{"entity": "label", "iuid": "4c38ef76351e45c5ace13c8848310194", "timestamp": "2026-08-12T21:41:58.058Z", "links": {"self": {"href": "https://publications.scilifelab.se/label/Bioinformatics%20Support%20and%20Infrastructure.json"}, "display": {"href": "https://publications.scilifelab.se/label/Bioinformatics%20Support%20and%20Infrastructure"}}, "value": "Bioinformatics Support and Infrastructure", "started": "2013", "ended": "2020", "created": "2017-05-02T12:09:58.823Z", "modified": "2021-03-15T14:14:26.477Z", "accounts": [{"entity": "account", "iuid": "32a436398938412b93e7ddcef018c708", "timestamp": "2026-08-12T21:41:58.058Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/christopher.erdmann%40scilifelab.uu.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/christopher.erdmann%40scilifelab.uu.se"}}, "email": "christopher.erdmann@scilifelab.uu.se", "name": "Christopher Erdmann", "orcid": "", "role": "curator", "status": "enabled", "login": "2024-08-16T11:56:57.787Z", "created": "2024-08-16T10:01:32.844Z", "modified": "2025-10-17T13:05:06.782Z"}, {"entity": "account", "iuid": "6a38350bd21f4fb6aeeb1530037a99ae", "timestamp": "2026-08-12T21:41:58.058Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/sune.joubert%40scilifelab.uu.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/sune.joubert%40scilifelab.uu.se"}}, "email": "sune.joubert@scilifelab.uu.se", "name": "Sun\u00e9 Joubert", "orcid": "", "role": "curator", "status": "enabled", "login": "2025-10-31T11:15:37.113Z", "created": "2024-08-16T10:01:02.800Z", "modified": "2025-10-31T11:15:37.113Z"}, {"entity": "account", "iuid": "6afeaa5195a2419f83672482d152927d", "timestamp": "2026-08-12T21:41:58.058Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/lucile.soler%40scilifelab.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/lucile.soler%40scilifelab.se"}}, "email": "lucile.soler@scilifelab.se", "name": "Lucile Soler", "orcid": "0000-0002-0121-2393", "role": "curator", "status": "enabled", "login": "2025-11-20T14:54:45.731Z", "created": "2025-11-20T14:52:29.099Z", "modified": "2025-11-20T14:54:45.731Z"}, {"entity": "account", "iuid": "a1502773318145e7ae779288ee307fea", "timestamp": "2026-08-12T21:41:58.058Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/dag.ahren%40scilifelab.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/dag.ahren%40scilifelab.se"}}, "email": "dag.ahren@scilifelab.se", "name": "Dag Ahr\u00e9n", "orcid": "0000-0003-4713-0032", "role": "curator", "status": "enabled", "login": "2025-11-20T13:29:32.830Z", "created": "2025-11-20T06:53:43.368Z", "modified": "2025-11-20T13:29:32.830Z"}, {"entity": "account", "iuid": "c053e1c9be3d48518bbcf83d50911361", "timestamp": "2026-08-12T21:41:58.058Z", "links": {"self": {"href": 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"account", "iuid": "d0dbe4021e344760b9b9735dde5958b4", "timestamp": "2026-08-12T21:41:58.058Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/henrik.lantz%40nbis.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/henrik.lantz%40nbis.se"}}, "email": "henrik.lantz@nbis.se", "name": "Henrik Lantz", "orcid": "", "role": "curator", "status": "enabled", "login": "2026-04-09T11:02:25.469Z", "created": "2019-01-15T11:28:02.331Z", "modified": "2026-04-09T11:02:25.469Z"}, {"entity": "account", "iuid": "e784b33982ad47a8b2d4786bf1e62cbe", "timestamp": "2026-08-12T21:41:58.058Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/bengt.sennblad%40scilifelab.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/bengt.sennblad%40scilifelab.se"}}, "email": "bengt.sennblad@scilifelab.se", "name": "Bengt Sennblad", "orcid": "", "role": "curator", "status": "enabled", "login": "2026-04-09T13:17:39.453Z", "created": "2023-12-20T10:47:23.547Z", "modified": "2026-04-09T13:17:39.453Z"}, {"entity": "account", "iuid": "f440beaba75d4f83a5d4c9d5744d285a", "timestamp": "2026-08-12T21:41:58.058Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/jonas.hagberg%40scilifelab.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/jonas.hagberg%40scilifelab.se"}}, "email": "jonas.hagberg@scilifelab.se", "name": "Jonas Hagberg", "orcid": "", "role": "curator", "status": "enabled", "login": "2019-12-12T09:34:46.269Z", "created": "2019-01-15T11:28:40.471Z", "modified": "2025-03-07T13:47:39.652Z"}], "publications_count": 594, "publications": [{"entity": "publication", "iuid": "302ea24f73a84f0e8853a9e9b53eb13f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/302ea24f73a84f0e8853a9e9b53eb13f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/302ea24f73a84f0e8853a9e9b53eb13f"}}, "title": "Dimethyl Fumarate, But Not Rituximab, Reduces Serum GFAP Levels and PIRMA in Relapsing\u2013Remitting MS", "authors": [{"family": "Shawket", "given": "F", "initials": "F"}, {"family": "Lycke", "given": "J", "initials": "J"}, {"family": "Salzer", "given": "J", "initials": "J"}, {"family": "Piehl", "given": "F", "initials": "F", "orcid": "0000-0001-8329-5219", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee04062fbee34836a4fa3f4d2e8076cd.json"}}, {"family": "Fink", "given": "K", "initials": "K"}, {"family": "Lange", "given": "N", "initials": "N"}, {"family": "Mellerg\u00e5rd", "given": "J", "initials": "J", "orcid": "0000-0003-0120-3734", "researcher": {"href": "https://publications.scilifelab.se/researcher/f471bdcfc7fc4c2fb282484ac7e148bd.json"}}, {"family": "Malmestr\u00f6m", "given": "C", "initials": "C"}, {"family": "Sundstr\u00f6m", "given": "P", "initials": "P"}, {"family": "Erngren", "given": "I", "initials": "I", "orcid": "0000-0001-7867-9525", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8a16aaaf5194acba6b8649690a101d8.json"}}, {"family": "al\u2010Grety", "given": "A", "initials": "A"}, {"family": "Freyhult", "given": "E", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "Kultima", "given": "K", "initials": "K", "orcid": "0000-0002-0680-1410", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ae376585168459681f5e2cae0c75b96.json"}}, {"family": "Burman", "given": "J", "initials": "J"}, {"family": "Svenningsson", "given": "A", "initials": "A", "orcid": "0000-0003-0663-2220", "researcher": {"href": "https://publications.scilifelab.se/researcher/73156fb41b544d82ad4c022d2ca12fc3.json"}}], "type": "journal-article", "published": "2026-04-12", "journal": {"title": "Ann Clin Transl Neurol", "issn": "2328-9503", "issn-l": "2328-9503"}, "abstract": "Serum neurofilament light chain (sNfL) and glial fibrillary acidic protein (sGFAP) levels are believed to reflect mainly acute and chronic disease processes in multiple sclerosis (MS), respectively. In this study, we investigated whether dimethyl fumarate (DMF) and rituximab (RTX) differentially affect these biomarkers.\n\nRIFUND-MS was a 2-year, rater-blinded, 1:1 randomized controlled multicenter trial comparing DMF and RTX in relapsing-remitting multiple sclerosis (RRMS). Serum samples for analysis of sNFL and sGFAP were collected at baseline and 0, 6, 12 and 24. Log-transformed biomarker data were analyzed with linear mixed models, based on intention to treat (ITT), per protocol (PP) and accounting for therapy switches. Cox proportional hazards models were performed to evaluate progression outcomes.\n\nOf 200 participants, 197 were analyzed. Based on ITT, sNfL decreased significantly in both arms from baseline to month 24; by 50.7% (CI 43.7%-56.8%; p < 0.001) with RTX, and by 46.4% (CI 38.6%-53.2%; p < 0.001) with DMF, no differences between treatments (global p-value: ITT = 0.06; PP = 0.08; switch group = 0.15). In contrast, sGFAP remained stable in RTX (3.6% decrease; CI -7.8%-13.8%, p = 0.81) but decreased with DMF (18.4%; CI 8.5%-27.2%; p < 0.001). Global analyses favored DMF (ITT = 0.02; PP = 0.004; switch group = 0.74). The risk of progression independent of relapse and MRI activity (PIRMA) was higher with RTX (HR 3.3, CI 1.1-10, p = 0.04).\n\nBoth RTX and DMF reduced sNfL levels, consistent with suppression of acute inflammatory disease activity. However, only DMF was associated with a sustained reduction in sGFAP and a lower risk of non-inflammatory disability progression. These findings suggest that DMF may exert additional effects on astrocyte-related or compartmentalized CNS pathology beyond peripheral immune modulation.", "doi": "10.1002/acn3.70395", "pmid": "41968564", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-04-14T06:47:42.291Z", "modified": "2026-04-16T09:41:54.416Z"}, {"entity": "publication", "iuid": "1e2a6a80e6314c9e9c235060aee84268", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e2a6a80e6314c9e9c235060aee84268.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e2a6a80e6314c9e9c235060aee84268"}}, "title": "TNF\u03b1 signaling in radiation-induced chronic bowel dysfunction suggests therapeutic potential for IBD biologics", "authors": [{"family": "Devarakonda", "given": "Sravani", "initials": "S"}, {"family": "Patel", "given": "Piyush", "initials": "P"}, {"family": "Toft Mor\u00e9n", "given": "Amelie", "initials": "A"}, {"family": "Bergmark", "given": "Karin", "initials": "K"}, {"family": "Bamfarahnak", "given": "Mohammad", "initials": "M"}, {"family": "Buske", "given": "Patrik A", "initials": "PA"}, {"family": "Peng", "given": "Yueling", "initials": "Y"}, {"family": "Thorsell", "given": "Annika", "initials": "A"}, {"family": "Li", "given": "Yuan", "initials": "Y"}, {"family": "Fagman", "given": "Henrik", "initials": "H"}, {"family": "Fransson", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-4762-901X", "researcher": {"href": "https://publications.scilifelab.se/researcher/30428cafc89647768f6c69eecf98efcf.json"}}, {"family": "Heden", "given": "Lisen", "initials": "L"}, {"family": "Gustafsson", "given": "Karin", "initials": "K"}, {"family": "Zhu", "given": "Changlian", "initials": "C"}, {"family": "Hedenstr\u00f6m", "given": "Per", "initials": "P"}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ", "orcid": "0000-0001-9522-9729", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c6a2dde2d8f40ef82dfba0cf1b52c0d.json"}}, {"family": "Bull", "given": "Cecilia", "initials": "C"}], "type": "journal-article", "published": "2026-04-09", "journal": {"title": "Mol. Med.", "issn": "1528-3658", "volume": "32", "issue": "1", "issn-l": "1076-1551"}, "abstract": null, "doi": "10.1186/s10020-026-01441-4", "pmid": "41957709", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-04-10T07:07:13.665Z", "modified": "2026-04-16T09:42:11.163Z"}, {"entity": "publication", "iuid": "8be8d00d65424632a6066715fa2207b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8be8d00d65424632a6066715fa2207b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8be8d00d65424632a6066715fa2207b8"}}, "title": "Lectin pathway of complement in SLE: MAP-1 as a marker of haematological manifestations and elevated type I interferon activity.", "authors": [{"family": "Lindel\u00f6f", "given": "Linnea", "initials": "L", "orcid": "0000-0002-3654-8874", "researcher": {"href": "https://publications.scilifelab.se/researcher/65f6c8233c5547f2885b3e55bbec2601.json"}}, {"family": "Garred", "given": "Peter", "initials": "P"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Wahl V\u00e6lum", "given": "Sasha", "initials": "S", "orcid": "0009-0006-1378-9591", "researcher": {"href": "https://publications.scilifelab.se/researcher/6668483bc5d1464f839e525848a5b84c.json"}}, {"family": "Holten Petersen", "given": "Lotte", "initials": "L"}, {"family": "Leonard", "given": "Dag", "initials": "D", "orcid": "0000-0002-6275-7282", "researcher": {"href": "https://publications.scilifelab.se/researcher/42ed25c2f495484db4757f4fef51abae.json"}}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Oke", "given": "Vilija", "initials": "V", "orcid": "0000-0002-1834-2688", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5115e955050467694c2e2396706066a.json"}}, {"family": "Niewold", "given": "Timothy B", "initials": "TB", "orcid": "0000-0003-3532-6660", "researcher": {"href": "https://publications.scilifelab.se/researcher/89b178dc1ef34fa4b4ef34e71b9ac1e5.json"}}, {"family": "Diaz-Gallo", "given": "Lina-Marcela", "initials": "LM", "orcid": "0000-0002-5688-0102", "researcher": {"href": "https://publications.scilifelab.se/researcher/7fc169ccfb154ef29c62f78044e27a7b.json"}}, {"family": "Saevarsdottir", "given": "Saedis", "initials": "S"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I", "orcid": "0000-0002-4514-7706", "researcher": {"href": "https://publications.scilifelab.se/researcher/90121ddba7fe4f928c1b121b162c2509.json"}}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3396-3244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ab5989c3c604a96bf42b1b6f90434a0.json"}}, {"family": "Eriksson", "given": "Oskar", "initials": "O"}], "type": "journal article", "published": "2026-04-09", "journal": {"title": "Lupus Sci Med", "issn": "2053-8790", "volume": "13", "issue": "1", "issn-l": "2053-8790"}, "abstract": "SLE is a systemic autoimmune disease in which the complement system plays a key pathogenic role, yet the contribution of the lectin pathway remains unclear. Lectin pathway-dependent complement activation is initiated by pattern-recognition molecules complexed with mannose-binding lectin (MBL)-associated serine proteases (MASPs) and MBL-associated proteins (MAPs). Here, we combined biochemical and genetic analyses to explore associations between MASP/MAP proteins, SLE manifestations and autoantibody specificities.\n\nSerum concentrations of MASP-3, MAP-1 and MASP-2 were measured using ELISA in Swedish patients with SLE (n=522) and population-based matched controls (n=322). Serum type I interferon activity was measured by a cell-based reporter assay. Associations with SLE manifestations and autoantibodies were explored using logistic regression models. Single-nucleotide genetic variants spanning the MASP1 and MASP2 genes were analysed for associations with MASP/MAP levels and SLE manifestations.\n\nPatients with MAP-1 serum concentrations in the highest quartile had significantly higher rates of discoid rash (OR 2.8 (95% CI 1.4 to 5.7)), haematological manifestations (OR 2.1 (95% CI 1.1 to 3.7)) and autoantibodies against Sm, RNP, SSA and SSB (ORs 2.4 (95% CI 1.3 to 4.6) to 3.6 (95% CI 1.7 to 7.7)). Patients in the highest quartiles of MAP-1 and MASP-2 had lower rates of anti-\u03b22GP1 and anti-cardiolipin IgG and IgA anti-phospholipid antibodies (ORs 0.29 (95% CI 0.12 to 0.68) to 0.56 (95% CI 0.31 to 1.0)). Serum MAP-1 levels correlated with type I interferon activity (Spearman's rho 0.34, p<0.0001), which mediated the associations of MAP-1 with haematological manifestations and Sm/RNP autoantibodies. Significant protein quantitative trait loci for MAP-1 and MASP-2 were identified; however, these did not show consistent associations with SLE or specific SLE manifestations.\n\nThese results demonstrate a distinct clinical and serological SLE profile associated with components of the lectin pathway. The lectin pathway-regulatory protein MAP-1 displayed the strongest associations and may serve as a marker of SLE manifestations with a type I interferon signature.", "doi": "10.1136/lupus-2025-001890", "pmid": "41956715", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pii", "key": "13/1/e001890"}], "notes": [], "created": "2026-04-15T06:40:16.897Z", "modified": "2026-04-15T06:40:17.508Z"}, {"entity": "publication", "iuid": "9bc3232d9f3b460cb3a8d08f5d9bd344", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9bc3232d9f3b460cb3a8d08f5d9bd344.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9bc3232d9f3b460cb3a8d08f5d9bd344"}}, "title": "Single-cell analysis of inhibitory efferent neurons of the zebrafish lateral line.", "authors": [{"family": "Manuel", "given": "Remy", "initials": "R", "orcid": "0000-0001-6938-4864", "researcher": {"href": "https://publications.scilifelab.se/researcher/927f9373b9f44c68ab362fa91a4bb8a9.json"}}, {"family": "Ahemaiti", "given": "Aikeremu", "initials": "A"}, {"family": "Tuz-Sasik", "given": "Melek Umay", "initials": "MU", "orcid": "0000-0002-0906-7477", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bf8b429a428493d8ee662e648798951.json"}}, {"family": "Boije", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2026-04-08", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "21", "issue": "4", "pages": "e0346255", "issn-l": "1932-6203"}, "abstract": "The zebrafish lateral line system is a sensory network made up of neuromasts, which contain hair cells to detect water flow. Neuromasts signal via sensory afferent neurons and their activity is modulated by efferent neurons. Inhibitory efferent neurons consist of REN, ROLE, and RELL cells and previous work has shown that neuromasts can be innervated by multiple efferent neurons, suggesting potential functional differences. To explore this, we performed single-cell RNA sequencing on REN, ROLE, and RELL neurons in 5-day-old zebrafish larvae. GO analysis across differentially expressed genes did not reveal pathways that suggest differences in cellular function. Comparing markers for neurotransmitter phenotype showed all inhibitory efferent neurons to be cholinergic, but also expressed genes related to other neurotransmitters. Expression of selected genes related to rhombomere location, axon guidance, or gap junctions was similar across efferent neurons. Expression of genes encoding proteins related to membrane potential suggest that REN neurons might be more sensitive to glutamate and may have different action potential dynamics, although functional validation remains to be done. In addition, we assessed neuromast innervation by ROLE and RELL neurons. We found that both ROLE and RELL neurons synapse to approximately 50% of hair cells within a neuromast, compared to approximately 75% innervation by all inhibitory efferent neurons combined. In addition, we did not observe flow polarity bias by innervating efferent axons. However, we did find that RELL neurons had a lower number of synaptic boutons compared to ROLE, which may reflect differences in synaptic output capacity. Taken that our transcriptional analysis did not reveal major intrinsic molecular differences, but we did observe differences in neuromast innervation, raises the possibility that functional differences, if present, may come from upstream inputs. Future work, such as retrograde tracing, could help map these input partners and clarify how different types of efferent neurons contribute to sensory modulation.", "doi": "10.1371/journal.pone.0346255", "pmid": "41950195", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13061224"}, {"db": "pii", "key": "PONE-D-25-53779"}], "notes": [], "created": "2026-04-09T11:03:25.812Z", "modified": "2026-05-27T11:38:01.833Z"}, {"entity": "publication", "iuid": "de64661fcabe49c2a64125eae6173df5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de64661fcabe49c2a64125eae6173df5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de64661fcabe49c2a64125eae6173df5"}}, "title": "Pre-diagnostic and diagnostic D-vitamin levels and risk of bladder cancer - A nested case-control study with follow-up at diagnosis", "authors": [{"family": "Hultdin", "given": "Johan", "initials": "J", "orcid": "0000-0002-9599-0961", "researcher": {"href": "https://publications.scilifelab.se/researcher/17ea31f8b74a4a3cbbddd262227dc95d.json"}}, {"family": "Tellstr\u00f6m", "given": "Andreas", "initials": "A"}, {"family": "Freyhult", "given": "Eva", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "Landstr\u00f6m", "given": "Mar\u00e9ne", "initials": "M", "orcid": "0000-0001-6737-7230", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2f02fcfb1c1497d81a6f343bc0e6928.json"}}, {"family": "Ljungberg", "given": "B\u00f6rje", "initials": "B", "orcid": "0000-0002-4121-3753", "researcher": {"href": "https://publications.scilifelab.se/researcher/36db1e6702414edfac81ab7dfa1430e9.json"}}], "type": "journal-article", "published": "2026-04-00", "journal": {"title": "Clinical Nutrition Open Science", "issn": "2667-2685", "pages": "100658", "issn-l": null}, "abstract": null, "doi": "10.1016/j.nutos.2026.100658", "pmid": null, "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-04-10T07:13:00.773Z", "modified": "2026-04-10T07:13:01.100Z"}, {"entity": "publication", "iuid": "2253e344ebd94022a1be7f7534701531", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2253e344ebd94022a1be7f7534701531.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2253e344ebd94022a1be7f7534701531"}}, "title": "Sex chromosome evolution mediated by a large inversion and a possible switch of the sex determination gene.", "authors": [{"family": "Mao", "given": "Xiaomeng", "initials": "X"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Karrenberg", "given": "Sophie", "initials": "S"}], "type": "journal article", "published": "2026-03-19", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "27", "issue": "1", "issn-l": "1474-7596"}, "abstract": "Sex chromosomes often evolve faster than autosomes and commonly degenerate after recombination arrest. However, the underlying evolutionary processes are under persistent debate. In particular, it is unclear whether or not recombination arrest generally evolves in a stepwise manner and how switches in sex determination genes contribute to sex chromosome evolution. Here, we investigate sex chromosome evolution in the dioecious plant genus Salix.\n\nWe identify Z- and W-regions (~ 8 Mb) on chromosome 15 of the dwarf willow Salix herbacea using a new haplotype-resolved assembly. The W-region harbours a large (5 Mb) embedded inversion. Analyses of synteny with other Salix species, sequence divergence between sex chromosomes and sequence degeneration suggest that this inversion recently incorporated pseudoautosomal sequence into the W-region, extending its length nearly three-fold. The W-region exclusively contains seven pairs of inverted partial repeats of the male essential floral identity gene PISTILLATA, suggesting a possible PISTILLATA suppression mechanism by interfering RNA in females. Such PISTILLATA pseudogenes are also found in other Salix species with ZW sex determination but not in those with XY sex determination.\n\nOur study provides rare and compelling support for the long-standing theory of inversions underlying stepwise recombination reduction and raises the hypothesis that the turnover of sex chromosomes in the Salicaceae family might be associated with a switch of the sex determination gene.", "doi": "10.1186/s13059-026-04038-6", "pmid": "41857659", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Long read": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC13064059"}, {"db": "pii", "key": "10.1186/s13059-026-04038-6"}], "notes": [], "created": "2026-04-10T06:39:04.743Z", "modified": "2026-08-12T15:12:37.561Z"}, {"entity": "publication", "iuid": "934abbdaa93042c99b863e927fd9b3eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/934abbdaa93042c99b863e927fd9b3eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/934abbdaa93042c99b863e927fd9b3eb"}}, "title": "Targeted CSF metabolomics and conformal prediction improve diagnostic accuracy of normal pressure hydrocephalus.", "authors": [{"family": "Hofling", "given": "Ulrika", "initials": "U"}, {"family": "Jakobsson", "given": "Jenny", "initials": "J"}, {"family": "Erngren", "given": "Ida", "initials": "I"}, {"family": "Ekman", "given": "Oskar", "initials": "O"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Sreenivasan", "given": "Akshai Parakkal", "initials": "AP"}, {"family": "Siljebo", "given": "Jakob", "initials": "J"}, {"family": "Libard", "given": "Sylwia", "initials": "S"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "L\u00f6wenmark", "given": "Malin", "initials": "M"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Kultima", "given": "Kim", "initials": "K"}, {"family": "Virhammar", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2026-02-07", "journal": {"title": "Fluids Barriers CNS", "issn": "2045-8118", "volume": "23", "issue": "1", "issn-l": null}, "abstract": "Idiopathic normal pressure hydrocephalus (iNPH) is a progressive but treatable neurological disorder. Yet, diagnosis is often confounded by overlapping symptoms and biomarker profiles with Alzheimer\u2019s disease (AD), mild cognitive impairment (MCI), and frontotemporal dementia (FTD). We aimed to determine whether cerebrospinal fluid (CSF) metabolomic profiling, combined with uncertainty-aware machine learning using conformal prediction (CP), could improve diagnostic differentiation of iNPH.\n\nCSF samples were collected from 120 patients with iNPH, 44 healthy controls, and 152 individuals with AD, MCI, or FTD. Targeted metabolomics of 59 metabolites was performed using liquid chromatography\u2013high-resolution mass spectrometry. Group differences were assessed using age- and sex-adjusted regression models. Multivariate classification with partial least squares discriminant analysis (PLS-DA) incorporated metabolites, demographics, and conventional biomarkers (amyloid-\u03b242, tau, phosphorylated tau). CP was applied to address individual-level diagnostic uncertainty.\n\nEight metabolites (proline, threonine, histidine, tyrosine, tryptophan, isobutyrylcarnitine, citric acid, and dehydroascorbic acid) were consistently reduced in iNPH (q < 0.05), independent of ventricular volume and cortical tau or amyloid-\u03b2 pathology. An integrated PLS-DA model combining metabolomic, demographic, and AD-biomarker data achieved excellent discrimination (AUC = 0.97). CP provided calibrated case-level confidence, identifying clear-cut and uncertain cases while maintaining high accuracy (94% for iNPH, 97% for not-iNPH).\n\niNPH exhibits a distinct CSF metabolomic signature reflecting altered amino acid metabolism, mitochondrial function, and oxidative stress. Integrating metabolomic data with established biomarkers enhances diagnostic accuracy, while CP adds individualized uncertainty estimates to improve diagnostic confidence and guide treatment decisions.\n\nThe online version contains supplementary material available at 10.1186/s12987-026-00771-z.", "doi": "10.1186/s12987-026-00771-z", "pmid": "41654915", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12930833"}, {"db": "pii", "key": "10.1186/s12987-026-00771-z"}], "notes": [], "created": "2026-04-10T07:10:24.128Z", "modified": "2026-04-10T07:10:24.131Z"}, {"entity": "publication", "iuid": "9fc4953605de40198d0d1f18d4d4caf2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9fc4953605de40198d0d1f18d4d4caf2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9fc4953605de40198d0d1f18d4d4caf2"}}, "title": "Inflammatory protein profiles and shunt response in iNPH", "authors": [{"family": "Braun", "given": "Madelene", "initials": "M", "orcid": "0000-0001-8844-1756", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb656d2129504868a45c01ae52cdb700.json"}}, {"family": "Ekblom", "given": "Maria", "initials": "M"}, {"family": "Freyhult", "given": "Eva", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": "Nyholm", "given": "Dag", "initials": "D"}, {"family": "Kultima", "given": "Kim", "initials": "K", "orcid": "0000-0002-0680-1410", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ae376585168459681f5e2cae0c75b96.json"}}, {"family": "Virhammar", "given": "Johan", "initials": "J", "orcid": "0000-0001-9901-2949", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7c5d8e520cf483e9d4fbb1ce459aec5.json"}}], "type": "journal-article", "published": "2026-01-07", "journal": {"title": "Fluids Barriers CNS", "issn": "2045-8118", "volume": "23", "issue": "1", "pages": "5", "issn-l": null}, "abstract": "Neuroinflammation in the context of idiopathic normal pressure hydrocephalus (iNPH) is poorly studied. Currently, no single objective test can reliably predict outcomes after shunt surgery. The aim was to investigate whether neuroinflammatory proteins in cerebrospinal fluid (CSF) are associated with the characteristic symptoms of iNPH and whether they can predict outcome after shunting.\n\nNeuroinflammatory proteins were analyzed from preoperative CSF using proximity extension assay (PEA). In total, 92 proteins were analyzed from 74 patients with iNPH referred to shunt surgery at a single center, with follow-up at the same hospital. Symptoms were assessed before surgery and at follow-up (primarily 12 months post-surgery), graded with the Swedish iNPH scale. Associations between protein levels and preoperative symptoms, as well as outcome, were analyzed using linear regression models adjusted for age and sex; outcome models were additionally adjusted for baseline symptom level. Benjamini-Hochberg with a false discovery rate (FDR) of 5% was used to control for multiple analyses.\n\nOf the 92 analyzed proteins, 60 had detectable values greater than 50% and were included in the analyses. No associations between preoperative symptom severity and levels of inflammatory proteins remained statistically significant after correction for multiple comparisons (FDR 5%). After adjustment, CST5 showed a significant negative association with postoperative improvement in balance and continence domains (b = -34, q = 0.017 and b = -35, q = 0.026, respectively) but not for outcome in the total iNPH scale. A general trend was observed where higher levels of inflammatory proteins were linked to less favourable outcomes, although these did not remain statistically significant after correction.\n\nCST5 emerged as the only protein significantly associated with postoperative improvement after shunt surgery, suggesting a potential role in iNPH pathophysiology. Furthermore, no associations were observed between preoperative symptom severity and levels of inflammatory CSF proteins.\n\nThe online version contains supplementary material available at 10.1186/s12987-025-00751-9.", "doi": "10.1186/s12987-025-00751-9", "pmid": "41501840", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12784546"}, {"db": "pii", "key": "10.1186/s12987-025-00751-9"}], "notes": [], "created": "2026-02-10T10:00:00.564Z", "modified": "2026-03-24T09:15:02.947Z"}, {"entity": "publication", "iuid": "f8ff8e625f5d45218a355407b7607936", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8ff8e625f5d45218a355407b7607936.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8ff8e625f5d45218a355407b7607936"}}, "title": "Co-exposure to PFAS and hydroxylated PCBs is associated with increased odds of multiple sclerosis", "authors": [{"family": "Vaivade", "given": "Aina", "initials": "A"}, {"family": "Sreenivasan", "given": "Akshai Parakkal", "initials": "AP", "orcid": "0000-0002-7293-6487", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b2f62a3bda9471d9227a6924b8adf7c.json"}}, {"family": "Erngren", "given": "Ida", "initials": "I", "orcid": "0000-0001-7867-9525", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8a16aaaf5194acba6b8649690a101d8.json"}}, {"family": "Freyhult", "given": "Eva", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "Emami Khoonsari", "given": "Payam", "initials": "P"}, {"family": "Siljebo", "given": "Jakob", "initials": "J"}, {"family": "Al-Grety", "given": "Asma", "initials": "A"}, {"family": "Carlsson", "given": "Henrik", "initials": "H", "orcid": "0000-0001-5558-6641", "researcher": {"href": "https://publications.scilifelab.se/researcher/de9581804a0b4b22991b34ebe89e9017.json"}}, {"family": "\u00c5kerfeldt", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "Hedstr\u00f6m", "given": "Anna Karin", "initials": "AK", "orcid": "0000-0002-6612-4749", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4a1c4b315cd4a09b8f98a87b6cd2fba.json"}}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}, {"family": "Alfredsson", "given": "Lars", "initials": "L", "orcid": "0000-0003-1688-6697", "researcher": {"href": "https://publications.scilifelab.se/researcher/6df230614a8a448e8607e03480169658.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Burman", "given": "Joachim", "initials": "J", "orcid": "0000-0002-7045-1806", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b9b82661abc49baaeac34bfcfc45321.json"}}, {"family": "Kultima", "given": "Kim", "initials": "K", "orcid": "0000-0002-0680-1410", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ae376585168459681f5e2cae0c75b96.json"}}], "type": "journal-article", "published": "2026-01-00", "journal": {"title": "Environment International", "issn": "0160-4120", "issn-l": "0160-4120", "volume": "207", "issue": null, "pages": "109993"}, "abstract": "Persistent organic pollutants often co-occur in human exposure environments, yet their combined effects on disease risk remain poorly understood. This study examined associations between serum concentrations of 14 per- and polyfluorinated substances (PFAS) and three hydroxylated polychlorinated biphenyls (OH-PCBs) and the onset of multiple sclerosis (MS), utilizing data from the Swedish population-based Epidemiological Investigation of Multiple Sclerosis (EIMS) cohort, comprising 907 MS cases and 907 matched controls. We employed single-substance logistic regression and quantile g-computation to evaluate cumulative and individual compound associations. We considered linear and non-linear risk patterns while adjusting for lifestyle factors and MS-associated HLA alleles. Our analysis revealed non-linear associations for several individual compounds, particularly perfluorooctane sulfonic acid (PFOS), perfluorononanoic acid, 2,2',3,4',5,5',6-heptachloro-4-biphenylol (4-OH-CB187), and 2,2',4,4',5,5'-, Hexachloro-3-biphenylol (3-OH-CB153), with increased odds of MS. Interaction analyses further indicated that the association between PFOS and MS odds was modified by the presence of the HLA-B*44:02 allele, known for its protective effect on MS risk. Mixture modeling highlighted that combined exposures to PFAS and OH-PCBs significantly increased MS odds, even when associations for individual compounds were weak or absent. These findings emphasize the complexity of associations between environmental contaminants, lifestyle and genetic risk factors, and the odds of MS. They underscore the importance of addressing co-exposure in environmental health research and call for further studies to elucidate underlying biological mechanisms.", "doi": "10.1016/j.envint.2025.109993", "pmid": "41411973", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0160-4120(25)00744-5"}], "notes": [], "created": "2026-02-10T09:53:14.232Z", "modified": "2026-03-24T09:16:23.730Z"}, {"entity": "publication", "iuid": "32a8f043a851424b897c3a1e3ae8c497", "links": {"self": {"href": "https://publications.scilifelab.se/publication/32a8f043a851424b897c3a1e3ae8c497.json"}, "display": {"href": "https://publications.scilifelab.se/publication/32a8f043a851424b897c3a1e3ae8c497"}}, "title": "Exploratory study linking plasma proteomics to cardiotoxicity in Hodgkin lymphoma.", "authors": [{"family": "Ulfstedt", "given": "Johan Mattsson", "initials": "JM"}, {"family": "Risebro", "given": "Ragnhild", "initials": "R"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Christersson", "given": "Christina", "initials": "C"}, {"family": "M\u00f6rth", "given": "Charlott", "initials": "C"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M"}, {"family": "Robelius", "given": "Anna", "initials": "A"}, {"family": "Enblad", "given": "Gunilla", "initials": "G"}, {"family": "Molin", "given": "Daniel", "initials": "D"}], "type": "journal article", "published": "2025-12-26", "journal": {"title": "Cardiooncology", "issn": "2057-3804", "volume": "12", "issue": "1", "pages": "13", "issn-l": null}, "abstract": "Cardiovascular toxicity is a well-known complication of chemotherapy, especially doxorubicin (DXR), and irradiation of the mediastinum for classical Hodgkin lymphoma (cHL). Due to the excellent prognosis in cHL, the mortality rate in late toxicity historically exceeds that of relapse of lymphoma. This highlights the need for strategies to minimize toxicity.Our aim was to characterize the prevalence of cardiovascular diseases (CVDs) in our cohort of cHL patients treated with DXR with or without radiotherapy according to standard practice and to identify any plasma protein associations with preexisting or emerging CVD posttreatment.\n\nWe analyzed 182 different proteins in plasma samples from 56 cHL patients and 60 controls using Olink multiplex protein panels Oncology II and Cardiovascular III. The analysis was supplemented with separate analyses of N-terminal pro-brain natriuretic peptide (NTpro-BNP), troponin I and C-reactive protein (CRP). The patient samples were prospectively collected prior to, during and after treatment.\n\nOur analysis revealed a statistically significant association between the compound endpoint of heart failure and ischemic heart disease and the protein biomarkers cysteine rich protein 61 (CYR61), glycoprotein nonmetastatic melanoma protein B (GPNMB) and activated leukocyte cell adhesion molecule (ALCAM) in samples collected after treatment for cHL.\n\nThis exploratory study identified three new biomarkers reflecting different biological processes associated with CVD in patients treated for cHL. Adding biomarkers to risk prediction in this population has the potential to identify patients with a high risk of cardiovascular events who need focused follow-up.\n\nThe online version contains supplementary material available at 10.1186/s40959-025-00426-2.", "doi": "10.1186/s40959-025-00426-2", "pmid": "41449437", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12853685"}, {"db": "pii", "key": "10.1186/s40959-025-00426-2"}], "notes": [], "created": "2026-02-10T09:56:00.336Z", "modified": "2026-02-10T09:56:00.355Z"}, {"entity": "publication", "iuid": "c998995ead0244f1b2aa6425b4c94d94", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c998995ead0244f1b2aa6425b4c94d94.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c998995ead0244f1b2aa6425b4c94d94"}}, "title": "Pharmacological activation of p53 induces dose-dependent changes in endothelial cell fate during angiogenic sprouting", "authors": [{"family": "Al-Radi", "given": "Omayma", "initials": "O"}, {"family": "Ingelshed", "given": "Katrine", "initials": "K"}, {"family": "Eichhorn", "given": "Lisa", "initials": "L"}, {"family": "Josefsson", "given": "Heidi", "initials": "H", "orcid": "0009-0001-0493-4877", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba8b17ae27f45ceb95d633757087213.json"}}, {"family": "Krkoska", "given": "Martin", "initials": "M"}, {"family": "Br\u00e4utigam", "given": "Lars", "initials": "L"}, {"family": "Lindstr\u00f6m", "given": "Susanne", "initials": "S", "orcid": "0009-0009-7396-9529", "researcher": {"href": "https://publications.scilifelab.se/researcher/fed14c3020094d9a8ca1ace96cbbe7b2.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Kheder", "given": "Sania", "initials": "S"}, {"family": "Cerrato", "given": "Carmine P", "initials": "CP"}, {"family": "Ferm\u00e9", "given": "Suzon", "initials": "S"}, {"family": "Bosdotter", "given": "Cecilia", "initials": "C"}, {"family": "Allalou", "given": "Amin", "initials": "A", "orcid": "0000-0003-4028-8443", "researcher": {"href": "https://publications.scilifelab.se/researcher/98fffa8e99254fb597bf07dea61d8e37.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b7add45d810457eb84a72aebbc7b82c.json"}}, {"family": "Vojtesek", "given": "Borivoj", "initials": "B"}, {"family": "Lane", "given": "David P", "initials": "DP"}, {"family": "Kannan", "given": "Pavitra", "initials": "P", "orcid": "0000-0002-9170-6062", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4f0b833cc604caf8dcff52dcbaa4fb9.json"}}], "type": "journal-article", "published": "2025-12-08", "journal": {"title": "Cell Death Dis", "issn": "2041-4889", "volume": "16", "issue": "1", "pages": "883", "issn-l": "2041-4889"}, "abstract": "The cell cycle is a key regulator of endothelial cell specification into tip and stalk cell phenotypes, which are essential for angiogenesis in both normal development and pathological conditions. While the tumor suppressor p53 is known to regulate the cell cycle and influence cell fate, its role in modulating the cell fate of these phenotypes remains unclear. Using non-genotoxic small molecule and stapled peptide compounds to pharmacologically activate p53 via MDM2 inhibition, we demonstrate that graded levels of p53 induce distinct cellular fates in normal endothelial cells. Low levels of p53 induce reversible cell cycle arrest by reducing DNA replication, while high levels induce senescence and cell death. Surprisingly, all tested levels of p53 activation reduced the growth of venous blood vessels in vitro and in zebrafish embryo models. This reduction in sprouting may stem from distinct cellular responses in tip-like and non-tip-like cells to pharmacological p53 activation: low p53 levels primarily reduced proliferation in non-tip-like cells, whereas high levels decreased the frequency of tip-like cells and the expression of genes associated with tip and stalk cell identities. Our findings show for the first time that pharmacological p53 activation modulates endothelial cell fate in a dose-dependent manner during sprouting angiogenesis. They also highlight the potential of using graded p53 modulation as a therapeutic strategy to target abnormal tip or stalk cell development in pathological angiogenesis, such as in cancer.", "doi": "10.1038/s41419-025-08292-7", "pmid": "41360924", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12698774"}, {"db": "pii", "key": "10.1038/s41419-025-08292-7"}], "notes": [], "created": "2025-12-12T12:24:13.109Z", "modified": "2026-01-09T07:55:39.395Z"}, {"entity": "publication", "iuid": "e7e4997a81904bfca3075b1e45f9cb0e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e7e4997a81904bfca3075b1e45f9cb0e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e7e4997a81904bfca3075b1e45f9cb0e"}}, "title": "Validation of a Genetic Risk Score Combined with Clinical Variables for Predicting Pulmonary Fibrosis in early Rheumatoid Arthritis.", "authors": [{"family": "Brink", "given": "Mikael", "initials": "M", "orcid": "0000-0001-7675-3488", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecbce4cc891249c5b96f71b6586aa777.json"}}, {"family": "Wheeler", "given": "Austin", "initials": "A", "orcid": "0000-0002-8816-7782", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcae89f571644e0c9aeb200574256acb.json"}}, {"family": "England", "given": "Bryant R", "initials": "BR", "orcid": "0000-0002-9649-3588", "researcher": {"href": "https://publications.scilifelab.se/researcher/3197cc141bd449728e5e65659fc2cada.json"}}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}], "type": "journal article", "published": "2025-11-14", "journal": {"title": "Arthritis Care Res (Hoboken)", "issn": "2151-4658", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "Pulmonary fibrosis (PF) is a severe extra-articular manifestation of rheumatoid arthritis (RA). The study aimed to externally validate a genetic risk score (GRS) and a combined risk score for predicting the risk of RA-associated PF in an independent cohort of early-RA patients.\r\n\r\nThis study utilized an inception cohort of 1118 patients diagnosed with RA from northern Sweden between 1996 and 2016. Clinical data were systematically collected, and genotyping was performed for 12 single-nucleotide polymorphisms (SNPs) associated with idiopathic pulmonary fibrosis. Statistical analyses, including logistic regression and area under the curve (AUC) assessments, were conducted to evaluate the performance of the GRS and in combination with clinical data as combined risk score in predicting RA-PF development.\r\n\r\nOf the 1115 patients with complete data, 60 (5.6%) were diagnosed with PF. PF was significantly associated with age, rheumatoid factor positivity, disease activity, and MUC5B (rs35705950) and FAM13A(rs2609255) SNPs. The GRS demonstrated a significant association with RA-PF (odds ratio 2.6, (95%CI 1.6, 4.5), while the combined risk score exhibited superior performance (AUC 0.75, p<0.001) compared to the GRS alone (AUC 0.62). The combined risk score outperformed the GRS in discriminating RA-PF, indicating its potential utility in clinical practice.\r\n\r\nThis study provides external validation of the VARA-ILD-GRS and VARA-ILD combined risk score in an RA cohort, demonstrating their generalizability and effectiveness in identifying high-risk individuals for RA-ILD. The findings support the integration of genetic and clinical data in risk stratification models, which could significantly improve screening strategies for RA patients at risk of developing PF.", "doi": "10.1002/acr.25696", "pmid": "41236136", "labels": {"Clinical Genomics": "Service", "Clinical Genomics Ume\u00e5": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-26T09:18:10.968Z", "modified": "2026-02-10T09:57:37.145Z"}, {"entity": "publication", "iuid": "394d345f587e4a8fa382227d3718c80e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/394d345f587e4a8fa382227d3718c80e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/394d345f587e4a8fa382227d3718c80e"}}, "title": "HAPP: High-accuracy pipeline for processing deep metabarcoding data.", "authors": [{"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Granqvist", "given": "Emma", "initials": "E", "orcid": "0000-0002-1513-1674", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b07f15f8724fdbbcdf34e6d6837147.json"}}, {"family": "Iwaszkiewicz-Eggebrecht", "given": "Ela", "initials": "E", "orcid": "0000-0003-1412-1711", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c085bb455d44ceac2f050f5c38f683.json"}}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L", "orcid": "0000-0001-9751-5745", "researcher": {"href": "https://publications.scilifelab.se/researcher/000321fd81b9457db66140246bbd9066.json"}}, {"family": "van Dijk", "given": "Laura J A", "initials": "LJA"}, {"family": "Goodsell", "given": "Robert", "initials": "R"}, {"family": "Godeiro", "given": "Nerivania N", "initials": "NN", "orcid": "0000-0002-1669-6124", "researcher": {"href": "https://publications.scilifelab.se/researcher/990e5c3362f94d76af29742ab5876a8a.json"}}, {"family": "Bellini", "given": "Bruno C", "initials": "BC"}, {"family": "Orsholm", "given": "Johanna", "initials": "J"}, {"family": "\u0141ukasik", "given": "Piotr", "initials": "P"}, {"family": "Miraldo", "given": "Andreia", "initials": "A"}, {"family": "Roslin", "given": "Tomas", "initials": "T"}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Ronquist", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3929-251X", "researcher": {"href": "https://publications.scilifelab.se/researcher/440662f277ea4756a08a7f5925b3f485.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "PLoS Comput. Biol.", "issn": "1553-7358", "issn-l": "1553-734X", "volume": "21", "issue": "11", "pages": "e1013558"}, "abstract": "Deep metabarcoding offers an efficient and reproducible approach to biodiversity monitoring, but noisy data and incomplete reference databases challenge accurate diversity estimation and taxonomic annotation. Here, we introduce a novel algorithm, NEEAT, for removing spurious operational taxonomic units (OTUs) originating from nuclear-embedded mitochondrial DNA sequences (NUMTs) or sequencing errors. It integrates 'echo' signals across samples with the identification of unusual evolutionary patterns among similar DNA sequences. We also extensively benchmark current tools for chimera removal, taxonomic annotation and OTU clustering of deep metabarcoding data. The best performing tools/parameter settings are integrated into HAPP, a high-accuracy pipeline for processing deep metabarcoding data. Tests using CO1 data from BOLD and large-scale metabarcoding data on insects demonstrate that HAPP significantly outperforms existing methods, while enabling efficient analysis of extensive datasets by parallelizing computations across taxonomic groups.", "doi": "10.1371/journal.pcbi.1013558", "pmid": "41202092", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12622834"}, {"db": "pii", "key": "PCOMPBIOL-D-25-00687"}], "notes": [], "created": "2025-11-21T11:45:11.315Z", "modified": "2025-11-21T12:27:09.804Z"}, {"entity": "publication", "iuid": "ca5a160aa916465286ca5da0958e09ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ca5a160aa916465286ca5da0958e09ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ca5a160aa916465286ca5da0958e09ea"}}, "title": "Growth failure in aggrecan deficiency is due to decreased extracellular matrix and impaired growth plate chondrocyte hypertrophy.", "authors": [{"family": "Bendre", "given": "Ameya", "initials": "A"}, {"family": "Ottosson", "given": "Lars", "initials": "L"}, {"family": "Baroncelli", "given": "Marta", "initials": "M"}, {"family": "Dou", "given": "Zelong", "initials": "Z"}, {"family": "Nilsson", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Bone", "issn": "1873-2763", "volume": "200", "pages": "117594", "issn-l": null}, "abstract": "Heterozygous loss-of-function mutations in the aggrecan (ACAN) gene cause autosomal dominant short stature often associated with advanced bone age, early-onset osteoarthritis and intervertebral disc disease (SSOAOD). These mutations are relatively common in patients with idiopathic short stature. However, the pathogenic mechanism of growth failure in this condition is not fully understood. Here, we studied the heterozygous cartilage matrix deficiency mouse (Acan+/-), which harbors a 7 bp microdeletion in aggrecan and develops postnatal growth cessation despite being born of normal size. Using detailed histomorphometric analysis, we found that the growth failure was primarily due to decreased extracellular matrix and impaired chondrocyte hypertrophy, whereas proliferation was largely unaffected. Furthermore, single-cell transcriptomic profiling revealed decreased total Acan mRNA expression in the Acan+/- chondrocytes. Notably, Akt signalling, which is important for hypertrophic differentiation was suppressed in Acan+/- pre-hypertrophic and hypertrophic chondrocytes. The decreased Akt signalling was associated with increased expression of calcium-calmodulin dependent protein kinase 1D (Camk1D), which negatively regulates Akt signalling, thereby providing a potential mechanism for the impaired hypertrophic differentiation. These findings reveal key cellular and molecular causes of growth failure in aggrecan deficiency and suggest that boosting proteoglycan expression and Akt signalling may help restore growth.", "doi": "10.1016/j.bone.2025.117594", "pmid": "40685060", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pii", "key": "S8756-3282(25)00206-6"}], "notes": [], "created": "2025-10-16T17:17:25.970Z", "modified": "2025-10-16T17:17:25.976Z"}, {"entity": "publication", "iuid": "a7fed56865ca4e36b3a0de3c2580cd45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a7fed56865ca4e36b3a0de3c2580cd45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a7fed56865ca4e36b3a0de3c2580cd45"}}, "title": "Comparing methods collecting mucosal secretions and detecting SARS-CoV-2 spike IgA in three laboratories across three countries.", "authors": [{"family": "Bladh", "given": "Oscar", "initials": "O"}, {"family": "Aguilera", "given": "Katherina", "initials": "K"}, {"family": "Sheikh-Mohamed", "given": "Salma", "initials": "S"}, {"family": "Nardulli", "given": "Jessica", "initials": "J"}, {"family": "Bhavsar", "given": "Disha", "initials": "D"}, {"family": "Fitzgerald", "given": "Dylan", "initials": "D"}, {"family": "Singh", "given": "Gagandeep", "initials": "G"}, {"family": "Ward", "given": "Lesley A", "initials": "LA"}, {"family": "Kleiner", "given": "Giulio", "initials": "G"}, {"family": "Chao", "given": "Gary Y C", "initials": "GYC"}, {"family": "Norin", "given": "Nina Greilert", "initials": "NG"}, {"family": "Pongr\u00e1cz", "given": "Tam\u00e1s", "initials": "T"}, {"family": "Gleason", "given": "Charles", "initials": "C"}, {"family": "Berkell", "given": "Matilda", "initials": "M"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M"}, {"family": "Krammer", "given": "Florian", "initials": "F"}, {"family": "Gommerman", "given": "Jennifer L", "initials": "JL"}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C"}, {"family": "Simon", "given": "Viviana", "initials": "V"}], "type": "journal article", "published": "2025-10-24", "journal": {"title": "Vaccine", "issn": "1873-2518", "volume": "65", "pages": "127792", "issn-l": null}, "abstract": "Mucosal IgA is key in preventing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. Several mucosal vaccines are in development, and consistent methodologies assessing mucosal IgA are crucial for evaluation across clinical trials.\n\nWe compared SARS-CoV-2 ancestral spike-specific IgA and secretory IgA (SIgA) in nasal secretions and saliva from 20 adults enrolled at Danderyd Hospital, Stockholm, Sweden, and 23 adults enrolled at the Icahn School of Medicine at Mount Sinai, New York, USA. Nasal secretions were collected by Nasosorption\u00ae and nasal swabs, and saliva by passive drooling, Salivette\u00ae, and saliva swabs. Antibody levels were measured in all samples using an electrochemiluminescence assay (ECL) and two enzyme-linked immunosorbent assays (ELISAs).\n\nSpike-specific IgA and SIgA levels measured by ECL correlated well with those measured by ELISA across nasal and saliva samples (range 0.42-0.94, p < 0.01), except for saliva collected by saliva swabs yielding lower IgA concentrations and weaker correlations (range - 0.21-0.27). Spike-specific IgA levels also correlated well across collection methods (range 0.7-0.9, p < 0.0001), with a weaker correlation between saliva collected by passive drooling and saliva swab (r = 0.55, p < 0.001). Although antibody levels correlated well between nasal secretions and saliva collected by passive drooling or Salivette\u00ae (range 0.64-0.86, p < 0.01), the overall levels were > 3-fold higher in nasal secretions compared to saliva (p < 0.01).\n\nThis multi-center study demonstrates an overall good comparability between spike-specific IgA and SIgA across assays and collection methods, except for saliva swabs. Our findings suggest that nasal secretions may be preferable due to higher spike-specific IgA levels compared to in saliva.", "doi": "10.1016/j.vaccine.2025.127792", "pmid": "41046839", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0264-410X(25)01089-8"}], "notes": [], "created": "2025-11-21T12:51:55.694Z", "modified": "2025-11-25T19:19:35.240Z"}, {"entity": "publication", "iuid": "5030ff3ac322493db0bee8969ebf9d14", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5030ff3ac322493db0bee8969ebf9d14.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5030ff3ac322493db0bee8969ebf9d14"}}, "title": "Reliable on-treatment prognostication and target identification with a customized assay for circulating tumor DNA in patients with newly diagnosed pancreatic cancer.", "authors": [{"family": "Petersson", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-5574-9217", "researcher": {"href": "https://publications.scilifelab.se/researcher/98f02e97bd25493c993d1a2568935885.json"}}, {"family": "Svensson", "given": "Maja", "initials": "M"}, {"family": "Hau", "given": "Sofie Olsson", "initials": "SO"}, {"family": "Bergstr\u00f6m", "given": "Rebecka", "initials": "R", "orcid": "0000-0001-7609-0733", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c52bb8b2ae249049f0da222bcdfe932.json"}}, {"family": "Lindberg", "given": "Johan", "initials": "J", "orcid": "0000-0003-3610-6774", "researcher": {"href": "https://publications.scilifelab.se/researcher/1369ca149def47a8abb8abb90b23ca66.json"}}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Chattopadhyay", "given": "Subhayan", "initials": "S", "orcid": "0000-0002-8599-2971", "researcher": {"href": "https://publications.scilifelab.se/researcher/78358668578b4661bed1f6a37365fae4.json"}}, {"family": "Eberhard", "given": "Jakob", "initials": "J"}, {"family": "Heidenblad", "given": "Markus", "initials": "M", "orcid": "0000-0002-0668-2263", "researcher": {"href": "https://publications.scilifelab.se/researcher/b49a0816fc794c27a25b34731e8ca7bf.json"}}, {"family": "Leandersson", "given": "Karin", "initials": "K", "orcid": "0000-0001-8254-3137", "researcher": {"href": "https://publications.scilifelab.se/researcher/4736923f382845c2990efb251340bfb4.json"}}, {"family": "Gisselsson", "given": "David", "initials": "D", "orcid": "0000-0002-0301-426X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3653582762b14f9a9ad2fe6aba511115.json"}}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K", "orcid": "0000-0003-2257-5000", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b7c5c8216d943d2b344d9de5622770b.json"}}], "type": "journal article", "published": "2025-10-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "34481", "issn-l": "2045-2322"}, "abstract": "The vast majority of patients with pancreatic cancer present with unresectable disease and precision medicine is lagging behind. Circulating tumor DNA (ctDNA) has emerged as a promising tool, both as a proxy for tumor burden and for capturing tumor heterogeneity, but optimal gene panels and prognostic cutoffs remain to be determined. Herein, we applied ultra-deep ctDNA sequencing using a customized panel targeting 23 genes and six frequently altered chromosomes on plasma samples obtained before, during and after chemotherapy from 60 patients enrolled in a prospective clinical study. At baseline, positive versus negative ctDNA was not prognostic, neither in the adjuvant nor in the palliative setting, but in palliative patients, an independent prognostic cutoff could be calculated from the absolute number of mutated DNA molecules. Median overall survival was 3.7 months in the ctDNAhigh compared to 11.9 months in the ctDNAlow group (p < 0.0001), and the cutoff remained prognostic at one and three months. Moreover, relevant genetic alterations were highly concordant in ctDNA and paired tumor tissue. These findings demonstrate the potential clinical utility of a customized and focused gene panel for prognostication and target identification over time in patients with newly diagnosed pancreatic cancer, in particular in the palliative setting.ClinicalTrials.gov number: NCT03724994.", "doi": "10.1038/s41598-025-22369-5", "pmid": "41044171", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Clinical Genomics Lund": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12494785"}, {"db": "pii", "key": "10.1038/s41598-025-22369-5"}, {"db": "ClinicalTrials.gov", "key": "NCT03724994"}], "notes": [], "created": "2025-10-16T17:14:10.829Z", "modified": "2025-11-18T20:46:37.775Z"}, {"entity": "publication", "iuid": "486383c9deab4e7ebdff990f1767aee7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/486383c9deab4e7ebdff990f1767aee7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/486383c9deab4e7ebdff990f1767aee7"}}, "title": "Quantitative temporal analysis of pancreatic islet T lymphocyte and macrophage infiltration heralded by serum IgE in congenic BioBreeding (BB) Gimap5-/- rats at risk for insulitis and acute onset diabetes.", "authors": [{"family": "J\u00f6nsson", "given": "Josefine", "initials": "J", "orcid": "0000-0003-0709-2828", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a4b2eb9eef5496eb27e76fc9fca120a.json"}}, {"family": "Faxius", "given": "Linda", "initials": "L"}, {"family": "T\u00e5ngrot", "given": "Jeanette", "initials": "J"}, {"family": "Vance", "given": "Krysten", "initials": "K", "orcid": "0000-0001-5647-1504", "researcher": {"href": "https://publications.scilifelab.se/researcher/25ed382328ed4627b4d1eed3e125fdfb.json"}}, {"family": "Jerman", "given": "Stephanie", "initials": "S"}, {"family": "Bowman", "given": "Doug", "initials": "D"}, {"family": "Bogdani", "given": "Marika", "initials": "M"}, {"family": "Ericsson", "given": "Peter", "initials": "P"}, {"family": "Bennet", "given": "Rasmus", "initials": "R"}, {"family": "Ramelius", "given": "Anita", "initials": "A", "orcid": "0000-0003-2407-7785", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb1bdf74e09d4101a0aea80b7d79559d.json"}}, {"family": "Lernmark", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0003-1735-0499", "researcher": {"href": "https://publications.scilifelab.se/researcher/87c2498b4a66469d9fe7c21f56e2eddd.json"}}], "type": "journal article", "published": "2025-10-03", "journal": {"title": "Inflamm Res", "issn": "1420-908X", "volume": "74", "issue": "1", "pages": "134", "issn-l": null}, "abstract": "The objective was to determine the association between serum IgE levels and the infiltration order of T lymphocytes and macrophages in pancreatic islets in relation to the loss of insulin and glucagon cells in presymptomatic congenic BB Gimap5-DP (Diabetes Prone) rats.\n\nCongenic prediabetes BB Gimap5-DP and control Gimap5-DR (Diabetes Resistant) rats were followed every other day from 29 to 32 days of age until peak serum IgE (\u2264 55 days of age).\n\nSerum IgE was measured using ELISA. The HALO\u2122 platform facilitated quantitative image analysis of infiltrating T lymphocytes, macrophages, and target organ insulin and glucagon cells. Whole genome sequencing (WGS) was employed to identify candidate type 1 diabetes genes.\n\nSerum IgE levels increased with age in normoglycemic BB Gimap5-DP rats. Quantification of infiltrating cells per mm2 in and around the islets indicated that T lymphocytes are the initial infiltrators, followed by macrophages. Elevated serum IgE levels inversely correlated with beta-cell mass (total mg insulin/mg pancreas). WGS refined the risk segment for islet inflammation to 1.02 Mbp, leaving 10 candidate genes, including Gimap4 and Gimap5.\n\nElevated IgE levels herald T lymphocyte and macrophage infiltration. Pancreatic islet inflammation was linked to Gimap4, Gimap5, and other potential candidate genes on rat chromosome 4.", "doi": "10.1007/s00011-025-02101-9", "pmid": "41042382", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12494634"}, {"db": "pii", "key": "10.1007/s00011-025-02101-9"}], "notes": [], "created": "2025-11-17T15:46:13.623Z", "modified": "2025-11-28T10:40:57.524Z"}, {"entity": "publication", "iuid": "aeb92fd9030f40e5b001042ea6594c76", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aeb92fd9030f40e5b001042ea6594c76.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aeb92fd9030f40e5b001042ea6594c76"}}, "title": "Developmental low-dose bisphenol A exposure leads to extensive transcriptome female masculinization and male feminization later in life.", "authors": [{"family": "Lind", "given": "Thomas", "initials": "T", "orcid": "0000-0003-2791-688X", "researcher": {"href": "https://publications.scilifelab.se/researcher/343532f8d9b44c848895493afbf32289.json"}}, {"family": "Dunder", "given": "Linda", "initials": "L"}, {"family": "Lejonklou", "given": "Margareta H", "initials": "MH"}, {"family": "Lind", "given": "P Monica", "initials": "PM"}, {"family": "Melhus", "given": "H\u00e5kan", "initials": "H"}, {"family": "Lind", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2025-10-01", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "5", "issue": "1", "pages": "410", "issn-l": null}, "abstract": "Bisphenol A (BPA) is an endocrine disruptor, and exposure to low doses in utero has been associated with the development of metabolic diseases. Previous studies have suggested that bone marrow (BM) may be particularly susceptible to BPA exposure.\n\nHere, we investigate how developmental exposure to low levels of BPA affects the BM transcriptome and the blood metabolic profile in Fischer 344 rats later in life. We compare these effects to those observed in human metabolic syndrome (MetS) using a population-based cohort.\n\nThe results show an unexpectedly extensive sex-biased effect on the BM transcriptome from a BPA dose approximately eight times lower than the recent temporary European Food Safety Authority (EFSA) human tolerable daily intake (TDI) and a higher dose considered safe in 2015. BPA exposure induces sex-specific changes in gene expression, progressing toward a hypometabolic cancer-like state in females and a hypermetabolic autoimmunity-like state in males, with a blood metabolic profile that significantly overlaps with human MetS in a cross-sectional study.\n\nWe conclude that developmental low-dose BPA exposure might induce metabolic syndrome specifically in males, possibly by affecting T cell activity in a sex-specific manner. Our study provides biologically plausible and convincing evidence for significant effects from low-dose BPA exposure, supporting the substantial lowering of the human BPA TDI by EFSA based on its critical effects on T cells.", "doi": "10.1038/s43856-025-01119-8", "pmid": "41034487", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Swedish Metabolomics Centre": "Service", "Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12488919"}, {"db": "pii", "key": "10.1038/s43856-025-01119-8"}], "notes": [], "created": "2025-11-17T15:52:20.678Z", "modified": "2025-11-27T08:05:30.935Z"}, {"entity": "publication", "iuid": "f4701608c6464c3288865cdcb70e61c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4701608c6464c3288865cdcb70e61c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4701608c6464c3288865cdcb70e61c9"}}, "title": "Low-Dose Aspirin for PI3K-Altered Localized Colorectal Cancer.", "authors": [{"family": "Martling", "given": "Anna", "initials": "A", "orcid": "0000-0001-5998-4735", "researcher": {"href": "https://publications.scilifelab.se/researcher/dab7d4e9839b4cd5be9393a04b089d33.json"}}, {"family": "Hed Myrberg", "given": "Ida", "initials": "I"}, {"family": "Nilbert", "given": "Mef", "initials": "M"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Granath", "given": "Fredrik", "initials": "F"}, {"family": "Eklund", "given": "Martin", "initials": "M"}, {"family": "\u00d6resland", "given": "Tom", "initials": "T"}, {"family": "Iversen", "given": "Lene H", "initials": "LH"}, {"family": "Haapam\u00e4ki", "given": "Carola", "initials": "C"}, {"family": "Janson", "given": "Martin", "initials": "M"}, {"family": "Westberg", "given": "Karin", "initials": "K"}, {"family": "Segelman", "given": "Josefin", "initials": "J"}, {"family": "Ersson", "given": "Urban", "initials": "U"}, {"family": "Prytz", "given": "Mattias", "initials": "M"}, {"family": "Angenete", "given": "Eva", "initials": "E", "orcid": "0000-0001-9966-4904", "researcher": {"href": "https://publications.scilifelab.se/researcher/07bd63b6d277460ca830518ed23fa31e.json"}}, {"family": "Bergstr\u00f6m", "given": "Rebecka", "initials": "R", "orcid": "0000-0001-7609-0733", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c52bb8b2ae249049f0da222bcdfe932.json"}}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Glimelius", "given": "Bengt", "initials": "B"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "ALASCCA Study Group", "given": "", "initials": ""}], "type": "clinical trial, phase iii", "published": "2025-09-18", "journal": {"title": "N. Engl. J. Med.", "issn": "1533-4406", "volume": "393", "issue": "11", "pages": "1051-1064", "issn-l": "0028-4793"}, "abstract": "Aspirin reduces the incidence of colorectal adenoma and colorectal cancer among high-risk persons. Observational studies suggest that aspirin may also improve disease-free survival after diagnosis, particularly among patients with tumors harboring somatic PIK3CA mutations. However, data from randomized trials are lacking.\n\nWe conducted a double-blind, randomized, placebo-controlled trial involving patients with stage I, II, or III rectal cancer or stage II or III colon cancer with somatic alterations in PI3K pathway genes. The patients were assigned in a 1:1 ratio to receive 160 mg of aspirin or matched placebo once daily for 3 years. Patients with prespecified PIK3CA hotspot mutations in exon 9 or 20 (group A alterations) and those with other moderate- or high-impact somatic variants in PIK3CA, PIK3R1, or PTEN (group B alterations) were eligible for randomization. The primary end point was colorectal cancer recurrence, assessed in a time-to-event analysis, in patients with group A alterations. Secondary end points included colorectal cancer recurrence in patients with group B alterations, disease-free survival, and safety.\n\nAlterations in PI3K pathway genes were detected in 1103 of 2980 patients (37.0%) with complete genomic data. Of 515 patients with group A alterations and 588 patients with group B alterations, 314 and 312, respectively, were assigned to receive aspirin or placebo. The estimated 3-year cumulative incidence of recurrence was 7.7% with aspirin and 14.1% with placebo (hazard ratio, 0.49; 95% confidence interval [CI], 0.24 to 0.98; P = 0.04) among patients with group A alterations and 7.7% and 16.8%, respectively (hazard ratio, 0.42; 95% CI, 0.21 to 0.83), among those with group B alterations. The estimated 3-year disease-free survival was 88.5% with aspirin and 81.4% with placebo (hazard ratio, 0.61; 95% CI, 0.34 to 1.08) among patients with group A alterations and 89.1% and 78.7%, respectively (hazard ratio, 0.51; 95% CI, 0.29 to 0.88), among those with group B alterations. Severe adverse events occurred in 16.8% of aspirin recipients and 11.6% of placebo recipients.\n\nAspirin led to a significantly lower incidence of colorectal cancer recurrence than placebo among patients with PIK3CA hotspot mutations in exon 9 or 20 and appeared to have a similar benefit among those with other somatic alterations in PI3K pathway genes. (Funded by the Swedish Research Council and others; ALASCCA ClinicalTrials.gov number, NCT02647099; EudraCT number, 2015-004240-19.).", "doi": "10.1056/NEJMoa2504650", "pmid": "40961426", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "ClinicalTrials.gov", "key": "NCT02647099"}, {"db": "EudraCT", "key": "2015-004240-19"}], "notes": [], "created": "2025-10-06T11:47:12.777Z", "modified": "2025-11-18T20:46:30.247Z"}, {"entity": "publication", "iuid": "df68d30a60804dbab4be6450c496ca2e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df68d30a60804dbab4be6450c496ca2e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df68d30a60804dbab4be6450c496ca2e"}}, "title": "Subtelomeric elements provide stability to short telomeres in telomerase-negative cells of the budding yeast Naumovozyma castellii.", "authors": [{"family": "Jaiswal", "given": "Rishi K", "initials": "RK"}, {"family": "Garibo Domingo", "given": "Teresa", "initials": "T"}, {"family": "Grunchec", "given": "H\u00e9lo\u00efse", "initials": "H"}, {"family": "Singh", "given": "Komudi", "initials": "K"}, {"family": "Pirooznia", "given": "Mehdi", "initials": "M", "orcid": "0000-0002-4210-6458", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b65f2a816224c6f91b136a2a6e0ecc0.json"}}, {"family": "Elhaik", "given": "Eran", "initials": "E"}, {"family": "Cohn", "given": "Marita", "initials": "M", "orcid": "0000-0002-3370-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f6375da7f964ac49517c2e41de8c074.json"}}], "type": "journal article", "published": "2025-09-03", "journal": {"title": "Curr Genet", "issn": "1432-0983", "issn-l": null, "volume": "71", "issue": "1", "pages": "19"}, "abstract": "Telomerase plays an important role in sustaining eukaryotic linear chromosomes, as elongation of telomeres is needed to counterbalance the shortening occurring in each replication round. Nevertheless, in telomerase-deficient cells, Alternative Lengthening of Telomeres (ALT) pathways can maintain telomeres by employing recombination-based mechanisms. In the budding yeast Naumovozyma castellii, effective activation of the ALT pathway leads to bypass of senescence and supports long-term growth. We found that telomere structures in N. castellii ALT cells are stably maintained at a shortened uniform length over extensive numbers of generations. This is correlated to the spreading of a subtelomeric sequence, TelKO element, to all telomeres. Genome sequencing of the wild-type strain revealed variants of the TelKO element, differing in their lengths, and separate ALT strains are maintained by spreading of distinct TelKO element variants. Although short uniform telomere structures are predominant, sporadic telomere lengthening events occur by addition of long repeated arrays of TelKO elements. The telomere-binding protein Rap1 can bind to TelKO sequences in vitro, indicating a functional role of TelKO elements in providing stability to shortened ALT telomeres. Our results suggest that stable maintenance and telomere functionality may be achieved by incorporating the distal subtelomeric TelKO sequences into the telomeric chromatin cap.", "doi": "10.1007/s00294-025-01325-w", "pmid": "40900359", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12408736"}, {"db": "pii", "key": "10.1007/s00294-025-01325-w"}], "notes": [], "created": "2025-11-04T10:56:32.978Z", "modified": "2025-11-28T10:41:08.037Z"}, {"entity": "publication", "iuid": "ebe4355205e54bc3b50d10a1a62fb6e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ebe4355205e54bc3b50d10a1a62fb6e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ebe4355205e54bc3b50d10a1a62fb6e8"}}, "title": "Genetic Adaptation to Brackish Water and Spawning Season in European Cisco.", "authors": [{"family": "Deng", "given": "Qiaoling", "initials": "Q", "orcid": "0000-0002-3776-1132", "researcher": {"href": "https://publications.scilifelab.se/researcher/bdfda2d3f64742e8a09bbded5f322f96.json"}}, {"family": "Goodall", "given": "Jake", "initials": "J", "orcid": "0000-0003-0960-4241", "researcher": {"href": "https://publications.scilifelab.se/researcher/457d1a2733cc4a569ffeb70750999199.json"}}, {"family": "Bergenius Nord", "given": "Mikaela", "initials": "M"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Cocco", "given": "Arianna", "initials": "A"}, {"family": "Delling", "given": "Bo", "initials": "B", "orcid": "0000-0001-9148-9574", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c1c3f7ddf0945d18660ecbaa85303b0.json"}}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3101-2285", "researcher": {"href": "https://publications.scilifelab.se/researcher/0db39539bdd94519a418e6dd7a287cc8.json"}}, {"family": "Heintz", "given": "Julia", "initials": "J"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "M"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "R"}, {"family": "Palm", "given": "Stefan", "initials": "S", "orcid": "0000-0002-9890-8265", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ebffe35bae646eb8a15163b0cb0820f.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Pippel", "given": "Martin", "initials": "M", "orcid": "0000-0002-8134-5929", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f59d0c98de64ac1a62234792258ee62.json"}}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Vasem\u00e4gi", "given": "Anti", "initials": "A", "orcid": "0000-0002-2184-5534", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad9186f5720d493980b92869fb504cb8.json"}}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2025-09-03", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": null, "issue": null, "pages": "e70094"}, "abstract": "How species adapt to diverse environmental conditions is essential for understanding evolution and the maintenance of biodiversity. The European cisco (Coregonus albula) is a salmonid that occurs in both fresh and brackish water, and this together with the presence of sympatric spring- and autumn-spawning lacustrine populations provides an opportunity for studying the genetics of adaptation in relation to salinity and timing of reproduction. Here, we present a high-quality reference genome of the European cisco based on PacBio HiFi long read sequencing and HiC-directed scaffolding. We generated low-coverage whole-genome sequencing data from 336 individuals across 12 population samples to explore population structure and genetics of ecological adaptation. We found a major subdivision between two groups of populations most likely reflecting colonisation from different glacial refugia. Within the two major groups, we detected further genetic differentiation between spring- and autumn-spawning populations and between populations from freshwater lakes, rivers and brackish water (Bothnian Bay). A genome-wide screen for genetic differentiation among populations identified a set of outlier SNPs strongly correlated with spawning timing and salinity. Several of the genes associated with spawning time, including BHLHE40, TIMELESS and CPT1A, have previously been shown to have a role in circadian rhythm biology. As many as 17 loci were associated with genetic differentiation between populations reproducing in fresh and brackish water. This study provides insights into the genomic basis of ecological adaptation in European cisco with implications for sustainable fishery management.", "doi": "10.1111/mec.70094", "pmid": "40903929", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Other": null, "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-09-08T14:16:37.667Z", "modified": "2025-11-21T12:48:41.202Z"}, {"entity": "publication", "iuid": "c027601d1dfd4b72a6c77d6aada03e78", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c027601d1dfd4b72a6c77d6aada03e78.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c027601d1dfd4b72a6c77d6aada03e78"}}, "title": "Multilayered Epigenetic Analysis Identifies a Molecular Portrait for Psychological Resilience in Patients With Breast Cancer.", "authors": [{"family": "Richter", "given": "Corinna", "initials": "C"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Axelsson", "given": "Ulrika", "initials": "U"}, {"family": "Lundberg", "given": "Kristina", "initials": "K"}, {"family": "Ryd\u00e9n", "given": "Lisa", "initials": "L"}, {"family": "Johnsson", "given": "Per", "initials": "P"}, {"family": "Ringdahl", "given": "Ulrika", "initials": "U"}, {"family": "Hallberg", "given": "Ingalill Rahm", "initials": "IR"}, {"family": "Borrebaeck", "given": "Carl A K", "initials": "CAK"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Biol Psychiatry Glob Open Sci", "issn": "2667-1743", "volume": "5", "issue": "5", "pages": "100545", "issn-l": null}, "abstract": "Psychological resilience refers to a person's positive adaptation when faced with adversities, such as a breast cancer (BC) diagnosis. Highly resilient patients are more likely to regain stability and be protected from health conditions such as depression, anxiety, and posttraumatic stress disorder. We aimed to identify epigenetic markers that distinguish high- and low-resilient patients in a BC cohort at time of diagnosis.\n\nGenome-wide DNA methylation was determined in participants selected from a prospectively collected cohort of 1040 newly diagnosed BC patients with known resilience status. DNA methylation of those displaying the highest and lowest scores (n = 425), as measured by the Connor-Davidson Resilience Scale, was analyzed in whole blood, using a multilayered bioinformatic approach. Sample subsets were created to identify differentially methylated probes (DMPs) and differentially methylated regions (DMRs), and fold change and area size were used to estimate the strength of methylation differences. The key regions associated with psychological resilience allowed us to build a classifier, using a random forest model, which was validated using an independent cohort (n = 80).\n\nDMPs and DMRs that consistently distinguished samples derived from high- and low-resilient patients were identified, and methylation differences followed a dose-response pattern related to resilience levels. DMRs included LY6G5C, ZFP57, CDH9, ZNF727, and C8orf31, where LY6G5C was found to be the most consistent DMR. Psychological resilience status could be predicted in the independent cohort with an area under the curve of 0.74 and a sensitivity and specificity of 0.67 and 0.72, respectively.\n\nLY6G5C was identified as a novel marker for psychological resilience, paving the way for a more conceptual and comprehensive molecular understanding.", "doi": "10.1016/j.bpsgos.2025.100545", "pmid": "40697488", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12281357"}, {"db": "pii", "key": "S2667-1743(25)00099-0"}], "notes": [], "created": "2025-11-17T10:18:22.349Z", "modified": "2025-11-17T10:18:22.358Z"}, {"entity": "publication", "iuid": "99d94470f07541c2b23fad1eefd0f74b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/99d94470f07541c2b23fad1eefd0f74b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/99d94470f07541c2b23fad1eefd0f74b"}}, "title": "Genomic studies in Linum shed light on the evolution of the distyly supergene and the molecular basis of convergent floral evolution.", "authors": [{"family": "Zervakis", "given": "Panagiotis-Ioannis", "initials": "PI", "orcid": "0000-0002-5197-3502", "researcher": {"href": "https://publications.scilifelab.se/researcher/295e9debf36c4641aa6c346e915b64ef.json"}}, {"family": "Postel", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0003-0502-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/0481ff1051564262af4e5384cbd17ac3.json"}}, {"family": "Losvik", "given": "Aleksandra", "initials": "A", "orcid": "0000-0001-7669-9266", "researcher": {"href": "https://publications.scilifelab.se/researcher/e85c35a0abd54a7087c94942290179be.json"}}, {"family": "Fracassetti", "given": "Marco", "initials": "M", "orcid": "0000-0002-2962-2669", "researcher": {"href": "https://publications.scilifelab.se/researcher/695213cdd1a645cbbf10d44122237b18.json"}}, {"family": "Sol\u00e9r", "given": "Lucile", "initials": "L", "orcid": "0000-0002-0121-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/f701059f90fe4c7c9b969079e74aac57.json"}}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E", "orcid": "0000-0003-3752-1806", "researcher": {"href": "https://publications.scilifelab.se/researcher/9257ccdfc6484cd9a95f9b2f17f9a8d1.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Churcher", "given": "Allison", "initials": "A", "orcid": "0000-0003-1902-3002", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97e6fb500a043f08d4f882e802cd91b.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X", "volume": "247", "issue": "6", "pages": "2964-2981"}, "abstract": "Distyly, an example of convergent evolution, is governed by a supergene, the S-locus, in several species. Recent studies highlight similar genomic architectures of independently evolved S-loci, but its mode of origin and whether similar regulatory pathways underlie the convergent evolution of distyly remains unclear. We examined the evolution of supergenes and mechanisms underlying distyly in Linum species that diverged c. 33 million years ago (Ma). Using haplotype-resolved genomes and population genomics, we identified and characterized the S-loci of Linum perenne (distylous) and Linum grandiflorum (style length dimorphic), and compared them to that of Linum tenue (distylous). We then tested for a conserved hormonal mechanism regulating style length polymorphism in Linum. The S-locus supergene was consistently hemizygous in short-styled individuals across all three species, although it showed variation in size, gene content, repeat elements and extent of recombination suppression. Two S-linked candidate genes, TSS1 (style length) and WDR-44 (anther height/pollen self-incompatibility), were conserved. Consistent with a brassinosteroid-dependent role of TSS1, epibrassinolide treatment revealed a conserved, morph-specific effect on style length. S-locus structural polymorphism, candidate distyly genes and mechanisms regulating style length remain conserved > 30 Ma in Linum. In combination with findings from other systems, our results suggest that the brassinosteroid pathway frequently contributes to style length polymorphism.", "doi": "10.1111/nph.70392", "pmid": "40682296", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Other": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12371154"}], "notes": [], "created": "2025-08-19T13:25:54.698Z", "modified": "2025-11-19T10:24:41.159Z"}, {"entity": "publication", "iuid": "4cb1f3bbbd73476d85743dd1a3b24932", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4cb1f3bbbd73476d85743dd1a3b24932.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4cb1f3bbbd73476d85743dd1a3b24932"}}, "title": "Early germline sequestration in a basidiomycete fungus.", "authors": [{"family": "Thor\u00e9n", "given": "Markus Hiltunen", "initials": "MH", "orcid": "0000-0002-8880-872X", "researcher": {"href": "https://publications.scilifelab.se/researcher/77b54361528b4c7c8f5122d91d58b36d.json"}}, {"family": "Olsson", "given": "Boel", "initials": "B", "orcid": "0009-0006-4157-2664", "researcher": {"href": "https://publications.scilifelab.se/researcher/219a75999b65464ca3d405ac20898743.json"}}, {"family": "Vonk", "given": "Peter Jan", "initials": "PJ", "orcid": "0000-0001-5325-7430", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5684212a1f5478cab0943d5064e74a7.json"}}, {"family": "Siljestam", "given": "Mattias", "initials": "M", "orcid": "0000-0002-3720-4926", "researcher": {"href": "https://publications.scilifelab.se/researcher/653d5e0ec2bc4925a19db2697ad61a2d.json"}}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J", "orcid": "0000-0003-1518-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/db7ebacfd8764a988ee41f2e5ab23e50.json"}}, {"family": "Ryberg", "given": "Martin", "initials": "M", "orcid": "0000-0002-6795-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0a8578a1ace4105be91ec8116c84365.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2025-08-14", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "389", "issue": "6761", "pages": "720-723"}, "abstract": "In sexual organisms, inheritance of new mutations is highly dependent on the timing of germline definition. Here, we used the fairy ring-forming fungus Marasmius oreades to challenge the general assumption of a late germline separation in the Fungi. We collected mushrooms from different parts of rings over a 7-year period and identified new mutations in different tissues by whole-genome sequencing. We found evidence that fertile and sterile tissues had accumulated different mutations, suggesting that the germ line, destined for spore production, is already defined in the mycelium in this species. Moreover, the germ line carried fewer mutations than sterile tissues, indicating a lower mutation rate. Our findings suggest that early germline sequestration is more widespread than previously considered across multicellular life.", "doi": "10.1126/science.adu8580", "pmid": "40811541", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-08-29T12:41:10.841Z", "modified": "2025-11-21T13:14:48.967Z"}, {"entity": "publication", "iuid": "741f4c91234245268da4ddfa1e0b9efa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/741f4c91234245268da4ddfa1e0b9efa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/741f4c91234245268da4ddfa1e0b9efa"}}, "title": "Lrig3-deficient mice exhibit strain-specific alterations in liver fat accumulation, intestinal morphology, and middle ear inflammation.", "authors": [{"family": "Herdenberg", "given": "Carl", "initials": "C"}, {"family": "Henriksson", "given": "Roger", "initials": "R"}, {"family": "Hedman", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0001-6891-6996", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b1b2d57a55e415aa17acbd0318a019e.json"}}, {"family": "Rondahl", "given": "Veronica", "initials": "V"}], "type": "journal article", "published": "2025-08-10", "journal": {"title": "Gene", "issn": "1879-0038", "issn-l": "0378-1119", "volume": "960", "issue": null, "pages": "149539"}, "abstract": "The transmembrane protein leucine-rich repeats and immunoglobulin-like domains 3 (LRIG3) regulates fat metabolism and bone morphogenetic protein (BMP) signaling. Lrig3-deficient mice exhibit impaired development of the snout and the inner ear lateral canal, neural defects, and cardiac hypertrophy in adulthood. However, no thorough and unbiased analysis of the physiological functions of Lrig3 has previously been performed. To address this knowledge gap, we performed histopathological examination of 42 tissues and organs from 1-year-old female C57BL/6JBomTac and 129S1-U mice with different Lrig3 genotypes. Among the scored pathologies, three were significantly associated with Lrig3 genotype: spontaneous macrovesicular hepatocellular degeneration (hepatocellular steatosis) was less prevalent in Lrig3-deficient C57BL/6JBomTac mice, whereas dilated or flaccid ileum and otitis media were more common in Lrig3-deficient 129S1-U mice. To further investigate hepatic steatosis phenotypes, 8-week-old C57BL/6JBomTac mice of both sexes and different Lrig3 genotypes were subjected to consuming a high-fat diet (HFD) for 8 weeks. The HFD regimen led to relatively few cases of hepatocellular steatosis, with no significant differences among the genotypes; however, female Lrig3-deficient mice presented reduced microvesicular hepatocellular degeneration compared with their wild-type littermates. This study revealed that Lrig3 regulates liver fat accumulation, intestinal morphology, and middle ear inflammation in a mouse strain-dependent manner.", "doi": "10.1016/j.gene.2025.149539", "pmid": "40320098", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pii", "key": "S0378-1119(25)00327-0"}], "notes": [], "created": "2025-09-08T07:06:55.862Z", "modified": "2025-11-19T13:14:56.377Z"}, {"entity": "publication", "iuid": "ab9b4fd3312a411fa7600da6cc9fc651", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab9b4fd3312a411fa7600da6cc9fc651.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab9b4fd3312a411fa7600da6cc9fc651"}}, "title": "Precise mapping of single-stranded DNA breaks by sequence-templated erroneous DNA polymerase end-labelling.", "authors": [{"family": "Wenson", "given": "Leonie", "initials": "L", "orcid": "0000-0002-1864-1258", "researcher": {"href": "https://publications.scilifelab.se/researcher/989e0534adbd426386cec5526c5e9668.json"}}, {"family": "Heldin", "given": "Johan", "initials": "J", "orcid": "0000-0002-0915-5303", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8a546798d014cd3a44537ae5db9f889.json"}}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Erbilgin", "given": "Y\u00fccel", "initials": "Y"}, {"family": "Salman", "given": "Bar\u0131\u015f", "initials": "B", "orcid": "0000-0002-7657-8576", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb919f7fcc794c8898fe800056d42f38.json"}}, {"family": "Sundqvist", "given": "Anders", "initials": "A"}, {"family": "Schaal", "given": "Wesley", "initials": "W", "orcid": "0000-0001-6770-0878", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab184845a24f4effb22ec2b338ab8960.json"}}, {"family": "Sandbaumh\u00fcter", "given": "Friederike A", "initials": "FA"}, {"family": "Jansson", "given": "Erik T", "initials": "ET"}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7ddc09e57745909175e41ac2d1b647.json"}}, {"family": "Davidsson", "given": "Anton", "initials": "A"}, {"family": "Stenerl\u00f6w", "given": "Bo", "initials": "B", "orcid": "0000-0001-8878-8071", "researcher": {"href": "https://publications.scilifelab.se/researcher/22437ff9315d43089232926973feb0d2.json"}}, {"family": "Espinoza", "given": "Jaime A", "initials": "JA", "orcid": "0000-0002-0731-2715", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cdf2cd80f5b4f87adf6d936b6390ee8.json"}}, {"family": "Lindstr\u00f6m", "given": "Mikael", "initials": "M", "orcid": "0000-0003-1148-8497", "researcher": {"href": "https://publications.scilifelab.se/researcher/5aa942fbfbee4257a129b3e7888f5b6d.json"}}, {"family": "Lennartsson", "given": "Johan", "initials": "J"}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O", "orcid": "0000-0003-2883-1925", "researcher": {"href": "https://publications.scilifelab.se/researcher/68df823efa304c0b9962684ac1515808.json"}}], "type": "journal article", "published": "2025-08-04", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "16", "issue": "1", "pages": "7130"}, "abstract": "The ability to analyze whether DNA contains lesions is essential in identifying mutagenic substances. Currently, the detection of single-stranded DNA breaks (SSBs) lacks precision. To address this limitation, we develop a method for sequence-templated erroneous end-labelling sequencing (STEEL-seq), which enables the mapping of SSBs. The method requires a highly error-prone DNA polymerase, so we engineer a chimeric DNA polymerase, Sloppymerase, capable of replicating DNA in the absence of one nucleotide. Following the omission of a specific nucleotide (e.g., dATP) from the reaction mixture, Sloppymerase introduces mismatches directly downstream of SSBs at positions where deoxyadenosine should occur. This mismatch pattern, coupled with the retention of sequence information flanking these sites, ensures that the identified hits are bona fide SSBs. STEEL-seq is compatible with a variety of sequencing technologies, as demonstrated using Sanger, Illumina, PacBio, and Nanopore systems. Using STEEL-seq, we determine the SSB/base pair frequency in the human genome to range between 0.7 and 3.8 \u00d7 10-6 with an enrichment in active promoter regions.", "doi": "10.1038/s41467-025-62512-4", "pmid": "40759655", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12322144"}, {"db": "pii", "key": "10.1038/s41467-025-62512-4"}], "notes": [], "created": "2025-08-19T13:16:23.958Z", "modified": "2025-11-28T10:45:45.544Z"}, {"entity": "publication", "iuid": "bf8f3c333e934ca6989a77551e9e1a73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf8f3c333e934ca6989a77551e9e1a73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf8f3c333e934ca6989a77551e9e1a73"}}, "title": "Genomic and secretomic analyses of Blastobotrys yeasts reveal key xylanases for biomass decomposition.", "authors": [{"family": "Ravn", "given": "Jonas", "initials": "J", "orcid": "0000-0003-4328-2530", "researcher": {"href": "https://publications.scilifelab.se/researcher/26e5ad3ac36c49678bf382fb87b43e42.json"}}, {"family": "Ristinmaa", "given": "Amanda S", "initials": "AS", "orcid": "0000-0003-0120-0330", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e92b57ec1b14304be945f243b66717a.json"}}, {"family": "Mazurkewich", "given": "Scott", "initials": "S", "orcid": "0000-0002-9238-0615", "researcher": {"href": "https://publications.scilifelab.se/researcher/39a1e4f9d3a74121937087f8875a975a.json"}}, {"family": "Dias", "given": "Guilherme B", "initials": "GB", "orcid": "0000-0002-1459-3148", "researcher": {"href": "https://publications.scilifelab.se/researcher/73778a1096e04b5d94f8d5c6f3584d99.json"}}, {"family": "Larsbrink", "given": "Johan", "initials": "J", "orcid": "0000-0001-8386-2914", "researcher": {"href": "https://publications.scilifelab.se/researcher/99badc395dbc46d1a43ae5c3d39fd8aa.json"}}, {"family": "Geijer", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-4158-2938", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad8eab8b087d47c4bce77ee2661628fb.json"}}], "type": "journal article", "published": "2025-08-01", "journal": {"title": "Appl. Microbiol. Biotechnol.", "issn": "1432-0614", "issn-l": "0175-7598", "volume": "109", "issue": "1", "pages": "175"}, "abstract": "Xylanolytic enzyme systems in ascomycetous yeasts remain underexplored, despite the presence of yeasts in various xylan-rich ecological niches. In this study, we investigated the secreted xylanolytic machineries of three Blastobotrys species-B. mokoenaii, B. illinoisensis, and B. malaysiensis-by integrating genome annotation, bioinformatics, and secretome analyses of cultures grown on beechwood glucuronoxylan. Our findings demonstrate that these yeasts effectively hydrolyze xylan through the secretion of xylanases from the glycoside hydrolase (GH) family 11, which play a central role in cleaving the xylan backbone. Additionally, the yeasts produce a diverse array of other CAZymes, including members of GH families 3, 5, and 67, with putative roles in xylan degradation. We also report on the heterologous expression and functional characterization of the GH30_7 xylanase BmXyn30A from B. mokoenaii, which exhibits both glucuronoxylanase and xylobiohydrolase activities. We demonstrate additive effects between GH family 30 BmXyn30A and GH family 11 BmXyn11A during the hydrolysis of beechwood glucuronoxylan, where the enzymes exhibit complementary roles that enhance the deconstruction of this complex hemicellulose substrate. These findings broaden our understanding of the xylanolytic systems in yeasts and underscore the potential of Blastobotrys species as cell factories and natural xylanase producers. The enzymes they produce hold promise for biorefining applications, enabling efficient utilization of renewable xylan-rich plant biomass resources. KEY POINTS: \u2022 Extracellular GH11 xylanases dominate glucuronoxylan degradation in Blastobotrys yeasts. \u2022 Yeast GH30_7 enzyme shows multifaceted activity, supporting complex xylan breakdown. \u2022 Blastobotrys yeasts show promise as cell factories for industrial biotechnology applications.", "doi": "10.1007/s00253-025-13556-5", "pmid": "40748385", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12316802"}, {"db": "pii", "key": "10.1007/s00253-025-13556-5"}], "notes": [], "created": "2025-08-19T13:52:12.110Z", "modified": "2025-11-17T16:43:09.377Z"}, {"entity": "publication", "iuid": "8731474c0874412e8ff9f33c698c18a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8731474c0874412e8ff9f33c698c18a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8731474c0874412e8ff9f33c698c18a1"}}, "title": "Profiling of the microRNA transcriptome in feline whole blood.", "authors": [{"family": "Ohlsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0003-1116-0141", "researcher": {"href": "https://publications.scilifelab.se/researcher/91d12e64d2d740669ec499319b66c22e.json"}}, {"family": "Han\u00e5s", "given": "Sofia", "initials": "S"}, {"family": "Holst", "given": "Bodil S", "initials": "BS"}, {"family": "Lorent", "given": "Julie", "initials": "J"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}, {"family": "H\u00f6glund", "given": "Katja", "initials": "K"}, {"family": "Tidholm", "given": "Anna", "initials": "A"}, {"family": "Ljungvall", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-6617-0454", "researcher": {"href": "https://publications.scilifelab.se/researcher/12b19ecb541c4d13a685b574390e8104.json"}}, {"family": "H\u00e4ggstr\u00f6m", "given": "Jens", "initials": "J", "orcid": "0000-0003-3402-023X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e1779188e20402294f12861a8232e71.json"}}], "type": "journal article", "published": "2025-07-31", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "27962", "issn-l": "2045-2322"}, "abstract": "Circulating microRNAs (miRNAs) are potential biomarkers for numerous diseases. Characterization of the whole blood (WB) miRNA-transcriptome (miRNome) in cats is lacking, which limits the potential use of miRNAs as biomarkers for diseases such as feline cardiovascular disease. The aims of the present study were to profile and evaluate circulating miRNAs in feline WB by high-throughput sequencing of the total miRNome in WB from twelve domestic mixed breed (DOM) and Norwegian Forest (NFO) cats stringently diagnosed with or without preclinical hypertrophic cardiomyopathy (HCM). A total of 459 mature miRNAs were identified in feline WB, of which 40 were potential novel feline miRNAs. A majority, 85.3%, of the miRNAs showed sequence similarity with human miRNAs. An effect of breed was found, with up to thirteen WB miRNAs being differentially abundant between breeds. The majority of the significant breed-specific miRNAs in feline WB could be associated with regulation of haematopoietic cells. One miRNA, miR-204-5p, was potentially associated with preclinical HCM in NFO cats, but the results need to be confirmed in a larger and sex-unbiased cohort. In conclusion, here we used miRNome-sequencing to identify hundreds of circulating miRNAs in feline WB. Breed should be considered when evaluating the miRNome in feline WB.", "doi": "10.1038/s41598-025-09478-x", "pmid": "40745193", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12313912"}, {"db": "pii", "key": "10.1038/s41598-025-09478-x"}], "notes": [], "created": "2025-09-05T08:24:52.249Z", "modified": "2025-09-09T13:12:41.462Z"}, {"entity": "publication", "iuid": "79cda722345d4dddadc80c3f12903789", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79cda722345d4dddadc80c3f12903789.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79cda722345d4dddadc80c3f12903789"}}, "title": "Cytokines, chemokines and antibodies against histone-3/4 citrullinated peptides in rheumatoid arthritis patients with pulmonary fibrosis.", "authors": [{"family": "Johansson", "given": "Linda", "initials": "L", "orcid": "0000-0001-7071-4699", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b9129e8ce7846e5b35b50f1ff4493e2.json"}}, {"family": "Pratesi", "given": "Federico", "initials": "F", "orcid": "0000-0002-7226-0907", "researcher": {"href": "https://publications.scilifelab.se/researcher/978ceb177a5545c89fe32f0689843120.json"}}, {"family": "Errante", "given": "Fosca", "initials": "F", "orcid": "0000-0001-7790-9886", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f4b94b4ee454c8fa990418b921272ab.json"}}, {"family": "Pacini", "given": "Lorenzo", "initials": "L", "orcid": "0000-0003-0737-2213", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8e5edfce6ae432cb0b3333cd9a8ebfd.json"}}, {"family": "Migliorini", "given": "Paola", "initials": "P", "orcid": "0000-0001-6433-4964", "researcher": {"href": "https://publications.scilifelab.se/researcher/1de011ca211242b3bb0639adc36c47e3.json"}}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}], "type": "journal article", "published": "2025-07-30", "journal": {"title": "Arthritis Res. Ther.", "issn": "1478-6362", "volume": "27", "issue": "1", "pages": "160", "issn-l": "1478-6354"}, "abstract": "Rheumatoid arthritis (RA) associated interstitial lung disease (ILD) is the most common pulmonary manifestations of RA, with a progressive course and a poor survival. An early detection and better treatment is essential to improve outcome. We evaluated 16 analytes that could be relevant for the development of RA ILD.\n\nIn an inception cohort of 1118 early RA patients, pulmonary fibrosis (PF) were identified in 60 patients after a mean follow-up of 5.3 years using high resolution computer tomography (HRCT). As controls, 124 early RA patients without PF and 94 matched population controls without known rheumatic disease were studied. Analysis of antibodies against histones 3 and 4 derived citrullinated peptides (CitH3/H4), and cytokines/chemokines levels were performed in plasma samples collected at RA diagnosis using in-house ELISA and Luminex analysis.\n\nAnti-CitH3(114-135) antibodies were the only antibody with increased frequency and levels in patients with PF versus without PF. The highest OR for PF development were found when combining positivity for anti-CitH3(114-135) and -CitH4(31-50) antibodies, OR 2.26. Levels of IL1\u03b1, IL1\u00df, TNF\u03b1, VEGFA and MIP\u03b1 remained significantly elevated in patients with PF compared without PF, after adjustments and Bonferroni corrections. Several of the cytokines/chemokines correlated significantly with the histone antibodies in patients without PF. Partial least squares discriminant analysis including antibodies against citrullinated histon peptides and cytokines/chemokines identified significantly in PF in non-smokers.\n\nAntibodies against CitH3 peptides and several of the analysed cytokines/chemokines in samples collected at diagnosis were associated with subsequent delevopment of PF in patients with RA.", "doi": "10.1186/s13075-025-03603-x", "pmid": "40739515", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12308956"}, {"db": "pii", "key": "10.1186/s13075-025-03603-x"}], "notes": [], "created": "2025-11-21T11:45:04.126Z", "modified": "2025-11-21T11:45:04.707Z"}, {"entity": "publication", "iuid": "e4171e3c321d427eab5134bacfa87814", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e4171e3c321d427eab5134bacfa87814.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e4171e3c321d427eab5134bacfa87814"}}, "title": "Cross-generational genomic prediction of Norway spruce (Picea abies) wood properties: an evaluation using independent validation.", "authors": [{"family": "Hayatgheibi", "given": "Haleh", "initials": "H"}, {"family": "Hallingb\u00e4ck", "given": "Henrik R", "initials": "HR"}, {"family": "Gezan", "given": "Salvador A", "initials": "SA"}, {"family": "Lundqvist", "given": "Sven-Olof", "initials": "SO"}, {"family": "Grahn", "given": "Thomas", "initials": "T"}, {"family": "Scheepers", "given": "Gerhard", "initials": "G"}, {"family": "Ranade", "given": "Sonali Sachin", "initials": "SS"}, {"family": "K\u00e4rkk\u00e4inen", "given": "Katri", "initials": "K"}, {"family": "Garc\u00eda Gil", "given": "M Rosario", "initials": "MR"}], "type": "journal article", "published": "2025-07-21", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "26", "issue": "1", "pages": "680", "issn-l": "1471-2164"}, "abstract": "The evaluation of genomic selection (GS) efficiency in forestry has primarily relied on cross-validation schemes that split the same population within a single generation for both training and validation. While useful, this approach may not be reliable for multigenerational breeding. To our knowledge, this is the first study to assess genomic prediction in Norway spruce using a large dataset spanning two generations in two environments. We trained pedigree-based (ABLUP) and marker-based (GBLUP) prediction models under three approaches: forward prediction, backward prediction, and across-environment prediction. The models were evaluated for ring-width, solid-wood and tracheid characteristics, using ~ 6,000 phenotyped and ~ 2,500 genotyped individual. Predictive ability (PA) and prediction accuracy (ACC) were estimated using an independent validation method, ensuring no individuals were shared between training and validation datasets. To assess the trade-off between comprehensive radial history and practical direct methods, we compared GBLUP models trained with cumulative area-weighted density (AWE-GBLUP) and single annual-ring density (SAD-GBLUP) from mother plus-trees. These models were validated using early and mature-stage progeny density measurements across two trials.\n\nDespite the smaller number of individuals used in the GBLUP models, both PA and ACC were generally comparable to those of the ABLUP model, particularly for cross-environment predictions. Overall, forward and backward predictions were significantly higher for density-related and tracheid properties, suggesting that across-generation predictions are feasible for wood properties but may be challenging for growth and low-heritability traits. Notably, SAD-GBLUP provided comparable prediction accuracies to AWE-GBLUP, supporting the use of more practical and cost-effective phenotyping methods in operational breeding programs.\n\nOur findings highlight the need for context-specific models to improve the accuracy and reliability of genomic prediction in forest tree breeding. Future efforts might aim to expand training populations, incorporate non-additive genetic effects, and validate model performance across cambial ages while accounting for climatic variability during the corresponding growth years. Overall, this study offers a valuable foundation for implementing GS in Norway spruce breeding programs.", "doi": "10.1186/s12864-025-11861-x", "pmid": "40691535", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12278512"}, {"db": "pii", "key": "10.1186/s12864-025-11861-x"}], "notes": [], "created": "2025-11-17T16:50:45.625Z", "modified": "2025-11-17T16:50:45.629Z"}, {"entity": "publication", "iuid": "19a4115c6ad14acaaf738a62c51e4f69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19a4115c6ad14acaaf738a62c51e4f69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19a4115c6ad14acaaf738a62c51e4f69"}}, "title": "Genome analyses suggest recent speciation and postglacial isolation in the Norwegian lemming.", "authors": [{"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Feinauer", "given": "Isabelle S", "initials": "IS", "orcid": "0009-0004-4615-0810", "researcher": {"href": "https://publications.scilifelab.se/researcher/18d95245a50e408a9643a18b7c0fc3d2.json"}}, {"family": "Soares", "given": "Andr\u00e9 E R", "initials": "AER"}, {"family": "Lagerholm", "given": "Vendela K", "initials": "VK"}, {"family": "N\u00e4svall", "given": "Karin", "initials": "K", "orcid": "0000-0002-2970-4189", "researcher": {"href": "https://publications.scilifelab.se/researcher/9173164aadbe47b0b4132d2c6e654cf3.json"}}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA", "orcid": "0009-0002-8357-5186", "researcher": {"href": "https://publications.scilifelab.se/researcher/5419b796720a47c8aa7a26ca663a96bd.json"}}, {"family": "Prost", "given": "Stefan", "initials": "S", "orcid": "0000-0002-6229-3596", "researcher": {"href": "https://publications.scilifelab.se/researcher/809ba200bb864ec9abf0d0cad09c5a42.json"}}, {"family": "Kuzmina", "given": "Elena A", "initials": "EA"}, {"family": "Smirnov", "given": "Nickolay G", "initials": "NG"}, {"family": "Stewart", "given": "John R", "initials": "JR", "orcid": "0000-0002-3506-5264", "researcher": {"href": "https://publications.scilifelab.se/researcher/62e8f2e54f1a4f1d96d8f4ae1de97a93.json"}}, {"family": "Knul", "given": "Monika V", "initials": "MV", "orcid": "0000-0002-0650-0992", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff550d1088bb4857a28277ae1db41452.json"}}, {"family": "Noiret", "given": "Pierre", "initials": "P"}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M", "orcid": "0000-0001-8865-0937", "researcher": {"href": "https://publications.scilifelab.se/researcher/79253311b1c64b599c8987b947459391.json"}}, {"family": "Ehrich", "given": "Dorothee", "initials": "D"}, {"family": "Pokrovsky", "given": "Ivan", "initials": "I"}, {"family": "Fedorov", "given": "Vadim B", "initials": "VB", "orcid": "0000-0003-3938-4200", "researcher": {"href": "https://publications.scilifelab.se/researcher/017b3cc7d41e46feb13e4e919b0c2dd5.json"}}, {"family": "Goropashnaya", "given": "Anna V", "initials": "AV", "orcid": "0009-0005-4712-6297", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e89f839e5c24f0dbef8deadb3a17f8d.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}], "type": "journal article", "published": "2025-07-15", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "122", "issue": "28", "pages": "e2424333122"}, "abstract": "The Norwegian lemming (Lemmus lemmus) is a small rodent distributed across the Fennoscandian mountain tundra and the Kola Peninsula. The Norwegian lemming likely evolved during the Late Pleistocene and inhabited Fennoscandia shortly prior to the Last Glacial Maximum. However, the exact timing and origins of the species, and its phylogenetic position relative to the closely related Siberian lemming (Lemmus sibiricus) remain disputed. Moreover, the presence of ancient or contemporary gene flow between both species is largely untested. The Norwegian lemming displays characteristic phenotypic and behavioral adaptations (e.g., coat color, aggression) that are not present in other Lemmus species. We generated a de novo genome assembly for the Norwegian lemming and resequenced nine modern and two ancient Lemmus spp. genomes. We show that all Lemmus species form distinct monophyletic clades, with concordant topology between the mitochondrial and nuclear genome phylogenies. The Siberian lemming is divided into two distinct but paraphyletic clades, one in the east and one in the west, where the western clade represents a sister taxon to the Norwegian lemming. We estimate that the Norwegian and western Siberian lemming diverged shortly before the Last Glacial Maximum, making the Norwegian lemming one of the youngest known mammalian species. We did not find any indication of gene flow between L. lemmus and L. sibiricus, suggesting postglacial isolation of L. lemmus. Furthermore, we identify species-specific genomic differences in genes related to coat color and fat transport, which are likely associated with the distinctive coloration and overwintering behavior observed in the Norwegian lemming.", "doi": "10.1073/pnas.2424333122", "pmid": "40587810", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12280882"}], "notes": [], "created": "2025-07-01T06:45:31.166Z", "modified": "2025-11-14T11:07:37.863Z"}, {"entity": "publication", "iuid": "936a7690dbce49328330eb645143c8cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/936a7690dbce49328330eb645143c8cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/936a7690dbce49328330eb645143c8cf"}}, "title": "Transcriptomic Patterns in Adult and Pediatric Patients with IgA Nephropathy or IgA Vasculitis with Nephropathy.", "authors": [{"family": "Levin", "given": "Anna", "initials": "A", "orcid": "0000-0002-1299-6920", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff22b37b69144ccc899c5e50be3abc5f.json"}}, {"family": "Schwarz", "given": "Angelina", "initials": "A", "orcid": "0009-0000-7828-9260", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee209747d3c64713a3aad7b1ff6c5748.json"}}, {"family": "van Hoef", "given": "Vincent", "initials": "V", "orcid": "0000-0003-1707-7066", "researcher": {"href": "https://publications.scilifelab.se/researcher/05c9836d67fa498381e8ee228464bada.json"}}, {"family": "Wijkstr\u00f6m", "given": "Julia", "initials": "J", "orcid": "0000-0001-6183-5878", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c20445221e242689b8473bdc2cc7a4b.json"}}, {"family": "Bruchfeld", "given": "Annette", "initials": "A", "orcid": "0000-0002-9752-9941", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc6ee3e8a4124c5f8d6506ab762949ae.json"}}, {"family": "Herthelius", "given": "Maria", "initials": "M", "orcid": "0000-0003-3306-2235", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe439528adab4cf6988826204b3a2929.json"}}, {"family": "Wennberg", "given": "Lars", "initials": "L", "orcid": "0000-0002-3313-3374", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d7c30072ecb4c70b53bb1abc7f072f3.json"}}, {"family": "B\u00e1r\u00e1ny", "given": "Peter", "initials": "P", "orcid": "0000-0001-6501-8293", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1694c39562e4675bc23cbf9366a0e18.json"}}, {"family": "Witasp", "given": "Anna", "initials": "A"}, {"family": "Wernerson", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2025-07-01", "journal": {"title": "J. Am. Soc. Nephrol.", "issn": "1533-3450", "issn-l": "1046-6673", "volume": null, "issue": null, "pages": null}, "abstract": "Disease manifestations and progression of IgA Nephropathy vary widely between individuals, particularly between children and adults. To further understand these differences, we examined the transcriptional profiles in kidney biopsies from both adult and paediatric IgA nephropathy patients in relation to normal kidneys.\r\n\r\nKidney biopsies from 95 participants, 71 adults and 13 children with histopathologically verified IgA nephropathy or IgA vasculitis with nephropathy as well as 11 living donors, were microdissected into glomerular and tubulointerstitial fractions and subjected to RNA sequencing. Differential gene expression analysis was performed across groups, and functional enrichment analyses were conducted using Gene ontology and Kyoto Encyclopedia of Genes and Genomes. Histopathological grading (Oxford and part of the Banff classifications) and clinical data (at time of biopsy and up to five years of follow-up) were analysed in relation to normalized RNA counts.\r\n\r\nDifferentially expressed genes obtained from all patients versus living donors, both glomerular and tubulointerstitial fractions, were enriched for immune system and complement activation pathways. When comparing of adults to children within the IgA nephropathy/IgA vasculitis with nephropathy group, 5562 and 3539 differentially expressed genes in each fraction were identified with pathway enrichment of including processes related to the endoplasmic reticulum and mitochondrial activity (glomeruli), as well as T cell activation (tubulointerstitium).\r\n\r\nDistinct transcriptional profiles with enrichment of inflammation and immune response pathways were revealed in patients compared to living donors. However, the transcriptomic signatures across adult and paediatric patients were not consistent, highlighting differences in pathways involved in endoplasmic reticular, mitochondrial and T cell activity when comparing adults and children.", "doi": "10.1681/ASN.0000000787", "pmid": "40591410", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pii", "key": "00001751-990000000-00696"}], "notes": [], "created": "2025-11-20T15:20:22.134Z", "modified": "2025-11-21T12:59:19.906Z"}, {"entity": "publication", "iuid": "4f31e8206ab542c7a81fb00a1819e982", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f31e8206ab542c7a81fb00a1819e982.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f31e8206ab542c7a81fb00a1819e982"}}, "title": "Uncemented hip arthroplasty and denosumab: increased postoperative dipeptide concentrations and identification of potential new bone turnover biomarkers.", "authors": [{"family": "Kultima", "given": "Kim", "initials": "K", "orcid": "0000-0002-0680-1410", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ae376585168459681f5e2cae0c75b96.json"}}, {"family": "Ashtiani", "given": "Saman Hosseini", "initials": "SH"}, {"family": "Erngren", "given": "Ida", "initials": "I"}, {"family": "Khoonsari", "given": "Payam Emami", "initials": "PE"}, {"family": "Carlsson", "given": "Henrik", "initials": "H"}, {"family": "Herman", "given": "Stephanie", "initials": "S"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Mallmin", "given": "Hans", "initials": "H"}, {"family": "Hailer", "given": "Nils P", "initials": "NP"}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "JBMR Plus", "issn": "2473-4039", "volume": "9", "issue": "7", "pages": "ziaf091", "issn-l": null}, "abstract": "Denosumab is a potent antagonist of RANKL and is widely used to treat severe postmenopausal osteoporosis. Using high-resolution mass spectrometry (HRMS), we aimed to identify molecular mediators associated with the rapid reactivation of osteoclasts following discontinuation of denosumab. In a previously reported randomized controlled trial, 64 patients undergoing uncemented total hip arthroplasty were randomized to receive 2 doses of 60 mg denosumab or placebo, administered 1-3 d and 6 mo postoperatively. Serum samples were analyzed using untargeted HRMS coupled with liquid chromatography, and bone turnover markers were assessed. Data were evaluated using linear mixed-effects models and machine learning techniques. After surgery, 83 metabolite features showed significant concentration changes (p < .0001). Denosumab-treated patients exhibited increased levels of the dipeptides di-L-phenylalanine, phenylalanylleucine, and alpha-Asp-Phe, and decreased levels of fibrinopeptide A and related peptides 24 mo after surgery. The oxidized peptide AP(Ox)GDRGEP(Ox)GPP(Ox)GP, derived from the collagen type I alpha 1 chain (COL1A1) and referred to as COL1A1-OxP, showed a strong correlation with the bone formation marker procollagen type 1 amino-terminal propeptide (P1NP) (p = 4.4E-83). Similarly, the tripeptide DL-alpha-aspartyl-DL-valyl-DL-proline (DVP) correlated highly with the bone resorption marker carboxy-terminal telopeptide of type 1 collagen (CTX) (p = 1.1E-222). P1NP and CTX levels were suppressed at 3, 6, and 12 mo postoperatively but exceeded baseline levels by 24 mo. Global metabolic shifts were observed postoperatively, with distinct profiles between treatment groups. The observed increase in specific dipeptides may reflect mechanisms contributing to rebound bone loss following denosumab withdrawal. Fibrinopeptide A and its analogs may play a protective role, while COL1A1-OxP and DVP represent potential new markers of bone turnover. These findings suggest metabolomics-based biomarkers could aid clinical decision-making by allowing earlier detection of rebound effects and guiding individualized treatment strategies after denosumab therapy. Clinical trial registration number: ClinicalTrials.gov, NCT01630941 (URL: https://clinicaltrials.gov/); European Union Clinical Trials Register (EU CTR), EudraCT No. 2011-001481-18 (https://www.clinicaltrialsregister.eu/).", "doi": "10.1093/jbmrpl/ziaf091", "pmid": "40584156", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12202150"}, {"db": "pii", "key": "ziaf091"}, {"db": "ClinicalTrials.gov", "key": "NCT01630941"}], "notes": [], "created": "2025-11-21T12:10:46.965Z", "modified": "2025-11-21T12:10:47.024Z"}, {"entity": "publication", "iuid": "8da9f8bb7e024de5b9d404a6ed360d99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8da9f8bb7e024de5b9d404a6ed360d99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8da9f8bb7e024de5b9d404a6ed360d99"}}, "title": "Angiopoietin-TIE2 feedforward circuit promotes PIK3CA-driven venous malformations.", "authors": [{"family": "Kraft", "given": "Marle", "initials": "M", "orcid": "0000-0002-3523-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bac6d144f4143b7ad9ad0a9058d95a0.json"}}, {"family": "Schoofs", "given": "Hans", "initials": "H", "orcid": "0000-0003-3429-912X", "researcher": {"href": "https://publications.scilifelab.se/researcher/32c662013aae42298c0776802f3628fa.json"}}, {"family": "Petkova", "given": "Milena", "initials": "M", "orcid": "0000-0002-7186-7256", "researcher": {"href": "https://publications.scilifelab.se/researcher/458b9dbc408c4118b97be343da8b3b49.json"}}, {"family": "Andrade", "given": "Jorge", "initials": "J", "orcid": "0000-0002-4577-8620", "researcher": {"href": "https://publications.scilifelab.se/researcher/477b341b9d0048dab408f6106fc5b915.json"}}, {"family": "Grosso", "given": "Ana Rita", "initials": "AR", "orcid": "0000-0001-6974-4209", "researcher": {"href": "https://publications.scilifelab.se/researcher/07a33297431f417eaabbdbe477c06c4f.json"}}, {"family": "Benedito", "given": "Rui", "initials": "R", "orcid": "0000-0003-2458-3055", "researcher": {"href": "https://publications.scilifelab.se/researcher/e15242bf49384c309118be8db7abe19a.json"}}, {"family": "De Roo", "given": "An-Katrien", "initials": "AK", "orcid": "0000-0002-0000-1260", "researcher": {"href": "https://publications.scilifelab.se/researcher/108ee3be589741e28c1e676b248ec20f.json"}}, {"family": "Boon", "given": "Laurence M", "initials": "LM", "orcid": "0000-0001-8273-3328", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bdedae62ce74bd08d22df3bd007e76a.json"}}, {"family": "Vikkula", "given": "Miikka", "initials": "M", "orcid": "0000-0002-6236-338X", "researcher": {"href": "https://publications.scilifelab.se/researcher/14ec2db8cf364aa383bcac2ebf64cc39.json"}}, {"family": "Kapp", "given": "Friedrich G", "initials": "FG", "orcid": "0000-0002-2729-6177", "researcher": {"href": "https://publications.scilifelab.se/researcher/392ca5f5f1914e0585da18619bda2c00.json"}}, {"family": "H\u00e4gerling", "given": "Ren\u00e9", "initials": "R", "orcid": "0000-0002-6830-2043", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc9254578d4a4ee8b7d24b2e4a3025ab.json"}}, {"family": "Potente", "given": "Michael", "initials": "M", "orcid": "0000-0002-5689-0036", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2fbc439106a4708b03a324aa5499f47.json"}}, {"family": "M\u00e4kinen", "given": "Taija", "initials": "T", "orcid": "0000-0002-9338-1257", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf99a0589d1f4532b532bfc575edaada.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Nat Cardiovasc Res", "issn": "2731-0590", "volume": "4", "issue": "7", "pages": "801-820", "issn-l": null}, "abstract": "Venous malformations (VMs) are vascular anomalies lacking curative treatments, often caused by somatic PIK3CA mutations that hyperactivate the PI3K\u03b1-AKT-mTOR signaling pathway. Here, we identify a venous-specific signaling circuit driving disease progression, where excessive PI3K\u03b1 activity amplifies upstream TIE2 receptor signaling through autocrine and paracrine mechanisms. In Pik3caH1047R-driven VM mouse models, single-cell transcriptomics and lineage tracking revealed clonal expansion of mutant endothelial cells with a post-capillary venous phenotype, characterized by suppression of the AKT-inhibited FOXO1 and its target genes, including the TIE2 antagonist ANGPT2. An imbalance in TIE2 ligands, likely exacerbated by aberrant recruitment of smooth muscle cells producing the agonist ANGPT1, increased TIE2 activity in both mouse and human VMs. While mTOR blockade had limited effects on advanced VMs in mice, inhibiting TIE2 or ANGPT effectively suppressed their growth. These findings uncover a PI3K-FOXO1-ANGPT-TIE2 circuit as a core driver of PIK3CA-related VMs and highlight TIE2 as a promising therapeutic target.", "doi": "10.1038/s44161-025-00655-9", "pmid": "40410415", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12259471"}, {"db": "pii", "key": "10.1038/s44161-025-00655-9"}], "notes": [], "created": "2025-11-18T11:56:53.465Z", "modified": "2025-11-28T10:48:02.845Z"}, {"entity": "publication", "iuid": "e60c8cab27a24067b89de060bdcc92e4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e60c8cab27a24067b89de060bdcc92e4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e60c8cab27a24067b89de060bdcc92e4"}}, "title": "The plasma proteome reveals distinct signaling pathways associated with PR3-ANCA positive and MPO-ANCA positive vasculitis.", "authors": [{"family": "Hellbacher", "given": "Erik", "initials": "E"}, {"family": "van Hoef", "given": "Vincent", "initials": "V"}, {"family": "Johansson", "given": "Alina", "initials": "A"}, {"family": "Knight", "given": "Ann", "initials": "A"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Bruchfeld", "given": "Annette", "initials": "A"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Ohlsson", "given": "Sophie", "initials": "S"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Dahlqvist", "given": "Johanna", "initials": "J"}], "type": "journal article", "published": "2025-06-18", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "16", "pages": "1600754", "issn-l": "1664-3224"}, "abstract": "Despite recent advances, the pathophysiological mechanisms underlying anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitides (AAV) remain incompletely understood, and comparative proteomic analyses of AAV subtypes are lacking. This study aimed to identify key molecular signaling pathways activated in AAV and to elucidate molecular distinctions between AAV with proteinase 3 ANCA (PR3-AAV) and AAV with myeloperoxidase ANCA (MPO-AAV).\n\nPlasma samples from 41 cases with active PR3-AAV, 24 with active MPO-AAV and 138 population controls were analyzed for 185 proteins using proximity extension assay and Luminex. Differential expression was assessed between PR3-AAV, MPO-AAV and controls using univariate and partial least squares discriminant analyses. Protein-protein interactions and pathway enrichment were explored using STRING and Cytoscape databases.\n\nCompared with controls, 31 proteins were significantly upregulated in PR3-AAV and 29 in MPO-AAV; 18 were shared, whereas 13 and 11 were specific to PR3-AAV and MPO-AAV, respectively. Shared proteins were enriched in general immune pathways, including IL-6 signaling. AAV subgroup-specific proteins were combined with proteins differentiating between PR3-AAV and MPO-AAV in a direct comparison. MMP-1, MMP-9, HGF, and OSM were uniquely upregulated in PR3-AAV, while TNF, TNF-R1/R2, TNFRSF14, and TNFRSF9 were prominent in MPO-AAV. Functional enrichment analyses underscored STAT3 signaling in PR3-AAV and TNF signaling in MPO-AAV.\n\nThis study identifies distinct and shared signaling pathways in PR3-AAV and MPO-AAV, highlighting STAT3 and TNF pathways as potential subtype-specific mechanisms. These findings offer insight into AAV pathogenesis and may guide the development of more targeted, less toxic treatments tailored to AAV subtypes.", "doi": "10.3389/fimmu.2025.1600754", "pmid": "40607391", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12213373"}], "notes": [], "created": "2025-11-18T17:41:37.997Z", "modified": "2025-11-18T17:41:38.003Z"}, {"entity": "publication", "iuid": "674ed939c1a74109b72a53ce6576ea0d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/674ed939c1a74109b72a53ce6576ea0d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/674ed939c1a74109b72a53ce6576ea0d"}}, "title": "Unlocking novel T cell-based immunotherapy for hepatocellular carcinoma through neoantigen-driven T cell receptor isolation.", "authors": [{"family": "Maravelia", "given": "Panagiota", "initials": "P"}, {"family": "Yao", "given": "Haidong", "initials": "H", "orcid": "0009-0007-4791-5063", "researcher": {"href": "https://publications.scilifelab.se/researcher/03a40cff36064374912d40cc5a9c65db.json"}}, {"family": "Cai", "given": "Curtis", "initials": "C", "orcid": "0000-0002-3490-4361", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ea25e71e96246d89437270a12cc9e47.json"}}, {"family": "Nascimento Silva", "given": "Daniela", "initials": "D", "orcid": "0000-0003-2165-4989", "researcher": {"href": "https://publications.scilifelab.se/researcher/061bbf2c5a864c5c9e852fcab907d29e.json"}}, {"family": "Fransson", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-4762-901X", "researcher": {"href": "https://publications.scilifelab.se/researcher/30428cafc89647768f6c69eecf98efcf.json"}}, {"family": "Nilsson", "given": "Ola B", "initials": "OB", "orcid": "0000-0002-7516-1760", "researcher": {"href": "https://publications.scilifelab.se/researcher/096ce3bf888b4ad395d53bb3c11f6946.json"}}, {"family": "Lu", "given": "Yong-Chen William", "initials": "YW", "orcid": "0000-0002-0275-9825", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa8d7936625c42078b815953810ee136.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P", "orcid": "0000-0003-1210-5961", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc0cba74e74a4c39a8f96319cb9a3034.json"}}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Gatto", "given": "Francesca", "initials": "F"}, {"family": "Rovesti", "given": "Giulia", "initials": "G", "orcid": "0000-0002-2761-9482", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd6c4824c71c44378a7f45649766f4cd.json"}}, {"family": "Carlsten", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9815-0012", "researcher": {"href": "https://publications.scilifelab.se/researcher/7dadae83c2494c7abc65118f04e1b6b6.json"}}, {"family": "Sallberg", "given": "Matti", "initials": "M", "orcid": "0000-0002-8858-5132", "researcher": {"href": "https://publications.scilifelab.se/researcher/89d4712be75441d6b49aca02c600bc70.json"}}, {"family": "St\u00e5l", "given": "Per", "initials": "P"}, {"family": "Jorns", "given": "Carl", "initials": "C", "orcid": "0000-0001-7727-8113", "researcher": {"href": "https://publications.scilifelab.se/researcher/59d387bd893f45bdb3663a0ef3aae88a.json"}}, {"family": "Buggert", "given": "Marcus", "initials": "M", "orcid": "0000-0003-0633-1719", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a54e4b5136642eeafa77ac5118a0c81.json"}}, {"family": "Pasetto", "given": "Anna", "initials": "A", "orcid": "0000-0002-5254-2173", "researcher": {"href": "https://publications.scilifelab.se/researcher/781c8b467fa144e494d13c7a3e80b4fc.json"}}], "type": "journal article", "published": "2025-06-06", "journal": {"title": "Gut", "issn": "1468-3288", "volume": "74", "issue": "7", "pages": "1125-1136", "issn-l": "0017-5749"}, "abstract": "Tumour-infiltrating T cells can mediate both antitumour immunity and promote tumour progression by creating an immunosuppressive environment. This dual role is especially relevant in hepatocellular carcinoma (HCC), characterised by a unique microenvironment and limited success with current immunotherapy.\n\nWe evaluated T cell responses in patients with advanced HCC by analysing tumours, liver flushes and liver-draining lymph nodes, to understand whether reactive T cell populations could be identified despite the immunosuppressive environment.\n\nT cells isolated from clinical samples were tested for reactivity against predicted neoantigens. Single-cell RNA sequencing was employed to evaluate the transcriptomic and proteomic profiles of antigen-experienced T cells. Neoantigen-reactive T cells expressing 4-1BB were isolated and characterised through T-cell receptor (TCR)-sequencing.\n\nBioinformatic analysis identified 542 candidate neoantigens from seven patients. Of these, 78 neoantigens, along with 11 hotspot targets from HCC driver oncogenes, were selected for ex vivo T cell stimulation. Reactivity was confirmed in co-culture assays for 14 targets, with most reactive T cells derived from liver flushes and lymph nodes. Liver flush-derived T cells exhibited central memory and effector memory CD4+ with cytotoxic effector profiles. In contrast, tissue-resident memory CD4+ and CD8+ T cells with an exhausted profile were primarily identified in the draining lymph nodes.\n\nThese findings offer valuable insights into the functional profiles of neoantigen-reactive T cells within and surrounding the HCC microenvironment. T cells isolated from liver flushes and tumour-draining lymph nodes may serve as a promising source of reactive T cells and TCRs for further use in immunotherapy for HCC.", "doi": "10.1136/gutjnl-2024-334148", "pmid": "39832892", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12611799"}, {"db": "pii", "key": "gutjnl-2024-334148"}], "notes": [], "created": "2025-11-19T08:23:34.477Z", "modified": "2025-11-21T15:22:04.326Z"}, {"entity": "publication", "iuid": "14a490b69be949de8cbbefbdfbe5d0e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14a490b69be949de8cbbefbdfbe5d0e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14a490b69be949de8cbbefbdfbe5d0e5"}}, "title": "Data of the Insect Biome Atlas: a metabarcoding survey of the terrestrial arthropods of Sweden and Madagascar.", "authors": [{"family": "Miraldo", "given": "A", "initials": "A", "orcid": "0000-0001-6107-006X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b1de25c21dc4c5fb541f4e8766de4b7.json"}}, {"family": "Sundh", "given": "J", "initials": "J", "orcid": "0000-0003-3053-9392", "researcher": {"href": "https://publications.scilifelab.se/researcher/655b68ac26af42ad9fb4dfe0869e15ea.json"}}, {"family": "Iwaszkiewicz-Eggebrecht", "given": "E", "initials": "E"}, {"family": "Buczek", "given": "M", "initials": "M"}, {"family": "Goodsell", "given": "R", "initials": "R"}, {"family": "Johansson", "given": "H", "initials": "H"}, {"family": "Fisher", "given": "B L", "initials": "BL", "orcid": "0000-0002-4653-3270", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e4747cc54254e8181f595e6fe21b953.json"}}, {"family": "Raharinjanahary", "given": "D", "initials": "D"}, {"family": "Rajoelison", "given": "E T", "initials": "ET"}, {"family": "Ranaivo", "given": "C", "initials": "C"}, {"family": "Randrianandrasana", "given": "C", "initials": "C"}, {"family": "Rafanomezantsoa", "given": "J-J", "initials": "J"}, {"family": "Manoharan", "given": "L", "initials": "L"}, {"family": "Granqvist", "given": "E", "initials": "E", "orcid": "0000-0002-1513-1674", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b07f15f8724fdbbcdf34e6d6837147.json"}}, {"family": "van Dijk", "given": "L J A", "initials": "LJA"}, {"family": "Alberg", "given": "L", "initials": "L"}, {"family": "\u00c5hl\u00e9n", "given": "D", "initials": "D"}, {"family": "Aspebo", "given": "M", "initials": "M"}, {"family": "\u00c5str\u00f6m", "given": "S", "initials": "S"}, {"family": "Bellviken", "given": "A", "initials": "A"}, {"family": "Bergman", "given": "P-E", "initials": "P"}, {"family": "Bj\u00f6rklund", "given": "S", "initials": "S"}, {"family": "Bj\u00f6rkman", "given": "M P", "initials": "MP", "orcid": "0000-0001-5768-1976", "researcher": {"href": "https://publications.scilifelab.se/researcher/9821ee4a87c74dde82d9a6a4ebc2b1fc.json"}}, {"family": "Deng", "given": "J", "initials": "J"}, {"family": "Desborough", "given": "L", "initials": "L"}, {"family": "Dolff", "given": "E", "initials": "E"}, {"family": "Eliasson", "given": "A", "initials": "A"}, {"family": "Elmquist", "given": "H", "initials": "H"}, {"family": "Emanuelsson", "given": "H", "initials": "H"}, {"family": "Erixon", "given": "R", "initials": "R"}, {"family": "Fahlen", "given": "L", "initials": "L"}, {"family": "Frogner", "given": "C", "initials": "C"}, {"family": "F\u00fcrst", "given": "P", "initials": "P"}, {"family": "Grabs", "given": "A", "initials": "A"}, {"family": "Grudd", "given": "H", "initials": "H", "orcid": "0000-0002-9033-2505", "researcher": {"href": "https://publications.scilifelab.se/researcher/97348870e86e4c75ae6ce0be4cc99699.json"}}, {"family": "Guasconi", "given": "D", "initials": "D"}, {"family": "Gunnarsson", "given": "M", "initials": "M"}, {"family": "H\u00e4ggqvist", "given": "S", "initials": "S"}, {"family": "Hed", "given": "A", "initials": "A"}, {"family": "H\u00f6rnstr\u00f6m", "given": "E", "initials": "E"}, {"family": "J\u00f6nsson", "given": "A", "initials": "A"}, {"family": "Kanerot", "given": "S", "initials": "S"}, {"family": "Karlsson", "given": "A", "initials": "A"}, {"family": "Karlsson", "given": "D", "initials": "D", "orcid": "0000-0003-4639-823X", "researcher": {"href": "https://publications.scilifelab.se/researcher/09ecfa3c78df4076bce64c7eeb36ee4f.json"}}, {"family": "Klinth", "given": "M", "initials": "M"}, {"family": "Kraft", "given": "T", "initials": "T", "orcid": "0000-0002-1143-5494", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd6da126be9d48658afb96aac9532ead.json"}}, {"family": "Lahti", "given": "R", "initials": "R"}, {"family": "Larsson", "given": "M", "initials": "M"}, {"family": "Lernefalk", "given": "H", "initials": "H"}, {"family": "Lestander", "given": "Y", "initials": "Y"}, {"family": "Lindholm", "given": "L-T", "initials": "L"}, {"family": "Lindholm", "given": "M", "initials": "M"}, {"family": "Ljung", "given": "U", "initials": "U"}, {"family": "Ljung", "given": "K", "initials": "K"}, {"family": "Lundberg", "given": "J", "initials": "J", "orcid": "0000-0003-4316-9183", "researcher": {"href": "https://publications.scilifelab.se/researcher/86b74c200f2b402cad6b82cdf63259c9.json"}}, {"family": "Lundin", "given": "E", "initials": "E", "orcid": "0000-0002-3785-8305", "researcher": {"href": "https://publications.scilifelab.se/researcher/842e65aa96ef4dcaa8af13bf9e3f73f8.json"}}, {"family": "Malmenius", "given": "M", "initials": "M"}, {"family": "Marquina", "given": "D", "initials": "D"}, {"family": "Martinelli", "given": "J", "initials": "J"}, {"family": "Mertz", "given": "L", "initials": "L"}, {"family": "Nilsson", "given": "J", "initials": "J"}, {"family": "Patchett", "given": "A", "initials": "A"}, {"family": "Persson", "given": "N", "initials": "N"}, {"family": "Persson", "given": "J", "initials": "J"}, {"family": "Prus-Frankowska", "given": "M", "initials": "M"}, {"family": "Regazzoni", "given": "E", "initials": "E"}, {"family": "Rosander", "given": "K-G", "initials": "K"}, {"family": "Rydg\u00e5rd", "given": "M", "initials": "M"}, {"family": "Sandblom", "given": "C", "initials": "C"}, {"family": "Skord", "given": "J", "initials": "J"}, {"family": "St\u00e5lhandske", "given": "T", "initials": "T"}, {"family": "Svensson", "given": "F", "initials": "F"}, {"family": "Szpryngiel", "given": "S", "initials": "S", "orcid": "0000-0003-2965-2873", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec77cb9136184887b68a4ae8c4360927.json"}}, {"family": "Tajani", "given": "K", "initials": "K"}, {"family": "Tyboni", "given": "M", "initials": "M"}, {"family": "Ugarph", "given": "C", "initials": "C"}, {"family": "Vestermark", "given": "L", "initials": "L"}, {"family": "Vilhelmsson", "given": "J", "initials": "J"}, {"family": "Wahlgren", "given": "N", "initials": "N"}, {"family": "Wass", "given": "A", "initials": "A"}, {"family": "Wetterstrand", "given": "P", "initials": "P"}, {"family": "\u0141ukasik", "given": "P", "initials": "P", "orcid": "0000-0002-4164-6487", "researcher": {"href": "https://publications.scilifelab.se/researcher/71d69a579a304425b70249e7db42ad67.json"}}, {"family": "Tack", "given": "A J M", "initials": "AJM", "orcid": "0000-0002-3550-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f9cf8fde705481281edab32bc9156e5.json"}}, {"family": "Andersson", "given": "A F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Roslin", "given": "T", "initials": "T", "orcid": "0000-0002-2957-4791", "researcher": {"href": "https://publications.scilifelab.se/researcher/04d92328b67e47ab82257567c07cf12f.json"}}, {"family": "Ronquist", "given": "F", "initials": "F"}], "type": "journal article", "published": "2025-05-21", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "12", "issue": "1", "pages": "835"}, "abstract": "We present the data from the Insect Biome Atlas project (IBA), characterizing the terrestrial arthropod faunas of Sweden and Madagascar. Over 12 months, Malaise trap samples were collected weekly (biweekly or monthly in the winter, when feasible) at 203 locations within 100 sites in Sweden and weekly at 50 locations within 33 sites in Madagascar; this was complemented by soil and litter samples from each site. The field samples comprise 4,749 Malaise trap, 192 soil and 192 litter samples from Sweden and 2,566 Malaise trap and 190 litter samples from Madagascar. Samples were processed using mild lysis or homogenization, followed by DNA metabarcoding of CO1 (418 bp). The data comprise 698,378 non-chimeric sequence variants from Sweden and 687,866 from Madagascar, representing 33,989 (33,046 Arthropoda) and 77,599 (77,380 Arthropoda) operational taxonomic units, respectively. These are the most comprehensive data presented on these faunas so far, allowing unique analyses of the size, composition, spatial turnover and seasonal dynamics of the sampled communities. They also provide an invaluable baseline against which to gauge future changes.", "doi": "10.1038/s41597-025-05151-0", "pmid": "40399316", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12095508"}, {"db": "pii", "key": "10.1038/s41597-025-05151-0"}], "notes": [], "created": "2025-11-19T08:51:31.233Z", "modified": "2025-11-21T12:26:09.639Z"}, {"entity": "publication", "iuid": "dfca2e28bc7947fdad65ae9bd1ac974e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfca2e28bc7947fdad65ae9bd1ac974e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfca2e28bc7947fdad65ae9bd1ac974e"}}, "title": "Oligodendroglia vulnerability in the human dorsal striatum in Parkinson's disease.", "authors": [{"family": "Barba-Reyes", "given": "Juan M", "initials": "JM"}, {"family": "Harder", "given": "Lisbeth", "initials": "L"}, {"family": "Marco Salas", "given": "Sergio", "initials": "S"}, {"family": "Jaisa-Aad", "given": "Methasit", "initials": "M"}, {"family": "Mu\u00f1oz-Castro", "given": "Clara", "initials": "C"}, {"family": "Garma", "given": "Leonardo D", "initials": "LD"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Nilsson", "given": "Mats", "initials": "M"}, {"family": "Hyman", "given": "Bradley T", "initials": "BT"}, {"family": "Serrano-Pozo", "given": "Alberto", "initials": "A"}, {"family": "Mu\u00f1oz-Manchado", "given": "Ana B", "initials": "AB"}], "type": "journal article", "published": "2025-05-05", "journal": {"title": "Acta Neuropathol.", "issn": "1432-0533", "volume": "149", "issue": "1", "pages": "46", "issn-l": "0001-6322"}, "abstract": "Oligodendroglia are the responsible cells for myelination in the central nervous system and their involvement in Parkinson's disease (PD) is poorly understood. We performed sn-RNA-seq and image-based spatial transcriptomics of human caudate nucleus and putamen (dorsal striatum) from PD and control brain donors to elucidate the diversity of oligodendroglia and how they are affected by the disease. We profiled a total of ~ 200.000 oligodendroglial nuclei, defining 15 subclasses, from precursor to mature cells, 4 of which are disease-associated. These PD-specific populations are characterized by the overexpression of heat shock proteins, as well as distinct expression signatures related to immune responses, myelination alterations, and disrupted cell signaling pathways. We have also identified impairments in cell communication and oligodendrocyte development, evidenced by changes in neurotransmitter receptors expression and cell adhesion molecules. In addition, we observed significant disruptions in oligodendrocyte development, with aberrant differentiation trajectories and shifts in cell proportions, particularly in the transition from mature oligodendrocytes to disease-associated states. Quantitative immunohistochemical analysis revealed decreased myelin levels in the PD striatum, which correlated with transcriptomic alterations. Furthermore, spatial transcriptomics mapping revealed the distinct localization of disease-associated populations within the striatum, with evidence of impaired myelin integrity. Thus, we uncover oligodendroglia as a critical cell type in PD and a potential new therapeutic target for myelin-based interventions.", "doi": "10.1007/s00401-025-02884-5", "pmid": "40323467", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "In Situ Sequencing": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12053221"}, {"db": "pii", "key": "10.1007/s00401-025-02884-5"}], "notes": [], "created": "2025-11-19T08:34:23.054Z", "modified": "2025-11-28T06:50:44.043Z"}, {"entity": "publication", "iuid": "b0c1d831145149dea42f664622f9d614", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0c1d831145149dea42f664622f9d614.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0c1d831145149dea42f664622f9d614"}}, "title": "The overlooked trio: sleep duration, sampling time and physical exercise alter levels of olink-assessed blood biomarkers of cardiovascular risk.", "authors": [{"family": "Brand\u00e3o", "given": "Luiz Eduardo Mateus", "initials": "LEM"}, {"family": "Zhang", "given": "Lei", "initials": "L"}, {"family": "Grip", "given": "Anastasia", "initials": "A"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "K\u00e5ks", "given": "Emil", "initials": "E"}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Sigurdardottir", "given": "Fjola", "initials": "F"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}, {"family": "Espes", "given": "Daniel", "initials": "D"}, {"family": "Omland", "given": "Torbj\u00f8rn", "initials": "T"}, {"family": "Khoonsari", "given": "Payam Emami", "initials": "PE"}, {"family": "Benedict", "given": "Christian", "initials": "C"}, {"family": "Cedernaes", "given": "Jonathan", "initials": "J"}], "type": "letter", "published": "2025-04-29", "journal": {"title": "Biomark Res", "issn": "2050-7771", "volume": "13", "issue": "1", "pages": "67", "issn-l": null}, "abstract": "Biomarker profiling from biofluids such as blood are widely measured in clinical research, using for example Olink proteomics panels. One such research focus area is cardiovascular disease (CVD), for which chronic sleep restriction (SR) is a risk factor. However, it remains unclear whether blood levels of commonly measured CVD biomarkers are sensitive to acute dynamic factors such as SR, physical exercise (PEx), and time of day. In this crossover design, 16 normal-weight, healthy men underwent three highly standardized in-lab nights of SR (4.25 h/night) and normal sleep (NS, 8.5 h/night) in randomized order, with 88 CVD blood protein biomarkers quantified using the Olink technology (and selected validation using ELISA) in the morning, evening, and immediately before and repeatedly after 30 min of high-intensity exercise. We found significant time-of-day-dependent changes in several CVD biomarkers. Whereas several proteins were exercise-induced across sleep conditions (such as the canonical exerkines IL- 6 and BDNF), exercise-induced proteomic dynamics differed in response to recurrent SR, compared with following NS. Moreover, SR compared with NS resulted in a biomarker profile previously associated with increased prospective risk of several CVDs across large-scale cohorts (such as higher circulating levels of IL-27 and LGALS9). Our findings highlight how dynamic physiology can modulate CVD biomarker levels. These results also underscore the need to consider sleep duration as a key determinant of cardiovascular health-an emphasis reflected in recent American Heart Association guidelines. Further studies in women, older individuals, and patients with prior CVD, and across different chronotypes and dietary schedules are warranted.", "doi": "10.1186/s40364-025-00776-0", "pmid": "40301994", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12038921"}, {"db": "pii", "key": "10.1186/s40364-025-00776-0"}], "notes": [], "created": "2025-10-06T11:43:23.271Z", "modified": "2025-11-25T19:21:06.056Z"}, {"entity": "publication", "iuid": "eba679997f32456a948f17cc10289938", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eba679997f32456a948f17cc10289938.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eba679997f32456a948f17cc10289938"}}, "title": "Prognostic Value of the Circulating Tumor DNA Fraction in Metastatic Castration-resistant Prostate Cancer: Results from the ProBio Platform Trial.", "authors": [{"family": "Crippa", "given": "Alessio", "initials": "A"}, {"family": "Laere", "given": "Bram De", "initials": "B"}, {"family": "Discacciati", "given": "Andrea", "initials": "A"}, {"family": "Larsson", "given": "Berit", "initials": "B"}, {"family": "Persson", "given": "Maria", "initials": "M"}, {"family": "Johansson", "given": "Susanne", "initials": "S"}, {"family": "D'hondt", "given": "Sanne", "initials": "S"}, {"family": "Hj\u00e4lm-Eriksson", "given": "Marie", "initials": "M"}, {"family": "Pettersson", "given": "Linn", "initials": "L"}, {"family": "Enblad", "given": "Gunilla", "initials": "G"}, {"family": "Ull\u00e9n", "given": "Anders", "initials": "A"}, {"family": "Lumen", "given": "Nicolaas", "initials": "N"}, {"family": "Karlsson", "given": "Camilla Thellenberg", "initials": "CT"}, {"family": "Sandz\u00e9n", "given": "Johan", "initials": "J"}, {"family": "J\u00e4nes", "given": "Elin", "initials": "E"}, {"family": "Ghysel", "given": "Christophe", "initials": "C"}, {"family": "Olsson", "given": "Martha", "initials": "M"}, {"family": "Sautois", "given": "Brieuc", "initials": "B"}, {"family": "Schatteman", "given": "Peter", "initials": "P"}, {"family": "Roock", "given": "Wendy De", "initials": "W"}, {"family": "Bruwaene", "given": "Siska Van", "initials": "SV"}, {"family": "Verbiene", "given": "Ingrida", "initials": "I"}, {"family": "Darras", "given": "Jochen", "initials": "J"}, {"family": "Everaert", "given": "Els", "initials": "E"}, {"family": "Maeseneer", "given": "Daan De", "initials": "D"}, {"family": "Anden", "given": "Mats", "initials": "M"}, {"family": "Strijbos", "given": "Michiel", "initials": "M"}, {"family": "Luyten", "given": "Daisy", "initials": "D"}, {"family": "Mortezavi", "given": "Ashkan", "initials": "A"}, {"family": "Oldenburg", "given": "Jan", "initials": "J"}, {"family": "Ost", "given": "Piet", "initials": "P"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Eklund", "given": "Martin", "initials": "M"}, {"family": "ProBio Investigators", "given": "", "initials": ""}], "type": "journal article", "published": "2025-04-21", "journal": {"title": "Eur Urol Oncol", "issn": "2588-9311", "issn-l": null}, "abstract": "The aim of this study was to evaluate the prognostic value of undetectable circulating tumor DNA (ctDNA) and the dose-response relationship between ctDNA levels and survival outcomes in metastatic castration-resistant prostate cancer (mCRPC).\n\nWe analyzed data for patients enrolled in the ProBio trial up to November 2022 who received an androgen receptor pathway inhibitor or taxane. We compared survival outcomes between patients with undetectable ctDNA and those with detectable ctDNA randomized to physician's choice or investigational arms. Time to no longer clinically benefiting (NLCB) and overall survival (OS) were assessed using Bayesian survival models, with results reported as survival time ratios (STRs). Dose-response relationships were estimated using spike-at-zero models.\n\nA total of 220 patients were included, of whom 139 had detectable ctDNA (56 in the physician's choice arm, 83 in investigational arms) and 81 had undetectable ctDNA. In comparison to the undetectable ctDNA group, the physician's choice arm had 60% shorter time to NLCB (STR 0.40, 90% credible interval [CrI] 0.31-0.51) and 51% shorter OS (STR 0.49, 90% CrI 0.38-0.61). Similar results were observed in comparison to the investigational arms. Dose-response analysis revealed that the undetectable ctDNA group had twofold longer time to NLCB (STR 2.05, 90% CrI 1.66-2.57) and 1.6-fold longer OS (STR 1.63, 90% CrI 1.33-2.05) in comparison to the subgroup with a ctDNA fraction of 2.5%. Every 10-point increment in the ctDNA fraction corresponded to a 10% reduction in NLCB and OS times.\n\nUndetectable ctDNA at baseline predicts superior prognosis in mCRPC, suggesting potential for treatment de-escalation and less intensive monitoring for this subgroup of patients. This trial is registered on ClinicalTrials.gov as NCT03903835.", "doi": "10.1016/j.euo.2025.02.002", "pmid": "40263079", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S2588-9311(25)00037-9"}, {"db": "ClinicalTrials.gov", "key": "NCT03903835"}], "notes": [], "created": "2025-11-18T17:28:38.658Z", "modified": "2025-11-18T20:45:43.260Z"}, {"entity": "publication", "iuid": "db834613fba7481d870d2cb2fd958282", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db834613fba7481d870d2cb2fd958282.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db834613fba7481d870d2cb2fd958282"}}, "title": "In vivo composition of the mitochondrial nucleoid in mice.", "authors": [{"family": "Garc\u00eda-Villegas", "given": "Rodolfo", "initials": "R"}, {"family": "Odenthal", "given": "Franka", "initials": "F"}, {"family": "Giannoula", "given": "Yvonne", "initials": "Y"}, {"family": "Bonekamp", "given": "Nina A", "initials": "NA"}, {"family": "K\u00fchl", "given": "Inge", "initials": "I"}, {"family": "Park", "given": "Chan Bae", "initials": "CB"}, {"family": "Sp\u00e5hr", "given": "Henrik", "initials": "H"}, {"family": "Motori", "given": "Elisa", "initials": "E"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Larsson", "given": "Nils-G\u00f6ran", "initials": "NG"}], "type": "journal article", "published": "2025-04-15", "journal": {"title": "Biochimica et Biophysica Acta (BBA) - Molecular Cell Research", "issn": "1879-2596", "pages": "119955", "issn-l": "0167-4889"}, "abstract": "Mitochondrial DNA (mtDNA) is compacted into dynamic structures called mitochondrial nucleoids (mt-nucleoids), with the mitochondrial transcription factor A (TFAM) as the core packaging protein. We generated bacterial artificial chromosome (BAC) transgenic mice expressing FLAG-tagged TFAM protein (Tfam-FLAGBAC mice) to investigate the mt-nucleoid composition in vivo. Importantly, we show that the TFAM-FLAG protein is functional and complements the absence of the wild-type TFAM protein in homozygous Tfam knockout mice. We performed immunoprecipitation experiments from different mouse tissues and identified 12 proteins as core mt-nucleoid components by proteomics analysis. Among these, eight proteins correspond to mtDNA replication and transcription factors, while the other four are involved in the mitoribosome assembly. In addition, we used the Tfam-FLAGBAC mice to identify ten proteins that may stabilize TFAM-FLAG upon depletion of the mitochondrial RNA polymerase despite the absence of mtDNA and induction of the LONP1 protease. Finally, we evaluated the changes in mt-nucleoids caused by very high levels of TFAM unraveling nine interactors that could counteract the high TFAM levels to maintain active mtDNA transcription. Altogether, we demonstrate that the Tfam-FLAGBAC mice are a valuable tool for investigating the mt-nucleoid composition in vivo.", "doi": "10.1016/j.bbamcr.2025.119955", "pmid": "40246179", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0167-4889(25)00060-6"}], "notes": [], "created": "2025-04-25T09:31:35.087Z", "modified": "2025-04-25T09:31:35.092Z"}, {"entity": "publication", "iuid": "ef163e2ed5814790a0934534c9cd7801", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef163e2ed5814790a0934534c9cd7801.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef163e2ed5814790a0934534c9cd7801"}}, "title": "Hyperplex PCR enables highly multiplexed analysis of point mutations in wastewater: Long-term SARS-CoV-2 variant surveillance in Sweden as a case study.", "authors": [{"family": "Soares", "given": "Ruben R G", "initials": "RRG"}, {"family": "Varg", "given": "Javier Edo", "initials": "JE"}, {"family": "Szab\u00f3", "given": "Attila", "initials": "A"}, {"family": "Kluge", "given": "Mariana", "initials": "M"}, {"family": "Petrini", "given": "Filip", "initials": "F"}, {"family": "Psallida", "given": "Margarita", "initials": "M"}, {"family": "Olszewski", "given": "Pawe\u0142", "initials": "P"}, {"family": "Nikou", "given": "Danai V", "initials": "DV"}, {"family": "Owusu-Agyeman", "given": "Isaac", "initials": "I"}, {"family": "Perez-Zabaleta", "given": "Mariel", "initials": "M"}, {"family": "Cetecioglu", "given": "Zeynep", "initials": "Z"}, {"family": "Naseem", "given": "Umear", "initials": "U"}, {"family": "Malmberg", "given": "Maja", "initials": "M"}, {"family": "Sz\u00e9kely", "given": "Anna J", "initials": "AJ"}], "type": "journal article", "published": "2025-04-15", "journal": {"title": "Water Res.", "issn": "1879-2448", "volume": "274", "pages": "123154", "issn-l": "0043-1354"}, "abstract": "Wastewater-based surveillance (WBS) allows the analysis of pathogens, chemicals or other biomarkers in wastewater to derive unbiased epidemiological information at population scale. After re-gaining attention during the SARS-CoV-2 pandemic, the field holds promise as a surveillance and early warning system by tracking emerging pathogens with pandemic potential. Expanding the current toolbox of analytical techniques for wastewater analysis, we explored the use of Hyperplex PCR (hpPCR) to analyse SARS-CoV-2 mutations in wastewater samples collected weekly in up to 22 sites across Sweden between October 2022 and December 2023. The samples were tested using a probe panel ranging from 10- to 18-plex, continuously adapted within 1-2 weeks to quantify relevant mutations of concern over time. For cross-validation, the samples were simultaneously analysed with commonly used methods including quantitative PCR (qPCR) and next-generation sequencing (NGS). hpPCR is demonstrated herein to provide (1) systematic single nucleotide specificity with a straightforward probe design, (2) high multiplexity with minimal panel re-optimization requirements and (3) 4-5-week earlier mutation detection relative to NGS with comparable performance of mutation frequency quantification (Pearson r = 0.88, n = 50). Hence, hpPCR is shown to be a powerful complementary tool to the current workflow involving NGS and qPCR by facilitating the assembly of dynamic high-plex panels compatible with high-frequency monitoring of multiple key pathogens and/or variants in WBS.", "doi": "10.1016/j.watres.2025.123154", "pmid": "39847906", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pii", "key": "S0043-1354(25)00068-5"}], "notes": [], "created": "2025-11-24T10:14:36.366Z", "modified": "2025-11-24T10:14:36.393Z"}, {"entity": "publication", "iuid": "a609fcce04e94ce4a51830b45ac8941d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a609fcce04e94ce4a51830b45ac8941d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a609fcce04e94ce4a51830b45ac8941d"}}, "title": "A Million Years of Mammoth Mitogenome Evolution.", "authors": [{"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}}, {"family": "Thomas Thorpe", "given": "Jessica A", "initials": "JA", "orcid": "0000-0003-2302-2387", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd7ce837837546e48d5debf6d6aa9b41.json"}}, {"family": "Li", "given": "Wenxi", "initials": "W", "orcid": "0009-0001-5130-9521", "researcher": {"href": "https://publications.scilifelab.se/researcher/f001ea19092e433b9abc9431fe45b63e.json"}}, {"family": "Dehasque", "given": "Marianne", "initials": "M", "orcid": "0000-0002-4640-8306", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdb54cf4aebb4cde9e3030a801fc9746.json"}}, {"family": "Pe\u010dnerov\u00e1", "given": "Patricia", "initials": "P", "orcid": "0000-0001-9350-1987", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d148327b05a4c7ea53d5567eb87c74e.json"}}, {"family": "Barlow", "given": "Axel", "initials": "A", "orcid": "0000-0002-5532-9458", "researcher": {"href": "https://publications.scilifelab.se/researcher/293d4982ed124c75896e1838bab18b8f.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "Henneberger", "given": "Kirstin", "initials": "K"}, {"family": "Jin", "given": "Chenyu", "initials": "C", "orcid": "0000-0002-2392-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/165a756337e8489f9621bbaa73fd4f7b.json"}}, {"family": "Moreland", "given": "Kelsey N", "initials": "KN", "orcid": "0000-0002-3571-0876", "researcher": {"href": "https://publications.scilifelab.se/researcher/b44fb07639f84500b325ea44d7faf08d.json"}}, {"family": "Paijmans", "given": "Johanna L A", "initials": "JLA", "orcid": "0000-0002-1938-7052", "researcher": {"href": "https://publications.scilifelab.se/researcher/bac46fda6c98402aa8743eeacef7a962.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Westbury", "given": "Michael V", "initials": "MV", "orcid": "0000-0003-0478-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c4a764072a0474abe4ca97c7b220676.json"}}, {"family": "Wijnands", "given": "Flore", "initials": "F", "orcid": "0009-0009-6254-8964", "researcher": {"href": "https://publications.scilifelab.se/researcher/06418b4f9e90443d94452c87fb0b0588.json"}}, {"family": "Barnes", "given": "Ian", "initials": "I", "orcid": "0000-0001-8322-6918", "researcher": {"href": "https://publications.scilifelab.se/researcher/daed8b59096b411dac9ad2bbe6ac84b4.json"}}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M", "orcid": "0000-0001-8865-0937", "researcher": {"href": "https://publications.scilifelab.se/researcher/79253311b1c64b599c8987b947459391.json"}}, {"family": "Hall", "given": "Elizabeth", "initials": "E", "orcid": "0000-0001-6998-0156", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcfa42cd57c645ba868b8ab621a1be14.json"}}, {"family": "Hewitson", "given": "Susan", "initials": "S", "orcid": "0000-0003-0091-012X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0a989b12c524e859eb20fdc38d2c111.json"}}, {"family": "Mol", "given": "Dick", "initials": "D", "orcid": "0009-0005-4772-4625", "researcher": {"href": "https://publications.scilifelab.se/researcher/9baa2917aafa4ab59b27c7be2a2f246a.json"}}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P", "orcid": "0000-0001-6547-9890", "researcher": {"href": "https://publications.scilifelab.se/researcher/14e81a9e6a164940a46a57249be26006.json"}}, {"family": "Sablin", "given": "Mikhail", "initials": "M", "orcid": "0000-0002-2773-7454", "researcher": {"href": "https://publications.scilifelab.se/researcher/3355f7b5b291492b8ff2119fd74adbaf.json"}}, {"family": "Vartanyan", "given": "Sergey", "initials": "S", "orcid": "0000-0001-7806-4053", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c472e06d8fa43a0b8a5575d5aec48e8.json"}}, {"family": "Zazula", "given": "Grant D", "initials": "GD", "orcid": "0000-0001-8436-1783", "researcher": {"href": "https://publications.scilifelab.se/researcher/077650a2501a49eaa9aba0a8b8fc4a56.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications.scilifelab.se/researcher/1088a8b6a9af4cc396c610383576690f.json"}}, {"family": "Lister", "given": "Adrian M", "initials": "AM", "orcid": "0000-0002-7985-138X", "researcher": {"href": "https://publications.scilifelab.se/researcher/156889b432944198909e4842f841a296.json"}}, {"family": "Hofreiter", "given": "Michael", "initials": "M", "orcid": "0000-0003-0441-4705", "researcher": {"href": "https://publications.scilifelab.se/researcher/f18713dbd0044cb2bd6dfc3bad1cf349.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2025-04-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "42", "issue": "4", "pages": null}, "abstract": "The genomic study of specimens dating to the Early and Middle Pleistocene (EP and MP), a period spanning from 2.6 million years ago (Ma) to 126 thousand years ago (ka), has the potential to elucidate the evolutionary processes that shaped present-day biodiversity. Obtaining genomic data from this period is challenging, but mitochondrial DNA, given its higher abundance compared to nuclear DNA, could play an important role to understand evolutionary processes at this time scale. In this study, we report 34 new mitogenomes, including two EP and nine MP mammoth (Mammuthus spp.) specimens from Siberia and North America and analyze them jointly with >200 publicly available mitogenomes to reconstruct a transect of mammoth mitogenome diversity throughout the last million years. We find that our EP mitogenomes fall outside the diversity of all Late Pleistocene (LP) mammoths, while those derived from MP mammoths are basal to LP mammoth Clades 2 and 3, supporting an ancient Siberian origin of these lineages. In contrast, the geographical origin of Clade 1 remains unresolved. With these new deep-time mitogenomes, we observe diversification events across all clades that appear consistent with previously hypothesized MP and LP demographic changes. Furthermore, we improve upon an existing methodology for molecular clock dating of specimens >50 ka, demonstrating that specimens need to be individually dated to avoid biases in their age estimates. Both the molecular and analytical improvements presented here highlight the importance of deep-time genomic data to discover long-lost genetic diversity, enabling better assessments of evolutionary histories.", "doi": "10.1093/molbev/msaf065", "pmid": "40202893", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11980863"}, {"db": "pii", "key": "8107989"}], "notes": [], "created": "2025-05-05T12:32:34.796Z", "modified": "2025-11-28T10:49:58.497Z"}, {"entity": "publication", "iuid": "87266d8a6f284e2198986f59a2abeff9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87266d8a6f284e2198986f59a2abeff9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87266d8a6f284e2198986f59a2abeff9"}}, "title": "Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows.", "authors": [{"family": "Marco Salas", "given": "Sergio", "initials": "S", "orcid": "0000-0002-4636-0322", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db8123d7b0f47afbb06b0559fcd79ff.json"}}, {"family": "Kuemmerle", "given": "Louis B", "initials": "LB", "orcid": "0000-0002-9193-1243", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d339771ed9a4559ad56a63e9e4e9e80.json"}}, {"family": "Mattsson-Langseth", "given": "Christoffer", "initials": "C"}, {"family": "Tismeyer", "given": "Sebastian", "initials": "S"}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5471168acdf94b63b1eab431fd1e8442.json"}}, {"family": "Hu", "given": "Taobo", "initials": "T", "orcid": "0000-0001-5124-7167", "researcher": {"href": "https://publications.scilifelab.se/researcher/b693c14571864cfcb6f3b36cce183f12.json"}}, {"family": "Rehman", "given": "Habib", "initials": "H", "orcid": "0000-0002-8671-982X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dff0d9994c0f4237a5afbcd66d706dbf.json"}}, {"family": "Grillo", "given": "Marco", "initials": "M", "orcid": "0000-0003-2155-0645", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcd8bec6567444558acbcbd1b3d28f7a.json"}}, {"family": "Czarnewski", "given": "Paulo", "initials": "P"}, {"family": "Helgadottir", "given": "Saga", "initials": "S"}, {"family": "Tiklova", "given": "Katarina", "initials": "K"}, {"family": "Andersson", "given": "Axel", "initials": "A", "orcid": "0000-0002-4714-3127", "researcher": {"href": "https://publications.scilifelab.se/researcher/34027f6b47684ff4be205e2d547c5f8a.json"}}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Chatzinikolaou", "given": "Maria", "initials": "M"}, {"family": "Theis", "given": "Fabian J", "initials": "FJ", "orcid": "0000-0002-2419-1943", "researcher": {"href": "https://publications.scilifelab.se/researcher/15139e290953411590201d9bb402da1f.json"}}, {"family": "Luecken", "given": "Malte D", "initials": "MD", "orcid": "0000-0001-7464-7921", "researcher": {"href": "https://publications.scilifelab.se/researcher/40b82068719d43448992741da54e00bd.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Ishaque", "given": "Naveed", "initials": "N", "orcid": "0000-0002-8426-901X", "researcher": {"href": "https://publications.scilifelab.se/researcher/38be333e07614a13bf8c559e7935381a.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "22", "issue": "4", "pages": "813-823", "issn-l": "1548-7091"}, "abstract": "The Xenium In Situ platform is a new spatial transcriptomics product commercialized by 10x Genomics, capable of mapping hundreds of genes in situ at subcellular resolution. Given the multitude of commercially available spatial transcriptomics technologies, recommendations in choice of platform and analysis guidelines are increasingly important. Herein, we explore 25 Xenium datasets generated from multiple tissues and species, comparing scalability, resolution, data quality, capacities and limitations with eight other spatially resolved transcriptomics technologies and commercial platforms. In addition, we benchmark the performance of multiple open-source computational tools, when applied to Xenium datasets, in tasks including preprocessing, cell segmentation, selection of spatially variable features and domain identification. This study serves as an independent analysis of the performance of Xenium, and provides best practices and recommendations for analysis of such datasets.", "doi": "10.1038/s41592-025-02617-2", "pmid": "40082609", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "BioImage Informatics": "Collaborative", "In Situ Sequencing": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC11978515"}, {"db": "pii", "key": "10.1038/s41592-025-02617-2"}], "notes": [], "created": "2025-11-21T12:56:02.504Z", "modified": "2025-11-28T06:50:06.581Z"}, {"entity": "publication", "iuid": "26b9ef3adace47b583a8720138aa1f04", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26b9ef3adace47b583a8720138aa1f04.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26b9ef3adace47b583a8720138aa1f04"}}, "title": "Fibromyalgia patients have altered lipid concentrations associated with disease symptom severity and anti-satellite glial cell IgG antibodies.", "authors": [{"family": "Jakobsson", "given": "Jenny E", "initials": "JE"}, {"family": "Menezes", "given": "Joana", "initials": "J"}, {"family": "Krock", "given": "Emerson", "initials": "E"}, {"family": "Hunt", "given": "Matthew A", "initials": "MA"}, {"family": "Carlsson", "given": "Henrik", "initials": "H"}, {"family": "Vaivade", "given": "Aina", "initials": "A"}, {"family": "Emami Khoonsari", "given": "Payam", "initials": "P"}, {"family": "Agalave", "given": "Nilesh M", "initials": "NM"}, {"family": "Sandstr\u00f6m", "given": "Angelica", "initials": "A"}, {"family": "Kadetoff", "given": "Diana", "initials": "D"}, {"family": "Tour Sohlin", "given": "Jeanette", "initials": "J"}, {"family": "Erngren", "given": "Ida", "initials": "I"}, {"family": "Al-Grety", "given": "Asma", "initials": "A"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Sandor", "given": "Katalin", "initials": "K"}, {"family": "Kosek", "given": "Eva", "initials": "E"}, {"family": "Svensson", "given": "Camilla I", "initials": "CI"}, {"family": "Kultima", "given": "Kim", "initials": "K"}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "J Pain", "issn": "1528-8447", "volume": "29", "pages": "105331", "issn-l": null}, "abstract": "Autoimmunity and immunoglobulin G (IgG) autoantibodies may contribute to pain in a subset of fibromyalgia (FM) patients. Previously, IgG from FM patients was found to induce pain-like behavior in mice and bind to satellite glial cells (anti-SGC IgG). The anti-SGC IgG levels were also associated with more severe symptomatology. Lipid metabolism in FM subjects is altered with lysophosphatidylcholines (LPCs) acting as pain mediators. The relationship between autoantibodies, lipid metabolism, and FM symptomatology remains unclear. Serum lipidomics with liquid chromatography mass spectrometry, anti-SGC IgG levels, and clinical measures were examined in 35 female FM subjects and 33 age- and body mass index-balanced healthy controls (HC). Fibromyalgia subjects with higher anti-SGC IgG levels experienced more intense pain than those with lower levels. Sixty-three lipids were significantly altered between FM subjects and HC or between FM subjects with severe (FM severe) and mild symptoms (FM mild). Compared to HC, FM subjects had lower concentrations of lipid species belonging to the classes LPC (n = 10), lysophosphatidylethanolamine (n = 7), phosphatidylcholine (n = 4), and triglyceride (n = 5), but higher concentrations of diglyceride (n = 3). Additionally, FM severe had higher LPC 19:0, 22:0, and 24:1 and lower sphingomyelin (n = 9) concentrations compared to FM mild. Positive associations were seen for LPC 22:0 and 24:1 with pain intensity and anti-SGC IgG levels in FM subjects. Taken together, these results suggest an association between altered lipid metabolism and autoimmune mechanisms in FM.", "doi": "10.1016/j.jpain.2025.105331", "pmid": "39922554", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1526-5900(25)00558-9"}], "notes": [], "created": "2025-11-21T12:09:30.182Z", "modified": "2025-11-21T12:09:30.222Z"}, {"entity": "publication", "iuid": "3f77b47c2c9d4cb4b7c69ccd9596688c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f77b47c2c9d4cb4b7c69ccd9596688c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f77b47c2c9d4cb4b7c69ccd9596688c"}}, "title": "A chromosome-level genome assembly of the European green toad (Bufotes viridis).", "authors": [{"family": "R\u00f6din-M\u00f6rch", "given": "Patrik", "initials": "P", "orcid": "0000-0001-6737-1488", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e6abe040b284d67b11f45db1e58540e.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Choi", "given": "Eunkyoung", "initials": "E", "orcid": "0009-0007-7147-9468", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4255b0cdeec4f43885e730affd1246b.json"}}, {"family": "Ciofi", "given": "Claudio", "initials": "C", "orcid": "0000-0001-8537-8659", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15012e62daf4c28b3c101550f460d35.json"}}, {"family": "Diedericks", "given": "Genevieve", "initials": "G", "orcid": "0000-0001-7700-8906", "researcher": {"href": "https://publications.scilifelab.se/researcher/7506eb0e88da4e4da970947289df5c4c.json"}}, {"family": "Diroma", "given": "Maria Angela", "initials": "MA", "orcid": "0000-0003-1427-8946", "researcher": {"href": "https://publications.scilifelab.se/researcher/93fd5ac3fe64467d9e617b2bf14fea71.json"}}, {"family": "Einarsd\u00f3ttir", "given": "El\u00edsabet", "initials": "E", "orcid": "0000-0003-3101-2285", "researcher": {"href": "https://publications.scilifelab.se/researcher/0db39539bdd94519a418e6dd7a287cc8.json"}}, {"family": "F\u00f6rs\u00e4ter", "given": "Kristofer", "initials": "K", "orcid": "0009-0009-7670-215X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2e8576dc5354bef84f13f2e6a3fc1b6.json"}}, {"family": "Heintz", "given": "Julia", "initials": "J", "orcid": "0009-0001-9345-1358", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7ebbb1f975844f7910676091d05a61e.json"}}, {"family": "Jons\u00e4ll", "given": "Linnea", "initials": "L", "orcid": "0009-0004-6729-0185", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9c8f571a5be4dfeb7ebf5b35f4b4ae7.json"}}, {"family": "Lantz", "given": "Henrik", "initials": "H", "orcid": "0000-0003-2419-0075", "researcher": {"href": "https://publications.scilifelab.se/researcher/85fa15d934214e00bb7818b865c4d754.json"}}, {"family": "Laurila", "given": "Anssi", "initials": "A", "orcid": "0000-0001-8090-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b55d6c459ef448c992a37db2a02c3ea.json"}}, {"family": "Leit\u00e3o", "given": "Henrique G", "initials": "HG", "orcid": "0000-0002-9212-4590", "researcher": {"href": "https://publications.scilifelab.se/researcher/991f0492e152466f8f02cb6b7365ca6b.json"}}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "M"}, {"family": "Natali", "given": "Chiara", "initials": "C", "orcid": "0000-0002-0293-171X", "researcher": {"href": "https://publications.scilifelab.se/researcher/df472019f49541f3bd455f1d8b1aea91.json"}}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "R"}, {"family": "Vinnere Pettersson", "given": "Olga", "initials": "O", "orcid": "0000-0002-5597-1870", "researcher": {"href": "https://publications.scilifelab.se/researcher/31689f508a984d0680d285c294669615.json"}}, {"family": "Soler", "given": "Lucile", "initials": "L", "orcid": "0000-0002-0121-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/f701059f90fe4c7c9b969079e74aac57.json"}}, {"family": "Svardal", "given": "Hannes", "initials": "H", "orcid": "0000-0001-7866-7313", "researcher": {"href": "https://publications.scilifelab.se/researcher/4aee397f0ff64641a9c2033d56c6effb.json"}}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E", "orcid": "0000-0003-3752-1806", "researcher": {"href": "https://publications.scilifelab.se/researcher/9257ccdfc6484cd9a95f9b2f17f9a8d1.json"}}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J", "orcid": "0000-0002-5840-779X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e1eb3c1903f4a97a4c585a2dee3b05f.json"}}], "type": "journal article", "published": "2025-03-18", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "issn-l": "2160-1836", "volume": "15", "issue": "3", "pages": null}, "abstract": "The European green toad (Bufotes viridis) is geographically widely distributed. While the species global conservation status is labeled as of least concern by the IUCN, it is declining in many parts of its range where populations are fragmented and isolated. A high-quality reference genome is an important resource for conservation genomic researchers who are trying to understand and interpret the genomic signals of population decline, inbreeding, and the accumulation of deleterious mutations. Here, we assembled and annotated a chromosome-level reference genome for B. viridis as part of the European Reference Genome Atlas pilot project. The genome assembly, with a size of \u223c3.89 Gb consists of 11 chromosomes and an additional 2,096 unplaced scaffolds. The final assembly had a scaffold N50 value of 478.39 Mb and covered 90.4% single copy tetrapod orthologs, and 46.7% repetitive elements. Finally, a total of 23,830 protein-coding genes matching a known gene, together with 56,974 mRNAs were predicted. This high-quality reference genome will benefit amphibian evolutionary genomics research and enable conservation genetic studies to inform practical conservation work on this species.", "doi": "10.1093/g3journal/jkaf002", "pmid": "39969399", "labels": {"NGI Stockholm (Genomics Production)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11917475"}, {"db": "pii", "key": "8024180"}], "notes": [], "created": "2025-02-28T07:50:03.734Z", "modified": "2025-11-21T12:40:15.314Z"}, {"entity": "publication", "iuid": "db7bafd701444e32b52fe11feea86f7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db7bafd701444e32b52fe11feea86f7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db7bafd701444e32b52fe11feea86f7b"}}, "title": "Sox9 and nuclear factor I transcription factors regulate the timing of neurogenesis and ependymal maturation in dopamine progenitors.", "authors": [{"family": "Lahti", "given": "Laura", "initials": "L", "orcid": "0000-0003-2929-1975", "researcher": {"href": "https://publications.scilifelab.se/researcher/30ee35dc36f440d197afe3cd433d64ca.json"}}, {"family": "Volakakis", "given": "Nikolaos", "initials": "N"}, {"family": "Gillberg", "given": "Linda", "initials": "L"}, {"family": "Yaghmaeian Salmani", "given": "Behzad", "initials": "B", "orcid": "0000-0002-4221-6243", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb9b5976d0b34622aff0e9a564b3ae54.json"}}, {"family": "Tiklov\u00e1", "given": "Katar\u00edna", "initials": "K", "orcid": "0000-0002-9529-4552", "researcher": {"href": "https://publications.scilifelab.se/researcher/14bbad41b8ed42268b71014ce111d247.json"}}, {"family": "Kee", "given": "Nigel", "initials": "N", "orcid": "0000-0002-7095-0760", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa213cf47c30423e8be78d0e8968b0b3.json"}}, {"family": "Lund\u00e9n-Miguel", "given": "Hilda", "initials": "H"}, {"family": "Werkman", "given": "Maarten", "initials": "M", "orcid": "0009-0000-6880-0897", "researcher": {"href": "https://publications.scilifelab.se/researcher/0eecf2c25f464784bf84003d051279ba.json"}}, {"family": "Piper", "given": "Michael", "initials": "M", "orcid": "0000-0002-6759-2560", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f040420470a4f11852954781cd23c15.json"}}, {"family": "Gronostajski", "given": "Richard", "initials": "R", "orcid": "0000-0003-4264-208X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff92d5fdb7fe4967a3f1af62077ef82e.json"}}, {"family": "Perlmann", "given": "Thomas", "initials": "T", "orcid": "0000-0003-4821-8036", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2c8dc93c324455b93aa392fcbb67315.json"}}], "type": "journal article", "published": "2025-03-15", "journal": {"title": "Development", "issn": "1477-9129", "issn-l": "0950-1991", "volume": "152", "issue": "6", "pages": null}, "abstract": "Correct timing of neurogenesis is crucial for generating the correct number and subtypes of glia and neurons in the embryo, and for preventing tumours and stem cell depletion in the adults. Here, we analyse how the midbrain dopamine (mDA) neuron progenitors transition into cell cycle arrest (G0) and begin to mature into ependymal cells. Comparison of mDA progenitors from different embryonic stages revealed upregulation of the genes encoding Sox9 and nuclear factor I transcription factors during development. Their conditional inactivation in the early embryonic midbrain led to delayed G0 entry and ependymal maturation in the entire midbrain ventricular zone, reduced gliogenesis and increased generation of neurons, including mDA neurons. In contrast, their inactivation in late embryogenesis did not result in mitotic re-entry, suggesting that these factors are necessary for G0 induction, but not for its maintenance. Our characterisation of adult ependymal cells by single-cell RNA sequencing and histology show that mDA-progenitor-derived cells retain several progenitor features but also secrete neuropeptides and contact neighbouring cells and blood vessels, indicating that these cells may form part of the circumventricular organ system.", "doi": "10.1242/dev.204421", "pmid": "39995267", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "367503"}], "notes": [], "created": "2025-04-07T09:04:57.491Z", "modified": "2025-11-28T10:53:42.874Z"}, {"entity": "publication", "iuid": "c5b4d283a9414611bfeae71de58abe32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c5b4d283a9414611bfeae71de58abe32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c5b4d283a9414611bfeae71de58abe32"}}, "title": "Genetic liability for anxiety and treatment response to the monoamine stabilizer OSU6162 in alcohol dependence: a retrospective secondary analysis.", "authors": [{"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Khemiri", "given": "Lotfi", "initials": "L"}, {"family": "Guterstam", "given": "Joar", "initials": "J"}, {"family": "Franck", "given": "Johan", "initials": "J"}, {"family": "Jayaram-Lindstr\u00f6m", "given": "Nitya", "initials": "N"}, {"family": "Melas", "given": "Philippe A", "initials": "PA"}], "type": "journal article", "published": "2025-03-12", "journal": {"title": "Pharmacol Rep", "issn": "2299-5684", "issn-l": null}, "abstract": "OSU6162, a monoamine stabilizer, has demonstrated efficacy in reducing alcohol and anxiety-related behaviors in preclinical settings. In a previous randomized, double-blind, placebo-controlled trial involving patients with alcohol dependence (AD), OSU6162 significantly reduced craving for alcohol but did not alter drinking behaviors. This retrospective secondary analysis explores whether genetic predispositions related to AD and associated traits might influence the response to OSU6162 treatment in original trial participants.\n\nPolygenic risk scores (PRSs) were calculated for 48 AD patients using PRSice-2 and genome-wide association study (GWAS) data for (i) alcohol use disorder and alcohol consumption, (ii) problematic alcohol use, (iii) drinks per week, (iv) major depression, and (v) anxiety (case-control comparisons and quantitative anxiety factor scores). Linear regression analyses, adjusted for population stratification, assessed interaction effects between PRSs and treatment type (OSU6162 or placebo) on various clinical outcomes.\n\nSignificant interactions were found between treatment type and anxiety factor score PRS at the genome-wide significance threshold. In the OSU6162-treated group, a higher anxiety PRS was associated with reductions in the number of drinks consumed (FDR = 0.0017), percentage of heavy drinking days (FDR = 0.0060), and percentage of drinking days (FDR = 0.0017), with a trend toward reduced blood phosphatidylethanol (PEth) levels (FDR = 0.068). These associations were absent in the placebo group.\n\nThese preliminary findings suggest that anxiety PRS may help predict response to OSU6162 treatment in AD. Further research with larger cohorts and more comprehensive genetic data is needed to confirm these results and advance personalized medicine approaches for alcohol use disorder.", "doi": "10.1007/s43440-025-00707-8", "pmid": "40069537", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s43440-025-00707-8"}], "notes": [], "created": "2025-03-31T07:45:02.876Z", "modified": "2025-03-31T07:45:03.018Z"}, {"entity": "publication", "iuid": "7b6d68bef27c42ccbf33580e86f46cdf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b6d68bef27c42ccbf33580e86f46cdf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b6d68bef27c42ccbf33580e86f46cdf"}}, "title": "Antisense-mediated regulation of exon usage in the elastic spring region of Titin modulates sarcomere function.", "authors": [{"family": "Celik", "given": "Selvi", "initials": "S", "orcid": "0000-0001-7032-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da057ac725d4fb0bdbaddbc06a8ea64.json"}}, {"family": "Hyrefelt", "given": "Ludvig", "initials": "L"}, {"family": "Czuba", "given": "Tomasz", "initials": "T"}, {"family": "Li", "given": "Yuan", "initials": "Y"}, {"family": "Assis", "given": "Juliana", "initials": "J", "orcid": "0000-0001-5995-8684", "researcher": {"href": "https://publications.scilifelab.se/researcher/09d17153a55c4eeaba108c7ecfb8fa3a.json"}}, {"family": "Martinez", "given": "Julia", "initials": "J"}, {"family": "Johansson", "given": "Markus", "initials": "M"}, {"family": "Andr\u00e9", "given": "Oscar", "initials": "O"}, {"family": "Synnergren", "given": "Jane", "initials": "J"}, {"family": "Sandstedt", "given": "Joakim", "initials": "J", "orcid": "0000-0002-6458-9550", "researcher": {"href": "https://publications.scilifelab.se/researcher/070e186990424c4b83225eb93efc2a66.json"}}, {"family": "Nordenfelt", "given": "Pontus", "initials": "P", "orcid": "0000-0002-9481-9951", "researcher": {"href": "https://publications.scilifelab.se/researcher/7aa3418ab23a4ec48c037d6d6ddea5b5.json"}}, {"family": "Vukusic", "given": "Kristina", "initials": "K", "orcid": "0000-0002-4243-0565", "researcher": {"href": "https://publications.scilifelab.se/researcher/342e325123674e74963ae7c4dd307874.json"}}, {"family": "Smith", "given": "J Gustav", "initials": "JG", "orcid": "0000-0001-6285-9935", "researcher": {"href": "https://publications.scilifelab.se/researcher/26e50df6bb7f4194a52546dbd5652e84.json"}}, {"family": "Gidl\u00f6f", "given": "Olof", "initials": "O", "orcid": "0000-0002-7402-3139", "researcher": {"href": "https://publications.scilifelab.se/researcher/83f5453e507041b995e0d69a74540c24.json"}}], "type": "journal article", "published": "2025-03-05", "journal": {"title": "Cardiovasc. Res.", "issn": "1755-3245", "issn-l": "0008-6363"}, "abstract": "Alternative splicing of Titin (TTN) I-band exons produce protein isoforms with variable size and elasticity, but the mechanisms whereby TTN splice factors regulate exon usage and thereby determining cardiomyocyte passive stiffness and diastolic function, is not well understood. Non-coding RNA transcripts from the antisense strand of protein-coding genes have been shown to regulate alternative splicing of the sense gene. The TTN gene locus harbours >80 natural antisense transcripts (NATs) with unknown function in the human heart. The aim of this study was to determine if TTN antisense transcripts play a role in alternative splicing of TTN.\n\nRNA-sequencing and RNA in situ hybridization (ISH) of cardiac tissue from heart failure patients (HF), unused donor hearts and human iPS-derived cardiomyocytes (iPS-CMs) were used to determine the expression and localization of TTN NATs. Live cell imaging was used to analyze the effect of NATs on sarcomere properties. RNA ISH, immunofluorescence was performed in iPS-CMs to study the interaction between NATs, TTN mRNA and splice factor protein RBM20.We found that TTN-AS1-276 was the predominant TTN NAT in the human heart and that it was upregulated in HF. Knock down of TTN-AS1-276 in human iPS-CMs resulted in decreased interaction between the splicing factor RBM20 and TTN pre-mRNA, decreased TTN I-band exon skipping, and markedly lower expression of the less compliant TTN isoform N2B. The effect on TTN exon usage was independent of sense-antisense exon overlap and polymerase II elongation rate. Furthermore, knockdown resulted in longer sarcomeres with preserved alignment, improved fractional shortening and relaxation times.\n\nWe demonstrate a role for TTN-AS1-276 in facilitating alternative splicing of TTN and regulating sarcomere properties. This transcript could constitute a target for improving cardiac passive stiffness and diastolic function in conditions such as heart failure with preserved ejection fraction.", "doi": "10.1093/cvr/cvaf037", "pmid": "40042822", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [{"db": "pii", "key": "8052712"}], "notes": [], "created": "2025-03-31T07:47:55.441Z", "modified": "2025-04-03T08:26:49.969Z"}, {"entity": "publication", "iuid": "b5e92260b7eb4e89a6a71c678e822438", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5e92260b7eb4e89a6a71c678e822438.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5e92260b7eb4e89a6a71c678e822438"}}, "title": "In-Depth Analysis of Disease Manifestations in Antineutrophil Cytoplasmic Antibody-Associated Vasculitides Identifies Distinct Clinical Phenotypes.", "authors": [{"family": "Lindberg", "given": "Hanna", "initials": "H"}, {"family": "Knight", "given": "Ann", "initials": "A"}, {"family": "Hellbacher", "given": "Erik", "initials": "E"}, {"family": "Norling", "given": "Olof", "initials": "O"}, {"family": "Berglin", "given": "Ewa", "initials": "E"}, {"family": "Stegmayr", "given": "Bernd", "initials": "B"}, {"family": "Baslund", "given": "Bo", "initials": "B"}, {"family": "Palm", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Haukeland", "given": "Hilde", "initials": "H"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Bruchfeld", "given": "Annette", "initials": "A"}, {"family": "Weiner", "given": "Maria", "initials": "M"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Segelmark", "given": "M\u00e5rten", "initials": "M"}, {"family": "Ohlsson", "given": "Sophie", "initials": "S"}, {"family": "Mohammad", "given": "Aladdin J", "initials": "AJ"}, {"family": "Sv\u00e4rd", "given": "Anna", "initials": "A"}, {"family": "Pullerits", "given": "Rille", "initials": "R"}, {"family": "Herlitz", "given": "Hans", "initials": "H"}, {"family": "S\u00f6derbergh", "given": "Annika", "initials": "A"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "Dahlqvist", "given": "Johanna", "initials": "J"}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "ACR Open Rheumatol", "issn": "2578-5745", "volume": "7", "issue": "3", "pages": "e70009", "issn-l": null}, "abstract": "The antineutrophil cytoplasmic antibody (ANCA)-associated vasculitides are heterogeneous disorders. The aim of this study was to identify and characterize subgroups of patients based on sex, ANCA, age at diagnosis, and organ involvement.\n\nIn total, 1,167 patients with granulomatosis with polyangiitis (GPA) or microscopic polyangiitis (MPA) were retrospectively recruited to the study. Data including cumulative involvement of 10 different organ systems, end-stage kidney disease (ESKD), sex, proteinase (PR) 3-ANCA, myeloperoxidase (MPO)-ANCA, age at diagnosis, disease duration, and relapse were obtained from medical records. Clinical variables were analyzed for associations with sex, age at diagnosis, and relapse using logistic regression analysis. Thirteen clinical variables were included in hierarchical cluster analyses using the Ward method.\n\nIn patients with GPA, PR3-ANCA, renal and pulmonary involvement, and ESKD were significantly associated with male sex, whereas MPO-ANCA was associated with female sex. Patients with GPA who were younger than 32 years of age at diagnosis were significantly more often females and had more ear-nose-throat involvement than patients older than 32 years. In patients with MPA, female patients were significantly younger at diagnosis than male patients. Relapse was significantly associated with young age at diagnosis and pulmonary involvement in GPA and with musculoskeletal involvement in MPA. Hierarchical cluster analyses identified five and seven patient clusters among individuals with GPA and MPA, respectively. PR3-/MPO-ANCA defined the largest clusters, whereas heart, gastrointestinal, and central nervous system involvement were hallmarks for three clusters for both patients with GPA and MPA.\n\nSex, age at diagnosis, and specific organ involvements define clinically relevant subgroups among patients with ANCA-associated vasculitides.", "doi": "10.1002/acr2.70009", "pmid": "40033657", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11876290"}], "notes": [], "created": "2025-11-17T10:12:19.867Z", "modified": "2025-11-17T10:12:19.927Z"}, {"entity": "publication", "iuid": "67fe70a7254545e7b2be4a509f5ff479", "links": {"self": {"href": "https://publications.scilifelab.se/publication/67fe70a7254545e7b2be4a509f5ff479.json"}, "display": {"href": "https://publications.scilifelab.se/publication/67fe70a7254545e7b2be4a509f5ff479"}}, "title": "Functionally characterizing obesity-susceptibility genes using CRISPR/Cas9, in vivo imaging and deep learning.", "authors": [{"family": "Mazzaferro", "given": "Eugenia", "initials": "E"}, {"family": "Mujica", "given": "Endrina", "initials": "E"}, {"family": "Zhang", "given": "Hanqing", "initials": "H"}, {"family": "Emmanouilidou", "given": "Anastasia", "initials": "A"}, {"family": "Jenseit", "given": "Anne", "initials": "A"}, {"family": "Evcimen", "given": "Bade", "initials": "B"}, {"family": "Metzendorf", "given": "Christoph", "initials": "C"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Loos", "given": "Ruth Jf", "initials": "RJ"}, {"family": "Vienberg", "given": "Sara Gry", "initials": "SG"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Allalou", "given": "Amin", "initials": "A"}, {"family": "den Hoed", "given": "Marcel", "initials": "M"}], "type": "journal article", "published": "2025-02-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "15", "issue": "1", "pages": "5408"}, "abstract": "Hundreds of loci have been robustly associated with obesity-related traits, but functional characterization of candidate genes remains a bottleneck. Aiming to systematically characterize candidate genes for a role in accumulation of lipids in adipocytes and other cardiometabolic traits, we developed a pipeline using CRISPR/Cas9, non-invasive, semi-automated fluorescence imaging and deep learning-based image analysis in live zebrafish larvae. Results from a dietary intervention show that 5 days of overfeeding is sufficient to increase the odds of lipid accumulation in adipocytes by 10 days post-fertilization (dpf, n = 275). However, subsequent experiments show that across 12 to 16 established obesity genes, 10 dpf is too early to detect an effect of CRISPR/Cas9-induced mutations on lipid accumulation in adipocytes (n = 1014), and effects on food intake at 8 dpf (n = 1127) are inconsistent with earlier results from mammals. Despite this, we observe effects of CRISPR/Cas9-induced mutations on ectopic accumulation of lipids in the vasculature (sh2b1 and sim1b) and liver (bdnf); as well as on body size (pcsk1, pomca, irs1); whole-body LDLc and/or total cholesterol content (irs2b and sh2b1); and pancreatic beta cell traits and/or glucose content (pcsk1, pomca, and sim1a). Taken together, our results illustrate that CRISPR/Cas9- and image-based experiments in zebrafish larvae can highlight direct effects of obesity genes on cardiometabolic traits, unconfounded by their - not yet apparent - effect on excess adiposity.", "doi": "10.1038/s41598-025-89823-2", "pmid": "39948378", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11825957"}, {"db": "pii", "key": "10.1038/s41598-025-89823-2"}], "notes": [], "created": "2025-09-08T11:37:27.351Z", "modified": "2025-11-28T10:47:20.122Z"}, {"entity": "publication", "iuid": "874f1c17b7aa431f977a1f680546f059", "links": {"self": {"href": "https://publications.scilifelab.se/publication/874f1c17b7aa431f977a1f680546f059.json"}, "display": {"href": "https://publications.scilifelab.se/publication/874f1c17b7aa431f977a1f680546f059"}}, "title": "Reducing methane emissions by developing low-fumarate high-ethanol eco-friendly rice.", "authors": [{"family": "Jin", "given": "Yunkai", "initials": "Y"}, {"family": "Liu", "given": "Tong", "initials": "T"}, {"family": "Hu", "given": "Jia", "initials": "J"}, {"family": "Sun", "given": "Kai", "initials": "K"}, {"family": "Xue", "given": "Lihong", "initials": "L"}, {"family": "Bettembourg", "given": "Mathilde", "initials": "M"}, {"family": "Bedada", "given": "Girma", "initials": "G"}, {"family": "Hou", "given": "Pengfu", "initials": "P"}, {"family": "Hao", "given": "Peiying", "initials": "P"}, {"family": "Tang", "given": "Jintian", "initials": "J"}, {"family": "Ye", "given": "Zihong", "initials": "Z"}, {"family": "Liu", "given": "Chunlin", "initials": "C"}, {"family": "Li", "given": "Peng", "initials": "P"}, {"family": "Pan", "given": "Aihu", "initials": "A"}, {"family": "Weng", "given": "Lushui", "initials": "L"}, {"family": "Xiao", "given": "Guoying", "initials": "G"}, {"family": "Moazzami", "given": "Ali A", "initials": "AA"}, {"family": "Yu", "given": "Xiaoping", "initials": "X"}, {"family": "Wu", "given": "Jun", "initials": "J"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}, {"family": "Sun", "given": "Chuanxin", "initials": "C"}], "type": "journal article", "published": "2025-02-03", "journal": {"title": "Mol Plant", "issn": "1752-9867", "issn-l": "1674-2052", "volume": "18", "issue": "2", "pages": "333-349"}, "abstract": "Methane in rice paddies is mainly produced by methanogenic communities feeding on carbon from root exudates and debris. However, the dominant root secretion governing methane emissions is not yet identified after decades of studies, even though secreted carbohydrates and organic acids have been shown to contribute to methane emissions. In this study, we discovered that fumarate and ethanol are two major rice-orchestrated secretions and play a key role in regulating methane emissions. Fumarate released in the rhizosphere is metabolized by microorganisms, supporting the growth of methanogenic archaea that produce methane as an end carbon product, while ethanol mitigates methane emissions through inhibition of methanogenic activity and growth as well as reducing fumarate synthesis in the rice root. Furthermore, we elucidated the route of fumarate metabolism in the anoxic rhizospheric zone. We found that fumarate in the rice root is produced from acetate via propionate and succinate, and when released into soil directly is oxidized to propionate before conversion via acetate into methane as the end product. The knowledge on fumarate and ethanol metabolism in rice was then used for hybrid breeding of new rice varieties with the property of low methane emission. Cultivation of these novel rice lines or employing our findings for rice cultivation managements showed up to 70% reductions in methane production from seven paddy field sites during 3 years of cultivation trials. Taken together, these findings offer great possibilities for effective mitigation of the global climatic impact of rice cultivation.", "doi": "10.1016/j.molp.2025.01.008", "pmid": "39904305", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pii", "key": "S1674-2052(25)00029-2"}], "notes": [], "created": "2025-09-08T11:37:21.068Z", "modified": "2025-11-21T12:24:20.380Z"}, {"entity": "publication", "iuid": "ff3859bb07664273873b0c450fa280cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff3859bb07664273873b0c450fa280cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff3859bb07664273873b0c450fa280cc"}}, "title": "A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei.", "authors": [{"family": "Jonsdottir", "given": "Thorey K", "initials": "TK", "orcid": "0000-0002-0618-4731", "researcher": {"href": "https://publications.scilifelab.se/researcher/43607032b6e9486889f0c34a4e0437f6.json"}}, {"family": "Paoletta", "given": "Martina S", "initials": "MS", "orcid": "0000-0001-7318-489X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f221d2972a8945b4b0d49bfa602c64a0.json"}}, {"family": "Ishizaki", "given": "Takahiro", "initials": "T", "orcid": "0000-0002-4677-5608", "researcher": {"href": "https://publications.scilifelab.se/researcher/adcbcb52e9ba4744a10527038143d759.json"}}, {"family": "Hernandez", "given": "Sophia", "initials": "S", "orcid": "0000-0002-7851-5501", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae5365af3a2f43548e1a2c72bf341e79.json"}}, {"family": "Ivanova", "given": "Maria", "initials": "M", "orcid": "0000-0003-1063-3576", "researcher": {"href": "https://publications.scilifelab.se/researcher/f179f259deb24b3a9dc6d8329cc42ee5.json"}}, {"family": "Herrera Curbelo", "given": "Alicia", "initials": "A"}, {"family": "Saiki", "given": "Paulina A", "initials": "PA"}, {"family": "Selinger", "given": "Martin", "initials": "M", "orcid": "0000-0002-5420-9702", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc68cdd8b8d748499e552a6e700d7e55.json"}}, {"family": "Das", "given": "Debojyoti", "initials": "D", "orcid": "0000-0001-6811-3333", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c763bab024a492d8e534a1e541c21dc.json"}}, {"family": "Henriksson", "given": "Johan", "initials": "J", "orcid": "0000-0002-7745-2844", "researcher": {"href": "https://publications.scilifelab.se/researcher/44339821900646b3881d4b4dfd09e8d5.json"}}, {"family": "Bushell", "given": "Ellen S C", "initials": "ESC", "orcid": "0000-0003-2863-4112", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6d25e8481034aaaafb7453ab00af664.json"}}], "type": "journal article", "published": "2025-01-11", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "53", "issue": "2", "pages": null}, "abstract": "Many Plasmodium genes remain uncharacterized due to low genetic tractability. Previous large-scale knockout screens have only been able to target about half of the genome in the more genetically tractable rodent malaria parasite Plasmodium berghei. To overcome this limitation, we have developed a scalable CRISPR system called P. berghei high-throughput (PbHiT), which uses a single cloning step to generate targeting vectors with 100-bp homology arms physically linked to a guide RNA (gRNA) that effectively integrate into the target locus. We show that PbHiT coupled with gRNA sequencing robustly recapitulates known knockout mutant phenotypes in pooled transfections. Furthermore, we provide an online resource of knockout and tagging designs to target the entire P. berghei genome and scale-up vector production using a pooled ligation approach. This work presents for the first time a tool for high-throughput CRISPR screens in Plasmodium for studying the parasite's biology at scale.", "doi": "10.1093/nar/gkaf005", "pmid": "39844455", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11754126"}, {"db": "pii", "key": "7973899"}], "notes": [], "created": "2025-11-19T10:27:39.428Z", "modified": "2025-11-24T10:10:45.104Z"}, {"entity": "publication", "iuid": "626dde82bebd4d8bb7880ecc0a2237e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/626dde82bebd4d8bb7880ecc0a2237e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/626dde82bebd4d8bb7880ecc0a2237e0"}}, "title": "Spatial transcriptomics unveils estrogen-modulated immune responses and structural alterations in the ectocervical mucosa of depot medroxyprogesterone acetate users.", "authors": [{"family": "Kaldhusdal", "given": "Vilde", "initials": "V"}, {"family": "Boger", "given": "Mathias Franzen", "initials": "MF"}, {"family": "Tjernlund", "given": "Annelie", "initials": "A"}, {"family": "Burgener", "given": "Adam D", "initials": "AD"}, {"family": "Bradley", "given": "Frideborg", "initials": "F", "orcid": "0000-0003-3006-7284", "researcher": {"href": "https://publications.scilifelab.se/researcher/d51eaeb949e94bd39ab3605d495dc647.json"}}, {"family": "Lajoie", "given": "Julie", "initials": "J"}, {"family": "Omollo", "given": "Kenneth", "initials": "K"}, {"family": "Kimani", "given": "Joshua", "initials": "J"}, {"family": "Fowke", "given": "Keith", "initials": "K"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Broliden", "given": "Kristina", "initials": "K", "orcid": "0000-0003-2224-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/95346da4e5984d48bbb50032797155e5.json"}}], "type": "journal article", "published": "2025-01-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "15", "issue": "1", "pages": "1014"}, "abstract": "The injectable contraceptive, depot medroxyprogesterone acetate (DMPA), is associated with compromised cervical mucosal barriers. High-resolution spatial transcriptomics is applied here to reveal the spatial localization of these altered molecular markers. Ectocervical tissue samples from Kenyan sex workers using DMPA, or non-hormonal contraceptives, underwent spatial transcriptomics and gene set enrichment analyses. Integrated systemic estradiol levels and bulk tissue gene expression data from a larger cohort enhanced the study's scope. Unsupervised clustering unveiled four epithelial and seven submucosal layers, showcasing spatially restricted and diverse functional epithelial responses, and a less structured submucosal spatial ordering. DMPA associated with mucosal-wide immunoglobulin gene upregulation, verified by CD20+ B-cell immunostaining, and upregulated immune markers adjacent to the basal membrane. Downregulated genes represented spatially restricted disrupted epithelial barrier integrity and submucosal extracellular matrix dysfunction. The transcriptional profile was associated with markers of estrogen regulation. Collectively, our findings reveal estrogen-modulated distinct ectocervical transcriptional profiles associated with DMPA usage. While upregulation of immunoglobulin genes occurs throughout the mucosa, activation of innate immune responses and dysregulation of barrier integrity markers are spatially restricted. These results extend previous analyses using bulk transcriptomics and provide insights into the molecular landscape influenced by DMPA, shedding light on contraceptive effects and health implications.", "doi": "10.1038/s41598-024-83775-9", "pmid": "39762272", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Spatial omics": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11704007"}, {"db": "pii", "key": "10.1038/s41598-024-83775-9"}], "notes": [], "created": "2025-01-23T12:51:23.407Z", "modified": "2025-11-19T08:36:34.197Z"}, {"entity": "publication", "iuid": "408854eb0c68488e8f43d442b1150e6c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/408854eb0c68488e8f43d442b1150e6c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/408854eb0c68488e8f43d442b1150e6c"}}, "title": "Targeted metagenomics using probe capture detect a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics.", "authors": [{"family": "Siljanen", "given": "Henri M P", "initials": "HMP", "orcid": "0000-0002-3197-1438", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a1fb0f39c4547438d0cdb35457a312c.json"}}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L", "orcid": "0000-0001-9751-5745", "researcher": {"href": "https://publications.scilifelab.se/researcher/000321fd81b9457db66140246bbd9066.json"}}, {"family": "Hilts", "given": "Angus S", "initials": "AS"}, {"family": "Bagnoud", "given": "Alexandre", "initials": "A"}, {"family": "Alves", "given": "Ricardo J E", "initials": "RJE"}, {"family": "Jones", "given": "Christopher M", "initials": "CM"}, {"family": "Kerou", "given": "Melina", "initials": "M"}, {"family": "Sousa", "given": "Felipa L", "initials": "FL"}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}, {"family": "Biasi", "given": "Christina", "initials": "C"}, {"family": "Schleper", "given": "Christa", "initials": "C", "orcid": "0000-0002-1918-2735", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ef5a3f76ba14a498f4eb6f0a7eeb465.json"}}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "volume": "5", "issue": "1", "pages": "ycaf183", "issn-l": null}, "abstract": "Microorganisms are key players in the global cycling of nitrogen and carbon, controlling their availability and fluxes, including the emissions of the powerful greenhouse gases nitrous oxide and methane. Standard sequencing methods often reveal only a limited fraction of their diversity, because of their low relative abundance, the insufficient sequencing depth of traditional metagenomes of complex communities, and limitations in coverage of DNA amplification-based assays. Here, we developed and tested a targeted metagenomics approach based on probe capture and hybridization to simultaneously characterize the diversity of multiple key metabolic genes involved in inorganic nitrogen and methane cycling. We designed comprehensive probe libraries for each of the 14 target marker genes comprising 264 111 unique probes. In validation experiments with mock communities, targeted metagenomics yielded gene profiles similar to the original communities. Only GC content had a small effect on probe efficiency, as low GC targets were less efficiently detected than those with high GC, within the mock communities. Furthermore, the relative abundances of the marker genes obtained using targeted or traditional shotgun metagenomics were significantly correlated. In addition, using archaeal amoA genes as a case-study, targeted metagenomics identified a substantially higher taxonomic diversity and a larger number of sequence reads per sample, yielding diversity estimates 28 or 1.24 times higher than shotgun metagenomics or amplicon sequencing, respectively. Our results show that targeted metagenomics complements current approaches to characterize key microbial populations and functional guilds in biogeochemical cycles in different ecosystems, enabling more detailed, simultaneous characterization of multiple functional genes.", "doi": "10.1093/ismeco/ycaf183", "pmid": "41221508", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12598625"}, {"db": "pii", "key": "ycaf183"}], "notes": [], "created": "2025-11-21T12:38:28.515Z", "modified": "2025-11-21T12:38:28.801Z"}, {"entity": "publication", "iuid": "2c25ac8902974f2bad8f06180c49be2f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c25ac8902974f2bad8f06180c49be2f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c25ac8902974f2bad8f06180c49be2f"}}, "title": "Treatment of Periprosthetic Joint Infection with Intravenous Vancomycin: Do We Hit the Target?", "authors": [{"family": "Haglund", "given": "Rasmus", "initials": "R"}, {"family": "Tornberg", "given": "Ulrika", "initials": "U"}, {"family": "Claesson", "given": "Ann-Charlotte", "initials": "AC"}, {"family": "Freyhult", "given": "Eva", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "Hailer", "given": "Nils P", "initials": "NP", "orcid": "0000-0002-3233-2638", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c8bb8c013184ef7b482ffe6f8f1380b.json"}}], "type": "journal article", "published": "2024-12-18", "journal": {"title": "Antibiotics (Basel)", "issn": "2079-6382", "volume": "13", "issue": "12", "issn-l": null}, "abstract": "Background/objectives: Vancomycin is commonly used in the treatment of periprosthetic joint infection (PJI), and trough concentrations are measured to ascertain that they are within the therapeutic range. It has not been investigated what proportion of vancomycin concentrations during treatment of PJI patients is accurately within this range, how many dose adjustments are commonly needed, and which patient factors predispose towards aberrations from the desired range. Method: In this single-center cohort study, we investigated vancomycin trough concentrations in 108 patients with surgically treated PJI who received IV administered vancomycin treatment post-operatively. Patients were identified in our local arthroplasty register, and data beyond what was available in the register were collected from electronic medical charts. Results: Of the final study cohort, 41% were women, and the median age was 71 (IQR 63-79) years. Most patients had PJI of the hip (73%), the majority (54%) underwent a debridement, antibiotics and implant retention (DAIR) procedure prior to vancomycin treatment, and 39% received vancomycin-loaded bone cement during the preceding revision procedure. Of 791 vancomycin trough measurements, only 58.2% were within the target range of 15-20 mg/L, 18.5% were below, and 23.4% were above. A total of 71% of all patients required at least one dose adjustment, and the median length of vancomycin treatment was 8 days. We observed positive correlations of vancomycin trough concentrations with both age (Spearman's rho = 0.35, p < 0.001) and pre-treatment creatinine concentrations (Spearman's rho = 0.34, p < 0.001), but no statistically significant difference between patients who had received vancomycin-loaded bone cement and those who had not. Conclusions: In our PJI patients, a high proportion of vancomycin trough concentrations were outside the therapeutic range, despite adherence to local and national guidelines. We can also confirm that caution needs to be exerted in patients of advanced age and those with compromised kidney function. Alternative broad-spectrum antibiotics that do not require as extensive therapeutic drug monitoring should be further explored.", "doi": "10.3390/antibiotics13121226", "pmid": "39766617", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11727632"}, {"db": "pii", "key": "antibiotics13121226"}], "notes": [], "created": "2025-02-17T09:20:45.877Z", "modified": "2025-02-17T09:20:46.439Z"}, {"entity": "publication", "iuid": "4f9e6a051c0045ddad47e80c3ae180ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f9e6a051c0045ddad47e80c3ae180ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f9e6a051c0045ddad47e80c3ae180ab"}}, "title": "The AxBioTick study - immune gene expression signatures in human skin bitten by Borrelia-infected versus non-infected ticks.", "authors": [{"family": "Berth\u00e9n", "given": "Nellie Carlstr\u00f6mer", "initials": "NC"}, {"family": "Cronhjort", "given": "Samuel", "initials": "S"}, {"family": "Nordberg", "given": "Marika", "initials": "M"}, {"family": "Lindgren", "given": "Per-Eric", "initials": "PE", "orcid": "0000-0003-2767-3638", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4a6e70c9c514a48a40c3edf446ab5ce.json"}}, {"family": "Larsson", "given": "Marie", "initials": "M"}, {"family": "Wilhelmsson", "given": "Peter", "initials": "P"}, {"family": "Sj\u00f6wall", "given": "Johanna", "initials": "J"}], "type": "journal article", "published": "2024-12-18", "journal": {"title": "BMC Infect. Dis.", "issn": "1471-2334", "volume": "24", "issue": "1", "pages": "1422", "issn-l": "1471-2334"}, "abstract": "Borrelia infection is caused by Borrelia burgdorferi sensu lato and transmitted by Ixodes ricinus ticks, a common tick-borne infection in Northern Europe. The establishment of Borrelia infection depends on transmission of the spirochetes, as well as the immune response generated in the skin after a bite. Here we aim to investigate the local immune response in the skin after a tick bite and assess the possible direct effects of Borrelia, by applying gene expression analysis of the immune response in skin exposed to Borrelia-infected and non-infected ticks, respectively.\n\nSkin biopsies from the study participants were taken 7-10 days after the tick-bite. The ticks and skin biopsies were analysed by real-time PCR for Borrelia spp. and other tick-borne pathogens. Dermal transcriptome profiles derived from RNA sequencing with focus on immune system regulation were created. In addition, we performed enrichment analysis of dermal transcriptome profiles with focus on immune system regulation.\n\nSkin biopsies exposed to a Borrelia-positive tick induced an overall higher expression of immune-related genes. Cytokines involved in the regulation of T-cell and macrophage activation, pro-inflammatory regulators and Toll-like receptor 2, 3 and 7 involved in pathogen recognition were upregulated in skin exposed to Borrelia, although Borrelia DNA was not detected in the biopsies.\n\nThe evidence of upregulation of genes in Borrelia exposed skin suggests an influence on the immune system of ticks and spirochetes. Characterization of Borrelia-associated gene expression signatures in the skin could contribute to future diagnostics and increase our understanding of the development of various manifestations of Borrelia infection.", "doi": "10.1186/s12879-024-10279-2", "pmid": "39695466", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11654342"}, {"db": "pii", "key": "10.1186/s12879-024-10279-2"}], "notes": [], "created": "2025-02-19T13:35:30.819Z", "modified": "2025-04-07T07:25:35.903Z"}, {"entity": "publication", "iuid": "de5f9b658ce74f6096b9c352ea946d5b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de5f9b658ce74f6096b9c352ea946d5b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de5f9b658ce74f6096b9c352ea946d5b"}}, "title": "SARS-CoV-2 and HSV-1 Induce Amyloid Aggregation in Human CSF Resulting in Drastic Soluble Protein Depletion.", "authors": [{"family": "Christ", "given": "Wanda", "initials": "W", "orcid": "0000-0003-3886-5248", "researcher": {"href": "https://publications.scilifelab.se/researcher/38fe3a44fdb547b885cce5b6f490b2bc.json"}}, {"family": "Kapell", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-9304-558X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cffd944f88e54ed6a910183ba49ef656.json"}}, {"family": "Sobkowiak", "given": "Michal J", "initials": "MJ", "orcid": "0000-0003-2932-1994", "researcher": {"href": "https://publications.scilifelab.se/researcher/14f1eb990edf472cac56f24d7cae330c.json"}}, {"family": "Mermelekas", "given": "Georgios", "initials": "G"}, {"family": "Evertsson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Sork", "given": "Helena", "initials": "H", "orcid": "0000-0002-5390-4420", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5d08dad4f2d4ee0a3e3a8f060383da5.json"}}, {"family": "Saher", "given": "Osama", "initials": "O"}, {"family": "Bazaz", "given": "Safa", "initials": "S"}, {"family": "Gustafsson", "given": "Oskar", "initials": "O"}, {"family": "Cardenas", "given": "Eduardo I", "initials": "EI"}, {"family": "Villa", "given": "Viviana", "initials": "V"}, {"family": "Ricciarelli", "given": "Roberta", "initials": "R"}, {"family": "Sandberg", "given": "Johan K", "initials": "JK", "orcid": "0000-0002-6275-0750", "researcher": {"href": "https://publications.scilifelab.se/researcher/7468c415a46645a3a4c3d28badcff954.json"}}, {"family": "Bergquist", "given": "Jonas", "initials": "J", "orcid": "0000-0002-4597-041X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d745034529f3423abbea230b4e586d20.json"}}, {"family": "Sturchio", "given": "Andrea", "initials": "A"}, {"family": "Svenningsson", "given": "Per", "initials": "P", "orcid": "0000-0001-6727-3802", "researcher": {"href": "https://publications.scilifelab.se/researcher/5199496295334771ba3c5621a83a6f43.json"}}, {"family": "Malm", "given": "Tarja", "initials": "T", "orcid": "0000-0002-9530-7472", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1ab3c9695424308b07c375901a089f4.json"}}, {"family": "Espay", "given": "Alberto J", "initials": "AJ"}, {"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15f303cb2044cfa81719700137e3603.json"}}, {"family": "Lind\u00e9n", "given": "Anders", "initials": "A"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0001-9076-1441", "researcher": {"href": "https://publications.scilifelab.se/researcher/95c1b345ae434fb383b7fe6a1d053c80.json"}}, {"family": "El Andaloussi", "given": "Samir", "initials": "S", "orcid": "0000-0003-4468-9113", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd1036a42043441da3e444f4eac58010.json"}}, {"family": "Ezzat", "given": "Kariem", "initials": "K", "orcid": "0000-0003-4186-0675", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f2f1d3d8a5d467c8fc3b95388e4c606.json"}}], "type": "journal article", "published": "2024-11-20", "journal": {"title": "ACS Chem Neurosci", "issn": "1948-7193", "volume": "15", "issue": "22", "pages": "4095-4104", "issn-l": "1948-7193"}, "abstract": "The corona virus (SARS-CoV-2) pandemic and the resulting long-term neurological complications in patients, known as long COVID, have renewed interest in the correlation between viral infections and neurodegenerative brain disorders. While many viruses can reach the central nervous system (CNS) causing acute or chronic infections (such as herpes simplex virus 1, HSV-1), the lack of a clear mechanistic link between viruses and protein aggregation into amyloids, a characteristic of several neurodegenerative diseases, has rendered such a connection elusive. Recently, we showed that viruses can induce aggregation of purified amyloidogenic proteins via the direct physicochemical mechanism of heterogeneous nucleation (HEN). In the current study, we show that the incubation of HSV-1 and SARS-CoV-2 with human cerebrospinal fluid (CSF) leads to the amyloid aggregation of several proteins known to be involved in neurodegenerative diseases, such as APLP1 (amyloid \u03b2 precursor like protein 1), ApoE, clusterin, \u03b12-macroglobulin, PGK-1 (phosphoglycerate kinase 1), ceruloplasmin, nucleolin, 14-3-3, transthyretin, and vitronectin. Importantly, UV-inactivation of SARS-CoV-2 does not affect its ability to induce amyloid aggregation, as amyloid formation is dependent on viral surface catalysis via HEN and not its ability to replicate. Additionally, viral amyloid induction led to a dramatic drop in the soluble protein concentration in the CSF. Our results show that viruses can physically induce amyloid aggregation of proteins in human CSF and result in soluble protein depletion, thus providing a potential mechanism that may account for the association between persistent and latent/reactivating brain infections and neurodegenerative diseases.", "doi": "10.1021/acschemneuro.4c00636", "pmid": "39510798", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Global Proteomics and Proteogenomics": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2024-11-15T09:02:02.653Z", "modified": "2025-04-07T07:30:58.294Z"}, {"entity": "publication", "iuid": "9e68a455ebfb445fb36a31627cb0b31b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e68a455ebfb445fb36a31627cb0b31b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e68a455ebfb445fb36a31627cb0b31b"}}, "title": "Prospective Screening of Cancer Syndromes in Patients with Mesenchymal Tumors.", "authors": [{"family": "\u00d6fverholm", "given": "Ingegerd", "initials": "I", "orcid": "0000-0002-6907-8004", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ba94eeea4d24e9c8c354fe1256fd0ce.json"}}, {"family": "Lin", "given": "Yingbo", "initials": "Y", "orcid": "0000-0001-7190-2261", "researcher": {"href": "https://publications.scilifelab.se/researcher/3dfabc46c47741b9ace94b082d60184d.json"}}, {"family": "Mondini", "given": "Julia", "initials": "J"}, {"family": "Hardingz", "given": "John", "initials": "J"}, {"family": "Br\u00e4nstr\u00f6m", "given": "Robert", "initials": "R", "orcid": "0000-0001-6245-7223", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a5818dd9c4e4b9eae136c135d411c66.json"}}, {"family": "Tsagkozis", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-6631-2053", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae792176785f4fb3b5a1eb36478570f7.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Gellerbring", "given": "Anna", "initials": "A"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Chellappa", "given": "Venkatesh", "initials": "V"}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Haglund", "given": "Cecilia", "initials": "C"}, {"family": "Haglund de Flon", "given": "Felix", "initials": "F"}, {"family": "Wallander", "given": "Karin", "initials": "K", "orcid": "0000-0001-8166-9678", "researcher": {"href": "https://publications.scilifelab.se/researcher/db174787efd74dc1b84f1bf56b74a22d.json"}}], "type": "journal article", "published": "2024-11-13", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "16", "issue": "22", "pages": "3816", "issn-l": "2072-6694"}, "abstract": "The etiology of most mesenchymal tumors is unknown, and knowledge about syndromes with an increased risk of tumors in bone or soft tissue is sparse.\n\nWe present a prospective germline analysis of 312 patients with tumors suspected of being sarcomas at a tertiary sarcoma center. Germline and tumor whole genome sequencing, tumor transcriptome, and methylome analyses were performed.\n\nGermline pathogenic or likely pathogenic variants associated with an increased risk of tumors were detected in 24 patients (8%), of which 11 (4%) harbored a detectable second hit in the tumor. Second hits were confirmed in genes with (NF1, RB1, TP53, EXT2, and SDHC) and without (ATM, CDC73, MLH1, MSH6, POLG, and KCNQ1) known association with mesenchymal tumor predisposition. Sarcomas from two Lynch syndrome patients showed mismatch repair deficiency, predicting a treatment response to immune checkpoint inhibitors (Level 1 biomarker according to the FDA (Federal Drug Administration) and ESMO (European Society for Medical Oncology)). None of the three CHEK2 carriers had a second hit in the tumor, suggesting a weak link to sarcoma.\n\nWe conclude that second-hit analyses can be used in standard of care to identify syndrome-related tumors. This approach can help distinguish true manifestations of tumor syndromes from unrelated germline findings and enhance the understanding of germline predisposition in soft tissue tumors. Prospective screening using germline whole genome sequencing should be considered when comprehensive somatic sequencing is introduced into clinical practice.", "doi": "10.3390/cancers16223816", "pmid": "39594770", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Clinical Genomics Stockholm": "Service", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11592761"}, {"db": "pii", "key": "cancers16223816"}], "notes": [], "created": "2024-11-14T08:02:41.749Z", "modified": "2025-11-18T20:44:32.464Z"}, {"entity": "publication", "iuid": "69d9d19832db4ef089b2fd6d0cc1a381", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69d9d19832db4ef089b2fd6d0cc1a381.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69d9d19832db4ef089b2fd6d0cc1a381"}}, "title": "Spatial Multiomics Reveals Intratumoral Immune Heterogeneity with Distinct Cytokine Networks in Lung Cancer Brain Metastases.", "authors": [{"family": "Christensson", "given": "Gustav", "initials": "G", "orcid": "0009-0001-3968-218X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e6b1f1f505d4198a07eb08b8d57ee83.json"}}, {"family": "Bocci", "given": "Matteo", "initials": "M", "orcid": "0000-0002-8774-0006", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff52ba58701141f88766777a3d7ef21e.json"}}, {"family": "Kazi", "given": "Julhash U", "initials": "JU", "orcid": "0000-0002-0719-5336", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b14748d011440488dc7d42da3a6c0f.json"}}, {"family": "Durand", "given": "Geoffroy", "initials": "G", "orcid": "0000-0001-9004-7248", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb5b34538f984b95a79dd581071df344.json"}}, {"family": "Lanzing", "given": "Gustav", "initials": "G", "orcid": "0009-0002-4535-5668", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bc224db0f26432895fe37b362afa206.json"}}, {"family": "Pietras", "given": "Kristian", "initials": "K", "orcid": "0000-0001-6738-4705", "researcher": {"href": "https://publications.scilifelab.se/researcher/5be0a3ec07654822a91df964eab1d6e4.json"}}, {"family": "Gonzalez Velozo", "given": "Hugo", "initials": "H", "orcid": "0000-0003-2183-3637", "researcher": {"href": "https://publications.scilifelab.se/researcher/2049ae2a1a8c4a439a3468b3e7899144.json"}}, {"family": "Hagerling", "given": "Catharina", "initials": "C", "orcid": "0000-0001-5631-7988", "researcher": {"href": "https://publications.scilifelab.se/researcher/c300f9071e664c098b48bcb98e507aa3.json"}}], "type": "journal article", "published": "2024-11-01", "journal": {"title": "Cancer Res Commun", "issn": "2767-9764", "volume": "4", "issue": "11", "pages": "2888-2902", "issn-l": null}, "abstract": "The tumor microenvironment of brain metastases has become a focus in the development of immunotherapeutic drugs. However, countless patients with brain metastasis have not experienced clinical benefit. Thus, understanding the immune cell composition within brain metastases and how immune cells interact with each other and other microenvironmental cell types may be critical for optimizing immunotherapy. We applied spatial whole-transcriptomic profiling with extensive multiregional sampling (19-30 regions per sample) and multiplex IHC on formalin-fixed, paraffin-embedded lung cancer brain metastasis samples. We performed deconvolution of gene expression data to infer the abundances of immune cell populations and inferred spatial relationships from the multiplex IHC data. We also described cytokine networks between immune and tumor cells and used a protein language model to predict drug-target interactions. Finally, we performed deconvolution of bulk RNA data to assess the prognostic significance of immune-metastatic tumor cellular networks. We show that immune cell infiltration has a negative prognostic role in lung cancer brain metastases. Our in-depth multiomics analyses further reveal recurring intratumoral immune heterogeneity and the segregation of myeloid and lymphoid cells into distinct compartments that may be influenced by distinct cytokine networks. By using computational modeling, we identify drugs that may target genes expressed in both tumor core and regions bordering immune infiltrates. Finally, we illustrate the potential negative prognostic role of our immune-metastatic tumor cell networks. Our findings advocate for a paradigm shift from focusing on individual genes or cell types toward targeting networks of immune and tumor cells.\n\nImmune cell signatures are conserved across lung cancer brain metastases, and immune-metastatic tumor cell networks have a prognostic effect, implying that targeting cytokine networks between immune and metastatic tumor cells may generate more precise immunotherapeutic approaches.", "doi": "10.1158/2767-9764.CRC-24-0201", "pmid": "39400127", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Clinical Genomics Lund": "Service", "Bioinformatics (NBIS)": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11539001"}, {"db": "pii", "key": "749058"}], "notes": [], "created": "2024-11-12T19:07:23.294Z", "modified": "2024-11-14T09:14:34.771Z"}, {"entity": "publication", "iuid": "4a95cb368b7e43af872e0dd1190cd040", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a95cb368b7e43af872e0dd1190cd040.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a95cb368b7e43af872e0dd1190cd040"}}, "title": "The T\u03b2RI promotes migration and metastasis through thrombospondin 1 and ITGAV in prostate cancer cells.", "authors": [{"family": "Mu", "given": "Yabing", "initials": "Y", "orcid": "0000-0003-3193-1425", "researcher": {"href": "https://publications.scilifelab.se/researcher/626d44f4c6d7498ea7e2690e9f7008d5.json"}}, {"family": "Wallenius", "given": "Anders", "initials": "A"}, {"family": "Zang", "given": "Guangxiang", "initials": "G"}, {"family": "Zhu", "given": "Shaochun", "initials": "S", "orcid": "0000-0001-9945-6718", "researcher": {"href": "https://publications.scilifelab.se/researcher/50c472868ea0437bb9a5a1b0a574bc39.json"}}, {"family": "Rudolfsson", "given": "Stina", "initials": "S"}, {"family": "Aripaka", "given": "Karthik", "initials": "K", "orcid": "0000-0001-5071-6187", "researcher": {"href": "https://publications.scilifelab.se/researcher/2622fdbe964f4f99810cdc20c67a9fe0.json"}}, {"family": "Bergh", "given": "Anders", "initials": "A", "orcid": "0000-0001-5163-5821", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba7945f3e27f4628ba29c7003b3bdf36.json"}}, {"family": "Mateus", "given": "Andr\u00e9", "initials": "A"}, {"family": "Landstr\u00f6m", "given": "Mar\u00e9ne", "initials": "M", "orcid": "0000-0001-6737-7230", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2f02fcfb1c1497d81a6f343bc0e6928.json"}}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Oncogene", "issn": "1476-5594", "issn-l": "0950-9232", "volume": "43", "issue": "45", "pages": "3321-3334"}, "abstract": "TGF\u03b2 potently modifies the extracellular matrix (ECM), which is thought to favor tumor cell invasion. However, the mechanism whereby the cancer cells employ the ECM proteins to facilitate their motility is largely unknown. In this study we used RNA-seq and proteomic analysis to examine the proteins secreted by castration-resistant prostate cancer (CRPC) cells upon TGF\u03b2 treatment and found that thrombospondin 1 (THBS1) was observed to be one of the predominant proteins. The CRISPR Cas9, or siRNA techniques was used to downregulate TGF\u03b2 type I receptor (T\u03b2RI) to interfere with TGF\u03b2 signaling in various cancer cells in vitro. The interaction of ECM proteins with the T\u03b2RI in the migratory prostate cancer cells in response to TGF\u03b21 was demonstrated by several different techniques to reveal that THBS1 mediates cell migration by interacting with integrin subunit alpha V (ITGAV) and T\u03b2RI. Deletion of T\u03b2RI or THBS1 in cancer cells prevented their migration and invasion. THBS1 belongs to a group of tumorigenic ECM proteins induced via TGF\u03b2 signaling in CRPC cells, and high expression of THBS1 in human prostate cancer tissues correlated with the degree of malignancy. TGF\u03b2-induced production of THBS1 through T\u03b2RI facilitates the invasion and metastasis of CRPC cells as shown in vivo xenograft animal experiments.", "doi": "10.1038/s41388-024-03165-3", "pmid": "39304722", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41388-024-03165-3"}], "notes": [], "created": "2024-11-05T07:21:43.281Z", "modified": "2024-11-15T09:56:41.242Z"}, {"entity": "publication", "iuid": "dee72ceeb5c04e68a9949a9f0a6611c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dee72ceeb5c04e68a9949a9f0a6611c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dee72ceeb5c04e68a9949a9f0a6611c0"}}, "title": "Androgen receptor pathway inhibitors and taxanes in metastatic prostate cancer: an outcome-adaptive randomized platform trial.", "authors": [{"family": "De Laere", "given": "Bram", "initials": "B", "orcid": "0000-0002-1174-0384", "researcher": {"href": "https://publications.scilifelab.se/researcher/47cc88752e1f46919ff52bcdcfa449b7.json"}}, {"family": "Crippa", "given": "Alessio", "initials": "A", "orcid": "0000-0002-2254-2420", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ab060d9722e4712891ead272dec300c.json"}}, {"family": "Discacciati", "given": "Andrea", "initials": "A"}, {"family": "Larsson", "given": "Berit", "initials": "B"}, {"family": "Persson", "given": "Maria", "initials": "M"}, {"family": "Johansson", "given": "Susanne", "initials": "S"}, {"family": "D'hondt", "given": "Sanne", "initials": "S", "orcid": "0000-0002-7604-3117", "researcher": {"href": "https://publications.scilifelab.se/researcher/8538b2a9d70e46c6ad6b44caf85633ff.json"}}, {"family": "Bergstr\u00f6m", "given": "Rebecka", "initials": "R", "orcid": "0000-0001-7609-0733", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c52bb8b2ae249049f0da222bcdfe932.json"}}, {"family": "Chellappa", "given": "Venkatesh", "initials": "V"}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Banijamali", "given": "Mahsan", "initials": "M"}, {"family": "Kotsalaynen", "given": "Anastasijia", "initials": "A"}, {"family": "Schelstraete", "given": "C\u00e9line", "initials": "C"}, {"family": "Vanwelkenhuyzen", "given": "Jan Pieter", "initials": "JP", "orcid": "0000-0001-6180-1889", "researcher": {"href": "https://publications.scilifelab.se/researcher/4dddbc8fc0e44c2fbe5d8bf6e5ad4b41.json"}}, {"family": "Hj\u00e4lm-Eriksson", "given": "Marie", "initials": "M"}, {"family": "Pettersson", "given": "Linn", "initials": "L"}, {"family": "Ull\u00e9n", "given": "Anders", "initials": "A"}, {"family": "Lumen", "given": "Nicolaas", "initials": "N"}, {"family": "Enblad", "given": "Gunilla", "initials": "G", "orcid": "0000-0002-0594-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/11313af3f4a241ecb93af23ab2652195.json"}}, {"family": "Thellenberg Karlsson", "given": "Camilla", "initials": "C", "orcid": "0000-0002-7061-7255", "researcher": {"href": "https://publications.scilifelab.se/researcher/02886c70ff4440ff94feb0ae410827c5.json"}}, {"family": "J\u00e4nes", "given": "Elin", "initials": "E"}, {"family": "Sandz\u00e9n", "given": "Johan", "initials": "J", "orcid": "0009-0005-8044-3817", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7b0406af13f454380566cacc2012861.json"}}, {"family": "Schatteman", "given": "Peter", "initials": "P"}, {"family": "Nyre Vigmostad", "given": "Maria", "initials": "M", "orcid": "0009-0008-8574-686X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8344fb6a3e314ac9a2627b86bda6d7dc.json"}}, {"family": "Olsson", "given": "Martha", "initials": "M"}, {"family": "Ghysel", "given": "Christophe", "initials": "C"}, {"family": "Sautois", "given": "Brieuc", "initials": "B", "orcid": "0000-0002-0029-7735", "researcher": {"href": "https://publications.scilifelab.se/researcher/bec4ee008fb54f52b687976868948b5c.json"}}, {"family": "De Roock", "given": "Wendy", "initials": "W"}, {"family": "Van Bruwaene", "given": "Siska", "initials": "S"}, {"family": "Anden", "given": "Mats", "initials": "M"}, {"family": "Verbiene", "given": "Ingrida", "initials": "I"}, {"family": "De Maeseneer", "given": "Daan", "initials": "D", "orcid": "0000-0002-0339-5621", "researcher": {"href": "https://publications.scilifelab.se/researcher/af378de208c3417f9fed2e739fc8aba4.json"}}, {"family": "Everaert", "given": "Els", "initials": "E"}, {"family": "Darras", "given": "Jochen", "initials": "J"}, {"family": "Aksnessether", "given": "Bj\u00f8rg Y", "initials": "BY"}, {"family": "Luyten", "given": "Daisy", "initials": "D"}, {"family": "Strijbos", "given": "Michiel", "initials": "M"}, {"family": "Mortezavi", "given": "Ashkan", "initials": "A"}, {"family": "Oldenburg", "given": "Jan", "initials": "J"}, {"family": "Ost", "given": "Piet", "initials": "P"}, {"family": "Eklund", "given": "Martin", "initials": "M", "orcid": "0000-0001-5032-5266", "researcher": {"href": "https://publications.scilifelab.se/researcher/993bb5d3f6da4027a0c226f7903ce414.json"}}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H", "orcid": "0000-0002-1073-2753", "researcher": {"href": "https://publications.scilifelab.se/researcher/813ff17beb984198a103e3dbe61bae7e.json"}}, {"family": "Lindberg", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Nat. Med.", "issn": "1546-170X", "volume": "30", "issue": "11", "pages": "3291-3302", "issn-l": "1078-8956"}, "abstract": "ProBio is the first outcome-adaptive platform trial in prostate cancer utilizing a Bayesian framework to evaluate efficacy within predefined biomarker signatures across systemic treatments. Prospective circulating tumor DNA and germline DNA analysis was performed in patients with metastatic castration-resistant prostate cancer before randomization to androgen receptor pathway inhibitors (ARPIs), taxanes or a physician's choice control arm. The primary endpoint was the time to no longer clinically benefitting (NLCB). Secondary endpoints included overall survival and (serious) adverse events. Upon reaching the time to NLCB, patients could be re-randomized. The primary endpoint was met after 218 randomizations. ARPIs demonstrated ~50% longer time to NLCB compared to taxanes (median, 11.1 versus 6.9 months) and the physician's choice arm (median, 11.1 versus 7.4 months) in the biomarker-unselected or 'all' patient population. ARPIs demonstrated longer overall survival (median, 38.7 versus 21.7 and 21.8 months for taxanes and physician's choice, respectively). Biomarker signature findings suggest that the largest increase in time to NLCB was observed in AR (single-nucleotide variant/genomic structural rearrangement)-negative and TP53 wild-type patients and TMPRSS2-ERG fusion-positive patients, whereas no difference between ARPIs and taxanes was observed in TP53-altered patients. In summary, ARPIs outperform taxanes and physician's choice treatment in patients with metastatic castration-resistant prostate cancer with detectable circulating tumor DNA. ClinicalTrials.gov registration: NCT03903835 .", "doi": "10.1038/s41591-024-03204-2", "pmid": "39164518", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Clinical Genomics Stockholm": "Service", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11564108"}, {"db": "pii", "key": "10.1038/s41591-024-03204-2"}, {"db": "ClinicalTrials.gov", "key": "NCT03903835"}], "notes": [], "created": "2024-09-02T08:11:04.824Z", "modified": "2024-11-20T19:58:56.694Z"}, {"entity": "publication", "iuid": "08268f1a806b438592e6ec40184b8e77", "links": {"self": {"href": "https://publications.scilifelab.se/publication/08268f1a806b438592e6ec40184b8e77.json"}, "display": {"href": "https://publications.scilifelab.se/publication/08268f1a806b438592e6ec40184b8e77"}}, "title": "Changes in circulating extracellular vesicle cargo are associated with cognitive decline after major surgery: an observational case-control study.", "authors": [{"family": "Mkrtchian", "given": "Souren", "initials": "S"}, {"family": "Eldh", "given": "Maria", "initials": "M"}, {"family": "Ebberyd", "given": "Anette", "initials": "A"}, {"family": "Gabrielsson", "given": "Susanne", "initials": "S"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1"}, {"family": "Ricksten", "given": "Sven-Erik", "initials": "SE"}, {"family": "Danielson", "given": "Mattias", "initials": "M"}, {"family": "Oras", "given": "Jonatan", "initials": "J"}, {"family": "Wiklund", "given": "Andreas", "initials": "A"}, {"family": "Eriksson", "given": "Lars I", "initials": "LI"}, {"family": "G\u00f3mez-Gal\u00e1n", "given": "Marta", "initials": "M"}], "type": "journal article", "published": "2024-10-18", "journal": {"title": "Br J Anaesth", "issn": "1471-6771", "issn-l": null}, "abstract": "Postoperative neurocognitive decline is a frequent complication triggered by unclear signalling mechanisms. This observational case-control study investigated the effects of hip or knee replacement surgery on the composition of circulating extracellular vesicles (EVs), potential periphery-to-brain messengers, and their association with neurocognitive outcomes.\n\nWe mapped the microRNAome and proteome of plasma-derived EVs from 12 patients (six with good and six with poor neurocognitive outcomes at 3 months after surgery) at preoperative and postoperative timepoints (4, 8, 24, and 48 h). Complement C3-EV association was confirmed by flow cytometry in plasma- and cerebrospinal fluid (CSF)-derived EVs, with total plasma and CSF C3 and C3a concentrations determined using enzyme-linked immunosorbent assay.\n\nDifferential expression analysis found eight dysregulated EV microRNAs (miRNAs) exclusively in the poor neurocognitive outcomes group. Pathway analysis suggested potential downregulation of proliferative pathways and activation of extracellular matrix and inflammatory response pathways in EV target tissues. Proteome analysis revealed a time-dependent increase in immune-related EV proteins, including complement system proteins, notably EV surface-associated C3. Such upward kinetics was detected earlier in the poor neurocognitive outcomes group. Interestingly, CSF-derived EVs from the same group showed a drastic drop of C3 at 48 h with unchanged concentrations in the good neurocognitive outcomes group. Functionally, the complement system was activated in both patient groups in plasma, but only in the poor neurocognitive outcomes group in CSF.\n\nOur findings highlight the impact of surgery on plasma- and CSF-derived EVs, particularly in patients with poor neurocognitive outcomes, indicating a potential role for EVs. The small sample size necessitates verification with a larger patient cohort.", "doi": "10.1016/j.bja.2024.07.040", "pmid": "39426921", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0007-0912(24)00553-1"}], "notes": [], "created": "2024-11-12T17:24:49.138Z", "modified": "2024-11-25T10:12:06.927Z"}, {"entity": "publication", "iuid": "da684c22e3e442799b6027659f83a772", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da684c22e3e442799b6027659f83a772.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da684c22e3e442799b6027659f83a772"}}, "title": "LRPPRC and SLIRP synergize to maintain sufficient and orderly mammalian mitochondrial translation.", "authors": [{"family": "Rubalcava-Gracia", "given": "Diana", "initials": "D", "orcid": "0000-0002-4615-7375", "researcher": {"href": "https://publications.scilifelab.se/researcher/99b075c43c2244ee9a26fae7b09d523a.json"}}, {"family": "Bubb", "given": "Kristina", "initials": "K"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b7add45d810457eb84a72aebbc7b82c.json"}}, {"family": "Burr", "given": "Stephen P", "initials": "SP"}, {"family": "August", "given": "Amelie V", "initials": "AV"}, {"family": "Chinnery", "given": "Patrick F", "initials": "PF"}, {"family": "Koolmeister", "given": "Camilla", "initials": "C"}, {"family": "Larsson", "given": "Nils-G\u00f6ran", "initials": "NG", "orcid": "0000-0001-5100-996X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc68aa2893a4ab8845fc32d8d6bc59a.json"}}], "type": "journal article", "published": "2024-10-14", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "52", "issue": "18", "pages": "11266-11282"}, "abstract": "In mammals, the leucine-rich pentatricopeptide repeat protein (LRPPRC) and the stem-loop interacting RNA-binding protein (SLIRP) form a complex in the mitochondrial matrix that is required throughout the life cycle of most mitochondrial mRNAs. Although pathogenic mutations in the LRPPRC and SLIRP genes cause devastating human mitochondrial diseases, the in vivo function of the corresponding proteins is incompletely understood. We show here that loss of SLIRP in mice causes a decrease of complex I levels whereas other OXPHOS complexes are unaffected. We generated knock-in mice to study the in vivo interdependency of SLIRP and LRPPRC by mutating specific amino acids necessary for protein complex formation. When protein complex formation is disrupted, LRPPRC is partially degraded and SLIRP disappears. Livers from Lrpprc knock-in mice had impaired mitochondrial translation except for a marked increase in the synthesis of ATP8. Furthermore, the introduction of a heteroplasmic pathogenic mtDNA mutation (m.C5024T of the tRNAAla gene) into Slirp knockout mice causes an additive effect on mitochondrial translation leading to embryonic lethality and reduced growth of mouse embryonic fibroblasts. To summarize, we report that the LRPPRC/SLIRP protein complex is critical for maintaining normal complex I levels and that it also coordinates mitochondrial translation in a tissue-specific manner.", "doi": "10.1093/nar/gkae662", "pmid": "39087558", "labels": {"CRISPR Functional Genomics": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11472161"}, {"db": "pii", "key": "7725477"}], "notes": [], "created": "2024-08-15T09:12:09.742Z", "modified": "2024-11-20T16:24:11.423Z"}, {"entity": "publication", "iuid": "405374f0e9ac4e9e93fdfedb670b2ebb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/405374f0e9ac4e9e93fdfedb670b2ebb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/405374f0e9ac4e9e93fdfedb670b2ebb"}}, "title": "Estradiol-mediated enhancement of the human ectocervical epithelial barrier correlates with desmoglein-1 expression in the follicular menstrual phase.", "authors": [{"family": "Bradley", "given": "Frideborg", "initials": "F"}, {"family": "Stern", "given": "Alexandra", "initials": "A"}, {"family": "Franz\u00e9n Boger", "given": "Mathias", "initials": "M"}, {"family": "Mousavian", "given": "Zaynab", "initials": "Z"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Kaldhusdal", "given": "Vilde", "initials": "V"}, {"family": "Lajoie", "given": "Julie", "initials": "J"}, {"family": "Omollo", "given": "Kenneth", "initials": "K"}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Kimani", "given": "Joshua", "initials": "J"}, {"family": "Burgener", "given": "Adam D", "initials": "AD"}, {"family": "Tjernlund", "given": "Annelie", "initials": "A"}, {"family": "Sundling", "given": "Christopher", "initials": "C"}, {"family": "Fowke", "given": "Keith R", "initials": "KR"}, {"family": "Broliden", "given": "Kristina", "initials": "K"}], "type": "journal article", "published": "2024-10-08", "journal": {"title": "Front Endocrinol (Lausanne)", "issn": "1664-2392", "issn-l": null, "volume": "15", "issue": null, "pages": "1454006"}, "abstract": "The cervicovaginal epithelial barrier is crucial for defending the female reproductive tract against sexually transmitted infections. Hormones, specifically estradiol and progesterone, along with their respective receptor expressions, play an important role in modulating this barrier. However, the influence of estradiol and progesterone on gene and protein expression in the ectocervical mucosa of naturally cycling women is not well understood.\r\n\r\nMucosal and blood samples were collected from Kenyan female sex workers at high risk of sexually transmitted infections. All samples were obtained at two time points, separated by two weeks, aiming for the follicular and luteal phases of the menstrual cycle. Ectocervical tissue biopsies were analyzed by RNA-sequencing and in situ immunofluorescence staining, cervicovaginal lavage samples (CVL) were evaluated using protein profiling, and plasma samples were analyzed for hormone levels.\r\n\r\nUnsupervised clustering of RNA-sequencing data was performed using Weighted gene co-expression network analysis (WGCNA). In the follicular phase, estradiol levels positively correlated with a gene module representing epithelial structure and function, and negatively correlated with a gene module representing cell cycle regulation. These correlations were confirmed using regression analysis including adjustment for bacterial vaginosis status. Using WGCNA, no gene module correlated with progesterone levels in the follicular phase. In the luteal phase, no gene module correlated with either estradiol or progesterone levels. Protein profiling on CVL revealed that higher levels of estradiol during the follicular phase correlated with increased expression of epithelial barrier integrity markers, including DSG1. This contrasted to the limited correlations of protein expression with estradiol levels in the luteal phase. In situ imaging analysis confirmed that higher estradiol levels during the follicular phase correlated with increased DSG1 expression.\r\n\r\nWe demonstrate that estradiol levels positively correlate with specific markers of ectocervical epithelial structure and function, particularly DSG1, during the follicular phase of the menstrual cycle. Neither progesterone levels during the follicular phase nor estradiol and progesterone levels during the luteal phase correlated with any specific sets of gene markers. These findings align with the expression of estradiol and progesterone receptors in the ectocervical epithelium during these menstrual phases.", "doi": "10.3389/fendo.2024.1454006", "pmid": "39439565", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11493707"}], "notes": [], "created": "2024-11-12T12:10:56.423Z", "modified": "2025-11-17T10:23:13.822Z"}, {"entity": "publication", "iuid": "9e66df26102a493d9556d84de8d9766b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e66df26102a493d9556d84de8d9766b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e66df26102a493d9556d84de8d9766b"}}, "title": "Multiomic biomarkers after cardiac arrest.", "authors": [{"family": "Stopa", "given": "Victoria", "initials": "V"}, {"family": "Lileikyte", "given": "Gabriele", "initials": "G"}, {"family": "Bakochi", "given": "Anahita", "initials": "A"}, {"family": "Agarwal", "given": "Prasoon", "initials": "P"}, {"family": "Beske", "given": "Rasmus", "initials": "R"}, {"family": "Stammet", "given": "Pascal", "initials": "P"}, {"family": "Hassager", "given": "Christian", "initials": "C"}, {"family": "\u00c5rman", "given": "Filip", "initials": "F"}, {"family": "Nielsen", "given": "Niklas", "initials": "N"}, {"family": "Devaux", "given": "Yvan", "initials": "Y", "orcid": "0000-0002-5321-8543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b0c49e54c3742a99f8309fa11ff7852.json"}}], "type": "journal article", "published": "2024-09-27", "journal": {"title": "Intensive Care Med Exp", "issn": "2197-425X", "volume": "12", "issue": "1", "pages": "83", "issn-l": null}, "abstract": "Cardiac arrest is a sudden cessation of heart function, leading to an abrupt loss of blood flow and oxygen to vital organs. This life-threatening emergency requires immediate medical intervention and can lead to severe neurological injury or death. Methods and biomarkers to predict neurological outcome are available but lack accuracy. Such methods would allow personalizing healthcare and help clinical decisions. Extensive research has been conducted to identify prognostic omic biomarkers of cardiac arrest. With the emergence of technologies allowing to combine different levels of omics data, and with the help of artificial intelligence and machine learning, there is a potential to use multiomic signatures as prognostic biomarkers after cardiac arrest. This review article delves into the current knowledge of cardiac arrest biomarkers across various omic fields and suggests directions for future research aiming to integrate multiple omics data layers to improve outcome prediction and cardiac arrest patient's care.", "doi": "10.1186/s40635-024-00675-y", "pmid": "39331333", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11436561"}, {"db": "pii", "key": "10.1186/s40635-024-00675-y"}], "notes": [], "created": "2024-11-12T13:11:46.970Z", "modified": "2024-11-12T13:11:47.031Z"}, {"entity": "publication", "iuid": "e17d4a0e0e434723a36f929e80935cd5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e17d4a0e0e434723a36f929e80935cd5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e17d4a0e0e434723a36f929e80935cd5"}}, "title": "The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.", "authors": [{"family": "Mc Cartney", "given": "Ann M", "initials": "AM"}, {"family": "Formenti", "given": "Giulio", "initials": "G"}, {"family": "Mouton", "given": "Alice", "initials": "A"}, {"family": "De Panis", "given": "Diego", "initials": "D"}, {"family": "Marins", "given": "Lu\u00edsa S", "initials": "LS"}, {"family": "Leit\u00e3o", "given": "Henrique G", "initials": "HG"}, {"family": "Diedericks", "given": "Genevieve", "initials": "G"}, {"family": "Kirangwa", "given": "Joseph", "initials": "J"}, {"family": "Morselli", "given": "Marco", "initials": "M"}, {"family": "Salces-Ortiz", "given": "Judit", "initials": "J"}, {"family": "Escudero", "given": "Nuria", "initials": "N"}, {"family": "Iannucci", "given": "Alessio", "initials": "A"}, {"family": "Natali", "given": "Chiara", "initials": "C"}, {"family": "Svardal", "given": "Hannes", "initials": "H"}, {"family": "Fern\u00e1ndez", "given": "Rosa", "initials": "R"}, {"family": "De Pooter", "given": "Tim", "initials": "T"}, {"family": "Joris", "given": "Geert", "initials": "G"}, {"family": "Strazisar", "given": "Mojca", "initials": "M"}, {"family": "Wood", "given": "Jonathan M D", "initials": "JMD"}, {"family": "Herron", "given": "Katie E", "initials": "KE"}, {"family": "Seehausen", "given": "Ole", "initials": "O"}, {"family": "Watts", "given": "Phillip C", "initials": "PC"}, {"family": "Shaw", "given": "Felix", "initials": "F"}, {"family": "Davey", "given": "Robert P", "initials": "RP"}, {"family": "Minotto", "given": "Alice", "initials": "A"}, {"family": "Fern\u00e1ndez", "given": "Jos\u00e9 M", "initials": "JM"}, {"family": "B\u00f6hne", "given": "Astrid", "initials": "A"}, {"family": "Alegria", "given": "Carla", "initials": "C"}, {"family": "Alioto", "given": "Tyler", "initials": "T"}, {"family": "Alves", "given": "Paulo C", "initials": "PC"}, {"family": "Amorim", "given": "Isabel R", "initials": "IR"}, {"family": "Aury", "given": "Jean-Marc", "initials": "J"}, {"family": "Backstrom", "given": "Niclas", "initials": "N"}, {"family": "Baldrian", "given": "Petr", "initials": "P"}, {"family": "Baltrunaite", "given": "Laima", "initials": "L"}, {"family": "Barta", "given": "Endre", "initials": "E"}, {"family": "BedHom", "given": "Bertrand", "initials": "B"}, {"family": "Belser", "given": "Caroline", "initials": "C"}, {"family": "Bergsten", "given": "Johannes", "initials": "J"}, {"family": "Bertrand", "given": "Laurie", "initials": "L"}, {"family": "Bilandija", "given": "Helena", "initials": "H"}, {"family": "Binzer-Panchal", "given": "Mahesh", "initials": "M"}, {"family": "Bista", "given": "Iliana", "initials": "I"}, {"family": "Blaxter", "given": "Mark", "initials": "M"}, {"family": "Borges", "given": "Paulo A V", "initials": "PAV"}, {"family": "Dias", "given": "Guilherme Borges", "initials": "GB"}, {"family": "Bosse", "given": "Mirte", "initials": "M"}, {"family": "Brown", "given": "Tom", "initials": "T"}, {"family": "Bruggmann", "given": "R\u00e9my", "initials": "R"}, {"family": "Buena-Atienza", "given": "Elena", "initials": "E"}, {"family": "Burgin", "given": "Josephine", "initials": "J"}, {"family": "Buzan", "given": "Elena", "initials": "E"}, {"family": "Cariani", "given": "Alessia", "initials": "A"}, {"family": "Casadei", "given": "Nicolas", "initials": "N"}, {"family": "Chiara", "given": "Matteo", "initials": "M"}, {"family": "Chozas", "given": "Sergio", "initials": "S"}, {"family": "\u010ciampor", "given": "Fedor", "initials": "F"}, {"family": "Crottini", "given": "Angelica", "initials": "A"}, {"family": "Cruaud", "given": "Corinne", "initials": "C"}, {"family": "Cruz", "given": "Fernando", "initials": "F"}, {"family": "Dalen", "given": "Love", "initials": "L"}, {"family": "De Biase", "given": "Alessio", "initials": "A"}, {"family": "Del Campo", "given": "Javier", "initials": "J"}, {"family": "Delic", "given": "Teo", "initials": "T"}, {"family": "Dennis", "given": "Alice B", "initials": "AB"}, {"family": "Derks", "given": "Martijn F L", "initials": "MFL"}, {"family": "Diroma", "given": "Maria Angela", "initials": "MA"}, {"family": "Djan", "given": "Mihajla", "initials": "M"}, {"family": "Duprat", "given": "Simone", "initials": "S"}, {"family": "Eleftheriadi", "given": "Klara", "initials": "K"}, {"family": "Feulner", "given": "Philine G D", "initials": "PGD"}, {"family": "Flot", "given": "Jean-Fran\u00e7ois", "initials": "J"}, {"family": "Forni", "given": "Giobbe", "initials": "G"}, {"family": "Fosso", "given": "Bruno", "initials": "B"}, {"family": "Fournier", "given": "Pascal", "initials": "P"}, {"family": "Fournier-Chambrillon", "given": "Christine", "initials": "C"}, {"family": "Gabaldon", "given": "Toni", "initials": "T"}, {"family": "Garg", "given": "Shilpa", "initials": "S"}, {"family": "Gissi", "given": "Carmela", "initials": "C"}, {"family": "Giupponi", "given": "Luca", "initials": "L"}, {"family": "Gomez-Garrido", "given": "Jessica", "initials": "J"}, {"family": "Gonz\u00e1lez", "given": "Josefa", "initials": "J"}, {"family": "Grilo", "given": "Miguel L", "initials": "ML"}, {"family": "Gr\u00fcning", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Guerin", "given": "Thomas", "initials": "T"}, {"family": "Guiglielmoni", "given": "Nadege", "initials": "N"}, {"family": "Gut", "given": "Marta", "initials": "M"}, {"family": "Haesler", "given": "Marcel P", "initials": "MP"}, {"family": "Hahn", "given": "Christoph", "initials": "C"}, {"family": "Halpern", "given": "Balint", "initials": "B"}, {"family": "Harrison", "given": "Peter W", "initials": "PW"}, {"family": "Heintz", "given": "Julia", "initials": "J"}, {"family": "Hindrikson", "given": "Maris", "initials": "M"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Howe", "given": "Kerstin", "initials": "K"}, {"family": "Hughes", "given": "Graham M", "initials": "GM"}, {"family": "Istace", "given": "Benjamin", "initials": "B"}, {"family": "Cock", "given": "Mark J", "initials": "MJ"}, {"family": "Jan\u017eekovi\u010d", "given": "Franc", "initials": "F"}, {"family": "Jonsson", "given": "Zophonias O", "initials": "ZO"}, {"family": "Joye-Dind", "given": "Sagane", "initials": "S"}, {"family": "Koskim\u00e4ki", "given": "Janne J", "initials": "JJ"}, {"family": "Krystufek", "given": "Boris", "initials": "B"}, {"family": "Kubacka", "given": "Justyna", "initials": "J"}, {"family": "Kuhl", "given": "Heiner", "initials": "H"}, {"family": "Kusza", "given": "Szilvia", "initials": "S"}, {"family": "Labadie", "given": "Karine", "initials": "K"}, {"family": "L\u00e4hteenaro", "given": "Meri", "initials": "M"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Lavrinienko", "given": "Anton", "initials": "A"}, {"family": "Lecl\u00e8re", "given": "Lucas", "initials": "L"}, {"family": "Lopes", "given": "Ricardo Jorge", "initials": "RJ"}, {"family": "Madsen", "given": "Ole", "initials": "O"}, {"family": "Magdelenat", "given": "Ghislaine", "initials": "G"}, {"family": "Magoga", "given": "Giulia", "initials": "G"}, {"family": "Manousaki", "given": "Tereza", "initials": "T"}, {"family": "Mappes", "given": "Tapio", "initials": "T"}, {"family": "Marques", "given": "Joao Pedro", "initials": "JP"}, {"family": "Redondo", "given": "Gemma I Martinez", "initials": "GIM"}, {"family": "Maumus", "given": "Florian", "initials": "F"}, {"family": "McCarthy", "given": "Shane A", "initials": "SA"}, {"family": "Megens", "given": "Hendrik-Jan", "initials": "H"}, {"family": "Melo-Ferreira", "given": "Jose", "initials": "J"}, {"family": "Mendes", "given": "Sofia L", "initials": "SL"}, {"family": "Montagna", "given": "Matteo", "initials": "M"}, {"family": "Moreno", "given": "Joao", "initials": "J"}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "M"}, {"family": "Moura", "given": "M\u00f3nica", "initials": "M"}, {"family": "Musilova", "given": "Zuzana", "initials": "Z"}, {"family": "Myers", "given": "Eugene", "initials": "E"}, {"family": "Nash", "given": "Will J", "initials": "WJ"}, {"family": "Nater", "given": "Alexander", "initials": "A"}, {"family": "Nicholson", "given": "Pamela", "initials": "P"}, {"family": "Niell", "given": "Manuel", "initials": "M"}, {"family": "Nijland", "given": "Reindert", "initials": "R"}, {"family": "Noel", "given": "Benjamin", "initials": "B"}, {"family": "Noren", "given": "Karin", "initials": "K"}, {"family": "Oliveira", "given": "Pedro H", "initials": "PH"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "R"}, {"family": "Ometto", "given": "Lino", "initials": "L"}, {"family": "Oomen", "given": "Rebekah A", "initials": "RA"}, {"family": "Ossowski", "given": "Stephan", "initials": "S"}, {"family": "Palinauskas", "given": "Vaidas", "initials": "V"}, {"family": "Palsson", "given": "Snaebjorn", "initials": "S"}, {"family": "Panibe", "given": "Jerome P", "initials": "JP"}, {"family": "Pauperio", "given": "Joana", "initials": "J"}, {"family": "Pavlek", "given": "Martina", "initials": "M"}, {"family": "Payen", "given": "Emilie", "initials": "E"}, {"family": "Pawlowska", "given": "Julia", "initials": "J"}, {"family": "Pellicer", "given": "Jaume", "initials": "J"}, {"family": "Pesole", "given": "Graziano", "initials": "G"}, {"family": "Pimenta", "given": "Joao", "initials": "J"}, {"family": "Pippel", "given": "Martin", "initials": "M"}, {"family": "Pirttil\u00e4", "given": "Anna Maria", "initials": "AM"}, {"family": "Poulakakis", "given": "Nikos", "initials": "N"}, {"family": "Rajan", "given": "Jeena", "initials": "J"}, {"family": "M C Rego", "given": "R\u00faben", "initials": "R"}, {"family": "Resendes", "given": "Roberto", "initials": "R"}, {"family": "Resl", "given": "Philipp", "initials": "P"}, {"family": "Riesgo", "given": "Ana", "initials": "A"}, {"family": "Rodin-Morch", "given": "Patrik", "initials": "P"}, {"family": "Soares", "given": "Andre E R", "initials": "AER"}, {"family": "Fernandes", "given": "Carlos Rodriguez", "initials": "CR"}, {"family": "Romeiras", "given": "Maria M", "initials": "MM"}, {"family": "Roxo", "given": "Guilherme", "initials": "G"}, {"family": "R\u00fcber", "given": "Lukas", "initials": "L"}, {"family": "Ruiz-Lopez", "given": "Maria Jose", "initials": "MJ"}, {"family": "Saarma", "given": "Urmas", "initials": "U"}, {"family": "da Silva", "given": "Luis P", "initials": "LP"}, {"family": "Sim-Sim", "given": "Manuela", "initials": "M"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Sousa", "given": "Vitor C", "initials": "VC"}, {"family": "Santos", "given": "Carla Sousa", "initials": "CS"}, {"family": "Spada", "given": "Alberto", "initials": "A"}, {"family": "Stefanovic", "given": "Milomir", "initials": "M"}, {"family": "Steger", "given": "Viktor", "initials": "V"}, {"family": "Stiller", "given": "Josefin", "initials": "J"}, {"family": "St\u00f6ck", "given": "Matthias", "initials": "M"}, {"family": "Struck", "given": "Torsten H", "initials": "TH"}, {"family": "Sudasinghe", "given": "Hiranya", "initials": "H"}, {"family": "Tapanainen", "given": "Riikka", "initials": "R"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Trindade", "given": "Helena", "initials": "H"}, {"family": "Tukalenko", "given": "Yevhen", "initials": "Y"}, {"family": "Urso", "given": "Ilenia", "initials": "I"}, {"family": "Vacherie", "given": "Benoit", "initials": "B"}, {"family": "Van Belleghem", "given": "Steven M", "initials": "SM"}, {"family": "Van Oers", "given": "Kees", "initials": "K"}, {"family": "Vargas-Chavez", "given": "Carlos", "initials": "C"}, {"family": "Velickovic", "given": "Nevena", "initials": "N"}, {"family": "Vella", "given": "Noel", "initials": "N"}, {"family": "Vella", "given": "Adriana", "initials": "A"}, {"family": "Vernesi", "given": "Cristiano", "initials": "C"}, {"family": "Vicente", "given": "Sara", "initials": "S"}, {"family": "Villa", "given": "Sara", "initials": "S"}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Volckaert", "given": "Filip A M", "initials": "FAM"}, {"family": "Voros", "given": "Judit", "initials": "J"}, {"family": "Wincker", "given": "Patrick", "initials": "P"}, {"family": "Winkler", "given": "Sylke", "initials": "S"}, {"family": "Ciofi", "given": "Claudio", "initials": "C"}, {"family": "Waterhouse", "given": "Robert M", "initials": "RM"}, {"family": "Mazzoni", "given": "Camila J", "initials": "CJ"}], "type": "journal article", "published": "2024-09-17", "journal": {"title": "NPJ Biodivers", "issn": "2731-4243", "issn-l": null, "volume": "3", "issue": "1", "pages": "28"}, "abstract": "A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.", "doi": "10.1038/s44185-024-00054-6", "pmid": "39289538", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11408602"}, {"db": "pii", "key": "10.1038/s44185-024-00054-6"}], "notes": [], "created": "2024-10-28T09:59:00.105Z", "modified": "2024-11-12T11:36:01.896Z"}, {"entity": "publication", "iuid": "9fd78bfbc8fc471bb3dcdfab7e002017", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9fd78bfbc8fc471bb3dcdfab7e002017.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9fd78bfbc8fc471bb3dcdfab7e002017"}}, "title": "Exposure of Colon-Derived Epithelial Monolayers to Fecal Luminal Factors from Patients with Colon Cancer and Ulcerative Colitis Results in Distinct Gene Expression Patterns.", "authors": [{"family": "Magnusson", "given": "Maria K", "initials": "MK", "orcid": "0000-0002-8888-4968", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa4ee61498234362819679d3c13745a3.json"}}, {"family": "Bas Forsberg", "given": "Anna", "initials": "A"}, {"family": "Verveda", "given": "Alexandra", "initials": "A"}, {"family": "Sapnara", "given": "Maria", "initials": "M"}, {"family": "Lorent", "given": "Julie", "initials": "J"}, {"family": "Savolainen", "given": "Otto", "initials": "O"}, {"family": "Wettergren", "given": "Yvonne", "initials": "Y", "orcid": "0000-0001-8660-7169", "researcher": {"href": "https://publications.scilifelab.se/researcher/30df595b99b048388f92c2794fefcf80.json"}}, {"family": "Strid", "given": "Hans", "initials": "H"}, {"family": "Simr\u00e9n", "given": "Magnus", "initials": "M", "orcid": "0000-0002-1155-1313", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c749281a28d453e8e155a8eeaf4b75e.json"}}, {"family": "\u00d6hman", "given": "Lena", "initials": "L", "orcid": "0000-0001-8142-2106", "researcher": {"href": "https://publications.scilifelab.se/researcher/79239c8719b24eba951c4e1702952d5e.json"}}], "type": "journal article", "published": "2024-09-13", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "25", "issue": "18", "issn-l": null}, "abstract": "Microbiota and luminal components may affect epithelial integrity and thus participate in the pathophysiology of colon cancer (CC) and inflammatory bowel disease (IBD). Therefore, we aimed to determine the effects of fecal luminal factors derived from patients with CC and ulcerative colitis (UC) on the colonic epithelium using a standardized colon-derived two-dimensional epithelial monolayer. The complex primary human stem cell-derived intestinal epithelium model, termed RepliGut\u00ae Planar, was expanded and passaged in a two-dimensional culture which underwent stimulation for 48 h with fecal supernatants (FS) from CC patients (n = 6), UC patients with active disease (n = 6), and healthy subjects (HS) (n = 6). mRNA sequencing of monolayers was performed and cytokine secretion in the basolateral cell culture compartment was measured. The addition of fecal supernatants did not impair the integrity of the colon-derived epithelial monolayer. However, monolayers stimulated with fecal supernatants from CC patients and UC patients presented distinct gene expression patterns. Comparing UC vs. CC, 29 genes were downregulated and 33 genes were upregulated, for CC vs. HS, 17 genes were downregulated and five genes were upregulated, and for UC vs. HS, three genes were downregulated and one gene was upregulated. The addition of FS increased secretion of IL8 with no difference between the study groups. Fecal luminal factors from CC patients and UC patients induce distinct colonic epithelial gene expression patterns, potentially reflecting the disease pathophysiology. The culture of colonic epithelial monolayers with fecal supernatants derived from patients may facilitate the exploration of IBD- and CC-related intestinal microenvironmental and barrier interactions.", "doi": "10.3390/ijms25189886", "pmid": "39337373", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Chalmers Mass Spectrometry Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11431989"}, {"db": "pii", "key": "ijms25189886"}], "notes": [], "created": "2024-11-12T17:57:31.628Z", "modified": "2024-11-27T15:29:15.332Z"}, {"entity": "publication", "iuid": "01832646b322457db74029072c6f506d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/01832646b322457db74029072c6f506d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/01832646b322457db74029072c6f506d"}}, "title": "Dantrolene corrects cellular disease features of Darier disease and may be a novel treatment.", "authors": [{"family": "Hunt", "given": "Matthew", "initials": "M", "orcid": "0000-0002-7697-8086", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a2c3da4af5e4004a8ce0923bfe5a78d.json"}}, {"family": "Wang", "given": "Nuoqi", "initials": "N"}, {"family": "Pupinyo", "given": "Naricha", "initials": "N"}, {"family": "Curman", "given": "Philip", "initials": "P"}, {"family": "Torres", "given": "Monica", "initials": "M", "orcid": "0000-0001-6634-2562", "researcher": {"href": "https://publications.scilifelab.se/researcher/fed46315e9c64acaafcc55736df05b29.json"}}, {"family": "Jebril", "given": "William", "initials": "W"}, {"family": "Chatzinikolaou", "given": "Maria", "initials": "M", "orcid": "0000-0002-3539-9088", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fa3519e517549bc854f19983e649074.json"}}, {"family": "Lorent", "given": "Julie", "initials": "J"}, {"family": "Silberberg", "given": "Gilad", "initials": "G"}, {"family": "Bansal", "given": "Ritu", "initials": "R", "orcid": "0000-0003-4091-1696", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a4e6e164714455787187edf408d5091.json"}}, {"family": "Burner", "given": "Teresa", "initials": "T"}, {"family": "Zhou", "given": "Jing", "initials": "J"}, {"family": "Kimeswenger", "given": "Susanne", "initials": "S", "orcid": "0000-0002-0443-8558", "researcher": {"href": "https://publications.scilifelab.se/researcher/64b4ab3d129844309d35c94b5304090e.json"}}, {"family": "Hoetzenecker", "given": "Wolfram", "initials": "W"}, {"family": "Choate", "given": "Keith", "initials": "K"}, {"family": "Bachar-Wikstrom", "given": "Etty", "initials": "E", "orcid": "0000-0002-3283-6721", "researcher": {"href": "https://publications.scilifelab.se/researcher/388692a214e44e9ea7497b397d237bc0.json"}}, {"family": "Wikstrom", "given": "Jakob D", "initials": "JD", "orcid": "0000-0002-9241-6817", "researcher": {"href": "https://publications.scilifelab.se/researcher/25161d16ce27418db99fb2e5f2942dac.json"}}], "type": "journal article", "published": "2024-09-00", "journal": {"title": "EMBO Mol Med", "issn": "1757-4684", "volume": "16", "issue": "9", "pages": "1986-2001", "issn-l": "1757-4676"}, "abstract": "Darier disease (DD) is a rare severe acantholytic skin disease caused by mutations in the ATP2A2 gene that encodes for the sarco/endoplasmic reticulum calcium ATPase isoform 2 (SERCA2). SERCA2 maintains endoplasmic reticulum calcium homeostasis by pumping calcium into the ER, critical for regulating cellular calcium dynamics and cellular function. To date, there is no treatment that specifically targets the disease mechanisms in DD. Dantrolene sodium (Dl) is a ryanodine receptor antagonist that inhibits calcium release from ER to increase ER calcium levels and is currently used for non-dermatological indications. In this study, we first identified dysregulated genes and molecular pathways in DD patient skin, demonstrating downregulation of cell adhesion and calcium homeostasis pathways, as well as upregulation of ER stress and apoptosis. We then show in various in vitro models of DD and SERCA2 inhibition that Dl aided in the retention of ER calcium and promoted cell adhesion. In addition, Dl treatment reduced ER stress and suppressed apoptosis. Our findings suggest that Dl specifically targets pathogenic mechanisms of DD and may be a potential treatment.", "doi": "10.1038/s44321-024-00104-3", "pmid": "39060641", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11392931"}, {"db": "pii", "key": "10.1038/s44321-024-00104-3"}], "notes": [], "created": "2024-11-12T17:46:28.489Z", "modified": "2025-02-28T14:16:48.876Z"}, {"entity": "publication", "iuid": "ca128e901f5f4cf484de05f16bcca9cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ca128e901f5f4cf484de05f16bcca9cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ca128e901f5f4cf484de05f16bcca9cc"}}, "title": "Contemporary intergeneric hybridization and backcrossing among birds-of-paradise.", "authors": [{"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications.scilifelab.se/researcher/e272339ca04d4daf935b708b04c5c53e.json"}}, {"family": "Soares", "given": "Andr\u00e9 E R", "initials": "AER"}, {"family": "M\u00fcller", "given": "Ingo A", "initials": "IA"}, {"family": "P\u00e4ckert", "given": "Martin", "initials": "M", "orcid": "0000-0001-5045-0139", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b587876461a4066b09d2bd5d3eaffc1.json"}}, {"family": "Frahnert", "given": "Sylke", "initials": "S"}, {"family": "van Grouw", "given": "Hein", "initials": "H"}, {"family": "Kamminga", "given": "Pepijn", "initials": "P"}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2024-09-00", "journal": {"title": "Evolution Letters", "issn": "2056-3744", "issn-l": "2056-3744", "volume": "8", "issue": "5", "pages": "680-694"}, "abstract": "Despite large differences in morphology, behavior and lek-mating strategies the birds-of-paradise are known to hybridize occasionally, even across different genera. Many of these bird-of-paradise hybrids were originally described as distinct species based on large morphological differences when compared to recognized species. Nowadays, these specimens are generally recognized as hybrids based on morphological assessments. Having fascinated naturalists for centuries, hybrid specimens of birds-of-paradise have been collected and the specimens kept in Natural History Collections. In the present study, we utilize this remarkable resource in a museomics framework and evaluate the genomic composition of most described intergeneric hybrids and some intrageneric hybrids. We show that the majority of investigated specimens are first-generation hybrids and that the parental species, in most cases, are in line with prior morphological assessments. We also identify two specimens that are the result of introgressive hybridization between different genera. Additionally, two specimens exhibit hybrid morphologies but have no identifiable signals of hybridization, which may indicate that minor levels of introgression can have large morphological effects. Our findings provide direct evidence of contemporary introgressive hybridization taking place between genera of birds-of-paradise in nature, despite markedly different morphologies and lek-mating behaviors.", "doi": "10.1093/evlett/qrae023", "pmid": "39328285", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11424083"}, {"db": "pii", "key": "qrae023"}], "notes": [], "created": "2024-10-18T07:14:19.442Z", "modified": "2024-11-25T10:23:13.047Z"}, {"entity": "publication", "iuid": "faefdb3dcb9d48b4975d841d847375dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/faefdb3dcb9d48b4975d841d847375dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/faefdb3dcb9d48b4975d841d847375dc"}}, "title": "AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality.", "authors": [{"family": "Rashid", "given": "Usman", "initials": "U"}, {"family": "Wu", "given": "Chen", "initials": "C"}, {"family": "Shiller", "given": "Jason", "initials": "J"}, {"family": "Smith", "given": "Ken", "initials": "K"}, {"family": "Crowhurst", "given": "Ross", "initials": "R"}, {"family": "Davy", "given": "Marcus", "initials": "M"}, {"family": "Chen", "given": "Ting-Hsuan", "initials": "TH"}, {"family": "Carvajal", "given": "Ignacio", "initials": "I"}, {"family": "Bailey", "given": "Sarah", "initials": "S"}, {"family": "Thomson", "given": "Susan", "initials": "S"}, {"family": "Deng", "given": "Cecilia H", "initials": "CH", "orcid": "0000-0002-2954-762X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1055115ab09f46a6b77f684072b2b200.json"}}], "type": "journal article", "published": "2024-08-02", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "40", "issue": "8", "issn-l": "1367-4803"}, "abstract": "Genome assembly projects have grown exponentially due to breakthroughs in sequencing technologies and assembly algorithms. Evaluating the quality of genome assemblies is critical to ensure the reliability of downstream analysis and interpretation. To fulfil this task, we have developed the AssemblyQC pipeline that performs file-format validation, contaminant checking, contiguity measurement, gene- and repeat-space completeness quantification, telomere inspection, taxonomic assignment, synteny alignment, scaffold examination through Hi-C contact-map visualization, and assessments of completeness, consensus quality and phasing through k-mer analysis. It produces a comprehensive HTML report with method descriptions, tables, and visualizations.\n\nThe pipeline uses Nextflow for workflow orchestration and adheres to the best-practice established by the nf-core community. This pipeline offers a reproducible, scalable, and portable method to assess the quality of genome assemblies-the code is available online at GitHub: https://github.com/Plant-Food-Research-Open/assemblyqc.", "doi": "10.1093/bioinformatics/btae477", "pmid": "39078114", "labels": {"Bioinformatics Support and Infrastructure": "Technology development", "Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pii", "key": "7723991"}, {"db": "pmc", "key": "PMC11333564"}], "notes": [], "created": "2024-08-21T09:21:17.217Z", "modified": "2024-08-21T09:21:17.390Z"}, {"entity": "publication", "iuid": "083d4ea1eab4440d9429b817a041e0e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/083d4ea1eab4440d9429b817a041e0e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/083d4ea1eab4440d9429b817a041e0e9"}}, "title": "Exploring the interplay between antiretroviral therapy and the gut-oral microbiome axis in people living with HIV.", "authors": [{"family": "Narayanan", "given": "Aswathy", "initials": "A"}, {"family": "Kieri", "given": "Oscar", "initials": "O"}, {"family": "Vesterbacka", "given": "Jan", "initials": "J"}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L"}, {"family": "Chen", "given": "Puran", "initials": "P"}, {"family": "Ghorbani", "given": "Mahin", "initials": "M"}, {"family": "Ljunggren", "given": "Hans-Gustaf", "initials": "HG"}, {"family": "S\u00e4llberg Chen", "given": "Margaret", "initials": "M"}, {"family": "Aleman", "given": "Soo", "initials": "S"}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A"}, {"family": "Ray", "given": "Shilpa", "initials": "S"}, {"family": "Nowak", "given": "Piotr", "initials": "P"}], "type": "journal article", "published": "2024-08-01", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "17820", "issn-l": "2045-2322"}, "abstract": "The gut and oral microbiome is altered in people living with HIV (PLWH). While antiretroviral treatment (ART) is pivotal in restoring immune function in PLWH, several studies have identified an association between specific antiretrovirals, particularly integrase inhibitors (INSTI), and weight gain. In our study, we explored the differences in the oral and gut microbiota of PLWH under different ART regimens, and its correlation to Body Mass Index (BMI). Fecal and salivary samples were collected from PLWH (n = 69) and healthy controls (HC, n = 80). We performed taxonomy analysis to determine the microbial composition and relationship between microbial abundance and ART regimens, BMI, CD4+T-cell count, CD4/CD8 ratio, and ART duration. PLWH showed significantly lower richness compared to HC in both the oral and gut environment. The gut microbiome composition of INSTI-treated individuals was enriched with Faecalibacterium and Bifidobacterium, whereas non-nucleotide reverse transcriptase inhibitor (NNRTI)-treated individuals were enriched with Gordonibacter, Megasphaera, and Staphylococcus. In the oral microenvironment, Veillonella was significantly more abundant in INSTI-treated individuals and Fusobacterium and Alloprevotella in the NNRTI-treated individuals. Furthermore, Bifidobacterium and Dorea were enriched in gut milieu of PLWH with high BMI. Collectively, our findings identify distinct microbial profiles, which are associated with different ART regimens and BMI in PLWH on successful ART, thereby highlighting significant effects of specific antiretrovirals on the microbiome.", "doi": "10.1038/s41598-024-68479-4", "pmid": "39090139", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11294597"}, {"db": "pii", "key": "10.1038/s41598-024-68479-4"}], "notes": [], "created": "2024-11-15T09:06:45.594Z", "modified": "2024-11-25T10:21:34.231Z"}, {"entity": "publication", "iuid": "3bf46273f014498b80752db1b270c250", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3bf46273f014498b80752db1b270c250.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3bf46273f014498b80752db1b270c250"}}, "title": "Plasticity for the win: Flexible transcriptional response to host plant switches in the comma butterfly (Polygonia c-album).", "authors": [{"family": "Schneider", "given": "Katharina", "initials": "K", "orcid": "0009-0004-7727-594X", "researcher": {"href": "https://publications.scilifelab.se/researcher/27ac69b83e6e4a70ab1473838d162f61.json"}}, {"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}}, {"family": "Celorio-Mancera", "given": "Maria de la Paz", "initials": "MdlP"}, {"family": "Janz", "given": "Niklas", "initials": "N", "orcid": "0000-0002-6379-7905", "researcher": {"href": "https://publications.scilifelab.se/researcher/addc1292f6db4eeeacee907b4a534f52.json"}}, {"family": "Moberg", "given": "Dick", "initials": "D", "orcid": "0000-0001-5704-3915", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f9df1ca5bd343cdb148d7c8fbfc6f46.json"}}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.json"}}, {"family": "Nylin", "given": "S\u00f6ren", "initials": "S", "orcid": "0000-0003-4195-8920", "researcher": {"href": "https://publications.scilifelab.se/researcher/68d7f780ed30472eb2af408b0762c14d.json"}}], "type": "journal article", "published": "2024-08-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "33", "issue": "16", "pages": "e17479"}, "abstract": "Generalist plant-feeding insects are characterised by a broad host repertoire that can comprise several families or even different orders of plants. The genetic and physiological mechanisms underlying the use of such a wide host range are still not fully understood. Earlier studies indicate that the consumption of different host plants is associated with host-specific gene expression profiles. It remained, however, unclear if and how larvae can alter these profiles in the case of a changing host environment. Using the polyphagous comma butterfly (Polygonia c-album) we show that larvae can adjust their transcriptional profiles in response to a new host plant. The switch to some of the host plants, however, resulted in a larger transcriptional response and, thus, seems to be more challenging. At a physiological level, no correspondence for these patterns could be found in larval performance. This suggests that a high transcriptional but also phenotypic flexibility are essential for the use of a broad and diverse host range. We furthermore propose that host switch tests in the laboratory followed by transcriptomic investigations can be a valuable tool to examine not only plasticity in host use but also subtle and/or transient trade-offs in the evolution of host plant repertoires.", "doi": "10.1111/mec.17479", "pmid": "39036890", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-12T19:50:29.574Z", "modified": "2025-01-02T12:19:27.670Z"}, {"entity": "publication", "iuid": "c8247c4a542e4c94ae4a3ee22db83900", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c8247c4a542e4c94ae4a3ee22db83900.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c8247c4a542e4c94ae4a3ee22db83900"}}, "title": "Comparative Genomic Analysis of the Pattern of Evolution of Male and Female Reproductive Proteins in Seed Beetles.", "authors": [{"family": "Papachristos", "given": "Konstantinos", "initials": "K", "orcid": "0000-0002-4777-9088", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bf7a545a218455fa134b3dd8bb1b895.json"}}, {"family": "Sayadi", "given": "Ahmed", "initials": "A", "orcid": "0000-0002-5662-9145", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f74f301499b4f888e0ac7c5161ae161.json"}}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f.json"}}], "type": "journal article", "published": "2024-07-03", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "16", "issue": "7", "pages": null}, "abstract": "Male seminal fluid proteins often show signs of positive selection and divergent evolution, believed to reflect male-female coevolution. Yet, our understanding of the predicted concerted evolution of seminal fluid proteins and female reproductive proteins is limited. We sequenced, assembled, and annotated the genome of two species of seed beetles allowing a comparative analysis of four closely related species of these herbivorous insects. We compare the general pattern of evolution in genes encoding seminal fluid proteins and female reproductive proteins with those in digestive protein genes and well-conserved reference genes. We found that female reproductive proteins showed an overall ratio of nonsynonymous to synonymous substitutions (\u03c9) similar to that of conserved genes, while seminal fluid proteins and digestive proteins exhibited higher overall \u03c9 values. Further, seminal fluid proteins and digestive proteins showed a higher proportion of sites putatively under positive selection, and explicit tests showed no difference in relaxed selection between protein types. Evolutionary rate covariation analyses showed that evolutionary rates among seminal fluid proteins were on average more closely correlated with those in female reproductive proteins than with either digestive or conserved genes. Gene expression showed the expected negative covariation with \u03c9 values, except for male-biased genes where this negative relationship was reversed. In conclusion, seminal fluid proteins showed relatively rapid evolution and signs of positive selection. In contrast, female reproductive proteins evolved at a lower rate under selective constraints, on par with genes known to be well conserved. Although our findings provide support for concerted evolution of seminal fluid proteins and female reproductive proteins, they also suggest that these two classes of proteins evolve under partly distinct selective regimes.", "doi": "10.1093/gbe/evae143", "pmid": "38941482", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11251426"}, {"db": "pii", "key": "7701342"}], "notes": [], "created": "2024-11-12T10:52:28.961Z", "modified": "2024-11-25T10:24:28.390Z"}, {"entity": "publication", "iuid": "3469dac1b4fd46aaaede136329dabc22", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3469dac1b4fd46aaaede136329dabc22.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3469dac1b4fd46aaaede136329dabc22"}}, "title": "GABA-mediated inhibition of human CD4+ T cell functions is enhanced by insulin but impaired by high glucose levels.", "authors": [{"family": "Jin", "given": "Zhe", "initials": "Z"}, {"family": "Hammoud", "given": "Hayma", "initials": "H"}, {"family": "Bhandage", "given": "Amol Keshavasa", "initials": "AK"}, {"family": "Korol", "given": "Sergiy Vasylyovych", "initials": "SV"}, {"family": "Trujeque-Ramos", "given": "Olivia", "initials": "O"}, {"family": "Koreli", "given": "Stasini", "initials": "S"}, {"family": "Gong", "given": "Zhitao", "initials": "Z"}, {"family": "Chowdhury", "given": "Azasul Islam", "initials": "AI"}, {"family": "Sandbaumh\u00fcter", "given": "Friederike Andrea", "initials": "FA"}, {"family": "Jansson", "given": "Erik Tomas", "initials": "ET"}, {"family": "Lindsay", "given": "Robin Sean", "initials": "RS"}, {"family": "Christoffersson", "given": "Gustaf", "initials": "G"}, {"family": "Andr\u00e9n", "given": "Per Erik", "initials": "PE"}, {"family": "Carlsson", "given": "Per-Ola", "initials": "PO"}, {"family": "Bergsten", "given": "Peter", "initials": "P"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M"}, {"family": "Birnir", "given": "Bryndis", "initials": "B"}], "type": "journal article", "published": "2024-07-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "volume": "105", "pages": "105217", "issn-l": "2352-3964"}, "abstract": "\u03b3-aminobutyric acid (GABA), known as the main inhibitory neurotransmitter in the brain, exerts immunomodulatory functions by interaction with immune cells, including T cells. Metabolic programs of T cells are closely linked to their effector functions including proliferation, differentiation, and cytokine production. The physiological molecules glucose and insulin may provide environmental cues and guidance, but whether they coordinate to regulate GABA-mediated T cell immunomodulation is still being examined.\n\nCD4+ T cells that were isolated from blood samples from healthy individuals and from patients with type 1 diabetes (T1D) were activated in vitro. We carried out metabolic assays, multiple proximity extension assay (PEA), ELISA, qPCR, immunoblotting, immunofluorescence staining, flow cytometry analysis, MS-based proteomics, as well as electrophysiology and live-cell Ca2+ imaging.\n\nWe demonstrate that GABA-mediated reduction of metabolic activity and the release of inflammatory proteins, including IFN\u03b3 and IL-10, were abolished in human CD4+ T cells from healthy individuals and patients with T1D when the glucose concentration was elevated above levels typically observed in healthy people. Insulin increased GABAA receptor-subunit \u03c12 expression, enhanced the GABAA receptors-mediated currents and Ca2+ influx. GABA decreased, whereas insulin sustained, hexokinase activity and glycolysis in a glucose concentration-dependent manner.\n\nThese findings support that metabolic factors, such as glucose and insulin, influence the GABA-mediated immunomodulation of human primary T cells effector functions.\n\nThe Swedish Children's Diabetes Foundation, The Swedish Diabetes Foundation, The Swedish Research Council 2018-02952, EXODIAB, The Ernfors Foundation, The Thurings Foundation and the Science for Life Laboratory.", "doi": "10.1016/j.ebiom.2024.105217", "pmid": "38943728", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Spatial Mass Spectrometry": "Collaborative", "Affinity Proteomics Uppsala": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11260598"}, {"db": "pii", "key": "S2352-3964(24)00252-4"}], "notes": [], "created": "2024-11-12T20:19:19.496Z", "modified": "2024-11-27T22:22:24.282Z"}, {"entity": "publication", "iuid": "9716f3138ad84b71861f8fa3d241d1d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9716f3138ad84b71861f8fa3d241d1d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9716f3138ad84b71861f8fa3d241d1d6"}}, "title": "Hearing loss and its association with the proteome of perilymph, cerebrospinal fluid, and tumor tissue in patients with vestibular schwannoma.", "authors": [{"family": "Edvardsson Rasmussen", "given": "Jesper", "initials": "J"}, {"family": "Li", "given": "Peng", "initials": "P"}, {"family": "Laurell", "given": "G\u00f6ran", "initials": "G"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Eriksson", "given": "Per Olof", "initials": "PO"}], "type": "journal article", "published": "2024-06-19", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "14118", "issn-l": "2045-2322"}, "abstract": "This study examined the association between hearing loss in sporadic vestibular schwannoma patients and the proteome of perilymph (PL), cerebrospinal fluid (CSF), and vestibular schwannoma. Intraoperative sampling of PL and of CSF, and biopsy of vestibular schwannoma tissue, was performed in 32, 32, and 20 patients with vestibular schwannoma, respectively. Perilymph and CSF in three patients with meningioma and normal hearing were also sampled. The proteomes were identified by liquid chromatography coupled to high-resolution tandem mass spectrometry. Preoperative hearing function of the patients was evaluated with pure tone audiometry, with mean values at frequencies of 500, 1000, 2000, and 4000 Hz (PTA4) in the tumor-affected ear used to delineate three hearing groups. Analysis of the PL samples revealed significant upregulation of complement factor H-related protein 2 (CFHR2) in patients with severe to profound hearing loss after false discovery rate correction. Pathway analysis of biofunctions revealed higher activation scores in the severe/profound hearing loss group of leukocyte migration, viral infection, and migration of cells in PL. Upregulation of CFHR2 and activation of these pathways indicate chronic inflammation in the cochlea of vestibular schwannoma patients with severe to profound hearing loss compared with patients with normal hearing or mild hearing loss.", "doi": "10.1038/s41598-024-64352-6", "pmid": "38898156", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11187212"}, {"db": "pii", "key": "10.1038/s41598-024-64352-6"}], "notes": [], "created": "2024-11-12T19:33:28.441Z", "modified": "2024-11-12T19:33:28.448Z"}, {"entity": "publication", "iuid": "b789c181c1ab4a679ba3bd4e0df2e56f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b789c181c1ab4a679ba3bd4e0df2e56f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b789c181c1ab4a679ba3bd4e0df2e56f"}}, "title": "Comprehensive Genomic Profiling Alters Clinical Diagnoses in a Significant Fraction of Tumors Suspicious of Sarcoma.", "authors": [{"family": "\u00d6fverholm", "given": "Ingegerd", "initials": "I", "orcid": "0000-0002-6907-8004", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ba94eeea4d24e9c8c354fe1256fd0ce.json"}}, {"family": "Wallander", "given": "Karin", "initials": "K", "orcid": "0000-0001-8166-9678", "researcher": {"href": "https://publications.scilifelab.se/researcher/db174787efd74dc1b84f1bf56b74a22d.json"}}, {"family": "Haglund", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5484-8945", "researcher": {"href": "https://publications.scilifelab.se/researcher/7943ee4528064cafab37a2d91db8e480.json"}}, {"family": "Chellappa", "given": "Venkatesh", "initials": "V", "orcid": "0000-0003-1431-6949", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1af2e624b7d4783b0b61ff80ce8d8a1.json"}}, {"family": "Wejde", "given": "Johan", "initials": "J", "orcid": "0009-0009-1563-8158", "researcher": {"href": "https://publications.scilifelab.se/researcher/a974827370844ae0944a96892fb609da.json"}}, {"family": "Gellerbring", "given": "Anna", "initials": "A", "orcid": "0009-0002-4505-2173", "researcher": {"href": "https://publications.scilifelab.se/researcher/a267c2ecf411470a88bac75ab3ea58b2.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Renevey", "given": "Annick", "initials": "A", "orcid": "0000-0001-7411-6063", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0f6fb37ae984090b795b87229ffbd72.json"}}, {"family": "Caceres", "given": "Eva", "initials": "E", "orcid": "0000-0003-2890-2631", "researcher": {"href": "https://publications.scilifelab.se/researcher/df9019d6fdfc42c9b22d94c0af4bbd42.json"}}, {"family": "Tsagkozis", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-6631-2053", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae792176785f4fb3b5a1eb36478570f7.json"}}, {"family": "Mayrhofer", "given": "Markus", "initials": "M", "orcid": "0000-0003-3403-0083", "researcher": {"href": "https://publications.scilifelab.se/researcher/b08e9a0f0dc948dca3a3c40a1dd7c8cc.json"}}, {"family": "Papakonstantinou", "given": "Andri", "initials": "A", "orcid": "0000-0002-4232-4658", "researcher": {"href": "https://publications.scilifelab.se/researcher/92de2b7447a74c08ad49083ef803d4de.json"}}, {"family": "Linder-Stragliotto", "given": "Christina", "initials": "C", "orcid": "0009-0002-1247-7028", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ab128a5d5a2410ab055ae15e99374ed.json"}}, {"family": "Br\u00e4nstr\u00f6m", "given": "Robert", "initials": "R", "orcid": "0000-0001-6245-7223", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a5818dd9c4e4b9eae136c135d411c66.json"}}, {"family": "Larsson", "given": "Olle", "initials": "O", "orcid": "0000-0001-8173-2956", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cc0db662031464b8a5a56cc6ef3705e.json"}}, {"family": "Lindberg", "given": "Johan", "initials": "J", "orcid": "0000-0003-3610-6774", "researcher": {"href": "https://publications.scilifelab.se/researcher/1369ca149def47a8abb8abb90b23ca66.json"}}, {"family": "Lin", "given": "Yingbo", "initials": "Y", "orcid": "0000-0001-7190-2261", "researcher": {"href": "https://publications.scilifelab.se/researcher/3dfabc46c47741b9ace94b082d60184d.json"}}, {"family": "Haglund de Flon", "given": "Felix", "initials": "F", "orcid": "0000-0002-7015-3841", "researcher": {"href": "https://publications.scilifelab.se/researcher/891cbee146fa4e27bc8d26111283b854.json"}}], "type": "journal article", "published": "2024-06-14", "journal": {"title": "Clin. Cancer Res.", "issn": "1557-3265", "issn-l": "1078-0432", "volume": "30", "issue": "12", "pages": "2647-2658"}, "abstract": "Tumor classification is a key component in personalized cancer care. For soft-tissue and bone tumors, this classification is currently based primarily on morphology assessment and IHC staining. However, these standard-of-care methods can pose challenges for pathologists. We therefore assessed how whole-genome and whole-transcriptome sequencing (WGTS) impacted tumor classification and clinical management when interpreted together with histomorphology.\n\nWe prospectively evaluated WGTS in routine diagnostics of 200 soft-tissue and bone tumors suspicious for malignancy, including DNA and RNA isolation from the tumor, and DNA isolation from a peripheral blood sample or any non-tumor tissue.\n\nOn the basis of specific genomic alterations or absence of presumed findings, WGTS resulted in reclassification of 7% (13/197) of the histopathologic diagnoses. Four cases were downgraded from low-grade sarcomas to benign lesions, and two cases were reclassified as metastatic malignant melanomas. Fusion genes associated with specific tumor entities were found in 30 samples. For malignant soft-tissue and bone tumors, we identified treatment relevant variants in 15% of cases. Germline pathogenic variants associated with a hereditary cancer syndrome were found in 22 participants (11%).\n\nWGTS provides an important dimension of data that aids in the classification of soft-tissue and bone tumors, correcting a significant fraction of clinical diagnoses, and identifies molecular targets relevant for precision medicine. However, genetic findings need to be evaluated in their morphopathologic context, just as germline findings need to be evaluated in the context of patient phenotype and family history.", "doi": "10.1158/1078-0432.CCR-24-0384", "pmid": "38573684", "labels": {"Clinical Genomics Stockholm": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "742915"}], "notes": [], "created": "2024-04-05T14:18:38.329Z", "modified": "2024-11-21T07:20:56.782Z"}, {"entity": "publication", "iuid": "9fd0cd5c795f411f840ee9eeab721e36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9fd0cd5c795f411f840ee9eeab721e36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9fd0cd5c795f411f840ee9eeab721e36"}}, "title": "Long-term impact of digital media on brain development in children.", "authors": [{"family": "Nivins", "given": "Samson", "initials": "S"}, {"family": "Sauce", "given": "Bruno", "initials": "B"}, {"family": "Liebherr", "given": "Magnus", "initials": "M"}, {"family": "Judd", "given": "Nicholas", "initials": "N"}, {"family": "Klingberg", "given": "Torkel", "initials": "T"}], "type": "journal article", "published": "2024-06-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "13030", "issn-l": "2045-2322"}, "abstract": "Digital media (DM) takes an increasingly large part of children's time, yet the long-term effect on brain development remains unclear. We investigated how individual effects of DM use (i.e., using social media, playing video games, or watching television/videos) on the development of the cortex (i.e., global cortical surface area), striatum, and cerebellum in children over 4 years, accounting for both socioeconomic status and genetic predisposition. We used a prospective, multicentre, longitudinal cohort of children from the Adolescent Brain and Cognitive Development Study, aged 9.9 years when entering the study, and who were followed for 4 years. Annually, children reported their DM usage through the Youth Screen Time Survey and underwent brain magnetic resonance imaging scans every 2 years. Quadratic-mixed effect modelling was used to investigate the relationship between individual DM usage and brain development. We found that individual DM usage did not alter the development of cortex or striatum volumes. However, high social media usage was associated with a statistically significant change in the developmental trajectory of cerebellum volumes, and the accumulated effect of high-vs-low social media users on cerebellum volumes over 4 years was only \u03b2 = - 0.03, which was considered insignificant. Nevertheless, the developmental trend for heavy social media users was accelerated at later time points. This calls for further studies and longer follow-ups on the impact of social media on brain development.", "doi": "10.1038/s41598-024-63566-y", "pmid": "38844772", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11156852"}, {"db": "pii", "key": "10.1038/s41598-024-63566-y"}], "notes": [], "created": "2024-11-12T20:54:57.860Z", "modified": "2024-11-12T20:54:57.872Z"}, {"entity": "publication", "iuid": "ad7858d5972e4eebb3327e5c45183267", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ad7858d5972e4eebb3327e5c45183267.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ad7858d5972e4eebb3327e5c45183267"}}, "title": "Macrophages upregulate mural cell-like markers and support healing of ischemic injury by adopting functions important for vascular support.", "authors": [{"family": "Amoedo-Leite", "given": "Catarina", "initials": "C", "orcid": "0000-0002-7556-4826", "researcher": {"href": "https://publications.scilifelab.se/researcher/09c63612668841df817c18ab93d6f4e4.json"}}, {"family": "Parv", "given": "Kristel", "initials": "K"}, {"family": "Testini", "given": "Chiara", "initials": "C"}, {"family": "Herrera-Hidalgo", "given": "Carmen", "initials": "C"}, {"family": "Xu", "given": "Feifei", "initials": "F"}, {"family": "Giraud", "given": "Antoine", "initials": "A", "orcid": "0000-0002-8559-5781", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0d7d5e9c90a4dc8b798c366ce4aa6a7.json"}}, {"family": "Malaquias", "given": "Marta", "initials": "M"}, {"family": "Fasterius", "given": "Erik", "initials": "E"}, {"family": "Holl", "given": "Daniel", "initials": "D"}, {"family": "Seignez", "given": "Cedric", "initials": "C"}, {"family": "G\u00f6ritz", "given": "Christian", "initials": "C", "orcid": "0000-0003-0799-766X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3358941841740db8d22fd49e14bdea2.json"}}, {"family": "Christoffersson", "given": "Gustaf", "initials": "G"}, {"family": "Phillipson", "given": "Mia", "initials": "M", "orcid": "0000-0002-2387-0266", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ebf9ffcab3e4a19add4c6dd51b727b1.json"}}], "type": "journal article", "published": "2024-06-00", "journal": {"title": "Nat Cardiovasc Res", "issn": "2731-0590", "volume": "3", "issue": "6", "pages": "685-700", "issn-l": null}, "abstract": "Sterile inflammation after injury is important for tissue restoration. In injured human and mouse tissues, macrophages were recently found to accumulate perivascularly. This study investigates if macrophages adopt a mural cell phenotype important for restoration after ischemic injury. Single-cell RNA sequencing of fate-mapped macrophages from ischemic mouse muscles demonstrates a macrophage-toward-mural cell switch of a subpopulation of macrophages with downregulated myeloid cell genes and upregulated mural cell genes, including PDGFR\u03b2. This observation was further strengthened when including unspliced transcripts in the analysis. The macrophage switch was proven functionally relevant, as induction of macrophage-specific PDGFR\u03b2 deficiency prevented their perivascular macrophage phenotype, impaired vessel maturation and increased vessel leakiness, which ultimately reduced limb function. In conclusion, macrophages in adult ischemic tissue were demonstrated to undergo a cellular program to morphologically, transcriptomically and functionally resemble mural cells while weakening their macrophage identity. The macrophage-to-mural cell-like phenotypic switch is crucial for restoring tissue function and warrants further exploration as a potential target for immunotherapies to enhance healing.", "doi": "10.1038/s44161-024-00478-0", "pmid": "39196227", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11358018"}, {"db": "pii", "key": "10.1038/s44161-024-00478-0"}], "notes": [], "created": "2024-10-16T12:27:59.619Z", "modified": "2024-11-12T20:14:44.444Z"}, {"entity": "publication", "iuid": "0858552e404246c8892b6fb8fe3ae038", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0858552e404246c8892b6fb8fe3ae038.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0858552e404246c8892b6fb8fe3ae038"}}, "title": "Epigenetic dissection of human blood group genes reveals regulatory elements and detailed characteristics of KEL and four other loci.", "authors": [{"family": "Wu", "given": "Ping Chun", "initials": "PC"}, {"family": "McGowan", "given": "Eunike C", "initials": "EC"}, {"family": "Lee", "given": "Yan Quan", "initials": "YQ"}, {"family": "Ghosh", "given": "Sudip", "initials": "S"}, {"family": "Hansson", "given": "Jenny", "initials": "J", "orcid": "0000-0001-9174-8089", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec099f6b24134519b596b8e34567a492.json"}}, {"family": "Olsson", "given": "Martin L", "initials": "ML", "orcid": "0000-0003-1647-9610", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbb7eb4eb158425584c9f953683bded7.json"}}], "type": "journal article", "published": "2024-06-00", "journal": {"title": "Transfusion", "issn": "1537-2995", "volume": "64", "issue": "6", "pages": "1083-1096", "issn-l": null}, "abstract": "Blood typing is essential for safe transfusions and is performed serologically or genetically. Genotyping predominantly focuses on coding regions, but non-coding variants may affect gene regulation, as demonstrated in the ABO, FY and XG systems. To uncover regulatory loci, we expanded a recently developed bioinformatics pipeline for discovery of non-coding variants by including additional epigenetic datasets.\n\nMultiple datasets including ChIP-seq with erythroid transcription factors (TFs), histone modifications (H3K27ac, H3K4me1), and chromatin accessibility (ATAC-seq) were analyzed. Candidate regulatory regions were investigated for activity (luciferase assays) and TF binding (electrophoretic mobility shift assay, EMSA, and mass spectrometry, MS).\n\nIn total, 814 potential regulatory sites in 47 blood-group-related genes were identified where one or more erythroid TFs bound. Enhancer candidates in CR1, EMP3, ABCB6, and ABCC4 indicated by ATAC-seq, histone markers, and co-occupancy of 4 TFs (GATA1/KLF1/RUNX1/NFE2) were investigated but only CR1 and ABCC4 showed increased transcription. Co-occupancy of GATA1 and KLF1 was observed in the KEL promoter, previously reported to contain GATA1 and Sp1 sites. TF binding energy scores decreased when three naturally occurring variants were introduced into GATA1 and KLF1 motifs. Two of three GATA1 sites and the KLF1 site were confirmed functionally. EMSA and MS demonstrated increased GATA1 and KLF1 binding to the wild-type compared to variant motifs.\n\nThis combined bioinformatics and experimental approach revealed multiple candidate regulatory regions and predicted TF co-occupancy sites. The KEL promoter was characterized in detail, indicating that two adjacent GATA1 and KLF1 motifs are most crucial for transcription.", "doi": "10.1111/trf.17840", "pmid": "38644556", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-12T19:01:55.627Z", "modified": "2024-11-12T19:01:55.931Z"}, {"entity": "publication", "iuid": "d40e07b18139455486ee5ce7b0c9b69b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d40e07b18139455486ee5ce7b0c9b69b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d40e07b18139455486ee5ce7b0c9b69b"}}, "title": "Childhood screening for type 1 diabetes comparing automated multiplex Antibody Detection by Agglutination-PCR (ADAP) with single plex islet autoantibody radiobinding assays.", "authors": [{"family": "Lind", "given": "Alexander", "initials": "A"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "de Jesus Cortez", "given": "Felipe", "initials": "F"}, {"family": "Ramelius", "given": "Anita", "initials": "A"}, {"family": "Bennet", "given": "Rasmus", "initials": "R"}, {"family": "Robinson", "given": "Peter V", "initials": "PV"}, {"family": "Seftel", "given": "David", "initials": "D"}, {"family": "Gebhart", "given": "David", "initials": "D"}, {"family": "Tandel", "given": "Devangkumar", "initials": "D"}, {"family": "Maziarz", "given": "Marlena", "initials": "M"}, {"family": "Larsson", "given": "Helena Elding", "initials": "HE"}, {"family": "Lundgren", "given": "Markus", "initials": "M"}, {"family": "Carlsson", "given": "Annelie", "initials": "A"}, {"family": "Nilsson", "given": "Anna-Lena", "initials": "AL"}, {"family": "Fex", "given": "Malin", "initials": "M"}, {"family": "T\u00f6rn", "given": "Carina", "initials": "C"}, {"family": "Agardh", "given": "Daniel", "initials": "D"}, {"family": "Tsai", "given": "Cheng-Ting", "initials": "CT"}, {"family": "Lernmark", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Better Diabetes Diagnosis (BDD) study group", "given": "", "initials": ""}], "type": "journal article", "published": "2024-06-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "volume": "104", "pages": "105144", "issn-l": "2352-3964"}, "abstract": "Two or more autoantibodies against either insulin (IAA), glutamic acid decarboxylase (GADA), islet antigen-2 (IA-2A) or zinc transporter 8 (ZnT8A) denote stage 1 (normoglycemia) or stage 2 (dysglycemia) type 1 diabetes prior to stage 3 type 1 diabetes. Automated multiplex Antibody Detection by Agglutination-PCR (ADAP) assays in two laboratories were compared to single plex radiobinding assays (RBA) to define threshold levels for diagnostic specificity and sensitivity.\n\nIAA, GADA, IA-2A and ZnT8A were analysed in 1504 (54% females) population based controls (PBC), 456 (55% females) doctor's office controls (DOC) and 535 (41% females) blood donor controls (BDC) as well as in 2300 (48% females) patients newly diagnosed (1-10 years of age) with stage 3 type 1 diabetes. The thresholds for autoantibody positivity were computed in 100 10-fold cross-validations to separate patients from controls either by maximizing the \u03c72-statistics (chisq) or using the 98th percentile of specificity (Spec98). Mean and 95% CI for threshold, sensitivity and specificity are presented.\n\nThe ADAP ROC curves of the four autoantibodies showed comparable AUC in the two ADAP laboratories and were higher than RBA. Detection of two or more autoantibodies using chisq showed 0.97 (0.95, 0.99) sensitivity and 0.94 (0.91, 0.97) specificity in ADAP compared to 0.90 (0.88, 0.95) sensitivity and 0.97 (0.94, 0.98) specificity in RBA. Using Spec98, ADAP showed 0.92 (0.89, 0.95) sensitivity and 0.99 (0.98, 1.00) specificity compared to 0.89 (0.77, 0.86) sensitivity and 1.00 (0.99, 1.00) specificity in the RBA. The diagnostic sensitivity and specificity were higher in PBC compared to DOC and BDC.\n\nADAP was comparable in two laboratories, both comparable to or better than RBA, to define threshold levels for two or more autoantibodies to stage type 1 diabetes.\n\nSupported by The Leona M. and Harry B. Helmsley Charitable Trust (grant number 2009-04078), the Swedish Foundation for Strategic Research (Dnr IRC15-0067) and the Swedish Research Council, Strategic Research Area (Dnr 2009-1039). AL was supported by the DiaUnion collaborative study, co-financed by EU Interreg \u00d6KS, Capital Region of Denmark, Region Sk\u00e5ne and the Novo Nordisk Foundation.", "doi": "10.1016/j.ebiom.2024.105144", "pmid": "38723553", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11090024"}, {"db": "pii", "key": "S2352-3964(24)00179-8"}], "notes": [], "created": "2024-09-02T08:15:55.423Z", "modified": "2024-11-12T12:24:26.019Z"}, {"entity": "publication", "iuid": "bdd78162107c4a5b9a038380043407d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bdd78162107c4a5b9a038380043407d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bdd78162107c4a5b9a038380043407d2"}}, "title": "Bacterial diversity in semen from stallions in three European countries evaluated by 16S sequencing.", "authors": [{"family": "Malaluang", "given": "Pongpreecha", "initials": "P"}, {"family": "Niazi", "given": "Adnan", "initials": "A"}, {"family": "Guo", "given": "Yongzhi", "initials": "Y"}, {"family": "Nagel", "given": "Christina", "initials": "C"}, {"family": "Guimaraes", "given": "Tiago", "initials": "T"}, {"family": "Rocha", "given": "Antonio", "initials": "A"}, {"family": "Aurich", "given": "Christine", "initials": "C"}, {"family": "Morrell", "given": "Jane M", "initials": "JM"}], "type": "journal article", "published": "2024-06-00", "journal": {"title": "Vet Res Commun", "issn": "1573-7446", "issn-l": null, "volume": "48", "issue": "3", "pages": "1409-1421"}, "abstract": "The microbiome plays a significant role in shaping the health and functioning of the systems it inhabits. The seminal microbiome of stallions has implications for the health of the reproductive tract, sperm quality during preservation and antibiotic use in semen extenders. Diverse bacteria are present on the external genital tract and a mix of commensal microorganisms populates various parts of the reproductive tract, influencing the seminal bacterial content. Other sources of bacteria include the environment, semen collection equipment, and personnel. The bacterial load can adversely affect sperm quality and fertility, particularly in artificial insemination, where semen is extended and stored before use. Antibiotics are frequently used to inhibit bacterial growth, but their effectiveness varies depending on the bacterial strains present. The aim of this study was to assess the bacterial diversity in semen from 37 healthy stallions across three European nations (Germany, Portugal, and Sweden) using 16S sequencing. Semen samples were collected from individual stallions at three AI centers; DNA extraction, sequencing, and bioinformatic analysis were performed. Differences in bacterial diversity among the stallions were seen; although bacterial phyla were shared across the regions, differences were observed at the genus level. Climate, husbandry practices, and individual variability likely contribute to these differences. These findings underscore the importance of tailoring antibiotic strategies for semen preservation based on regional bacterial profiles. The study presents a comprehensive approach to understanding the intricacies of the stallion seminal microbiome and its potential implications for reproductive technologies and animal health.", "doi": "10.1007/s11259-024-10321-3", "pmid": "38305959", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11147884"}, {"db": "pii", "key": "10.1007/s11259-024-10321-3"}], "notes": [], "created": "2024-11-13T15:22:47.849Z", "modified": "2024-11-25T10:11:25.630Z"}, {"entity": "publication", "iuid": "f984c2d2de4c4dd39b5ce3c3921595b7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f984c2d2de4c4dd39b5ce3c3921595b7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f984c2d2de4c4dd39b5ce3c3921595b7"}}, "title": "Copy number variation and elevated genetic diversity at immune trait loci in Atlantic and Pacific herring.", "authors": [{"family": "Mohamadnejad Sangdehi", "given": "Fahime", "initials": "F"}, {"family": "Jamsandekar", "given": "Minal S", "initials": "MS"}, {"family": "Enbody", "given": "Erik D", "initials": "ED"}, {"family": "Pettersson", "given": "Mats E", "initials": "ME"}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal article", "published": "2024-05-10", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "459", "issn-l": "1471-2164"}, "abstract": "Genome-wide comparisons of populations are widely used to explore the patterns of nucleotide diversity and sequence divergence to provide knowledge on how natural selection and genetic drift affect the genome. In this study we have compared whole-genome sequencing data from Atlantic and Pacific herring, two sister species that diverged about 2 million years ago, to explore the pattern of genetic differentiation between the two species.\n\nThe genome comparison of the two species revealed high genome-wide differentiation but with islands of remarkably low genetic differentiation, as measured by an FST analysis. However, the low FST observed in these islands is not caused by low interspecies sequence divergence (dxy) but rather by exceptionally high estimated intraspecies nucleotide diversity (\u03c0). These regions of low differentiation and elevated nucleotide diversity, termed high-diversity regions in this study, are not enriched for repeats but are highly enriched for immune-related genes. This enrichment includes genes from both the adaptive immune system, such as immunoglobulin, T-cell receptor and major histocompatibility complex genes, as well as a substantial number of genes with a role in the innate immune system, e.g. novel immune-type receptor, tripartite motif and tumor necrosis factor receptor genes. Analysis of long-read based assemblies from two Atlantic herring individuals revealed extensive copy number variation in these genomic regions, indicating that the elevated intraspecies nucleotide diversities were partially due to the cross-mapping of short reads.\n\nThis study demonstrates that copy number variation is a characteristic feature of immune trait loci in herring. Another important implication is that these loci are blind spots in classical genome-wide screens for genetic differentiation using short-read data, not only in herring, likely also in other species harboring qualitatively similar variation at immune trait loci. These loci stood out in this study because of the relatively high genome-wide baseline for FST values between Atlantic and Pacific herring.", "doi": "10.1186/s12864-024-10380-5", "pmid": "38730342", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11088111"}, {"db": "pii", "key": "10.1186/s12864-024-10380-5"}], "notes": [], "created": "2024-08-02T12:07:07.600Z", "modified": "2025-02-28T14:22:01.056Z"}, {"entity": "publication", "iuid": "c0da1688f3a74822ac6329a2a61bbfdb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0da1688f3a74822ac6329a2a61bbfdb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0da1688f3a74822ac6329a2a61bbfdb"}}, "title": "Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum.", "authors": [{"family": "Guti\u00e9rrez-Valencia", "given": "Juanita", "initials": "J"}, {"family": "Zervakis", "given": "Panagiotis-Ioannis", "initials": "P"}, {"family": "Postel", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0003-0502-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/0481ff1051564262af4e5384cbd17ac3.json"}}, {"family": "Fracassetti", "given": "Marco", "initials": "M"}, {"family": "Losvik", "given": "Aleksandra", "initials": "A"}, {"family": "Mehrabi", "given": "Sara", "initials": "S"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Hughes", "given": "P William", "initials": "PW"}, {"family": "D\u00e9samor\u00e9", "given": "Aur\u00e9lie", "initials": "A"}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Abdelaziz", "given": "Mohamed", "initials": "M"}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Arroyo", "given": "Juan", "initials": "J"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2024-05-03", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "41", "issue": "5", "pages": null}, "abstract": "Distyly is an iconic floral polymorphism governed by a supergene, which promotes efficient pollen transfer and outcrossing through reciprocal differences in the position of sexual organs in flowers, often coupled with heteromorphic self-incompatibility. Distyly has evolved convergently in multiple flowering plant lineages, but has also broken down repeatedly, often resulting in homostylous, self-compatible populations with elevated rates of self-fertilization. Here, we aimed to study the genetic causes and genomic consequences of the shift to homostyly in Linum trigynum, which is closely related to distylous Linum tenue. Building on a high-quality genome assembly, we show that L. trigynum harbors a genomic region homologous to the dominant haplotype of the distyly supergene conferring long stamens and short styles in L. tenue, suggesting that loss of distyly first occurred in a short-styled individual. In contrast to homostylous Primula and Fagopyrum, L. trigynum harbors no fixed loss-of-function mutations in coding sequences of S-linked distyly candidate genes. Instead, floral gene expression analyses and controlled crosses suggest that mutations downregulating the S-linked LtWDR-44 candidate gene for male self-incompatibility and/or anther height could underlie homostyly and self-compatibility in L. trigynum. Population genomic analyses of 224 whole-genome sequences further demonstrate that L. trigynum is highly self-fertilizing, exhibits significantly lower genetic diversity genome-wide, and is experiencing relaxed purifying selection and less frequent positive selection on nonsynonymous mutations relative to L. tenue. Our analyses shed light on the loss of distyly in L. trigynum, and advance our understanding of a common evolutionary transition in flowering plants.", "doi": "10.1093/molbev/msae087", "pmid": "38709782", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11114476"}, {"db": "pii", "key": "7665594"}], "notes": [], "created": "2024-05-17T09:14:33.893Z", "modified": "2024-11-15T11:28:42.391Z"}, {"entity": "publication", "iuid": "3e379db93ab74874adbbade635e75d36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e379db93ab74874adbbade635e75d36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e379db93ab74874adbbade635e75d36"}}, "title": "Cyanotoxin Occurrence and Diversity in 98 Cyanobacterial Blooms from Swedish Lakes and the Baltic Sea.", "authors": [{"family": "Dirks", "given": "Caroline", "initials": "C"}, {"family": "Cappelli", "given": "Paolo", "initials": "P"}, {"family": "Blomqvist", "given": "Maria", "initials": "M"}, {"family": "Ekroth", "given": "Susanne", "initials": "S"}, {"family": "Johansson", "given": "Malin", "initials": "M"}, {"family": "Persson", "given": "Max", "initials": "M"}, {"family": "Drakare", "given": "Stina", "initials": "S", "orcid": "0000-0002-7389-2105", "researcher": {"href": "https://publications.scilifelab.se/researcher/74f83b22223740c186f2ed9aba19331e.json"}}, {"family": "Pekar", "given": "Heidi", "initials": "H"}, {"family": "Zuberovic Muratovic", "given": "Aida", "initials": "A"}], "type": "journal article", "published": "2024-04-27", "journal": {"title": "Mar Drugs", "issn": "1660-3397", "volume": "22", "issue": "5", "issn-l": "1660-3397"}, "abstract": "The Drinking Water Directive (EU) 2020/2184 includes the parameter microcystin LR, a cyanotoxin, which drinking water producers need to analyze if the water source has potential for cyanobacterial blooms. In light of the increasing occurrences of cyanobacterial blooms worldwide and given that more than 50 percent of the drinking water in Sweden is produced from surface water, both fresh and brackish, the need for improved knowledge about cyanotoxin occurrence and cyanobacterial diversity has increased. In this study, a total of 98 cyanobacterial blooms were sampled in 2016-2017 and identified based on their toxin production and taxonomical compositions. The surface water samples from freshwater lakes throughout Sweden including brackish water from eight east coast locations along the Baltic Sea were analyzed for their toxin content with LC-MS/MS and taxonomic composition with 16S rRNA amplicon sequencing. Both the extracellular and the total toxin content were analyzed. Microcystin's prevalence was highest with presence in 82% of blooms, of which as a free toxin in 39% of blooms. Saxitoxins were found in 36% of blooms in which the congener decarbamoylsaxitoxin (dcSTX) was detected for the first time in Swedish surface waters at four sampling sites. Anatoxins were most rarely detected, followed by cylindrospermopsin, which were found in 6% and 10% of samples, respectively. As expected, nodularin was detected in samples collected from the Baltic Sea only. The cyanobacterial operational taxonomic units (OTUs) with the highest abundance and prevalence could be annotated to Aphanizomenon NIES-81 and the second most profuse cyanobacterial taxon to Microcystis PCC 7914. In addition, two correlations were found, one between Aphanizomenon NIES-81 and saxitoxins and another between Microcystis PCC 7914 and microcystins. This study is of value to drinking water management and scientists involved in recognizing and controlling toxic cyanobacteria blooms.", "doi": "10.3390/md22050199", "pmid": "38786590", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11123207"}, {"db": "pii", "key": "md22050199"}], "notes": [], "created": "2024-11-15T09:52:12.278Z", "modified": "2024-11-15T09:52:12.425Z"}, {"entity": "publication", "iuid": "44a144fa740a407eb4a008fb12602fcd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/44a144fa740a407eb4a008fb12602fcd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/44a144fa740a407eb4a008fb12602fcd"}}, "title": "HIV-2 mediated effects on target and bystander cells induce plasma proteome remodeling.", "authors": [{"family": "Johansson", "given": "Emil", "initials": "E"}, {"family": "Nazziwa", "given": "Jamirah", "initials": "J"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Lindman", "given": "Jacob", "initials": "J"}, {"family": "Neptin", "given": "Malin", "initials": "M"}, {"family": "Karlson", "given": "Sara", "initials": "S"}, {"family": "Rezeli", "given": "Melinda", "initials": "M"}, {"family": "Biague", "given": "Antonio J", "initials": "AJ"}, {"family": "Medstrand", "given": "Patrik", "initials": "P"}, {"family": "M\u00e5nsson", "given": "Fredrik", "initials": "F"}, {"family": "Norrgren", "given": "Hans", "initials": "H"}, {"family": "Esbj\u00f6rnsson", "given": "Joakim", "initials": "J"}, {"family": "Jansson", "given": "Marianne", "initials": "M"}, {"family": "SWEGUB CORE group", "given": "", "initials": ""}], "type": "journal article", "published": "2024-04-19", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "27", "issue": "4", "pages": "109344", "issn-l": "2589-0042"}, "abstract": "Despite low or undetectable plasma viral load, people living with HIV-2 (PLWH2) typically progress toward AIDS. The driving forces behind HIV-2 disease progression and the role of viremia are still not known, but low-level replication in tissues is believed to play a role. To investigate the impact of viremic and aviremic HIV-2 infection on target and bystander cell pathology, we used data-independent acquisition mass spectrometry to determine plasma signatures of tissue and cell type engagement. Proteins derived from target and bystander cells in multiple tissues, such as the gastrointestinal tract and brain, were detected at elevated levels in plasma of PLWH2, compared with HIV negative controls. Moreover, viremic HIV-2 infection appeared to induce enhanced release of proteins from a broader range of tissues compared to aviremic HIV-2 infection. This study expands the knowledge on the link between plasma proteome remodeling and the pathological cell engagement in tissues during HIV-2 infection.", "doi": "10.1016/j.isci.2024.109344", "pmid": "38500818", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10945182"}, {"db": "pii", "key": "S2589-0042(24)00565-0"}], "notes": [], "created": "2024-09-02T08:20:14.400Z", "modified": "2024-11-12T12:23:48.346Z"}, {"entity": "publication", "iuid": "63e7b29f92a149148163f3d5af923fbd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63e7b29f92a149148163f3d5af923fbd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63e7b29f92a149148163f3d5af923fbd"}}, "title": "The HLA region in ANCA-associated vasculitis: characterisation of genetic associations in a Scandinavian patient population.", "authors": [{"family": "Lundtoft", "given": "Christian", "initials": "C"}, {"family": "Knight", "given": "Ann", "initials": "A"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS"}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "Berglin", "given": "Ewa", "initials": "E"}, {"family": "Palm", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Haukeland", "given": "Hilde", "initials": "H"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Bruchfeld", "given": "Annette", "initials": "A"}, {"family": "Segelmark", "given": "M\u00e5rten", "initials": "M"}, {"family": "Ohlsson", "given": "Sophie", "initials": "S"}, {"family": "Mohammad", "given": "Aladdin J", "initials": "AJ", "orcid": "0000-0002-7169-6936", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7010c3f5b91415dbc26c87d6a923f68.json"}}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "S\u00f6derkvist", "given": "Peter", "initials": "P"}, {"family": "Ronnblom", "given": "Lars", "initials": "L"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Jonsson", "given": "Roland", "initials": "R", "orcid": "0000-0002-9588-0260", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6edb43a7da34bf9af85c876b1b8974a.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Dahlqvist", "given": "Johanna", "initials": "J", "orcid": "0000-0002-6283-644X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fb2ab2d83b6437f9918f330e5fb81b2.json"}}], "type": "journal article", "published": "2024-04-04", "journal": {"title": "RMD Open", "issn": "2056-5933", "volume": "10", "issue": "2", "issn-l": "2056-5933"}, "abstract": "The antineutrophil cytoplasmic antibody (ANCA)-associated vasculitides (AAV) are inflammatory disorders with ANCA autoantibodies recognising either proteinase 3 (PR3-AAV) or myeloperoxidase (MPO-AAV). PR3-AAV and MPO-AAV have been associated with distinct loci in the human leucocyte antigen (HLA) region. While the association between MPO-AAV and HLA has been well characterised in East Asian populations where MPO-AAV is more common, studies in populations of European descent are limited. The aim of this study was to thoroughly characterise associations to the HLA region in Scandinavian patients with PR3-AAV as well as MPO-AAV.\n\nGenotypes of single-nucleotide polymorphisms (SNPs) located in the HLA region were extracted from a targeted exome-sequencing dataset comprising Scandinavian AAV cases and controls. Classical HLA alleles were called using xHLA. After quality control, association analyses were performed of a joint SNP/classical HLA allele dataset for cases with PR3-AAV (n=411) and MPO-AAV (n=162) versus controls (n=1595). Disease-associated genetic variants were analysed for association with organ involvement, age at diagnosis and relapse, respectively.\n\nPR3-AAV was significantly associated with both HLA-DPB1*04:01 and rs1042335 at the HLA-DPB1 locus, also after stepwise conditional analysis. MPO-AAV was significantly associated with HLA-DRB1*04:04. Neither carriage of HLA-DPB1*04:01 alleles in PR3-AAV nor of HLA-DRB1*04:04 alleles in MPO-AAV were associated with organ involvement, age at diagnosis or relapse.\n\nThe association to the HLA region was distinct in Scandinavian cases with MPO-AAV compared with cases of East Asian descent. In PR3-AAV, the two separate signals of association to the HLD-DPB1 region mediate potentially different functional effects.", "doi": "10.1136/rmdopen-2023-004039", "pmid": "38580345", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11002376"}, {"db": "pii", "key": "rmdopen-2023-004039"}], "notes": [], "created": "2024-04-15T06:10:27.649Z", "modified": "2024-11-25T10:28:43.870Z"}, {"entity": "publication", "iuid": "8822f79ce12c4158bd6128531eaf7657", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8822f79ce12c4158bd6128531eaf7657.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8822f79ce12c4158bd6128531eaf7657"}}, "title": "Kupffer cells dictate hepatic responses to the atherogenic dyslipidemic insult.", "authors": [{"family": "Di Nunzio", "given": "Giada", "initials": "G"}, {"family": "Hellberg", "given": "Sanna", "initials": "S", "orcid": "0000-0003-1791-3693", "researcher": {"href": "https://publications.scilifelab.se/researcher/053fd0cc678f48abb083aaf102f1cec4.json"}}, {"family": "Zhang", "given": "Yuyang", "initials": "Y", "orcid": "0000-0002-3806-6094", "researcher": {"href": "https://publications.scilifelab.se/researcher/d469b9b7fccd4f65a66b2cb87939a157.json"}}, {"family": "Ahmed", "given": "Osman", "initials": "O", "orcid": "0000-0002-2854-2552", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb219b9efad046f6badae392587f62b1.json"}}, {"family": "Wang", "given": "Jiawen", "initials": "J"}, {"family": "Zhang", "given": "Xueming", "initials": "X"}, {"family": "Bj\u00f6rck", "given": "Hanna M", "initials": "HM"}, {"family": "Chizh", "given": "Veronika", "initials": "V"}, {"family": "Schipper", "given": "Ruby", "initials": "R"}, {"family": "Aulin", "given": "Hanna", "initials": "H"}, {"family": "Francis", "given": "Roy", "initials": "R"}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Gister\u00e5", "given": "Anton", "initials": "A", "orcid": "0000-0002-4614-8030", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e2beec3559745a6ba1859252df4a547.json"}}, {"family": "Metso", "given": "Jari", "initials": "J"}, {"family": "Manf\u00e9", "given": "Valentina", "initials": "V"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Jauhiainen", "given": "Matti", "initials": "M"}, {"family": "Hagberg", "given": "Carolina E", "initials": "CE", "orcid": "0000-0002-5497-2855", "researcher": {"href": "https://publications.scilifelab.se/researcher/66bbd07c59044b279527c75f12cd4c04.json"}}, {"family": "Olofsson", "given": "Peder S", "initials": "PS", "orcid": "0000-0003-3473-5948", "researcher": {"href": "https://publications.scilifelab.se/researcher/527d940eee82480bae882e2c8b4af99f.json"}}, {"family": "Malin", "given": "Stephen G", "initials": "SG", "orcid": "0000-0001-7723-9579", "researcher": {"href": "https://publications.scilifelab.se/researcher/86c05018e1e9477181eb7aa86faef7d1.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "Nat Cardiovasc Res", "issn": "2731-0590", "volume": "3", "issue": "3", "pages": "356-371", "issn-l": null}, "abstract": "Apolipoprotein-B (APOB)-containing lipoproteins cause atherosclerosis. Whether the vasculature is the initially responding site or if atherogenic dyslipidemia affects other organs simultaneously is unknown. Here we show that the liver responds to a dyslipidemic insult based on inducible models of familial hypercholesterolemia and APOB tracing. An acute transition to atherogenic APOB lipoprotein levels resulted in uptake by Kupffer cells and rapid accumulation of triglycerides and cholesterol in the liver. Bulk and single-cell RNA sequencing revealed a Kupffer-cell-specific transcriptional program that was not activated by a high-fat diet alone or detected in standard liver function or pathological assays, even in the presence of fulminant atherosclerosis. Depletion of Kupffer cells altered the dynamic of plasma and liver lipid concentrations, indicating that these liver macrophages help restrain and buffer atherogenic lipoproteins while simultaneously secreting atherosclerosis-modulating factors into plasma. Our results place Kupffer cells as key sentinels in organizing systemic responses to lipoproteins at the initiation of atherosclerosis.", "doi": "10.1038/s44161-024-00448-6", "pmid": "39196121", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11358021"}, {"db": "pii", "key": "10.1038/s44161-024-00448-6"}], "notes": [], "created": "2024-10-14T13:20:41.587Z", "modified": "2025-02-28T14:16:26.867Z"}, {"entity": "publication", "iuid": "9670731db7d94785b128f5d9454c7b1e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9670731db7d94785b128f5d9454c7b1e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9670731db7d94785b128f5d9454c7b1e"}}, "title": "Differential gene expression in two consecutive pregnancies between same sex siblings and implications on maternal constraint.", "authors": [{"family": "Kallak", "given": "Theodora Kunovac", "initials": "TK"}, {"family": "Serapio", "given": "Solveig", "initials": "S"}, {"family": "Visser", "given": "Nadja", "initials": "N"}, {"family": "Lager", "given": "Susanne", "initials": "S"}, {"family": "Skalkidou", "given": "Alkistis", "initials": "A"}, {"family": "Ahlsson", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2024-02-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "4210", "issn-l": "2045-2322"}, "abstract": "The objective of this study was to investigate how placental gene expression differs in two consecutive pregnancies in same sex siblings, and its possible association with the \"maternal constraint\" hypothesis. Material was gathered from the BASIC study (Biological, Affect, Stress, Imaging, and Cognition in Pregnancy and the Puerperium), a population based prospective study that was started in 2009 in Uppsala. Over 900 specimens of placenta biopsies were collected and out of these 10 women gave birth twice, to the same sex child, and were included in this study. The total RNA was isolated and prepared from frozen villous tissue from the placenta and further analyzed by use of Ion AmpliSeq Human Transcriptome Gene Expression kit. A total of 234 genes differed significantly between the first and second pregnancy placentas, when adjusting for delivery mode, maternal BMI and gestational age. Of special interest was the down-regulated group of genes in the second pregnancy. Exemplified by Pentraxin 3, SRY-Box Transcription Factor 9, and Serum Amyloid A1, which all were associated with biological processes involved in the immune system and inflammation. Further, protein-protein interaction analysis visualized them as hub genes interacting with several of the other differentially expressed genes. How these altered gene expressions affect maternal constraint during pregnancy needs further validation in lager study cohorts and also future validation in functional assays.", "doi": "10.1038/s41598-024-54724-3", "pmid": "38378837", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10879170"}, {"db": "pii", "key": "10.1038/s41598-024-54724-3"}], "notes": [], "created": "2024-11-12T17:42:40.329Z", "modified": "2024-11-25T10:20:47.752Z"}, {"entity": "publication", "iuid": "d4450142a100484a9f16e92b92dc78ee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d4450142a100484a9f16e92b92dc78ee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d4450142a100484a9f16e92b92dc78ee"}}, "title": "Nigral transcriptomic profiles in Engrailed-1 hemizygous mouse models of Parkinson's disease reveal upregulation of oxidative phosphorylation-related genes associated with delayed dopaminergic neurodegeneration.", "authors": [{"family": "Belfiori", "given": "Lautaro Francisco", "initials": "LF"}, {"family": "Due\u00f1as Rey", "given": "Alfredo", "initials": "A"}, {"family": "Ralbovszki", "given": "Dorottya M\u00e1ria", "initials": "DM"}, {"family": "Jimenez-Ferrer", "given": "Itzia", "initials": "I"}, {"family": "Fredlund", "given": "Filip", "initials": "F"}, {"family": "Balikai", "given": "Sagar Shivayogi", "initials": "SS"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Brolin", "given": "Kajsa Atterling", "initials": "KA"}, {"family": "Swanberg", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2024-02-05", "journal": {"title": "Front Aging Neurosci", "issn": "1663-4365", "volume": "16", "pages": "1337365", "issn-l": null}, "abstract": "Parkinson's disease (PD) is the second most common neurodegenerative disorder, increasing both in terms of prevalence and incidence. To date, only symptomatic treatment is available, highlighting the need to increase knowledge on disease etiology in order to develop new therapeutic strategies. Hemizygosity for the gene Engrailed-1 (En1), encoding a conserved transcription factor essential for the programming, survival, and maintenance of midbrain dopaminergic neurons, leads to progressive nigrostriatal degeneration, motor impairment and depressive-like behavior in SwissOF1 (OF1-En1+/-). The neurodegenerative phenotype is, however, absent in C57Bl/6j (C57-En1+/-) mice. En1+/- mice are thus highly relevant tools to identify genetic factors underlying PD susceptibility.\n\nTranscriptome profiles were defined by RNAseq in microdissected substantia nigra from 1-week old OF1, OF1- En1+/-, C57 and C57- En1+/- male mice. Differentially expressed genes (DEGs) were analyzed for functional enrichment. Neurodegeneration was assessed in 4- and 16-week old mice by histology.\n\nNigrostriatal neurodegeneration was manifested in OF1- En1+/- mice by increased dopaminergic striatal axonal swellings from 4 to 16 weeks and decreased number of dopaminergic neurons in the SNpc at 16 weeks compared to OF1. In contrast, C57- En1+/- mice had no significant increase in axonal swellings or cell loss in SNpc at 16 weeks. Transcriptomic analyses identified 198 DEGs between OF1- En1+/- and OF1 mice but only 52 DEGs between C57- En1+/- and C57 mice. Enrichment analysis of DEGs revealed that the neuroprotective phenotype of C57- En1+/- mice was associated with a higher expression of oxidative phosphorylation-related genes compared to both C57 and OF1- En1+/- mice.\n\nOur results suggest that increased expression of genes encoding mitochondrial proteins before the onset of neurodegeneration is associated with increased resistance to PD-like nigrostriatal neurodegeneration. This highlights the importance of genetic background in PD models, how different strains can be used to model clinical and sub-clinical pathologies and provides insights to gene expression mechanisms associated with PD susceptibility and progression.", "doi": "10.3389/fnagi.2024.1337365", "pmid": "38374883", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10875038"}], "notes": [], "created": "2024-11-15T09:43:32.556Z", "modified": "2024-11-15T11:51:27.191Z"}, {"entity": "publication", "iuid": "fa3ec7c6d57645dca27002bd711dd76c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa3ec7c6d57645dca27002bd711dd76c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa3ec7c6d57645dca27002bd711dd76c"}}, "title": "A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern.", "authors": [{"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Dias", "given": "Guilherme", "initials": "G"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Soares", "given": "Andr\u00e9", "initials": "A"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Talla", "given": "Venkat", "initials": "V", "orcid": "0000-0003-2653-6770", "researcher": {"href": "https://publications.scilifelab.se/researcher/703518ce5a1f4e5ea04719016173a867.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}], "type": "journal article", "published": "2024-02-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "2", "issn-l": "1759-6653"}, "abstract": "The clouded apollo (Parnassius mnemosyne) is a palearctic butterfly distributed over a large part of western Eurasia, but population declines and fragmentation have been observed in many parts of the range. The development of genomic tools can help to shed light on the genetic consequences of the decline and to make informed decisions about direct conservation actions. Here, we present a high-contiguity, chromosome-level genome assembly of a female clouded apollo butterfly and provide detailed annotations of genes and transposable elements. We find that the large genome (1.5 Gb) of the clouded apollo is extraordinarily repeat rich (73%). Despite that, the combination of sequencing techniques allowed us to assemble all chromosomes (nc = 29) to a high degree of completeness. The annotation resulted in a relatively high number of protein-coding genes (22,854) compared with other Lepidoptera, of which a large proportion (21,635) could be assigned functions based on homology with other species. A comparative analysis indicates that overall genome structure has been largely conserved, both within the genus and compared with the ancestral lepidopteran karyotype. The high-quality genome assembly and detailed annotation presented here will constitute an important tool for forthcoming efforts aimed at understanding the genetic consequences of fragmentation and decline, as well as for assessments of genetic diversity, population structure, inbreeding, and genetic load in the clouded apollo butterfly.", "doi": "10.1093/gbe/evae031", "pmid": "38368625", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10901555"}, {"db": "pii", "key": "7610114"}], "notes": [], "created": "2024-02-29T15:15:06.133Z", "modified": "2025-02-28T14:18:02.771Z"}, {"entity": "publication", "iuid": "9548e88f13764743811099768c2ea421", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9548e88f13764743811099768c2ea421.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9548e88f13764743811099768c2ea421"}}, "title": "Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9-mediated genome engineering in HAP1 cells mimicking cancer profiles.", "authors": [{"family": "Geng", "given": "Keyi", "initials": "K", "orcid": "0000-0003-0892-7460", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0ce637276ce4cb0b81f9f039d261c61.json"}}, {"family": "Merino", "given": "Lara G", "initials": "LG", "orcid": "0000-0002-7208-953X", "researcher": {"href": "https://publications.scilifelab.se/researcher/afebb85c860744dc8ad5840caa6f06c0.json"}}, {"family": "Veiga", "given": "Ra\u00fcl G", "initials": "RG", "orcid": "0000-0002-8517-1559", "researcher": {"href": "https://publications.scilifelab.se/researcher/f012c55305964efb9155c1442c204759.json"}}, {"family": "Sommerauer", "given": "Christian", "initials": "C", "orcid": "0000-0001-7132-7172", "researcher": {"href": "https://publications.scilifelab.se/researcher/01320952391e4afe9b924dcf85b5d50a.json"}}, {"family": "Epperlein", "given": "Janine", "initials": "J", "orcid": "0000-0002-1595-5411", "researcher": {"href": "https://publications.scilifelab.se/researcher/83adf9175bcf4737b98bb83b3c715254.json"}}, {"family": "Brinkman", "given": "Eva K", "initials": "EK", "orcid": "0000-0003-3120-1174", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee3d3152bb82438e96b23d5f0cfc5ae5.json"}}, {"family": "Kutter", "given": "Claudia", "initials": "C", "orcid": "0000-0002-8047-0058", "researcher": {"href": "https://publications.scilifelab.se/researcher/61f2e0e6c9be43ac946b318d080d5cca.json"}}], "type": "journal article", "published": "2024-02-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "volume": "7", "issue": "2", "issn-l": "2575-1077"}, "abstract": "The CRISPR-Cas9 system is a powerful tool for studying gene functions and holds potential for disease treatment. However, precise genome editing requires thorough assessments to minimize unintended on- and off-target effects. Here, we report an unexpected 283-kb deletion on Chromosome 10 (10q23.31) in chronic myelogenous leukemia-derived HAP1 cells, which are frequently used in CRISPR screens. The deleted region encodes regulatory genes, including PAPSS2, ATAD1, KLLN, and PTEN We found that this deletion was not a direct consequence of CRISPR-Cas9 off-targeting but rather occurred frequently during the generation of CRISPR-Cas9-modified cells. The deletion was associated with global changes in histone acetylation and gene expression, affecting fundamental cellular processes such as cell cycle and DNA replication. We detected this deletion in cancer patient genomes. As in HAP1 cells, the deletion contributed to similar gene expression patterns among cancer patients despite interindividual differences. Our findings suggest that the unintended deletion of 10q23.31 can confound CRISPR-Cas9 studies and underscore the importance to assess unintended genomic changes in CRISPR-Cas9-modified cells, which could impact cancer research.", "doi": "10.26508/lsa.202302128", "pmid": "37984988", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10662290"}, {"db": "pii", "key": "7/2/e202302128"}], "notes": [], "created": "2023-12-01T13:23:58.904Z", "modified": "2025-02-28T14:23:40.585Z"}, {"entity": "publication", "iuid": "c6ee9d682b4440b98f597b4ff57d6037", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6ee9d682b4440b98f597b4ff57d6037.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6ee9d682b4440b98f597b4ff57d6037"}}, "title": "A survey of ficolin-3 activity in Systemic Lupus Erythematosus reveals a link to hematological disease manifestations and autoantibody profile.", "authors": [{"family": "Lindel\u00f6f", "given": "Linnea", "initials": "L"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Lundtoft", "given": "Christian", "initials": "C"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Enocsson", "given": "Helena", "initials": "H"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Diaz-Gallo", "given": "Lina-Marcela", "initials": "LM"}, {"family": "Bianchi", "given": "Matteo", "initials": "M"}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "DISSECT consortium", "given": "", "initials": ""}, {"family": "ImmunoArray consortium", "given": "", "initials": ""}, {"family": "Nilsson Ekdahl", "given": "Kristina", "initials": "K"}, {"family": "Nilsson", "given": "Bo", "initials": "B"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Eriksson", "given": "Oskar", "initials": "O"}], "type": "multicenter study", "published": "2024-02-00", "journal": {"title": "J. Autoimmun.", "issn": "1095-9157", "issn-l": "0896-8411", "volume": "143", "issue": null, "pages": "103166"}, "abstract": "The complement system plays a central role in the pathogenesis of Systemic Lupus Erythematosus (SLE), but most studies have focused on the classical pathway. Ficolin-3 is the main initiator of the lectin pathway of complement in humans, but its role in systemic autoimmune disease has not been conclusively determined. Here, we combined biochemical and genetic approaches to assess the contribution of ficolin-3 to SLE risk and disease manifestations. Ficolin-3 activity was measured by a functional assay in serum or plasma samples from Swedish SLE patients (n = 786) and controls matched for age and sex (n = 566). Genetic variants in an extended 300 kb genomic region spanning the FCN3 locus were analyzed for their association with ficolin-3 activity and SLE manifestations in a Swedish multicenter cohort (n = 985). Patients with ficolin-3 activity in the highest tertile showed a strong enrichment in an SLE cluster defined by anti-Sm/DNA/nucleosome antibodies (OR 3.0, p < 0.001) and had increased rates of hematological disease (OR 1.4, p = 0.078) and lymphopenia (OR = 1.6, p = 0.039). Genetic variants associated with low ficolin-3 activity mapped to an extended haplotype in high linkage disequilibrium upstream of the FCN3 gene. Patients carrying the lead genetic variant associated with low ficolin-3 activity had a lower frequency of hematological disease (OR 0.67, p = 0.018) and lymphopenia (OR 0.63, p = 0.031) and fewer autoantibodies (p = 0.0019). Loss-of-function variants in the FCN3 gene were not associated with SLE, but four (0.5 %) SLE patients developed acquired ficolin-3 deficiency where ficolin-3 activity in serum was depleted following diagnosis of SLE. Taken together, our results provide genetic and biochemical evidence that implicate the lectin pathway in hematological SLE manifestations. We also identify lectin pathway activation through ficolin-3 as a factor that contributes to the autoantibody response in SLE.", "doi": "10.1016/j.jaut.2023.103166", "pmid": "38219652", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0896-8411(23)00175-0"}], "notes": [], "created": "2024-01-16T08:53:44.077Z", "modified": "2025-02-28T14:12:16.457Z"}, {"entity": "publication", "iuid": "33c43a1cbf47448aa9aebd435898bee6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33c43a1cbf47448aa9aebd435898bee6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33c43a1cbf47448aa9aebd435898bee6"}}, "title": "Mutation of the cyclooxygenase 2 gene promoter and anastomotic leakage in colorectal cancer patients: retrospective cohort study.", "authors": [{"family": "Grahn", "given": "Oskar", "initials": "O", "orcid": "0000-0002-7206-6493", "researcher": {"href": "https://publications.scilifelab.se/researcher/873397967eed49369de7cc24c351244e.json"}}, {"family": "Holmgren", "given": "Klas", "initials": "K", "orcid": "0000-0002-8611-1304", "researcher": {"href": "https://publications.scilifelab.se/researcher/f25e5c40cc2c4a039ed4125767b25a4a.json"}}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Sund", "given": "Malin", "initials": "M", "orcid": "0000-0002-7516-9543", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6d2313e3364447789d52b5d4a44b318.json"}}, {"family": "Ruteg\u00e5rd", "given": "Martin", "initials": "M", "orcid": "0000-0002-0974-6373", "researcher": {"href": "https://publications.scilifelab.se/researcher/332b3ee932544076a00ce550821d516c.json"}}], "type": "journal article", "published": "2024-01-03", "journal": {"title": "BJS Open", "issn": "2474-9842", "volume": "8", "issue": "1", "issn-l": null}, "abstract": null, "doi": "10.1093/bjsopen/zrae004", "pmid": "38289394", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10826458"}, {"db": "pii", "key": "7591788"}], "notes": [], "created": "2024-09-02T08:22:00.645Z", "modified": "2024-11-12T12:22:17.508Z"}, {"entity": "publication", "iuid": "38e8ea2add274447af482c0b9e751d80", "links": {"self": {"href": "https://publications.scilifelab.se/publication/38e8ea2add274447af482c0b9e751d80.json"}, "display": {"href": "https://publications.scilifelab.se/publication/38e8ea2add274447af482c0b9e751d80"}}, "title": "The functional role of CST1 and CCL26 in asthma development.", "authors": [{"family": "Hoyer", "given": "Angela", "initials": "A", "orcid": "0000-0003-3295-5007", "researcher": {"href": "https://publications.scilifelab.se/researcher/7be4e1424a2f4fe58f7f5c1839e81616.json"}}, {"family": "Chakraborty", "given": "Sandip", "initials": "S"}, {"family": "Lilienthal", "given": "Ingrid", "initials": "I"}, {"family": "Konradsen", "given": "Jon R", "initials": "JR"}, {"family": "Katayama", "given": "Shintaro", "initials": "S"}, {"family": "S\u00f6derh\u00e4ll", "given": "Cilla", "initials": "C"}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "Immun Inflamm Dis", "issn": "2050-4527", "volume": "12", "issue": "1", "pages": "e1162", "issn-l": null}, "abstract": "Asthma is the most common chronic disease in children with an increasing prevalence. Its development is caused by genetic and environmental factors and allergic sensitization is a known trigger. Dog allergens affect up to 30% of all children and dog dander-sensitized children show increased expression of cystatin-1 (CST1) and eotaxin-3 (CCL26) in nasal epithelium. The aim of our study was to investigate the functional mechanism of CST1 and CCL26 in the alveolar basal epithelial cell line A549.\n\nA549 cells were transfected with individual overexpression vectors for CST1 and CCL26 and RNA sequencing was performed to examine the transcriptomics. edgeR was used to identify differentially expressed genes (= DEG, |log2 FC | \u2265 2, FDR < 0.01). The protein expression levels of A549 cells overexpressing CST1 and CCL26 were analyzed using the Target 96 inflammation panel from OLINK (antibody-mediated proximity extension-based assay; OLINK Proteomics). Differentially expressed proteins were considered with a |log2 FC| \u2265 1, p < .05.\n\nThe overexpression of CST1 resulted in a total of 27 DEG (1 upregulated and 26 downregulated) and the overexpression of CCL26 in a total of 137 DEG (0 upregulated and 137 downregulated). The gene ontology enrichment analysis showed a significant downregulation of type I and III interferon signaling pathway genes as well as interferon-stimulated genes. At the protein level, overexpression of CST1 induced a significantly increased expression of CCL3, whereas CCL26 overexpression led to increased expression of HGF, and a decrease of CXCL11, CCL20, CCL3 and CXCL10.\n\nOur results indicate that an overexpression of CST1 and CCL26 cause a downregulation of interferon related genes and inflammatory proteins. It might cause a higher disease susceptibility, mainly for allergic asthma, as CCL26 is an agonist for CCR-3-carrying cells, such as eosinophils and Th2 lymphocytes, mostly active in allergic asthma.", "doi": "10.1002/iid3.1162", "pmid": "38270326", "labels": {"Affinity Proteomics Stockholm": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10797655"}], "notes": [], "created": "2024-05-23T13:27:06.537Z", "modified": "2025-02-28T14:10:10.524Z"}, {"entity": "publication", "iuid": "c7dc193c604c4e5fa865e49344129528", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7dc193c604c4e5fa865e49344129528.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7dc193c604c4e5fa865e49344129528"}}, "title": "New chemical and microbial perspectives on vitamin B1 and vitamer dynamics of a coastal system.", "authors": [{"family": "Bittner", "given": "Meriel J", "initials": "MJ", "orcid": "0000-0002-3798-6315", "researcher": {"href": "https://publications.scilifelab.se/researcher/5abcc332fec3408f996fff6e2470f304.json"}}, {"family": "Bannon", "given": "Catherine C", "initials": "CC", "orcid": "0000-0002-8581-1069", "researcher": {"href": "https://publications.scilifelab.se/researcher/176684868401463e8e36980a8f297ab8.json"}}, {"family": "Rowland", "given": "Elden", "initials": "E", "orcid": "0000-0003-4756-9125", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c1d771d5585492681b9c2a296a78914.json"}}, {"family": "Sundh", "given": "John", "initials": "J", "orcid": "0000-0003-3053-9392", "researcher": {"href": "https://publications.scilifelab.se/researcher/655b68ac26af42ad9fb4dfe0869e15ea.json"}}, {"family": "Bertrand", "given": "Erin M", "initials": "EM", "orcid": "0000-0002-5950-6810", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc79515185fc4304bb690324be48adf2.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Paerl", "given": "Ryan W", "initials": "RW", "orcid": "0000-0003-3980-8181", "researcher": {"href": "https://publications.scilifelab.se/researcher/1267dafcedd84e77aa550169e4340998.json"}}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "issn-l": null, "volume": "4", "issue": "1", "pages": "ycad016"}, "abstract": "Vitamin B1 (thiamin, B1) is an essential micronutrient for cells, yet intriguingly in aquatic systems most bacterioplankton are unable to synthesize it de novo (auxotrophy), requiring an exogenous source. Cycling of this valuable metabolite in aquatic systems has not been fully investigated and vitamers (B1-related compounds) have only begun to be measured and incorporated into the B1 cycle. Here, we identify potential key producers and consumers of B1 and gain new insights into the dynamics of B1 cycling through measurements of B1 and vitamers (HMP: 4-amino-5-hydroxymethyl-2-methylpyrimidine, HET: 4-methyl-5-thiazoleethanol, FAMP: N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine) in the particulate and dissolved pool in a temperate coastal system. Dissolved B1 was not the primary limiting nutrient for bacterial production and was relatively stable across seasons with concentrations ranging from 74-117 pM, indicating a balance of supply and demand. However, vitamer concentration changed markedly with season as did transcripts related to vitamer salvage and transport suggesting use of vitamers by certain bacterioplankton, e.g. Pelagibacterales. Genomic and transcriptomic analyses showed that up to 78% of the bacterioplankton taxa were B1 auxotrophs. Notably, de novo B1 production was restricted to a few abundant bacterioplankton (e.g. Vulcanococcus, BACL14 (Burkholderiales), Verrucomicrobiales) across seasons. In summer, abundant picocyanobacteria were important putative B1 sources, based on transcriptional activity, leading to an increase in the B1 pool. Our results provide a new dynamic view of the players and processes involved in B1 cycling over time in coastal waters, and identify specific priority populations and processes for future study.", "doi": "10.1093/ismeco/ycad016", "pmid": "38390520", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10881298"}, {"db": "pii", "key": "ycad016"}, {"db": "figshare", "key": "10.6084/m9.figshare.23634429"}], "notes": [], "created": "2024-03-14T11:11:47.095Z", "modified": "2025-02-28T14:18:29.377Z"}, {"entity": "publication", "iuid": "437e080835214ee29720700ba7ce89d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/437e080835214ee29720700ba7ce89d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/437e080835214ee29720700ba7ce89d8"}}, "title": "Impact of the gut microbiome on immunological responses to COVID-19 vaccination in healthy controls and people living with HIV.", "authors": [{"family": "Ray", "given": "Shilpa", "initials": "S", "orcid": "0000-0002-9940-7366", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7aa8a3e3b554695989dfe15ee1e9239.json"}}, {"family": "Narayanan", "given": "Aswathy", "initials": "A"}, {"family": "Vesterbacka", "given": "Jan", "initials": "J"}, {"family": "Blennow", "given": "Ola", "initials": "O"}, {"family": "Chen", "given": "Puran", "initials": "P"}, {"family": "Gao", "given": "Yu", "initials": "Y"}, {"family": "Gabarrini", "given": "Giorgio", "initials": "G", "orcid": "0000-0001-6936-4919", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbb92481579b4a23afefbbed5ad59a9a.json"}}, {"family": "Ljunggren", "given": "Hans-Gustaf", "initials": "H"}, {"family": "Buggert", "given": "Marcus", "initials": "M"}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L"}, {"family": "Chen", "given": "Margaret S\u00e4llberg", "initials": "MS", "orcid": "0000-0002-3793-4064", "researcher": {"href": "https://publications.scilifelab.se/researcher/af31e38e29a24d208df80184c563357f.json"}}, {"family": "Aleman", "given": "Soo", "initials": "S"}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A"}, {"family": "Nowak", "given": "Piotr", "initials": "P"}], "type": "journal article", "published": "2023-12-20", "journal": {"title": "NPJ Biofilms Microbiomes", "issn": "2055-5008", "issn-l": "2055-5008", "volume": "9", "issue": "1", "pages": "104"}, "abstract": "Although mRNA SARS-CoV-2 vaccines are generally safe and effective, in certain immunocompromised individuals they can elicit poor immunogenic responses. Among these individuals, people living with HIV (PLWH) have poor immunogenicity to several oral and parenteral vaccines. As the gut microbiome is known to affect vaccine immunogenicity, we investigated whether baseline gut microbiota predicts immune responses to the BNT162b2 mRNA SARS-CoV-2 vaccine in healthy controls and PLWH after two doses of BNT162b2. Individuals with high spike IgG titers and high spike-specific CD4+ T-cell responses against SARS-CoV-2 showed low \u03b1-diversity in the gut. Here, we investigated and presented initial evidence that the gut microbial composition influences the response to BNT162b2 in PLWH. From our predictive models, Bifidobacterium and Faecalibacterium appeared to be microbial markers of individuals with higher spike IgG titers, while Cloacibacillus was associated with low spike IgG titers. We therefore propose that microbiome modulation could optimize immunogenicity of SARS-CoV-2 mRNA vaccines.", "doi": "10.1038/s41522-023-00461-w", "pmid": "38123600", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10733305"}, {"db": "pii", "key": "10.1038/s41522-023-00461-w"}], "notes": [], "created": "2024-01-02T13:29:41.728Z", "modified": "2025-11-21T12:35:21.101Z"}, {"entity": "publication", "iuid": "9efdc3a281a84030a7ec8c88d23e7a67", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9efdc3a281a84030a7ec8c88d23e7a67.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9efdc3a281a84030a7ec8c88d23e7a67"}}, "title": "Identification of Quantitative Trait Nucleotides and Development of Diagnostic Markers for Nine Fatty Acids in the Peanut.", "authors": [{"family": "Wang", "given": "Juan", "initials": "J"}, {"family": "Chen", "given": "Haoning", "initials": "H"}, {"family": "Li", "given": "Yuan", "initials": "Y"}, {"family": "Shi", "given": "Dachuan", "initials": "D", "orcid": "0000-0002-7823-5876", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f9474d4daa486aa5737e57ab62b778.json"}}, {"family": "Wang", "given": "Wenjiao", "initials": "W"}, {"family": "Yan", "given": "Caixia", "initials": "C"}, {"family": "Yuan", "given": "Mei", "initials": "M", "orcid": "0000-0002-3851-5603", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d8a70c94c94a5b88c345e0371a835d.json"}}, {"family": "Sun", "given": "Quanxi", "initials": "Q", "orcid": "0000-0002-4075-1955", "researcher": {"href": "https://publications.scilifelab.se/researcher/278bf206b3b644a9b60aa2ab5ba7538e.json"}}, {"family": "Chen", "given": "Jing", "initials": "J"}, {"family": "Mou", "given": "Yifei", "initials": "Y"}, {"family": "Qu", "given": "Chunjuan", "initials": "C"}, {"family": "Shan", "given": "Shihua", "initials": "S"}], "type": "journal article", "published": "2023-12-20", "journal": {"title": "Plants (Basel)", "issn": "2223-7747", "volume": "13", "issue": "1", "issn-l": null}, "abstract": "The cultivated peanut (Arachis hypogaea L.) is an important oilseed crop worldwide, and fatty acid composition is a major determinant of peanut oil quality. In the present study, we conducted a genome-wide association study (GWAS) for nine fatty acid traits using the whole genome sequences of 160 representative Chinese peanut landraces and identified 6-1195 significant SNPs for different fatty acid contents. Particularly for oleic acid and linoleic acid, two peak SNP clusters on Arahy.09 and Arahy.19 were found to contain the majority of the significant SNPs associated with these two fatty acids. Additionally, a significant proportion of the candidate genes identified on Arahy.09 overlap with those identified in early studies, among which three candidate genes are of special interest. One possesses a significant missense SNP and encodes a known candidate gene FAD2A. The second gene is the gene closest to the most significant SNP for linoleic acid. It codes for an MYB protein that has been demonstrated to impact fatty acid biosynthesis in Arabidopsis. The third gene harbors a missense SNP and encodes a JmjC domain-containing protein. The significant phenotypic difference in the oleic acid/linoleic acid between the genotypes at the first and third candidate genes was further confirmed with PARMS analysis. In addition, we have also identified different candidate genes (i.e., Arahy.ZV39IJ, Arahy.F9E3EA, Arahy.X9ZZC1, and Arahy.Z0ELT9) for the remaining fatty acids. Our findings can help us gain a better understanding of the genetic foundation of peanut fatty acid contents and may hold great potential for enhancing peanut quality in the future.", "doi": "10.3390/plants13010016", "pmid": "38202325", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10780752"}, {"db": "pii", "key": "plants13010016"}], "notes": [], "created": "2024-09-02T08:23:31.998Z", "modified": "2024-09-02T08:23:32.273Z"}, {"entity": "publication", "iuid": "eab4268374624f2ab14306ca0d1dd3b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eab4268374624f2ab14306ca0d1dd3b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eab4268374624f2ab14306ca0d1dd3b0"}}, "title": "Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta).", "authors": [{"family": "Landi", "given": "Michael", "initials": "M", "orcid": "0000-0001-5597-7802", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a48329b81f14ff191ed7a8c8cb562b8.json"}}, {"family": "Shah", "given": "Trushar", "initials": "T", "orcid": "0000-0002-0091-7981", "researcher": {"href": "https://publications.scilifelab.se/researcher/6db73454fcb34150bd72bcc5e850cb5e.json"}}, {"family": "Falquet", "given": "Laurent", "initials": "L", "orcid": "0000-0001-8102-7579", "researcher": {"href": "https://publications.scilifelab.se/researcher/bba0eeebd71e4f6ca50a2751f898fc6a.json"}}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Stavolone", "given": "Livia", "initials": "L"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E", "orcid": "0000-0002-1947-8288", "researcher": {"href": "https://publications.scilifelab.se/researcher/6970ca57259d498588ecf9e1ad28a9b0.json"}}, {"family": "Gisel", "given": "Andreas", "initials": "A", "orcid": "0000-0001-7218-9488", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2eb91acead14ec58845e9eda08742fa.json"}}], "type": "dataset", "published": "2023-12-09", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "10", "issue": "1", "pages": "887", "issn-l": "2052-4463"}, "abstract": "Cassava (Manihot esculenta Crantz) is a vital tropical root crop providing essential dietary energy to over 800 million people in tropical and subtropical regions. As a climate-resilient crop, its significance grows as the human population expands. However, yield improvement faces challenges from biotic and abiotic stress and limited breeding. Advanced sequencing and assembly techniques enabled the generation of a highly accurate, nearly complete, haplotype-resolved genome of the African cassava cultivar TMEB117. It is the most accurate cassava genome sequence to date with a base-level accuracy of QV > 64, N50 > 35 Mbp, and 98.9% BUSCO completeness. Over 60% of the genome comprises repetitive elements. We predicted over 45,000 gene models for both haplotypes. This achievement offers valuable insights into the heterozygosity genome organization of the cassava genome, with improved accuracy, completeness, and phased genomes. Due to its high susceptibility to African Cassava Mosaic Virus (ACMV) infections compared to other cassava varieties, TMEB117 provides an ideal reference for studying virus resistance mechanisms, including epigenetic variations and smallRNA expressions.", "doi": "10.1038/s41597-023-02800-0", "pmid": "38071206", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10710486"}, {"db": "pii", "key": "10.1038/s41597-023-02800-0"}], "notes": [], "created": "2023-12-11T06:42:02.155Z", "modified": "2024-01-05T16:18:41.036Z"}, {"entity": "publication", "iuid": "1b2932d08317470ebe2041e9a8bf6852", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b2932d08317470ebe2041e9a8bf6852.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b2932d08317470ebe2041e9a8bf6852"}}, "title": "Screening for Circulating Inflammatory Proteins Does Not Reveal Plasma Biomarkers of Constant Tinnitus.", "authors": [{"family": "Cederroth", "given": "Christopher R", "initials": "CR", "orcid": "0000-0001-7267-5136", "researcher": {"href": "https://publications.scilifelab.se/researcher/adbc4cbe122a4c23b4664de3ea5c28ae.json"}}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Freydin", "given": "Maxim B", "initials": "MB"}, {"family": "Edvall", "given": "Niklas K", "initials": "NK"}, {"family": "Trpchevska", "given": "Natalia", "initials": "N"}, {"family": "Jarach", "given": "Carlotta", "initials": "C"}, {"family": "Schlee", "given": "Winfried", "initials": "W"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM"}, {"family": "Lopez-Escamez", "given": "Jose-Antonio", "initials": "JA"}, {"family": "Gallus", "given": "Silvano", "initials": "S"}, {"family": "Canlon", "given": "Barbara", "initials": "B"}, {"family": "Bulla", "given": "Jan", "initials": "J"}, {"family": "Williams", "given": "Frances M K", "initials": "FMK"}], "type": "meta-analysis", "published": "2023-12-00", "journal": {"title": "J Assoc Res Otolaryngol", "issn": "1438-7573", "volume": "24", "issue": "6", "pages": "593-606", "issn-l": null}, "abstract": "Tinnitus would benefit from an objective biomarker. The goal of this study is to identify plasma biomarkers of constant and chronic tinnitus among selected circulating inflammatory proteins.\n\nA case-control retrospective study on 548 cases with constant tinnitus and 548 matched controls from the Swedish Tinnitus Outreach Project (STOP), whose plasma samples were examined using Olink's Inflammatory panel. Replication and meta-analysis were performed using the same method on samples from the TwinsUK cohort. Participants from LifeGene, whose blood was collected in Stockholm and Ume\u00e5, were recruited to STOP for a tinnitus subtyping study. An age and sex matching was performed at the individual level. TwinsUK participants (n = 928) were selected based on self-reported tinnitus status over 2 to 10 years. Primary outcomes include normalized levels for 96 circulating proteins, which were used as an index test. No reference standard was available in this study.\n\nAfter adjustment for age, sex, BMI, smoking, hearing loss, and laboratory site, the top proteins identified were FGF-21, MCP4, GDNF, CXCL9, and MCP-1; however, these were no longer statistically significant after correction for multiple testing. Stratification by sex did not yield any significant associations. Similarly, associations with hearing loss or other tinnitus-related comorbidities such as stress, anxiety, depression, hyperacusis, temporomandibular joint disorders, and headache did not yield any significant associations. Analysis in the TwinsUK failed in replicating the top candidates. Meta-analysis of STOP and TwinsUK did not reveal any significant association. Using elastic net regularization, models exhibited poor predictive capacity tinnitus based on inflammatory markers [sensitivity = 0.52 (95% CI 0.47-0.57), specificity = 0.53 (0.48-0.58), positive predictive value = 0.52 (0.47-0.56), negative predictive values = 0.53 (0.49-0.58), and AUC = 0.53 (0.49-0.56)].\n\nOur results did not identify significant associations of the selected inflammatory proteins with constant tinnitus. Future studies examining longitudinal relations among those with more severe tinnitus and using more recent expanded proteomics platforms and sampling of cerebrospinal fluid could increase the likelihood of identifying relevant molecular biomarkers.", "doi": "10.1007/s10162-023-00920-3", "pmid": "38079022", "labels": {"Affinity Proteomics Stockholm": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10752855"}, {"db": "pii", "key": "10.1007/s10162-023-00920-3"}], "notes": [], "created": "2023-12-11T21:30:53.303Z", "modified": "2024-11-12T12:27:06.170Z"}, {"entity": "publication", "iuid": "105f960199ea414c8b533eded245b31c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/105f960199ea414c8b533eded245b31c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/105f960199ea414c8b533eded245b31c"}}, "title": "Antigen-presenting autoreactive B cells activate regulatory T cells and suppress autoimmune arthritis in mice.", "authors": [{"family": "Aoun", "given": "Mike", "initials": "M", "orcid": "0000-0002-7814-3787", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e342417528f4a92a8e84558359b6bfa.json"}}, {"family": "Coelho", "given": "Ana", "initials": "A", "orcid": "0000-0001-7783-9750", "researcher": {"href": "https://publications.scilifelab.se/researcher/163d8babd72b406d94647b4cfd9d7e5b.json"}}, {"family": "Kr\u00e4mer", "given": "Alexander", "initials": "A", "orcid": "0000-0002-2288-2361", "researcher": {"href": "https://publications.scilifelab.se/researcher/50b1230e5acf4ad89344e8d1ae404ef2.json"}}, {"family": "Saxena", "given": "Amit", "initials": "A", "orcid": "0000-0002-1185-8649", "researcher": {"href": "https://publications.scilifelab.se/researcher/d230e0159adc4d7dbd1c3e7ded94dcec.json"}}, {"family": "Sabatier", "given": "Pierre", "initials": "P", "orcid": "0000-0002-2734-1791", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a75556311084e2b827ab1f646d7a16c.json"}}, {"family": "Beusch", "given": "Christian Michel", "initials": "CM", "orcid": "0000-0001-9100-8283", "researcher": {"href": "https://publications.scilifelab.se/researcher/278e50b11a3c4ef69b6e2708f99b5f3e.json"}}, {"family": "L\u00f6nnblom", "given": "Erik", "initials": "E", "orcid": "0000-0002-1311-2541", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f5683b51d554ff482bd76c0ded3aaa2.json"}}, {"family": "Geng", "given": "Manman", "initials": "M", "orcid": "0009-0003-7502-4699", "researcher": {"href": "https://publications.scilifelab.se/researcher/0370014234f54ad08bba271bc19f2703.json"}}, {"family": "Do", "given": "Nhu-Nguyen", "initials": "NN", "orcid": "0000-0001-6483-8062", "researcher": {"href": "https://publications.scilifelab.se/researcher/0de1bfd7cdc945378b2eb973237345bc.json"}}, {"family": "Xu", "given": "Zhongwei", "initials": "Z", "orcid": "0000-0001-5178-3437", "researcher": {"href": "https://publications.scilifelab.se/researcher/f056000b3af842bda8cdd411da7d44ad.json"}}, {"family": "Zhang", "given": "Jingdian", "initials": "J", "orcid": "0000-0002-5685-8386", "researcher": {"href": "https://publications.scilifelab.se/researcher/e208f3fec0f34151a5916ff260e2ace7.json"}}, {"family": "He", "given": "Yibo", "initials": "Y", "orcid": "0000-0003-0659-2150", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e734ee308394c35ba53ef6ed344cfa7.json"}}, {"family": "Romero Castillo", "given": "Laura", "initials": "L", "orcid": "0000-0002-0271-212X", "researcher": {"href": "https://publications.scilifelab.se/researcher/432706cab4ec46258698725df3b02f6c.json"}}, {"family": "Abolhassani", "given": "Hassan", "initials": "H", "orcid": "0000-0002-4838-0407", "researcher": {"href": "https://publications.scilifelab.se/researcher/20370042ca1045c3bcaac67821a93df2.json"}}, {"family": "Xu", "given": "Bingze", "initials": "B", "orcid": "0000-0002-5341-1722", "researcher": {"href": "https://publications.scilifelab.se/researcher/d262ebec52004d1f8bc77d43cafe0cc7.json"}}, {"family": "Viljanen", "given": "Johan", "initials": "J", "orcid": "0009-0003-7291-4178", "researcher": {"href": "https://publications.scilifelab.se/researcher/2519e15fb9c74494a72cfcea38c304ca.json"}}, {"family": "Rorbach", "given": "Joanna", "initials": "J", "orcid": "0000-0002-2891-2840", "researcher": {"href": "https://publications.scilifelab.se/researcher/a069374613a7403b818ce7ca400f3627.json"}}, {"family": "Fernandez Lahore", "given": "Gonzalo", "initials": "G", "orcid": "0000-0002-4291-0251", "researcher": {"href": "https://publications.scilifelab.se/researcher/520747ac45e94b0fb8f0fb08b849eecc.json"}}, {"family": "Gjertsson", "given": "Inger", "initials": "I", "orcid": "0000-0002-9301-4844", "researcher": {"href": "https://publications.scilifelab.se/researcher/56e95592e89f43cba8eb30bd32da1cc8.json"}}, {"family": "Kastbom", "given": "Alf", "initials": "A", "orcid": "0000-0001-7187-1477", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9b6d835959e4613995904bf3a01733c.json"}}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Kihlberg", "given": "Jan", "initials": "J", "orcid": "0000-0002-4205-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9805d4f39cc48f79a6e6ba076917021.json"}}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}, {"family": "Burkhardt", "given": "Harald", "initials": "H", "orcid": "0000-0002-6261-3131", "researcher": {"href": "https://publications.scilifelab.se/researcher/89e31cfcedb24f4ba63420e8ac7903a6.json"}}, {"family": "Holmdahl", "given": "Rikard", "initials": "R", "orcid": "0000-0002-4969-2576", "researcher": {"href": "https://publications.scilifelab.se/researcher/49e60d22dd1a4dd1a4ca5a50d9fc4fc7.json"}}], "type": "journal article", "published": "2023-11-06", "journal": {"title": "J. Exp. Med.", "issn": "1540-9538", "volume": "220", "issue": "11", "issn-l": "0022-1007"}, "abstract": "B cells undergo several rounds of selection to eliminate potentially pathogenic autoreactive clones, but in contrast to T cells, evidence of positive selection of autoreactive B cells remains moot. Using unique tetramers, we traced natural autoreactive B cells (C1-B) specific for a defined triple-helical epitope on collagen type-II (COL2), constituting a sizeable fraction of the physiological B cell repertoire in mice, rats, and humans. Adoptive transfer of C1-B suppressed arthritis independently of IL10, separating them from IL10-secreting regulatory B cells. Single-cell sequencing revealed an antigen processing and presentation signature, including induced expression of CD72 and CCR7 as surface markers. C1-B presented COL2 to T cells and induced the expansion of regulatory T cells in a contact-dependent manner. CD72 blockade impeded this effect suggesting a new downstream suppressor mechanism that regulates antigen-specific T cell tolerization. Thus, our results indicate that autoreactive antigen-specific na\u00efve B cells tolerize infiltrating T cells against self-antigens to impede the development of tissue-specific autoimmune inflammation.", "doi": "10.1084/jem.20230101", "pmid": "37695523", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10494526"}, {"db": "pii", "key": "276247"}], "notes": [], "created": "2023-11-16T12:01:57.118Z", "modified": "2024-01-16T13:48:31.724Z"}, {"entity": "publication", "iuid": "db348fd6274541babf929e604a62268d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db348fd6274541babf929e604a62268d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db348fd6274541babf929e604a62268d"}}, "title": "Early detection of the emerging SARS-CoV-2 BA.2.86 lineage through integrated genomic surveillance of wastewater and COVID-19 cases in Sweden, weeks 31 to 38 2023.", "authors": [{"family": "Espinosa-Gongora", "given": "Carmen", "initials": "C"}, {"family": "Berg", "given": "Carlo", "initials": "C"}, {"family": "Rehn", "given": "Moa", "initials": "M"}, {"family": "Varg", "given": "Javier Edo", "initials": "JE"}, {"family": "Dillner", "given": "Lena", "initials": "L"}, {"family": "Latorre-Margalef", "given": "Neus", "initials": "N"}, {"family": "Sz\u00e9kely", "given": "Anna J", "initials": "AJ"}, {"family": "Andersson", "given": "Emmi", "initials": "E"}, {"family": "Movert", "given": "Elin", "initials": "E"}], "type": "journal article", "published": "2023-11-00", "journal": {"title": "Euro Surveill.", "issn": "1560-7917", "volume": "28", "issue": "46", "issn-l": "1025-496X"}, "abstract": "The SARS-CoV-2 BA.2.86 Omicron subvariant was first detected in wastewater in Sweden in week 31 2023, using 21 highly specific markers from the 50 investigated. We report BA.2.86's introduction and subsequent spread to all 14 regions performing wastewater sampling, and on 70 confirmed COVID-19 cases, along with the emergence of sublineages JN.1 and JN.2. Further, we investigated two novel mutations defining the unique BA.2.86 branching in Sweden. Our integrated approach enabled variant tracking, offering evidence for well-informed public health interventions.", "doi": "10.2807/1560-7917.ES.2023.28.46.2300595", "pmid": "37971659", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10655203"}], "notes": [], "created": "2025-11-24T07:50:36.279Z", "modified": "2025-11-24T07:50:36.287Z"}, {"entity": "publication", "iuid": "c04937c70b4a447b91d3d2aec9bf40bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c04937c70b4a447b91d3d2aec9bf40bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c04937c70b4a447b91d3d2aec9bf40bc"}}, "title": "CGG toolkit: Software components for computational genomics.", "authors": [{"family": "Vasileiou", "given": "Dimitrios", "initials": "D"}, {"family": "Karapiperis", "given": "Christos", "initials": "C"}, {"family": "Baltsavia", "given": "Ismini", "initials": "I"}, {"family": "Chasapi", "given": "Anastasia", "initials": "A"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Janssen", "given": "Paul J", "initials": "PJ", "orcid": "0000-0002-7877-0270", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbeadef1d79643c49619e484d1773adf.json"}}, {"family": "Iliopoulos", "given": "Ioannis", "initials": "I"}, {"family": "Promponas", "given": "Vasilis J", "initials": "VJ"}, {"family": "Enright", "given": "Anton J", "initials": "AJ"}, {"family": "Ouzounis", "given": "Christos A", "initials": "CA", "orcid": "0000-0002-0086-8657", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e7eab67d5134be89b5f7cea5208e860.json"}}], "type": "journal article", "published": "2023-11-00", "journal": {"title": "PLoS Comput. Biol.", "issn": "1553-7358", "volume": "19", "issue": "11", "pages": "e1011498", "issn-l": "1553-734X"}, "abstract": "Public-domain availability for bioinformatics software resources is a key requirement that ensures long-term permanence and methodological reproducibility for research and development across the life sciences. These issues are particularly critical for widely used, efficient, and well-proven methods, especially those developed in research settings that often face funding discontinuities. We re-launch a range of established software components for computational genomics, as legacy version 1.0.1, suitable for sequence matching, masking, searching, clustering and visualization for protein family discovery, annotation and functional characterization on a genome scale. These applications are made available online as open source and include MagicMatch, GeneCAST, support scripts for CoGenT-like sequence collections, GeneRAGE and DifFuse, supported by centrally administered bioinformatics infrastructure funding. The toolkit may also be conceived as a flexible genome comparison software pipeline that supports research in this domain. We illustrate basic use by examples and pictorial representations of the registered tools, which are further described with appropriate documentation files in the corresponding GitHub release.", "doi": "10.1371/journal.pcbi.1011498", "pmid": "37934729", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10629618"}, {"db": "pii", "key": "PCOMPBIOL-D-23-00660"}], "notes": [], "created": "2023-12-01T10:26:42.813Z", "modified": "2023-12-01T10:26:42.887Z"}, {"entity": "publication", "iuid": "34c38b3d3f564542956074b47323ddb5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34c38b3d3f564542956074b47323ddb5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34c38b3d3f564542956074b47323ddb5"}}, "title": "Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis.", "authors": [{"family": "Mastropasqua", "given": "Francesca", "initials": "F", "orcid": "0000-0003-4237-2446", "researcher": {"href": "https://publications.scilifelab.se/researcher/30aece0009c94ace82728640c71682f7.json"}}, {"family": "Oksanen", "given": "Marika", "initials": "M", "orcid": "0000-0003-4140-4282", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a8727638dc49fe88b15052d5741fd5.json"}}, {"family": "Soldini", "given": "Cristina", "initials": "C"}, {"family": "Alatar", "given": "Shemim", "initials": "S", "orcid": "0009-0009-0738-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/0500cee4755b46479d0818314e5c05a7.json"}}, {"family": "Arora", "given": "Abishek", "initials": "A", "orcid": "0000-0002-6149-4417", "researcher": {"href": "https://publications.scilifelab.se/researcher/384ef4f8d6eb49d6873c87556843a7a2.json"}}, {"family": "Ballarino", "given": "Roberto", "initials": "R", "orcid": "0000-0001-7812-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb720f25876d45c39b9dad1b4b48a6fa.json"}}, {"family": "Molinari", "given": "Maya", "initials": "M"}, {"family": "Agostini", "given": "Federico", "initials": "F", "orcid": "0000-0002-5453-2737", "researcher": {"href": "https://publications.scilifelab.se/researcher/a21ea8b7e9a5427eb0e48a822c840b8b.json"}}, {"family": "Poulet", "given": "Axel", "initials": "A", "orcid": "0000-0002-3415-8960", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4dfc191bbfd4ed6922008f10531835c.json"}}, {"family": "Watts", "given": "Michelle", "initials": "M", "orcid": "0000-0002-3178-3429", "researcher": {"href": "https://publications.scilifelab.se/researcher/28a00d3b8c3e40e1b68fc333a7aa4fb7.json"}}, {"family": "Rabkina", "given": "Ielyzaveta", "initials": "I", "orcid": "0000-0001-5890-4115", "researcher": {"href": "https://publications.scilifelab.se/researcher/509d3fdbf53b45acbae3ddea4903a0ba.json"}}, {"family": "Becker", "given": "Martin", "initials": "M", "orcid": "0000-0001-8442-4246", "researcher": {"href": "https://publications.scilifelab.se/researcher/85eaa4173364473d83506125206a7193.json"}}, {"family": "Li", "given": "Danyang", "initials": "D", "orcid": "0000-0001-7470-6645", "researcher": {"href": "https://publications.scilifelab.se/researcher/01900295a1904ac886960b3eea5915f0.json"}}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM", "orcid": "0000-0002-2488-6024", "researcher": {"href": "https://publications.scilifelab.se/researcher/73c8590243874a0a9f18b9e7138ce9a9.json"}}, {"family": "Isaksson", "given": "Johan", "initials": "J", "orcid": "0000-0003-1033-2618", "researcher": {"href": "https://publications.scilifelab.se/researcher/af22620f762a4a5e80dca3f546223caa.json"}}, {"family": "Lundin Remnelius", "given": "Karl", "initials": "K"}, {"family": "Moslem", "given": "Mohsen", "initials": "M"}, {"family": "Jacob", "given": "Yannick", "initials": "Y", "orcid": "0000-0003-4741-0755", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f553bc5034e4768bad65bf8b1236e6a.json"}}, {"family": "Falk", "given": "Anna", "initials": "A", "orcid": "0000-0003-1634-8610", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b708dfb7f0548589bdee53d6e6b536e.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Santini", "given": "Emanuela", "initials": "E", "orcid": "0000-0002-8948-9652", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d176892d0f14922bab782fe4cd69e90.json"}}, {"family": "Borgkvist", "given": "Anders", "initials": "A", "orcid": "0000-0003-1698-0288", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c0f5180d7a74249bcfeb59386a7c65d.json"}}, {"family": "B\u00f6lte", "given": "Sven", "initials": "S", "orcid": "0000-0002-4579-4970", "researcher": {"href": "https://publications.scilifelab.se/researcher/bead50319cae447f90bcf7658d9edf56.json"}}, {"family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba19ec07147743c6942ea10c9a92482a.json"}}], "type": "journal article", "published": "2023-10-15", "journal": {"title": "Biol Open", "issn": "2046-6390", "volume": "12", "issue": "10", "issn-l": "2046-6390"}, "abstract": "Genetic variants affecting Heterogeneous Nuclear Ribonucleoprotein U (HNRNPU) have been identified in several neurodevelopmental disorders (NDDs). HNRNPU is widely expressed in the human brain and shows the highest postnatal expression in the cerebellum. Recent studies have investigated the role of HNRNPU in cerebral cortical development, but the effects of HNRNPU deficiency on cerebellar development remain unknown. Here, we describe the molecular and cellular outcomes of HNRNPU locus deficiency during in vitro neural differentiation of patient-derived and isogenic neuroepithelial stem cells with a hindbrain profile. We demonstrate that HNRNPU deficiency leads to chromatin remodeling of A/B compartments, and transcriptional rewiring, partly by impacting exon inclusion during mRNA processing. Genomic regions affected by the chromatin restructuring and host genes of exon usage differences show a strong enrichment for genes implicated in epilepsies, intellectual disability, and autism. Lastly, we show that at the cellular level HNRNPU downregulation leads to an increased fraction of neural progenitors in the maturing neuronal population. We conclude that the HNRNPU locus is involved in delayed commitment of neural progenitors to differentiate in cell types with hindbrain profile.", "doi": "10.1242/bio.060113", "pmid": "37815090", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10581386"}, {"db": "pii", "key": "330791"}], "notes": [], "created": "2023-11-16T12:03:03.393Z", "modified": "2024-01-16T13:48:31.943Z"}, {"entity": "publication", "iuid": "467d9682bec746ed878a1bacf430dbca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/467d9682bec746ed878a1bacf430dbca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/467d9682bec746ed878a1bacf430dbca"}}, "title": "Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients.", "authors": [{"family": "Sar\u00e9n", "given": "Tina", "initials": "T", "orcid": "0000-0001-5227-6779", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8f06b113565445f8dc2882a926229b6.json"}}, {"family": "Ramachandran", "given": "Mohanraj", "initials": "M", "orcid": "0000-0003-2685-0575", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3fefc78a0b040faa998efb8fde7b920.json"}}, {"family": "Gammelg\u00e5rd", "given": "Gustav", "initials": "G", "orcid": "0009-0008-5522-0103", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f8652afc79e4fe39e82bb49a5dc5307.json"}}, {"family": "L\u00f6vgren", "given": "Tanja", "initials": "T", "orcid": "0000-0003-2170-0682", "researcher": {"href": "https://publications.scilifelab.se/researcher/a578be87e95941fe8d59d344d03d1dd2.json"}}, {"family": "Mirabello", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7868-034X", "researcher": {"href": "https://publications.scilifelab.se/researcher/00052b54a3d24fd4a6e648f987d15e5f.json"}}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}, {"family": "Wikstr\u00f6m", "given": "Kristina", "initials": "K", "orcid": "0009-0000-1027-2534", "researcher": {"href": "https://publications.scilifelab.se/researcher/0922ad45252045e9b2ac4d8ad264a718.json"}}, {"family": "Hashemi", "given": "Jamileh", "initials": "J", "orcid": "0000-0002-4997-3765", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1dd38f2d9644c1c8a9bf870fc69ef2a.json"}}, {"family": "Freyhult", "given": "Eva", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "Ahlstr\u00f6m", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0002-8701-969X", "researcher": {"href": "https://publications.scilifelab.se/researcher/53e4a209929642ceaadf3e0aed6b8c69.json"}}, {"family": "Amini", "given": "Rose-Marie", "initials": "RM", "orcid": "0000-0003-0901-5252", "researcher": {"href": "https://publications.scilifelab.se/researcher/c157abcd61fa4900b5ad502b408d6d95.json"}}, {"family": "Hagberg", "given": "Hans", "initials": "H", "orcid": "0000-0001-7855-2452", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ec21157056f48e49cb2f7c528d16b1d.json"}}, {"family": "Loskog", "given": "Angelica", "initials": "A", "orcid": "0000-0001-8583-6138", "researcher": {"href": "https://publications.scilifelab.se/researcher/5730068a851041ecb0bce96c2954bb28.json"}}, {"family": "Enblad", "given": "Gunilla", "initials": "G", "orcid": "0000-0002-0594-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/11313af3f4a241ecb93af23ab2652195.json"}}, {"family": "Essand", "given": "Magnus", "initials": "M", "orcid": "0000-0002-9725-0422", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5afc47ab0814c09909af3c66217a3a6.json"}}], "type": "journal article", "published": "2023-10-13", "journal": {"title": "Clin. Cancer Res.", "issn": "1557-3265", "issn-l": "1078-0432", "volume": "29", "issue": "20", "pages": "4139-4152"}, "abstract": "Although CD19 chimeric antigen receptor T cells (CAR-T) therapy has shown remarkable success in B-cell malignancies, a substantial fraction of patients do not obtain a long-term clinical response. This could be influenced by the quality of the individual CAR-T infusion product. To shed some light on this, clinical outcome was correlated to characteristics of CAR-T infusion products.\n\nIn this phase II study, patients with B-cell lymphoma (n = 23) or leukemia (n = 1) received one or two infusions of third-generation CD19-directed CAR-Ts (2 \u00d7 108/m2). The clinical trial was registered at clinicaltrials.gov: NCT03068416. We investigated the transcriptional profile of individual CD19 CAR-T infusion products using targeted single-cell RNA sequencing and multicolor flow cytometry.\n\nTwo CAR-T infusions were not better than one in the settings used in this study. As for the CAR-T infusion products, we found that effector-like CD8+CAR-Ts with a high polyfunctionality, high cytotoxic and cytokine production profile, and low dysfunctional signature were associated with clinical response. An extended ex vivo expansion time during CAR-T manufacturing negatively influenced the proportion of effector CD8+CAR-Ts in the infusion product.\n\nWe identified cell-intrinsic characteristics of effector CD8+CAR-Ts correlating with response that could be used as an indicator for clinical outcome. The results in the study also serve as a guide to CAR-T manufacturing practices.", "doi": "10.1158/1078-0432.CCR-23-0178", "pmid": "37540566", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Affinity Proteomics Uppsala": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10570681"}, {"db": "pii", "key": "728314"}, {"db": "ClinicalTrials.gov", "key": "NCT03068416"}], "notes": [], "created": "2023-09-20T16:40:48.854Z", "modified": "2024-11-12T12:30:30.156Z"}, {"entity": "publication", "iuid": "29909db19bd74064be97cd0a000ef1a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29909db19bd74064be97cd0a000ef1a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29909db19bd74064be97cd0a000ef1a7"}}, "title": "Mitochondrial heteroplasmic shifts reveal a positive selection of breast cancer.", "authors": [{"family": "Li", "given": "Yanni", "initials": "Y", "orcid": "0000-0003-4550-8935", "researcher": {"href": "https://publications.scilifelab.se/researcher/29f30b9be82b470ea5123ddf3329c0f0.json"}}, {"family": "Sundquist", "given": "Kristina", "initials": "K"}, {"family": "Vats", "given": "Sakshi", "initials": "S"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Wang", "given": "Xiao", "initials": "X"}, {"family": "Chen", "given": "Yilun", "initials": "Y"}, {"family": "Hedelius", "given": "Anna", "initials": "A"}, {"family": "Saal", "given": "Lao H", "initials": "LH"}, {"family": "Sundquist", "given": "Jan", "initials": "J"}, {"family": "Memon", "given": "Ashfaque A", "initials": "AA"}], "type": "journal article", "published": "2023-10-05", "journal": {"title": "J Transl Med", "issn": "1479-5876", "volume": "21", "issue": "1", "pages": "696", "issn-l": "1479-5876"}, "abstract": "Breast cancer is, despite screening, not always detected early enough and is together with other tumor types known to shed genetic information in circulation. Unlike single-copy nuclear DNA, mitochondrial DNA (mtDNA) copies range from 100s to 10,000s per cell, thus providing a potentially alternative to identify potential missing cancer information in circulation at an early stage.\n\nTo characterize mitochondrial mutation landscapes in breast cancer, whole mtDNA sequencing and bioinformatics analyses were performed on 86 breast cancer biopsies and 50 available matched baseline cancer-free whole blood samples from the same individuals, selected from a cohort of middle-aged women in Sweden. To determine whether the mutations can be detected in blood plasma prior to cancer diagnosis, we further designed a nested case-control study (n = 663) and validated the shortlisted mutations using droplet digital PCR.\n\nWe detected different mutation landscapes between biopsies and matched whole blood samples. Compared to whole blood samples, mtDNA from biopsies had higher heteroplasmic mutations in the D-loop region (P = 0.02), RNR2 (P = 0.005), COX1 (P = 0.037) and CYTB (P = 0.006). Furthermore, the germline mtDNA mutations had higher heteroplasmy level than the lost (P = 0.002) and de novo mutations (P = 0.04). The nonsynonymous to synonymous substitution ratio (dN/dS) was higher for the heteroplasmic mutations (P = 7.25 \u00d7 10-12) than that for the homoplasmic mutations, but the de novo (P = 0.06) and lost mutations (P = 0.03) had lower dN/dS than the germline mutations. Interestingly, we found that the critical regions for mitochondrial transcription: MT-HSP1 (odds ratio [OR]: 21.41), MT-TFH (OR: 7.70) and MT-TAS2 (OR: 3.62), had significantly higher heteroplasmic mutations than the rest of the D-loop sub-regions. Finally, we found that the presence of mt.16093T > C mutation increases 67% risk of developing breast cancer.\n\nOur findings show that mitochondrial genetic landscape changes during cancer pathogenesis and positive selection of mtDNA heteroplasmic mutations in breast cancer. Most importantly, the mitochondrial mutations identified in biopsies can be traced back in matched plasma samples and could potentially be used as early breast cancer diagnostic biomarkers.", "doi": "10.1186/s12967-023-04534-4", "pmid": "37798736", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10557196"}, {"db": "pii", "key": "10.1186/s12967-023-04534-4"}], "notes": [], "created": "2023-11-16T12:29:55.895Z", "modified": "2023-11-16T12:29:55.935Z"}, {"entity": "publication", "iuid": "97328d83a5ff458481fbad51e7615b21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/97328d83a5ff458481fbad51e7615b21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/97328d83a5ff458481fbad51e7615b21"}}, "title": "Metabolomic and transcriptomic analyses identify external conditions and key genes underlying high levels of toxic glycoalkaloids in tubers of stress-sensitive potato cultivars.", "authors": [{"family": "Merino", "given": "Irene", "initials": "I"}, {"family": "Guasca", "given": "Alexandra Olarte", "initials": "AO"}, {"family": "Krmela", "given": "Ales", "initials": "A"}, {"family": "Arif", "given": "Usman", "initials": "U"}, {"family": "Ali", "given": "Ashfaq", "initials": "A"}, {"family": "Westerberg", "given": "Erik", "initials": "E"}, {"family": "Jalmi", "given": "Siddhi Kashinanth", "initials": "SK"}, {"family": "Hajslova", "given": "Jana", "initials": "J"}, {"family": "Schulzova", "given": "Vera", "initials": "V"}, {"family": "Sitbon", "given": "Folke", "initials": "F"}], "type": "journal article", "published": "2023-10-04", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "issn-l": "1664-462X", "volume": "14", "issue": null, "pages": "1210850"}, "abstract": "High levels of toxic steroidal glycoalkaloids (SGAs) in potato tubers constitute a recognized food quality problem. Tuber SGA levels vary between potato cultivars and can increase after post-harvest stresses such as wounding and light exposure. A few cultivars, e.g., 'Magnum Bonum' and 'Lenape,' have been withdrawn from commercial sales due to excessive SGA levels during some cultivation years. However, these sudden SGA increases are diffucult to predict, and their causes are not understood. To identify external and genetic factors that underlie sudden SGA increases in certain potato cultivars, we have here in a 2-year study investigated 'Magnum Bonum' and five additional table potato cultivars for their SGA levels after wounding and light exposure.\r\n\r\nResults showed that 'Magnum Bonum' has an unusual strong SGA response to light exposure, but not to wounding, whereas 'Bintje' displayed an opposite regulation. Levels of calystegine alkaloids were not significantly altered by treatments, implicating independent metabolic regulation of SGA and calystegine levels also under conditions of high SGA accumulation. Metabolomic and transcriptomic analyses identified a small number of key genes whose expression correlated with SGA differences between cultivars. Overexpression of two key genes in transgenic low-SGA potato cultivars increased their leaf SGA levels significantly.\r\n\r\nThe results show that a strong response to light can underlie the SGA peaks that occasionally occur in certain potato cultivars and indicate that a between-cultivar variation in the expression of single SGA key genes can account for cultivar SGA differerences. We propose that current attempts to mitigate the SGA hazard will benefit from an increased consideration of cultivar-dependent SGA responses to post-harvest conditions, particularly light exposure. The identified key SGA genes can now be used as a molecular tool in this work.", "doi": "10.3389/fpls.2023.1210850", "pmid": "37860257", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10582707"}], "notes": [], "created": "2023-11-16T12:04:12.160Z", "modified": "2024-01-16T13:48:32.011Z"}, {"entity": "publication", "iuid": "18f91b3acff84dd7bbb28f1ff7415c73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/18f91b3acff84dd7bbb28f1ff7415c73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/18f91b3acff84dd7bbb28f1ff7415c73"}}, "title": "Copy number variations and their effect on the plasma proteome.", "authors": [{"family": "Schmitz", "given": "Daniel", "initials": "D"}, {"family": "Li", "given": "Zhiwei", "initials": "Z"}, {"family": "Lo Faro", "given": "Valeria", "initials": "V"}, {"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "Ameur", "given": "Adam", "initials": "A"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2023-10-04", "journal": {"title": "Genetics", "issn": "1943-2631", "issn-l": "0016-6731", "volume": null, "issue": null, "pages": null}, "abstract": "Structural variations, including copy number variations (CNVs), affect around 20 million bases in the human genome and are common causes of rare conditions. CNVs are rarely investigated in complex disease research because most CNVs are not targeted on the genotyping arrays or the reference panels for genetic imputation. In this study, we characterize CNVs in a Swedish cohort (N = 1,021) using short-read whole genome sequencing (WGS) and use long-read WGS for validation in a sub-cohort (N = 15), and explore their effect on 438 plasma proteins. We detected 184,182 polymorphic CNVs and identified 15 CNVs to be associated with 16 proteins (p<8.22\u00d710-10). Of these, five CNVs could be perfectly validated using long-read sequencing, including a CNV which was associated to measurements of the osteoclast-associated immunoglobulin-like receptor (OSCAR) and located upstream of OSCAR, a gene important for bone health. Two other CNVs were identified to be clusters of many short repetitive elements and another represented a complex rearrangement including an inversion. Our findings provide insights into the structure of common CNVs and their effects on the plasma proteome, and highlights the importance of investigating common CNVs, also in relation to complex diseases.", "doi": "10.1093/genetics/iyad179", "pmid": "37793096", "labels": {"NGI Long read": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "7289162"}], "notes": [], "created": "2023-10-10T08:55:38.883Z", "modified": "2024-01-16T13:48:32.020Z"}, {"entity": "publication", "iuid": "c16cc0e41db14e1da25ba7d3ee32add2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c16cc0e41db14e1da25ba7d3ee32add2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c16cc0e41db14e1da25ba7d3ee32add2"}}, "title": "Quantification of proteomic profile changes in the hemolymph of crayfish during in vitro coagulation.", "authors": [{"family": "Mengal", "given": "Kifayatullah", "initials": "K"}, {"family": "Kor", "given": "Golara", "initials": "G"}, {"family": "Siino", "given": "Valentina", "initials": "V"}, {"family": "Bu\u0159i\u010d", "given": "Milo\u0161", "initials": "M"}, {"family": "Koz\u00e1k", "given": "Pavel", "initials": "P"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Niksirat", "given": "Hamid", "initials": "H"}], "type": "journal article", "published": "2023-10-00", "journal": {"title": "Dev. Comp. Immunol.", "issn": "1879-0089", "volume": "147", "pages": "104760", "issn-l": "0145-305X"}, "abstract": "Hemolymph is the circulatory fluid that fills the body cavity of crustaceans, analogous to blood in vertebrates. Hemolymph coagulation, similar to blood clotting in vertebrates, plays a crucial role in wound healing and innate immune responses. Despite extensive studies on the clotting process in crustaceans, no comparative quantitative analysis of the protein composition of non-clotted and clotted hemolymph in any decapod has been reported. In this study, we used label-free protein quantification with high-resolution mass spectrometry to identify the proteomic profile of hemolymph in crayfish and quantify significant changes in protein abundances between non-clotted and clotted hemolymph. Our analysis identified a total of two-hundred and nineteen proteins in both hemolymph groups. Furthermore, we discussed the potential functions of the top most high and low-abundant proteins in hemolymph proteomic profile. The quantity of most of the proteins was not significantly changed during coagulation between non-clotted and clotted hemolymph, which may indicate that clotting proteins are likely pre-synthesized, allowing for a swift coagulation response to injury. Four proteins still showed abundance differences (p < 0.05, fold change>2), including C-type lectin domain-containing proteins, Laminin A chain, Tropomyosin, and Reverse transcriptase domain-containing proteins. While the first three proteins were down-regulated, the last one was up-regulated. The down-regulation of structural and cytoskeletal proteins may affect the process of hemocyte degranulation needed for coagulation, while the up-regulation of an immune-related protein might be attributed to the phagocytosis ability of viable hemocytes during coagulation.", "doi": "10.1016/j.dci.2023.104760", "pmid": "37331675", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0145-305X(23)00130-1"}], "notes": [], "created": "2023-09-27T07:00:00.025Z", "modified": "2023-09-27T07:00:00.041Z"}, {"entity": "publication", "iuid": "4c52ba744a8a404a97e2fce750f07972", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4c52ba744a8a404a97e2fce750f07972.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4c52ba744a8a404a97e2fce750f07972"}}, "title": "Origin matters: Using a local reference genome improves measures in population genomics.", "authors": [{"family": "Thorburn", "given": "Doko-Miles J", "initials": "DJ", "orcid": "0000-0002-0120-8829", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad7b91e844dc4b50aa45e94baacc2081.json"}}, {"family": "Sagonas", "given": "Kostas", "initials": "K"}, {"family": "Binzer-Panchal", "given": "Mahesh", "initials": "M"}, {"family": "Chain", "given": "Frederic J J", "initials": "FJJ", "orcid": "0000-0001-6169-7399", "researcher": {"href": "https://publications.scilifelab.se/researcher/a24db39bdde04478a210da0176cbdbf6.json"}}, {"family": "Feulner", "given": "Philine G D", "initials": "PGD", "orcid": "0000-0002-8078-1788", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e9226f8674848faa5fcc8a1f756c614.json"}}, {"family": "Bornberg-Bauer", "given": "Erich", "initials": "E"}, {"family": "Reusch", "given": "Thorsten B H", "initials": "TBH"}, {"family": "Samonte-Padilla", "given": "Irene E", "initials": "IE"}, {"family": "Milinski", "given": "Manfred", "initials": "M"}, {"family": "Lenz", "given": "Tobias L", "initials": "TL"}, {"family": "Eizaguirre", "given": "Christophe", "initials": "C"}], "type": "journal article", "published": "2023-10-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "volume": "23", "issue": "7", "pages": "1706-1723", "issn-l": "1755-098X"}, "abstract": "Genome sequencing enables answering fundamental questions about the genetic basis of adaptation, population structure and epigenetic mechanisms. Yet, we usually need a suitable reference genome for mapping population-level resequencing data. In some model systems, multiple reference genomes are available, giving the challenging task of determining which reference genome best suits the data. Here, we compared the use of two different reference genomes for the three-spined stickleback (Gasterosteus aculeatus), one novel genome derived from a European gynogenetic individual and the published reference genome of a North American individual. Specifically, we investigated the impact of using a local reference versus one generated from a distinct lineage on several common population genomics analyses. Through mapping genome resequencing data of 60 sticklebacks from across Europe and North America, we demonstrate that genetic distance among samples and the reference genomes impacts downstream analyses. Using a local reference genome increased mapping efficiency and genotyping accuracy, effectively retaining more and better data. Despite comparable distributions of the metrics generated across the genome using SNP data (i.e. \u03c0, Tajima's D and FST ), window-based statistics using different references resulted in different outlier genes and enriched gene functions. A marker-based analysis of DNA methylation distributions had a comparably high overlap in outlier genes and functions, yet with distinct differences depending on the reference genome. Overall, our results highlight how using a local reference genome decreases reference bias to increase confidence in downstream analyses of the data. Such results have significant implications in all reference-genome-based population genomic analyses.", "doi": "10.1111/1755-0998.13838", "pmid": "37489282", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-12-01T13:18:00.367Z", "modified": "2023-12-01T13:18:00.481Z"}, {"entity": "publication", "iuid": "5f84008ef37d4592a6744d625c3bcab6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f84008ef37d4592a6744d625c3bcab6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f84008ef37d4592a6744d625c3bcab6"}}, "title": "Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae).", "authors": [{"family": "Steffen", "given": "Karin", "initials": "K"}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Churcher", "given": "Allison", "initials": "A"}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "C\u00e1rdenas", "given": "Paco", "initials": "P"}], "type": "journal article", "published": "2023-09-30", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "issn-l": "2160-1836", "volume": "13", "issue": "10", "pages": null}, "abstract": "Sponges are among the earliest branching extant animals. As such, genetic data from this group are valuable for understanding the evolution of various traits and processes in other animals. However, like many marine organisms, they are notoriously difficult to sequence, and hence, genomic data are scarce. Here, we present the draft genome assembly for the North Atlantic deep-sea high microbial abundance species Geodia barretti Bowerbank 1858, from a single individual collected on the West Coast of Sweden. The nuclear genome assembly has 4,535 scaffolds, an N50 of 48,447 bp and a total length of 144 Mb; the mitochondrial genome is 17,996 bp long. BUSCO completeness was 71.5%. The genome was annotated using a combination of ab initio and evidence-based methods finding 31,884 protein-coding genes.", "doi": "10.1093/g3journal/jkad192", "pmid": "37619978", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10542158"}, {"db": "pii", "key": "7250426"}], "notes": [], "created": "2023-09-04T12:08:12.851Z", "modified": "2024-01-16T13:48:32.035Z"}, {"entity": "publication", "iuid": "9926326bbebc4228bb5c62d45a0f25be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9926326bbebc4228bb5c62d45a0f25be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9926326bbebc4228bb5c62d45a0f25be"}}, "title": "Oral fungal profiling and risk of nasopharyngeal carcinoma: a population-based case-control study.", "authors": [{"family": "Chen", "given": "Yufeng", "initials": "Y"}, {"family": "Li", "given": "Wanxin", "initials": "W"}, {"family": "Chang", "given": "Ellen T", "initials": "ET"}, {"family": "Debelius", "given": "Justine W", "initials": "JW"}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L"}, {"family": "Zheng", "given": "Yuming", "initials": "Y"}, {"family": "Li", "given": "Yancheng", "initials": "Y"}, {"family": "Huang", "given": "Guangwu", "initials": "G"}, {"family": "Adami", "given": "Hans-Olov", "initials": "HO"}, {"family": "Knight", "given": "Rob", "initials": "R"}, {"family": "Cai", "given": "Yonglin", "initials": "Y"}, {"family": "Zhang", "given": "Zhe", "initials": "Z"}, {"family": "Ye", "given": "Weimin", "initials": "W"}], "type": "journal article", "published": "2023-09-28", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "volume": "96", "pages": "104813", "issn-l": "2352-3964"}, "abstract": "Dysbiosis of the oral mycobiome has been linked to some diseases, including cancers. However, the role of oral fungal communities in nasopharyngeal carcinoma (NPC) carcinogenesis has not previously been investigated.\n\nWe characterized the oral salivary fungal mycobiome in 476 untreated incident NPC patients and 537 population-based controls using fungal internal transcribed spacer (ITS)-2 sequencing. The relationship between oral fungal mycobiome and the risk of NPC was assessed through bioinformatic and biostatistical analyses.\n\nWe found that lower fungal alpha diversity was associated with an increased odds of NPC [lower vs. higher: observed features (adjusted odds ratio [OR] = 5.81, 95% confidence interval [CI] = 3.60-9.38); Simpson diversity (1.53, 1.03-2.29); Shannon diversity (2.03, 1.35-3.04)]. We also observed a significant difference in global fungal community patterns between cases and controls based on Bray-Curtis dissimilarity (P < 0.001). Carriage of oral fungal species, specifically, Saccharomyces cerevisiae, Candida tropicalis, Lodderomyces elongisporus, Candida albicans, and Fusarium poae, was associated with significantly higher odds of NPC, with ORs ranging from 1.56 to 4.66. Individuals with both low fungal and low bacterial alpha diversity had a profoundly elevated risk of NPC.\n\nOur results suggest that dysbiosis in the oral mycobiome, characterized by a loss of fungal community diversity and overgrowth of several fungal organisms, is associated with a substantially increased risk of NPC.\n\nThis work was funded by the US National Institutes of Health, the Swedish Research Council, the High-level Talents Research Start-up Project of Fujian Medical University, and the China Scholarship Council.", "doi": "10.1016/j.ebiom.2023.104813", "pmid": "37776725", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2352-3964(23)00379-1"}], "notes": [], "created": "2023-10-04T14:51:11.575Z", "modified": "2023-10-04T14:51:11.579Z"}, {"entity": "publication", "iuid": "9afbaeee322443f5b2209c9afa15ffc4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9afbaeee322443f5b2209c9afa15ffc4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9afbaeee322443f5b2209c9afa15ffc4"}}, "title": "Strict self-isolation did not protect Swedish cancer patients on active treatment from the risk of becoming seropositive for SARS-CoV-2.", "authors": [{"family": "Ginman", "given": "Beatrice", "initials": "B"}, {"family": "Pahnke", "given": "Simon", "initials": "S", "orcid": "0000-0002-3541-2027", "researcher": {"href": "https://publications.scilifelab.se/researcher/0040221ec27a44c4b05b7e886cd48bbb.json"}}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Hoffman", "given": "Tove", "initials": "T"}, {"family": "Kolstad", "given": "Linda", "initials": "L"}, {"family": "R\u00f6nnberg", "given": "Bengt", "initials": "B"}, {"family": "Lundkvist", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Hamberg Levedahl", "given": "Kerstin", "initials": "K"}, {"family": "Enblad", "given": "Gunilla", "initials": "G"}, {"family": "Glimelius", "given": "Ingrid", "initials": "I", "orcid": "0000-0001-6158-3041", "researcher": {"href": "https://publications.scilifelab.se/researcher/3db3caec5bef41d2b92cb8e3cf8221ea.json"}}], "type": "journal article", "published": "2023-09-20", "journal": {"title": "Acta Oncol", "issn": "1651-226X", "pages": "1-9", "issn-l": "0284-186X"}, "abstract": "Background: Swedish recommendations to reduce the risk of COVID-19 relied on each citizen's own sense of responsibility rather than mandatory lockdowns. We studied how COVID-19-related self-isolation and anxiety correlated to SARS-CoV-2 seropositivity and PCR-positivity in patients with active cancer treatment.Methods: In a longitudinal cohort study at Uppsala University Hospital patients and cancer personnel were included between April 1st 2020 to August 1st 2020. Serological testing for SARS-CoV-2 was done every 8-12-weeks until 30 March 2021. Patients completed a survey at inclusion regarding self-reported COVID-19-related anxiety and self-isolation.Results: A total of 622 patients [n = 475 with solid malignancies (SM), n = 147 with haematological malignancies (HM)], and 358 healthcare personnel were included. The seropositivity rate was lower for patients than for personnel; 10.5% for SM patients, 6.8% for HM patients, and 16.2% for personnel (p = 0.005). Strict adherence to self-isolation guidelines was reported by 54% of patients but was not associated with a lower risk of becoming seropositive [OR = 1.4 (0.8-2.5), p = 0.2]. High anxiety was expressed by 32% of patients, more often by SM patients than HM patients (34% vs 25% [OR = 1.6 (1.1-2.5, p = 0.03)]). Female gender [OR = 3.5 (2.4-5.2), p < 0.001] and being born outside of Europe [OR = 2.9 (1.4-6.4), p = 0.007] were both associated with high anxiety. Patients reporting high anxiety became seropositive to a similar degree as those with low anxiety [OR = 0.7 (0.3-1.2), p = 0.2]. HM patients with PCR-positive COVID-19 were more likely than SM patients to require oxygen therapy, including non-invasive ventilation/intubation (69% vs. 26%, p = 0.005).Conclusion: For Swedish patients on active cancer treatment, high self-assessed COVID-19-related anxiety or strict adherence to self-isolation guidelines were not associated with a lower risk of COVID-19. Patients with HM were less likely to develop serological antibody response after COVID-19 and were more likely to require advanced hospital care, but expressed less COVID-19-related anxiety than patients with SM.", "doi": "10.1080/0284186X.2023.2257873", "pmid": "37729083", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-11-16T12:20:43.626Z", "modified": "2023-11-16T12:20:43.691Z"}, {"entity": "publication", "iuid": "e335b68f25c64535bff7e2b859d6c729", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e335b68f25c64535bff7e2b859d6c729.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e335b68f25c64535bff7e2b859d6c729"}}, "title": "Ki67 and prostate specific antigen are prognostic in metastatic hormone na\u00efve prostate cancer.", "authors": [{"family": "Spyratou", "given": "Vasiliki", "initials": "V"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Bergh", "given": "Anders", "initials": "A"}, {"family": "Thellenberg-Karlsson", "given": "Camilla", "initials": "C"}, {"family": "Wikstr\u00f6m", "given": "Pernilla", "initials": "P"}, {"family": "Wel\u00e9n", "given": "Karin", "initials": "K", "orcid": "0000-0001-6480-636X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2212e6a5c0b844908cbce508027c2a54.json"}}, {"family": "Josefsson", "given": "Andreas", "initials": "A"}], "type": "journal article", "published": "2023-09-15", "journal": {"title": "Acta Oncol", "issn": "1651-226X", "pages": "1-9", "issn-l": "0284-186X"}, "abstract": "For metastatic hormone na\u00efve prostate cancer patients, androgen deprivation therapy (ADT) with escalation therapy including docetaxel and/or androgen targeting drugs is the standard therapy. However, de-escalation is preferable to avoid unnecessary side effects, especially from docetaxel, but markers to identify these patients are lacking. The purpose of the present study was to investigate the potential of PSA and Ki67 immunoreactive scores as prognostic and treatment-predictive markers.\n\nProstate biopsies from 92 patients with metastatic hormone na\u00efve PC (PSA > 80 ng/mL or clinical metastases) were immunohistochemically evaluated for PSA and Ki67. Gene expression analysis was performed with Clariom D microarrays to identify the phenotypic profile associated with the immunohistochemistry scores of biopsies. Cox regression analysis for progression free survival after ADT adjustment for age, ISUP, and serum PSA and Kaplan-Meier analyses were performed to assess prognostic values of Ki67, PSA, and the Ki67/PSA ratio.\n\nThe immunohistochemical score for PSA was the strongest prognostic factor for progression-free and overall survival after ADT. Consequently, the ratio between Ki67 and PSA displayed a stronger prognostic value than Ki67 itself. Further, mRNA expression data analysis showed an association between high Ki67/PSA ratio, cell-cycle regulation, and DNA damage repair. In an exploratory sub-analysis of 12 patients treated with early docetaxel as addition to ADT and matched controls, a high Ki67/PSA ratio showed potential to identify those who benefit from docetaxel.\n\nPSA and Ki67 immunoreactive scores are prognostic in the metastatic hormone-sensitive setting, with PSA being superior. The combination of Ki67 and PSA did not give additional prognostic value. The results suggest immunohistochemical scoring of PSA to have potential to improve identification of patients responding well to ADT alone.", "doi": "10.1080/0284186X.2023.2254480", "pmid": "37713321", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-11-16T12:13:26.712Z", "modified": "2023-11-16T12:13:26.751Z"}, {"entity": "publication", "iuid": "f9c4efe5667c4006a300f88f4274ea9f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9c4efe5667c4006a300f88f4274ea9f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9c4efe5667c4006a300f88f4274ea9f"}}, "title": "In vivo gene expression profile of Haemophilus influenzae during human pneumonia.", "authors": [{"family": "Polland", "given": "Linnea", "initials": "L", "orcid": "0000-0003-1912-265X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8181a22ea442432ea67839d6d5397f55.json"}}, {"family": "Ryd\u00e9n", "given": "Hanna", "initials": "H"}, {"family": "Su", "given": "Yi", "initials": "Y", "orcid": "0009-0001-4802-5210", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7f56487ba584ac5b08cfa6c06c6f7a6.json"}}, {"family": "Paulsson", "given": "Magnus", "initials": "M", "orcid": "0000-0003-1104-2727", "researcher": {"href": "https://publications.scilifelab.se/researcher/f833091b8f644a4ea2823034cb9220ca.json"}}], "type": "journal article", "published": "2023-09-14", "journal": {"title": "Microbiol Spectr", "issn": "2165-0497", "issn-l": null, "volume": "11", "issue": "5", "pages": "e0163923"}, "abstract": "Haemophilus influenzae is a major cause of community-acquired pneumonia. While studied extensively in various laboratory models, less is known about the cell function while inside the human lung. We present the first analysis of the global gene expression of H. influenzae while the bacteria are in the lung during pneumonia (in vivo conditions) and contrast it with bacterial isolates that have been cultured under standard laboratory conditions (in vitro conditions). Patients with pneumonia were recruited from emergency departments and intensive care units during 2018-2020 (n = 102). Lower respiratory samples were collected for bacterial culture and RNA extraction. Patient samples with H. influenzae (n = 8) and colonies from bacterial cultures (n = 6) underwent RNA sequencing. The reads were then pseudo-aligned to core and pan genomes created from 15 reference strains. While bacteria cultured in vitro clustered tightly by principal component analysis of core genome (n = 1067) gene expression, bacteria in the patient samples had more diverse transcriptomic signatures and did not group with their lab-cultured counterparts. In total, 328 core genes were significantly differentially expressed between in vitro and in vivo conditions. The most highly upregulated genes in vivo included tbpA and fbpA, which are involved in the acquisition of iron from transferrin, and the stress response gene msrAB. The biosynthesis of nucleotides/purines and molybdopterin-scavenging processes were also significantly enriched in vivo. In contrast, major metabolic pathways and iron-sequestering genes were downregulated under this condition. In conclusion, extensive transcriptomic differences were found between bacteria while in the human lung and bacteria that were cultured in vitro. IMPORTANCE The human-specific pathogen Haemophilus influenzae is generally not well suited for studying in animal models, and most laboratory models are unlikely to approximate the diverse environments encountered by bacteria in the human airways accurately. Thus, we have examined the global gene expression of H. influenzae during pneumonia. Extensive differences in the global gene expression profiles were found in H. influenzae while in the human lung compared to bacteria that were grown in the laboratory. In contrast, the gene expression profiles of isolates collected from different patients were found to cluster together when grown under the same laboratory conditions. Interesting observations were made of how H. influenzae acquires and uses iron and molybdate, endures oxidative stress, and regulates central metabolism while in the lung. Our results indicate important processes during infection and can guide future research on genes and pathways that are relevant in the pathogenesis of H. influenzae pneumonia.", "doi": "10.1128/spectrum.01639-23", "pmid": "37707456", "labels": {"Clinical Genomics Lund": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10581191"}], "notes": [], "created": "2023-11-21T19:14:53.780Z", "modified": "2024-11-15T10:17:47.196Z"}, {"entity": "publication", "iuid": "5815b34e01e64b45a0f6c2603917bb7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5815b34e01e64b45a0f6c2603917bb7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5815b34e01e64b45a0f6c2603917bb7e"}}, "title": "PLK1 as a cooperating partner for BCL2-mediated antiapoptotic program in leukemia.", "authors": [{"family": "Shah", "given": "Kinjal", "initials": "K"}, {"family": "Nasimian", "given": "Ahmad", "initials": "A"}, {"family": "Ahmed", "given": "Mehreen", "initials": "M", "orcid": "0000-0002-0422-2343", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba8dd2be2d5a469495a0abac5a597d61.json"}}, {"family": "Al Ashiri", "given": "Lina", "initials": "L"}, {"family": "Denison", "given": "Linn", "initials": "L"}, {"family": "Sime", "given": "Wondossen", "initials": "W", "orcid": "0000-0001-9518-2457", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b1353a0ded04eb88c564117345c556f.json"}}, {"family": "Bendak", "given": "Katerina", "initials": "K"}, {"family": "Kolosenko", "given": "Iryna", "initials": "I"}, {"family": "Siino", "given": "Valentina", "initials": "V"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b7add45d810457eb84a72aebbc7b82c.json"}}, {"family": "Palm-Apergi", "given": "Caroline", "initials": "C"}, {"family": "Massoumi", "given": "Ramin", "initials": "R"}, {"family": "Lock", "given": "Richard B", "initials": "RB"}, {"family": "Kazi", "given": "Julhash U", "initials": "JU", "orcid": "0000-0002-0719-5336", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b14748d011440488dc7d42da3a6c0f.json"}}], "type": "journal article", "published": "2023-09-07", "journal": {"title": "Blood Cancer J", "issn": "2044-5385", "volume": "13", "issue": "1", "pages": "139", "issn-l": "2044-5385"}, "abstract": "The deregulation of BCL2 family proteins plays a crucial role in leukemia development. Therefore, pharmacological inhibition of this family of proteins is becoming a prevalent treatment method. However, due to the emergence of primary and acquired resistance, efficacy is compromised in clinical or preclinical settings. We developed a drug sensitivity prediction model utilizing a deep tabular learning algorithm for the assessment of venetoclax sensitivity in T-cell acute lymphoblastic leukemia (T-ALL) patient samples. Through analysis of predicted venetoclax-sensitive and resistant samples, PLK1 was identified as a cooperating partner for the BCL2-mediated antiapoptotic program. This finding was substantiated by additional data obtained through phosphoproteomics and high-throughput kinase screening. Concurrent treatment using venetoclax with PLK1-specific inhibitors and PLK1 knockdown demonstrated a greater therapeutic effect on T-ALL cell lines, patient-derived xenografts, and engrafted mice compared with using each treatment separately. Mechanistically, the attenuation of PLK1 enhanced BCL2 inhibitor sensitivity through upregulation of BCL2L13 and PMAIP1 expression. Collectively, these findings underscore the dependency of T-ALL on PLK1 and postulate a plausible regulatory mechanism.", "doi": "10.1038/s41408-023-00914-7", "pmid": "37679323", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10484999"}, {"db": "pii", "key": "10.1038/s41408-023-00914-7"}], "notes": [], "created": "2023-09-27T06:59:53.705Z", "modified": "2023-09-27T06:59:53.911Z"}, {"entity": "publication", "iuid": "f7afab38bd424c0185c3ffb34ba09d6b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f7afab38bd424c0185c3ffb34ba09d6b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f7afab38bd424c0185c3ffb34ba09d6b"}}, "title": "An mTRAN-mRNA interaction mediates mitochondrial translation initiation in plants.", "authors": [{"family": "Tran", "given": "Huy Cuong", "initials": "HC", "orcid": "0000-0002-7670-2215", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf057352ae445079a2e9dc51b6326a7.json"}}, {"family": "Schmitt", "given": "Vivian", "initials": "V", "orcid": "0000-0001-9260-4853", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0a5170d13f44da38cd57fa9d14708c6.json"}}, {"family": "Lama", "given": "Sbatie", "initials": "S", "orcid": "0000-0003-0093-8915", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a6c32adfeea44ee97d6cdc08a90e6f7.json"}}, {"family": "Wang", "given": "Chuande", "initials": "C", "orcid": "0000-0002-3102-0931", "researcher": {"href": "https://publications.scilifelab.se/researcher/6858cc1751ec4393befbeea617c876f7.json"}}, {"family": "Launay-Avon", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-1993-313X", "researcher": {"href": "https://publications.scilifelab.se/researcher/483c9872afad41b6a916315884a1a7f1.json"}}, {"family": "Bernfur", "given": "Katja", "initials": "K", "orcid": "0000-0002-7927-9563", "researcher": {"href": "https://publications.scilifelab.se/researcher/4600cd5ea61b41e4ab9b85af90fb41b4.json"}}, {"family": "Sultan", "given": "Kristin", "initials": "K", "orcid": "0009-0002-5619-517X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7288f4347b8440479e0f908b705f9df5.json"}}, {"family": "Khan", "given": "Kasim", "initials": "K", "orcid": "0000-0001-7336-2764", "researcher": {"href": "https://publications.scilifelab.se/researcher/76561aa1400a457aa3aff29a105097f8.json"}}, {"family": "Brunaud", "given": "V\u00e9ronique", "initials": "V", "orcid": "0000-0002-6246-3161", "researcher": {"href": "https://publications.scilifelab.se/researcher/43f86a5a57ed40d09104ceb7563edc70.json"}}, {"family": "Liehrmann", "given": "Arnaud", "initials": "A", "orcid": "0000-0002-4936-1056", "researcher": {"href": "https://publications.scilifelab.se/researcher/17e728328c294053bafd99c21f861cbf.json"}}, {"family": "Castandet", "given": "Beno\u00eet", "initials": "B", "orcid": "0000-0003-1948-8651", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb78c62ee96e4a288be84f2cfb43e900.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b7add45d810457eb84a72aebbc7b82c.json"}}, {"family": "Rasmusson", "given": "Allan G", "initials": "AG", "orcid": "0000-0003-0734-5020", "researcher": {"href": "https://publications.scilifelab.se/researcher/9980e74c1d904c8f924e7e4298738c20.json"}}, {"family": "Mireau", "given": "Hakim", "initials": "H", "orcid": "0000-0002-2299-5139", "researcher": {"href": "https://publications.scilifelab.se/researcher/6af69c819fa94de6a4795daf00bf9e57.json"}}, {"family": "Delannoy", "given": "Etienne", "initials": "E", "orcid": "0000-0002-0866-2063", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9e67345f58e4739bd96805f89617b89.json"}}, {"family": "Van Aken", "given": "Olivier", "initials": "O", "orcid": "0000-0003-4024-968X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f8174aa4d9e4031822ea281b6f0f9dd.json"}}], "type": "journal article", "published": "2023-09-00", "journal": {"title": "Science", "issn": "1095-9203", "volume": "381", "issue": "6661", "pages": "eadg0995", "issn-l": "0036-8075"}, "abstract": "Plant mitochondria represent the largest group of respiring organelles on the planet. Plant mitochondrial messenger RNAs (mRNAs) lack Shine-Dalgarno-like ribosome-binding sites, so it is unknown how plant mitoribosomes recognize mRNA. We show that \"mitochondrial translation factors\" mTRAN1 and mTRAN2 are land plant-specific proteins, required for normal mitochondrial respiration chain biogenesis. Our studies suggest that mTRANs are noncanonical pentatricopeptide repeat (PPR)-like RNA binding proteins of the mitoribosomal \"small\" subunit. We identified conserved Adenosine (A)/Uridine (U)-rich motifs in the 5' regions of plant mitochondrial mRNAs. mTRAN1 binds this motif, suggesting that it is a mitoribosome homing factor to identify mRNAs. We demonstrate that mTRANs are likely required for translation of all plant mitochondrial mRNAs. Plant mitochondrial translation initiation thus appears to use a protein-mRNA interaction that is divergent from bacteria or mammalian mitochondria.", "doi": "10.1126/science.adg0995", "pmid": "37651534", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-09-27T06:59:56.729Z", "modified": "2023-09-27T06:59:57.550Z"}, {"entity": "publication", "iuid": "9fb879c926904883b9330093264e5427", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9fb879c926904883b9330093264e5427.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9fb879c926904883b9330093264e5427"}}, "title": "Inhibition of high level E2F in a RB1 proficient MYCN overexpressing chicken retinoblastoma model normalizes neoplastic behaviour.", "authors": [{"family": "Zhang", "given": "Hanzhao", "initials": "H"}, {"family": "Konjusha", "given": "Dardan", "initials": "D"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Tararuk", "given": "Tatsiana", "initials": "T"}, {"family": "Hallb\u00f6\u00f6k", "given": "Finn", "initials": "F"}], "type": "journal article", "published": "2023-08-22", "journal": {"title": "Cell Oncol (Dordr)", "issn": "2211-3436", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "Retinoblastoma, a childhood cancer, is most frequently caused by bi-allelic inactivation of RB1 gene. However, other oncogenic mutations such as MYCN amplification can induce retinoblastoma with proficient RB1. Previously, we established RB1-proficient MYCN-overexpressing retinoblastoma models both in human organoids and chicken. Here, we investigate the regulatory events in MYCN-induced retinoblastoma carcinogenesis based on the model in chicken.\r\n\r\nMYCN transformed retinal cells in culture were obtained from in vivo MYCN electroporated chicken embryo retina. The expression profiles were analysed by RNA sequencing. Chemical treatments, qRT-PCR, flow cytometry, immunohisto- and immunocytochemistry and western blot were applied to study the properties and function of these cells.\r\n\r\nThe expression profile of MYCN-transformed retinal cells in culture showed cone photoreceptor progenitor signature and robustly increased levels of E2Fs. This expression profile was consistently observed in long-term culture. Chemical treatments confirmed RB1 proficiency in these cells. The cells were insensitive to p53 activation but inhibition of E2f efficiently induced cell cycle arrest followed by apoptosis.\r\n\r\nIn conclusion, with proficient RB1, MYCN-induced high level of E2F expression dysregulates the cell cycle and contributes to retinoblastoma carcinogenesis. The increased level of E2f renders the cells to adopt a similar mechanistic phenotype to a RB1-deficient tumour.", "doi": "10.1007/s13402-023-00863-0", "pmid": "37606819", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s13402-023-00863-0"}], "notes": [], "created": "2023-11-02T09:10:58.573Z", "modified": "2024-01-16T13:48:32.442Z"}, {"entity": "publication", "iuid": "9c09757e502b4f28bedeb9e4e9f351d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c09757e502b4f28bedeb9e4e9f351d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c09757e502b4f28bedeb9e4e9f351d9"}}, "title": "Altered gut microbiota community structure and correlated immune system changes in dibutyl phthalate exposed mice.", "authors": [{"family": "Almamoun", "given": "Radwa", "initials": "R"}, {"family": "Pierozan", "given": "Paula", "initials": "P"}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L"}, {"family": "Karlsson", "given": "Oskar", "initials": "O"}], "type": "journal article", "published": "2023-08-05", "journal": {"title": "Ecotoxicol Environ Saf", "issn": "1090-2414", "volume": "262", "pages": "115321", "issn-l": null}, "abstract": "Di-n-butyl phthalate (DBP) is a ubiquitous environmental contaminant linked with various adverse health effects, including immune system dysfunction. Gut microbial dysbiosis can contribute to a wide range of pathogenesis, particularly immune disease. Here, we investigated the impact of DBP on the gut microbiome and examined correlations with immune system changes after five weeks oral exposure (10 or 100 mg/kg/day) in adult male mice. The fecal microbiome composition was characterized using 16S rRNA sequencing. DBP-treated mice displayed a significantly distinct microbial community composition, indicated by Bray-Curtis distance. Numerous amplicon sequence variants (ASVs) at the genus level were altered. Compared to the vehicle control group, the 10 mg/kg/day DBP group had 63 more abundant and 65 less abundant ASVs, while 60 ASVs were increased and 76 ASVs were decreased in the 100 mg/kg/day DBP group. Both DBP treatment groups showed higher abundances of ASVs assigned to Desulfovibrio (Proteobacteria phylum) and Enterorhabdus genera, while ASVs belonging to Parabacteroides, Lachnospiraceae UCG-006 and Lachnoclostridium were less common compared to the control group. Interestingly, an ASV belonging to Rumniniclostridium 6, which was less abundant in DBP-treated mice, demonstrated a negative correlation with the increased number of non-classical monocytes observed in the blood of DBP-treated animals. In addition, an ASV from Lachnospiraceae UCG-001, which was more abundant in the DBP-treated animals, showed a positive correlation with the non-classical monocyte increase. This study shows that DBP exposure greatly modifies the gut bacterial microbiome and indicates a potential contribution of microbial dysbiosis to DBP-induced immune system impairment, illustrating the importance of investigating how interactions between exposome components can affect health.", "doi": "10.1016/j.ecoenv.2023.115321", "pmid": "37549549", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0147-6513(23)00825-4"}], "notes": [], "created": "2023-08-16T13:14:28.168Z", "modified": "2024-01-16T13:48:32.526Z"}, {"entity": "publication", "iuid": "94f890155ce140bcbb88b88e967915d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/94f890155ce140bcbb88b88e967915d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/94f890155ce140bcbb88b88e967915d8"}}, "title": "An Okinawan-Based Nordic Diet Leads to Profound Effects on Gut Microbiota and Plasma Metabolites Linked to Glucose and Lipid Metabolism.", "authors": [{"family": "Manoharan", "given": "Lokeshwaran", "initials": "L", "orcid": "0000-0001-9751-5745", "researcher": {"href": "https://publications.scilifelab.se/researcher/000321fd81b9457db66140246bbd9066.json"}}, {"family": "Roth", "given": "Bodil", "initials": "B"}, {"family": "Bang", "given": "Corinna", "initials": "C"}, {"family": "Stenlund", "given": "Hans", "initials": "H", "orcid": "0000-0001-9943-296X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5259d6369f564651ace11d8bff689535.json"}}, {"family": "Ohlsson", "given": "Bodil", "initials": "B", "orcid": "0000-0002-9142-5244", "researcher": {"href": "https://publications.scilifelab.se/researcher/d61d0a97d7df49e5856419fc06769c23.json"}}], "type": "journal article", "published": "2023-07-24", "journal": {"title": "Nutrients", "issn": "2072-6643", "issn-l": "2072-6643", "volume": "15", "issue": "14", "pages": null}, "abstract": "Dietary interventions modify gut microbiota and clinical outcomes. Weight reduction and improved glucose and lipid homeostasis were observed after adopting an Okinawan-based Nordic diet (O-BN) in individuals with type 2 diabetes. The aim of the present study was to explore changes in metabolomics and gut microbiota during O-BN and correlate changes with clinical outcomes. A total of 30 patients (17 women), aged 57.5 \u00b1 8.2 years, diabetes duration 10.4 \u00b1 7.6 years, 90% over-weight, were included. Participants were provided an O-BN for 12 weeks. Before and after intervention, and 16 weeks afterwards, anthropometry and clinical data were estimated and questionnaires were collected, as well as samples of blood and stool. Plasma metabolomics were determined by gas- (GC-MS) or liquid- (LC-MS) chromatography-based mass spectrometry and fecal microbiota determination was based on 16S rRNA amplicons from regions V1-V2. During the intervention, weight (6.8%), waist circumference (6.1%), and levels of glucose, HbA1c, insulin, triglycerides, and cholesterol were decreased. Of 602 metabolites, 323 were changed for any or both periods; 199 (101 lipids) metabolites were decreased while 58 (43 lipids) metabolites were increased during the intervention. Changes in glucose homeostasis were linked to changes in, e.g., 1,5-anhydroglucitol, thyroxine, and chiro-inositol. Changes of microbe beta diversity correlated positively with food components and negatively with IL-18 (p = 0.045). Abundance differences at phylum and genus levels were found. Abundances of Actinobacteria, Bacteroidetes, Firmicutes, and Verrucomicrobia correlated with anthropometry, HbA1c, lipids, inflammation, and food. Changes in metabolites and microbiota were reversed after the intervention. The O-BN-induced changes in metabolomics and gut microbiota correspond to clinical outcomes of reduced weight and inflammation and improved glucose and lipid metabolism.", "doi": "10.3390/nu15143273", "pmid": "37513690", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Swedish Metabolomics Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10384944"}, {"db": "pii", "key": "nu15143273"}], "notes": [], "created": "2023-08-16T13:15:19.078Z", "modified": "2025-10-17T13:03:13.641Z"}, {"entity": "publication", "iuid": "5ce013509a834b4ea3ae487ebcc837c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5ce013509a834b4ea3ae487ebcc837c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5ce013509a834b4ea3ae487ebcc837c3"}}, "title": "Serum proteome profiles in patients treated with targeted temperature management after out-of-hospital cardiac arrest.", "authors": [{"family": "Lileikyte", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-6778-6269", "researcher": {"href": "https://publications.scilifelab.se/researcher/1499d28b68e544338790f7aa028027d0.json"}}, {"family": "Bakochi", "given": "Anahita", "initials": "A"}, {"family": "Ali", "given": "Ashfaq", "initials": "A"}, {"family": "Moseby-Knappe", "given": "Marion", "initials": "M"}, {"family": "Cronberg", "given": "Tobias", "initials": "T"}, {"family": "Friberg", "given": "Hans", "initials": "H"}, {"family": "Lilja", "given": "Gisela", "initials": "G"}, {"family": "Levin", "given": "Helena", "initials": "H"}, {"family": "\u00c5rman", "given": "Filip", "initials": "F"}, {"family": "Kjellstr\u00f6m", "given": "Sven", "initials": "S"}, {"family": "Dankiewicz", "given": "Josef", "initials": "J"}, {"family": "Hassager", "given": "Christian", "initials": "C"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Nielsen", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2023-07-17", "journal": {"title": "Intensive Care Med Exp", "issn": "2197-425X", "volume": "11", "issue": "1", "pages": "43", "issn-l": null}, "abstract": "Definition of temporal serum proteome profiles after out-of-hospital cardiac arrest may identify biological processes associated with severe hypoxia-ischaemia and reperfusion. It may further explore intervention effects for new mechanistic insights, identify candidate prognostic protein biomarkers and potential therapeutic targets. This pilot study aimed to investigate serum proteome profiles from unconscious patients admitted to hospital after out-of-hospital cardiac arrest according to temperature treatment and neurological outcome.\n\nSerum samples at 24, 48, and 72 h after cardiac arrest at three centres included in the Target Temperature Management after out-of-hospital cardiac arrest trial underwent data-independent acquisition mass spectrometry analysis (DIA-MS) to find changes in serum protein concentrations associated with neurological outcome at 6-month follow-up and targeted temperature management (TTM) at 33 \u00b0C as compared to 36 \u00b0C. Neurological outcome was defined according to Cerebral Performance Category (CPC) scale as \"good\" (CPC 1-2, good cerebral performance or moderate disability) or \"poor\" (CPC 3-5, severe disability, unresponsive wakefulness syndrome, or death).\n\nOf 78 included patients [mean age 66 \u00b1 12 years, 62 (80.0%) male], 37 (47.4%) were randomised to TTM at 36 \u00b0C. Six-month outcome was poor in 47 (60.3%) patients. The DIA-MS analysis identified and quantified 403 unique human proteins. Differential protein abundance testing comparing poor to good outcome showed 19 elevated proteins in patients with poor outcome (log2-fold change (FC) range 0.28-1.17) and 16 reduced proteins (log2(FC) between - 0.22 and - 0.68), involved in inflammatory/immune responses and apoptotic signalling pathways for poor outcome and proteolysis for good outcome. Analysis according to level of TTM showed a significant protein abundance difference for six proteins [five elevated proteins in TTM 36 \u00b0C (log2(FC) between 0.33 and 0.88), one reduced protein (log2(FC) - 0.6)] mainly involved in inflammatory/immune responses only at 48 h after cardiac arrest.\n\nSerum proteome profiling revealed an increase in inflammatory/immune responses and apoptosis in patients with poor outcome. In patients with good outcome, an increase in proteolysis was observed, whereas TTM-level only had a modest effect on the proteome profiles. Further validation of the differentially abundant proteins in response to neurological outcome is necessary to validate novel biomarker candidates that may predict prognosis after cardiac arrest.", "doi": "10.1186/s40635-023-00528-0", "pmid": "37455296", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10350448"}, {"db": "pii", "key": "10.1186/s40635-023-00528-0"}], "notes": [], "created": "2023-11-16T12:04:55.684Z", "modified": "2023-11-16T12:04:55.756Z"}, {"entity": "publication", "iuid": "b1ca32c9035c4f99ba117f53cb7df654", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1ca32c9035c4f99ba117f53cb7df654.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1ca32c9035c4f99ba117f53cb7df654"}}, "title": "SAG-RAD: A Method for Single-Cell Population Genomics of Unicellular Eukaryotes.", "authors": [{"family": "Gollnisch", "given": "Raphael", "initials": "R", "orcid": "0000-0001-6177-8877", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f78f6e8cacf4eba9104fbfd2ab26f66.json"}}, {"family": "Wallenius", "given": "Joel", "initials": "J"}, {"family": "Gribble", "given": "Kristin E", "initials": "KE"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Rengefors", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2023-05-02", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "40", "issue": "5", "pages": null}, "abstract": "Sequencing of reduced representation libraries enables genotyping of many individuals for population genomic studies. However, high amounts of DNA are required, and the method cannot be applied directly on single cells, preventing its use on most microbes. We developed and implemented the analysis of single amplified genomes followed by restriction-site-associated DNA sequencing to bypass labor-intensive culturing and to avoid culturing bias in population genomic studies of unicellular eukaryotes. This method thus opens the way for addressing important questions about the genetic diversity, gene flow, adaptation, dispersal, and biogeography of hitherto unexplored species.", "doi": "10.1093/molbev/msad095", "pmid": "37079883", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10202595"}, {"db": "pii", "key": "7133828"}], "notes": [], "created": "2023-05-24T12:59:17.974Z", "modified": "2024-01-16T13:48:33.441Z"}, {"entity": "publication", "iuid": "5344db944956481a84b2095e31dcc8be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5344db944956481a84b2095e31dcc8be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5344db944956481a84b2095e31dcc8be"}}, "title": "Characterization of the Mitochondrial Genetic Landscape in Abdominal Aortic Aneurysm.", "authors": [{"family": "Vats", "given": "Sakshi", "initials": "S", "orcid": "0000-0003-3419-6446", "researcher": {"href": "https://publications.scilifelab.se/researcher/af8ac632f4154dca88e58826ec866e60.json"}}, {"family": "Sundquist", "given": "Kristina", "initials": "K", "orcid": "0000-0001-8031-279X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2922bbc4c358426a8addc76424ae04d0.json"}}, {"family": "Li", "given": "Yanni", "initials": "Y"}, {"family": "Wang", "given": "Xiao", "initials": "X"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG", "orcid": "0000-0001-8603-8293", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d66c199ece143a6ab15222d8b55e3ea.json"}}, {"family": "Sundquist", "given": "Jan", "initials": "J", "orcid": "0000-0001-7228-5015", "researcher": {"href": "https://publications.scilifelab.se/researcher/308d053b6c3e472f960d353eeb87bd30.json"}}, {"family": "Zarrouk", "given": "Moncef", "initials": "M"}, {"family": "Gotts\u00e4ter", "given": "Anders", "initials": "A", "orcid": "0000-0003-0865-0000", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ed22ec8082248e986a9709c1521861f.json"}}, {"family": "Memon", "given": "Ashfaque A", "initials": "AA", "orcid": "0000-0002-1081-3553", "researcher": {"href": "https://publications.scilifelab.se/researcher/19670270fcaf4c878ca7d1063c696c04.json"}}], "type": "journal article", "published": "2023-04-18", "journal": {"title": "J Am Heart Assoc", "issn": "2047-9980", "volume": "12", "issue": "8", "pages": "e029248", "issn-l": "2047-9980"}, "abstract": "Background Abdominal aortic aneurysm (AAA) is a vascular disease with a mortality rate of >80% if ruptured. Mitochondrial dysfunction has been previously implicated in AAA pathogenesis. In this study, we aimed to characterize the mitochondrial genetic landscape in AAA. Methods and Results Whole mitochondrial genome sequencing and bioinformatics analysis were performed in comorbidity matched 48 cases without AAA and 48 cases with AAA, objectively diagnosed, and selected from a cohort of 65-year-old men recruited for a screening program. We identified differential mutational landscapes in men with and without AAA, with errors in mitochondrial DNA replication or repair as potential sources. Heteroplasmic insertions and overall heteroplasmy of structural rearrangements were significantly elevated in AAA cases. Three heteroplasmic variants were associated with risk factors of AAA: leukocyte concentration, plasma glucose, and cholesterol levels, respectively. Interestingly, mutations were more prevalent in regulatory part of the mitochondria, the displacement loop region, in AAA as compared with controls (P value <0.05), especially in the conserved and critical mitochondrial extended termination-associated sequence region. Moreover, we report a novel 24 bp mitochondrial DNA duplication present exclusively in cases with AAA (4%) and 75% of the unmatched AAA biopsies. Finally, the haplogroup cluster JTU was overrepresented in AAA and significantly associated with a positive family history of AAA (odds ratio, 2.9 [95% CI, 1.1-8.1]). Conclusions This is the first study investigating the mitochondrial genome in AAA, where important genetic alterations and haplogroups associated with AAA and clinical risk factors were identified. Our findings have the potential to fill in gaps in the missing genetic information on AAA.", "doi": "10.1161/JAHA.122.029248", "pmid": "37026541", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Affinity Proteomics Uppsala": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10227273"}], "notes": [], "created": "2023-05-17T07:17:15.312Z", "modified": "2023-11-29T19:15:25.793Z"}, {"entity": "publication", "iuid": "4371a4380e6d4e3294f5c4116411dd13", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4371a4380e6d4e3294f5c4116411dd13.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4371a4380e6d4e3294f5c4116411dd13"}}, "title": "Immune-interacting lymphatic endothelial subtype at capillary terminals drives lymphatic malformation.", "authors": [{"family": "Petkova", "given": "Milena", "initials": "M", "orcid": "0000-0002-7186-7256", "researcher": {"href": "https://publications.scilifelab.se/researcher/458b9dbc408c4118b97be343da8b3b49.json"}}, {"family": "Kraft", "given": "Marle", "initials": "M", "orcid": "0000-0002-3523-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bac6d144f4143b7ad9ad0a9058d95a0.json"}}, {"family": "Stritt", "given": "Simon", "initials": "S", "orcid": "0000-0002-4299-4934", "researcher": {"href": "https://publications.scilifelab.se/researcher/b561f8d6fb1a46d0ae76c66e440956a1.json"}}, {"family": "Martinez-Corral", "given": "Ines", "initials": "I", "orcid": "0000-0001-9194-2412", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f961131890c4422b8ce5a5d2d1f1dc9.json"}}, {"family": "Orts\u00e4ter", "given": "Henrik", "initials": "H", "orcid": "0000-0002-4046-4702", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f597cc7c8104728ae168db36a8ee9e7.json"}}, {"family": "Vanlandewijck", "given": "Michael", "initials": "M", "orcid": "0000-0002-0709-7808", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa2148fbafb44d59bd110e36bd77769c.json"}}, {"family": "Jakic", "given": "Bojana", "initials": "B", "orcid": "0000-0002-2339-5928", "researcher": {"href": "https://publications.scilifelab.se/researcher/31f0bb6137144060a45a40650aacadc7.json"}}, {"family": "Baselga", "given": "Eul\u00e0lia", "initials": "E", "orcid": "0000-0003-1086-8439", "researcher": {"href": "https://publications.scilifelab.se/researcher/12b835a79f01492e82d1280c8050e01b.json"}}, {"family": "Castillo", "given": "Sandra D", "initials": "SD", "orcid": "0000-0002-7007-3155", "researcher": {"href": "https://publications.scilifelab.se/researcher/de3d0367a9d8474197f66365c1b5c040.json"}}, {"family": "Graupera", "given": "Mariona", "initials": "M", "orcid": "0000-0003-4608-4185", "researcher": {"href": "https://publications.scilifelab.se/researcher/76ead57229884f90bff307099a9a70ea.json"}}, {"family": "Betsholtz", "given": "Christer", "initials": "C", "orcid": "0000-0002-8494-971X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a00cfe9d521047f280978d84d7dcf1b3.json"}}, {"family": "M\u00e4kinen", "given": "Taija", "initials": "T", "orcid": "0000-0002-9338-1257", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf99a0589d1f4532b532bfc575edaada.json"}}], "type": "journal article", "published": "2023-04-03", "journal": {"title": "J. Exp. Med.", "issn": "1540-9538", "volume": "220", "issue": "4", "issn-l": "0022-1007"}, "abstract": "Oncogenic mutations in PIK3CA, encoding p110\u03b1-PI3K, are a common cause of venous and lymphatic malformations. Vessel type-specific disease pathogenesis is poorly understood, hampering development of efficient therapies. Here, we reveal a new immune-interacting subtype of Ptx3-positive dermal lymphatic capillary endothelial cells (iLECs) that recruit pro-lymphangiogenic macrophages to promote progressive lymphatic overgrowth. Mouse model of Pik3caH1047R-driven vascular malformations showed that proliferation was induced in both venous and lymphatic ECs but sustained selectively in LECs of advanced lesions. Single-cell transcriptomics identified the iLEC population, residing at lymphatic capillary terminals of normal vasculature, that was expanded in Pik3caH1047R mice. Expression of pro-inflammatory genes, including monocyte/macrophage chemokine Ccl2, in Pik3caH1047R-iLECs was associated with recruitment of VEGF-C-producing macrophages. Macrophage depletion, CCL2 blockade, or anti-inflammatory COX-2 inhibition limited Pik3caH1047R-driven lymphangiogenesis. Thus, targeting the paracrine crosstalk involving iLECs and macrophages provides a new therapeutic opportunity for lymphatic malformations. Identification of iLECs further indicates that peripheral lymphatic vessels not only respond to but also actively orchestrate inflammatory processes.", "doi": "10.1084/jem.20220741", "pmid": "36688917", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9884640"}, {"db": "pii", "key": "213817"}], "notes": [], "created": "2023-11-16T12:40:26.995Z", "modified": "2024-01-16T13:48:33.714Z"}, {"entity": "publication", "iuid": "78254efb050a487a851142670d335532", "links": {"self": {"href": "https://publications.scilifelab.se/publication/78254efb050a487a851142670d335532.json"}, "display": {"href": "https://publications.scilifelab.se/publication/78254efb050a487a851142670d335532"}}, "title": "Microbial gene activity in straw residue amendments reveals carbon sequestration mechanisms in agricultural soils", "authors": [{"family": "Kozjek", "given": "Katja", "initials": "K", "orcid": "0000-0001-9381-7447", "researcher": {"href": "https://publications.scilifelab.se/researcher/89d979db71154d31af52f3e739a538a1.json"}}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L", "orcid": "0000-0001-9751-5745", "researcher": {"href": "https://publications.scilifelab.se/researcher/000321fd81b9457db66140246bbd9066.json"}}, {"family": "Urich", "given": "Tim", "initials": "T"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Hedlund", "given": "Katarina", "initials": "K"}], "type": "journal-article", "published": "2023-04-00", "journal": {"title": "Soil Biology and Biochemistry", "issn": "0038-0717", "volume": "179", "pages": "108994", "issn-l": null}, "abstract": null, "doi": "10.1016/j.soilbio.2023.108994", "pmid": null, "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-08-16T13:19:05.075Z", "modified": "2024-01-16T13:48:33.723Z"}, {"entity": "publication", "iuid": "9da6c0d047504eb782424ed88f7af2d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9da6c0d047504eb782424ed88f7af2d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9da6c0d047504eb782424ed88f7af2d1"}}, "title": "Analysis of human lung mast cells by single cell RNA sequencing.", "authors": [{"family": "R\u00f6nnberg", "given": "Elin", "initials": "E"}, {"family": "Ravindran", "given": "Avinash", "initials": "A"}, {"family": "Mazzurana", "given": "Luca", "initials": "L"}, {"family": "Gong", "given": "Yitao", "initials": "Y"}, {"family": "S\u00e4fholm", "given": "Jesper", "initials": "J"}, {"family": "Lorent", "given": "Julie", "initials": "J"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Orre", "given": "Ann-Charlotte", "initials": "AC"}, {"family": "Al-Ameri", "given": "Mamdoh", "initials": "M"}, {"family": "Adner", "given": "Mikael", "initials": "M"}, {"family": "Dahl\u00e9n", "given": "Sven-Erik", "initials": "SE"}, {"family": "Dahlin", "given": "Joakim S", "initials": "JS"}, {"family": "Mj\u00f6sberg", "given": "Jenny", "initials": "J"}, {"family": "Nilsson", "given": "Gunnar", "initials": "G"}], "type": "journal article", "published": "2023-03-30", "journal": {"title": "Front Immunol", "issn": "1664-3224", "issn-l": "1664-3224", "volume": "14", "issue": null, "pages": "1151754"}, "abstract": "Mast cells are tissue-resident cells playing major roles in homeostasis and disease conditions. Lung mast cells are particularly important in airway inflammatory diseases such as asthma. Human mast cells are classically divided into the subsets MCT and MCTC, where MCT express the mast cell protease tryptase and MCTC in addition express chymase, carboxypeptidase A3 (CPA3) and cathepsin G. Apart from the disctintion of the MCT and MCTC subsets, little is known about the heterogeniety of human lung mast cells and a deep analysis of their heterogeniety has previously not been performed. We therefore performed single cell RNA sequencing on sorted human lung mast cells using SmartSeq2. The mast cells showed high expression of classical mast cell markers. The expression of several individual genes varied considerably among the cells, however, no subpopulations were detected by unbiased clustering. Variable genes included the protease-encoding transcripts CMA1 (chymase) and CTSG (cathepsin G). Human lung mast cells are predominantly of the MCT subset and consistent with this, the expression of CMA1 was only detectable in a small proportion of the cells, and correlated moderately to CTSG. However, in contrast to established data for the protein, CPA3 mRNA was high in all cells and the correlation of CPA3 to CMA1 was weak.", "doi": "10.3389/fimmu.2023.1151754", "pmid": "37063885", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10100501"}], "notes": [], "created": "2023-04-21T12:24:24.121Z", "modified": "2024-01-16T13:48:33.785Z"}, {"entity": "publication", "iuid": "b497203a64f24a21b4e18fc5c671604c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b497203a64f24a21b4e18fc5c671604c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b497203a64f24a21b4e18fc5c671604c"}}, "title": "Serum immuno-oncology markers carry independent prognostic information in patients with newly diagnosed metastatic breast cancer, from a prospective observational study.", "authors": [{"family": "Gunnarsdottir", "given": "Frida Bj\u00f6rk", "initials": "FB"}, {"family": "Bendahl", "given": "P\u00e4r-Ola", "initials": "PO"}, {"family": "Johansson", "given": "Alexandra", "initials": "A"}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Ryd\u00e9n", "given": "Lisa", "initials": "L"}, {"family": "Bergenfelz", "given": "Caroline", "initials": "C"}, {"family": "Larsson", "given": "Anna-Maria", "initials": "AM"}], "type": "observational study", "published": "2023-03-21", "journal": {"title": "Breast Cancer Res.", "issn": "1465-542X", "volume": "25", "issue": "1", "pages": "29", "issn-l": "1465-5411"}, "abstract": "Metastatic breast cancer (MBC) is a challenging disease, and despite new therapies, prognosis is still poor for a majority of patients. There is a clinical need for improved prognostication where immuno-oncology markers can provide important information. The aim of this study was to evaluate serum immuno-oncology markers in MBC patients and their respective relevance for prediction of survival.\n\nWe investigated a broad panel of 92 immuno-oncology proteins in serum from 136 MBC patients included in a prospective observational study (NCT01322893) with long-term follow-up. Serum samples were collected before start of systemic therapy and analyzed using multiplex proximity extension assay (Olink Target 96 Immuno-Oncology panel). Multiple machine learning techniques were used to identify serum markers with highest importance for prediction of overall and progression-free survival (OS and PFS), and associations to survival were further evaluated using Cox regression analyses. False discovery rate was then used to adjust for multiple comparisons.\n\nUsing random forest and random survival forest analyses, we identified the top nine and ten variables of highest predictive importance for OS and PFS, respectively. Cox regression analyses revealed significant associations (P < 0.005) of higher serum levels of IL-8, IL-10 and CAIX with worse OS in multivariable analyses, adjusted for established clinical prognostic factors including circulating tumor cells (CTCs). Similarly, high serum levels of IL-8, IL-10, ADA and CASP8 significantly associated with worse PFS. Interestingly, high serum levels of FasL significantly associated with improved OS and PFS. In addition, CSF-1, IL-6, MUC16, TFNSFR4 and CD244 showed suggestive evidence (P < 0.05) for an association to survival in multivariable analyses. After correction for multiple comparisons, IL-8 still showed strong evidence for correlation to survival.\n\nTo conclude, we found six serum immuno-oncology markers that were significantly associated with OS and/or PFS in MBC patients, independently of other established prognostic factors including CTCs. Furthermore, an additional five serum immuno-oncology markers provided suggestive evidence for an independent association to survival. These findings highlight the relevance of immuno-oncology serum markers in MBC patients and support their usefulness for improved prognostication. Trial registration Clinical Trials (NCT01322893), registered March 25, 2011.", "doi": "10.1186/s13058-023-01631-6", "pmid": "36945037", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10031935"}, {"db": "pii", "key": "10.1186/s13058-023-01631-6"}, {"db": "ClinicalTrials.gov", "key": "NCT01322893"}], "notes": [], "created": "2023-04-12T12:40:50.720Z", "modified": "2023-04-12T12:40:50.722Z"}, {"entity": "publication", "iuid": "f704885669b14245bda026f2c18aafbf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f704885669b14245bda026f2c18aafbf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f704885669b14245bda026f2c18aafbf"}}, "title": "Gut Micro- and Mycobiota in Preeclampsia: Bacterial Composition Differences Suggest Role in Pathophysiology.", "authors": [{"family": "Meijer", "given": "Sofie", "initials": "S"}, {"family": "Pasquinelli", "given": "Elena", "initials": "E"}, {"family": "Renzi", "given": "Sonia", "initials": "S", "orcid": "0000-0002-0450-106X", "researcher": {"href": "https://publications.scilifelab.se/researcher/09e86deefd4e473596355f4099c08372.json"}}, {"family": "Lavasani", "given": "Shahram", "initials": "S", "orcid": "0000-0003-4922-9351", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c1b4da101d048ff874161c07bc98e6d.json"}}, {"family": "Nouri", "given": "Mehrnaz", "initials": "M"}, {"family": "Erlandsson", "given": "Lena", "initials": "L", "orcid": "0000-0003-4350-5909", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cb64013c9ec4577939b05f36a7286de.json"}}, {"family": "Cavalieri", "given": "Duccio", "initials": "D"}, {"family": "Hansson", "given": "Stefan R", "initials": "SR", "orcid": "0000-0002-7838-9074", "researcher": {"href": "https://publications.scilifelab.se/researcher/36d2357ed19142279abdedd8a17583ea.json"}}], "type": "journal article", "published": "2023-02-10", "journal": {"title": "Biomolecules", "issn": "2218-273X", "issn-l": null, "volume": "13", "issue": "2", "pages": null}, "abstract": "Preeclampsia is a severe pregnancy-related inflammatory disease without an effective treatment. The pathophysiology remains partly unknown. However, an increased inflammatory response and oxidative stress are part of the maternal systemic reaction. Recent data have suggested that dysbiosis of the gut microbiome plays a role in preeclampsia as well as other inflammatory diseases. However, dysbiosis in preeclampsia has not been studied in a Scandinavian population. Furthermore, although the fungal flora may also have anti-inflammatory properties, it has never been studied in preeclampsia. We included 25 preeclamptic and 29 healthy third-trimester women for the ITS and 16S sequencing of fungal and bacterial microbiota, respectively. Calprotectin was measured to assess systemic and intestinal inflammatory responses. The fungal diversity differed with BMI and gestational length, suggesting a link between fungi and the immune changes seen in pregnancy. An LEfSe analysis showed 18 significantly differentially abundant bacterial taxa in PE, including enriched Bacteroidetes and depleted Verrucomicrobia and Syntergistota at the phylum level and depleted Akkermansia at the genus level, suggesting a role in the pathophysiology of PE.", "doi": "10.3390/biom13020346", "pmid": "36830715", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9953204"}, {"db": "pii", "key": "biom13020346"}], "notes": [], "created": "2025-11-21T12:33:22.878Z", "modified": "2025-11-21T12:33:40.893Z"}, {"entity": "publication", "iuid": "402524da476a4884a9495be39fc7f50c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/402524da476a4884a9495be39fc7f50c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/402524da476a4884a9495be39fc7f50c"}}, "title": "Larval transcriptomes reflect the evolutionary history of plant-insect associations.", "authors": [{"family": "de la Paz Celorio-Mancera", "given": "Maria", "initials": "M", "orcid": "0000-0003-0296-0577", "researcher": {"href": "https://publications.scilifelab.se/researcher/2abfa65f99b44f1ba6f8f0e6f3d7d8a4.json"}}, {"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}}, {"family": "Pruisscher", "given": "Peter", "initials": "P"}, {"family": "Smialowska", "given": "Agata", "initials": "A"}, {"family": "Pires Braga", "given": "Mariana", "initials": "M", "orcid": "0000-0002-1253-2536", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab296645778b4d97959314bf28c8209a.json"}}, {"family": "Janz", "given": "Niklas", "initials": "N"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.json"}}, {"family": "Nylin", "given": "S\u00f6ren", "initials": "S"}], "type": "journal article", "published": "2023-02-04", "journal": {"title": "Evolution", "issn": "1558-5646", "volume": "77", "issue": "2", "pages": "519-533", "issn-l": "0014-3820"}, "abstract": "In this study, we investigated whether patterns of gene expression in larvae feeding on different plants can explain important aspects of the evolution of insect-plant associations, such as phylogenetic conservatism of host use and re-colonization of ancestral hosts that have been lost from the host repertoire. To this end, we performed a phylogenetically informed study comparing the transcriptomes of 4 nymphalid butterfly species in Polygonia and the closely related genus Nymphalis. Larvae were reared on Urtica dioica, Salix spp., and Ribes spp. Plant-specific gene expression was found to be similar across butterfly species, even in the case of host plants that are no longer used by two of the butterfly species. These results suggest that plant-specific transcriptomes can be robust over evolutionary time. We propose that adaptations to particular larval food plants can profitably be understood as an evolved set of modules of co-expressed genes, promoting conservatism in host use and facilitating re-colonization. Moreover, we speculate that the degree of overlap between plant-specific transcriptomes may correlate with the strength of trade-offs between plants as resources and hence to the probability of colonizing hosts and complete host shifts.", "doi": "10.1093/evolut/qpac049", "pmid": "36625474", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6881564"}], "notes": [], "created": "2023-05-17T08:45:56.948Z", "modified": "2024-01-16T13:48:33.977Z"}, {"entity": "publication", "iuid": "734914bad3564337bca7bf350f0924cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/734914bad3564337bca7bf350f0924cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/734914bad3564337bca7bf350f0924cd"}}, "title": "Immune gene expression in the mosquito vector Culex quinquefasciatus during an avian malaria infection", "authors": [{"family": "Garc\u00eda\u2010Longoria", "given": "Luz", "initials": "L", "orcid": "0000-0002-2589-5379", "researcher": {"href": "https://publications.scilifelab.se/researcher/96e4458356cc4ef99891ddc93ca32152.json"}}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D", "orcid": "0000-0003-4713-0032", "researcher": {"href": "https://publications.scilifelab.se/researcher/d634886b77ad4331916bebc0a3b8b0e3.json"}}, {"family": "Berthomieu", "given": "Arnaud", "initials": "A", "orcid": "0000-0003-0931-667X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b6ee5cb65c341059521186688507bb7.json"}}, {"family": "Kalbskopf", "given": "Victor", "initials": "V", "orcid": "0000-0001-7918-8883", "researcher": {"href": "https://publications.scilifelab.se/researcher/e479796b940c4cb7a35bc8b65329007d.json"}}, {"family": "Rivero", "given": "Ana", "initials": "A", "orcid": "0000-0002-7056-5846", "researcher": {"href": "https://publications.scilifelab.se/researcher/0edaac3fe9a54a5cbe6460f753f7cf9c.json"}}, {"family": "Hellgren", "given": "Olof", "initials": "O", "orcid": "0000-0002-4062-7276", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bca3b673a2447ecbc55eaf9edf56a02.json"}}], "type": "journal-article", "published": "2023-02-00", "journal": {"title": "Mol Ecol", "issn": "0962-1083", "issn-l": "0962-1083", "volume": "32", "issue": "4", "pages": "904-919"}, "abstract": null, "doi": "10.1111/mec.16799", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2022-11-25T08:16:35.901Z", "modified": "2024-01-19T12:37:03.506Z"}, {"entity": "publication", "iuid": "af6252a9803047d2a058d0bd90c207d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af6252a9803047d2a058d0bd90c207d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af6252a9803047d2a058d0bd90c207d9"}}, "title": "Identification of biomarkers and outcomes of endocrine disruption in human ovarian cortex using In Vitro Models.", "authors": [{"family": "Li", "given": "Tianyi", "initials": "T"}, {"family": "Vazakidou", "given": "Paraskevi", "initials": "P"}, {"family": "Leonards", "given": "Pim E G", "initials": "PEG"}, {"family": "Damdimopoulos", "given": "Anastasios", "initials": "A"}, {"family": "Panagiotou", "given": "Eleftheria Maria", "initials": "EM"}, {"family": "Arnelo", "given": "Catarina", "initials": "C"}, {"family": "Jansson", "given": "Kerstin", "initials": "K"}, {"family": "Pettersson", "given": "Karin", "initials": "K"}, {"family": "Papaikonomou", "given": "Kiriaki", "initials": "K"}, {"family": "van Duursen", "given": "Majorie", "initials": "M"}, {"family": "Damdimopoulou", "given": "Pauliina", "initials": "P"}], "type": "journal article", "published": "2023-02-00", "journal": {"title": "Toxicology", "issn": "1879-3185", "volume": "485", "pages": "153425", "issn-l": null}, "abstract": "Endocrine disrupting chemicals (EDCs) are raising concerns about adverse effects on fertility in women. However, there is a lack of information regarding mechanisms and effects in humans. Our study aims to identify mechanisms of endocrine disruption using two EDCs, diethylstilbestrol (DES) and ketoconazole (KTZ)1. Human ovarian cortical tissue obtained from Caesarean section patients was exposed to 10-9 M - 10-5 M KTZ and 10-10 M - 10-6 M DES in vitro for 6 days. Follicle survival and growth were studied via histology analysis and liquid-chromatography-mass spectrometry-based steroid quantification. RNA-sequencing was performed on COV434, KGN, and primary ovarian cells that were exposed for 24 h. Significantly lower unilaminar follicle densities were observed in DES 10-10 M group, whereas low KTZ exposure reduced secondary follicle density. KTZ 10-5 M reduced levels of pregnenolone and progesterone. RNA-sequencing revealed that 445 and 233 differentially expressed genes (false discovery rate < 0.1) altogether in DES and KTZ exposed groups. Gene set variation analysis showed that both chemicals modulated pathways that are important for folliculogenesis and steroidogenesis. We selected stearoyl-CoA desaturase (SCD) and 7-dehydrocholesterol reductase (DHCR7) for further validation. Up-regulation of both genes in response to KTZ was confirmed by qPCR and in situ RNA hybridization. Further validation with immunofluorescence focused on the expression of SCD in growing follicles in exposed ovarian tissue. In conclusion, SCD may serve as a potential novel human-relevant biomarker of EDC exposure and effects on ovaries.", "doi": "10.1016/j.tox.2023.153425", "pmid": "36621641", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0300-483X(23)00010-0"}], "notes": [], "created": "2023-12-01T13:21:44.238Z", "modified": "2023-12-01T13:21:44.241Z"}, {"entity": "publication", "iuid": "818ae71d23b34d728f0d3eb5a1db3dde", "links": {"self": {"href": "https://publications.scilifelab.se/publication/818ae71d23b34d728f0d3eb5a1db3dde.json"}, "display": {"href": "https://publications.scilifelab.se/publication/818ae71d23b34d728f0d3eb5a1db3dde"}}, "title": "Cerebellar granule neurons induce Cyclin D1 before the onset of motor symptoms in Huntington's disease mice.", "authors": [{"family": "Bauer", "given": "Susanne", "initials": "S"}, {"family": "Chen", "given": "Chwen-Yu", "initials": "CY"}, {"family": "Jonson", "given": "Maria", "initials": "M"}, {"family": "Kaczmarczyk", "given": "Lech", "initials": "L"}, {"family": "Magadi", "given": "Srivathsa Subramanya", "initials": "SS"}, {"family": "Jackson", "given": "Walker S", "initials": "WS", "orcid": "0000-0002-3003-5509", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f49c7978954d098514c5b1bfa9e34b.json"}}], "type": "journal article", "published": "2023-01-20", "journal": {"title": "Acta Neuropathol Commun", "issn": "2051-5960", "volume": "11", "issue": "1", "pages": "17", "issn-l": "2051-5960"}, "abstract": "Although Huntington's disease (HD) is classically defined by the selective vulnerability of striatal projection neurons, there is increasing evidence that cerebellar degeneration modulates clinical symptoms. However, little is known about cell type-specific responses of cerebellar neurons in HD. To dissect early disease mechanisms in the cerebellum and cerebrum, we analyzed translatomes of neuronal cell types from both regions in a new HD mouse model. For this, HdhQ200 knock-in mice were backcrossed with the calm 129S4 strain, to constrain experimental noise caused by variable hyperactivity of mice in a C57BL/6 background. Behavioral and neuropathological characterization showed that these S4-HdhQ200 mice had very mild behavioral abnormalities starting around 12 months of age that remained mild up to 18 months. By 9 months, we observed abundant Huntingtin-positive neuronal intranuclear inclusions (NIIs) in the striatum and cerebellum. The translatome analysis of GABAergic cells of the cerebrum further confirmed changes typical of HD-induced striatal pathology. Surprisingly, we observed the strongest response with 626 differentially expressed genes in glutamatergic neurons of the cerebellum, a population consisting primarily of granule cells, commonly considered disease resistant. Our findings suggest vesicular fusion and exocytosis, as well as differentiation-related pathways are affected in these neurons. Furthermore, increased expression of cyclin D1 (Ccnd1) in the granular layer and upregulated expression of polycomb group complex protein genes and cell cycle regulators Cbx2, Cbx4 and Cbx8 point to a putative role of aberrant cell cycle regulation in cerebellar granule cells in early disease.", "doi": "10.1186/s40478-022-01500-x", "pmid": "36670467", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9854201"}, {"db": "pii", "key": "10.1186/s40478-022-01500-x"}], "notes": [], "created": "2023-12-01T13:21:09.700Z", "modified": "2024-01-16T13:48:34.107Z"}, {"entity": "publication", "iuid": "d2e4fe5fe1f44218a1d65838b6bfb69a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d2e4fe5fe1f44218a1d65838b6bfb69a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d2e4fe5fe1f44218a1d65838b6bfb69a"}}, "title": "Single-cell analysis of myeloid cells in HPV+ tonsillar cancer.", "authors": [{"family": "Jimenez", "given": "David Gomez", "initials": "DG"}, {"family": "Altunbulakli", "given": "Can", "initials": "C"}, {"family": "Swoboda", "given": "Sabine", "initials": "S"}, {"family": "Sobti", "given": "Aastha", "initials": "A"}, {"family": "Askmyr", "given": "David", "initials": "D"}, {"family": "Ali", "given": "Ashfaq", "initials": "A"}, {"family": "Greiff", "given": "Lennart", "initials": "L"}, {"family": "Lindstedt", "given": "Malin", "initials": "M"}], "type": "journal article", "published": "2023-01-19", "journal": {"title": "Front Immunol", "issn": "1664-3224", "issn-l": "1664-3224", "volume": "13", "issue": null, "pages": "1087843"}, "abstract": "The incidence of human papillomavirus-positive (HPV+) tonsillar cancer has been sharply rising during the last decades. Myeloid cells represent an appropriate therapeutic target due to their proximity to virus-infected tumor cells, and their ability to orchestrate antigen-specific immunity, within the tonsil. However, the interrelationship of steady-state and inflammatory myeloid cell subsets, and their impact on patient survival remains unexplored. Here, we used single-cell RNA-sequencing to map the myeloid compartment in HPV+ tonsillar cancer. We observed an expansion of the myeloid compartment in HPV+ tonsillar cancer, accompanied by interferon-induced cellular responses both in dendritic cells (DCs) and monocyte-macrophages. Our analysis unveiled the existence of four DC lineages, two macrophage polarization processes, and their sequential maturation profiles. Within the DC lineages, we described a balance shift in the frequency of progenitor and mature cDC favoring the cDC1 lineage in detriment of cDC2s. Furthermore, we observed that all DC lineages apart from DC5s matured into a common activated DC transcriptional program involving upregulation of interferon-inducible genes. In turn, the monocyte-macrophage lineage was subjected to early monocyte polarization events, which give rise to either interferon-activated or CXCL-producing macrophages, the latter enriched in advanced tumor stages. We validated the existence of most of the single-cell RNA-seq clusters using 26-plex flow cytometry, and described a positive impact of cDC1 and interferon-activated DCs and macrophages on patient survival using gene signature scoring. The current study contributes to the understanding of myeloid ontogeny and dynamics in HPV-driven tonsillar cancer, and highlights myeloid biomarkers that can be used to assess patient prognosis.", "doi": "10.3389/fimmu.2022.1087843", "pmid": "36741389", "labels": {"Clinical Genomics Lund": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9893928"}], "notes": [], "created": "2023-02-20T13:50:15.982Z", "modified": "2023-06-02T11:49:44.196Z"}, {"entity": "publication", "iuid": "d9528bf8ef3e42c590e45cc2d0baf8ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9528bf8ef3e42c590e45cc2d0baf8ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9528bf8ef3e42c590e45cc2d0baf8ac"}}, "title": "GotEnzymes: an extensive database of enzyme parameter predictions.", "authors": [{"family": "Li", "given": "Feiran", "initials": "F", "orcid": "0000-0001-9155-5260", "researcher": {"href": "https://publications.scilifelab.se/researcher/249bec020dae419caad38538e87331f2.json"}}, {"family": "Chen", "given": "Yu", "initials": "Y", "orcid": "0000-0003-3326-9068", "researcher": {"href": "https://publications.scilifelab.se/researcher/36c1db44b0634b5ea85f45a5dba020e7.json"}}, {"family": "Anton", "given": "Mihail", "initials": "M"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2023-01-06", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "51", "issue": "D1", "pages": "D583-D586", "issn-l": "0305-1048"}, "abstract": "Enzyme parameters are essential for quantitatively understanding, modelling, and engineering cells. However, experimental measurements cover only a small fraction of known enzyme-compound pairs in model organisms, much less in other organisms. Artificial intelligence (AI) techniques have accelerated the pace of exploring enzyme properties by predicting these in a high-throughput manner. Here, we present GotEnzymes, an extensive database with enzyme parameter predictions by AI approaches, which is publicly available at https://metabolicatlas.org/gotenzymes for interactive web exploration and programmatic access. The first release of this data resource contains predicted turnover numbers of over 25.7 million enzyme-compound pairs across 8099 organisms. We believe that GotEnzymes, with the readily-predicted enzyme parameters, would bring a speed boost to biological research covering both experimental and computational fields that involve working with candidate enzymes.", "doi": "10.1093/nar/gkac831", "pmid": "36169223", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Support and Infrastructure": "Collaborative", "Systems Biology": "Technology development", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9825421"}, {"db": "pii", "key": "6725766"}], "notes": [], "created": "2022-11-25T08:13:46.214Z", "modified": "2023-05-17T11:36:45.867Z"}, {"entity": "publication", "iuid": "61e6bc05d92f4403aba21ee521531b70", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61e6bc05d92f4403aba21ee521531b70.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61e6bc05d92f4403aba21ee521531b70"}}, "title": "ASV portal: an interface to DNA-based biodiversity data in the Living Atlas.", "authors": [{"family": "Prager", "given": "Maria", "initials": "M", "orcid": "0000-0003-4897-8422", "researcher": {"href": "https://publications.scilifelab.se/researcher/4edcc39683ae4adb9f8000321271ae44.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Ronquist", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3929-251X", "researcher": {"href": "https://publications.scilifelab.se/researcher/440662f277ea4756a08a7f5925b3f485.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2023-01-05", "journal": {"title": "BMC Bioinformatics", "issn": "1471-2105", "volume": "24", "issue": "1", "pages": "6", "issn-l": "1471-2105"}, "abstract": "The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited functionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Amplicon Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas.\n\nThe ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure.\n\nThe ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.", "doi": "10.1186/s12859-022-05120-z", "pmid": "36604610", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9817246"}, {"db": "pii", "key": "10.1186/s12859-022-05120-z"}], "notes": [], "created": "2023-11-23T14:14:28.588Z", "modified": "2023-11-23T14:14:28.644Z"}, {"entity": "publication", "iuid": "18d1940c083c4e4780bea26c0c4df967", "links": {"self": {"href": "https://publications.scilifelab.se/publication/18d1940c083c4e4780bea26c0c4df967.json"}, "display": {"href": "https://publications.scilifelab.se/publication/18d1940c083c4e4780bea26c0c4df967"}}, "title": "Experimental Life History Evolution Results in Sex-specific Evolution of Gene Expression in Seed Beetles.", "authors": [{"family": "Immonen", "given": "Elina", "initials": "E", "orcid": "0000-0003-1121-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6c9af5588c64dfdacba192b65524d43.json"}}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Stojkovi\u0107", "given": "Biljana", "initials": "B"}, {"family": "Savkovi\u0107", "given": "Uro\u0161", "initials": "U"}, {"family": "\u0110or\u0111evi\u0107", "given": "Mirko", "initials": "M"}, {"family": "Liljestrand-R\u00f6nn", "given": "Johanna", "initials": "J"}, {"family": "Wiberg", "given": "R Axel W", "initials": "RAW"}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f.json"}}], "type": "journal article", "published": "2023-01-04", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "15", "issue": "1", "pages": null}, "abstract": "The patterns of reproductive timing and senescence vary within and across species owing to differences in reproductive strategies, but our understanding of the molecular underpinnings of such variation is incomplete. This is perhaps particularly true for sex differences. We investigated the evolution of sex-specific gene expression associated with life history divergence in replicated populations of the seed beetle Acanthoscelides obtectus, experimentally evolving under (E)arly or (L)ate life reproduction for >200 generations which has resulted in strongly divergent life histories. We detected 1,646 genes that were differentially expressed in E and L lines, consistent with a highly polygenic basis of life history evolution. Only 30% of differentially expressed genes were similarly affected in males and females. The evolution of long life was associated with significantly reduced sex differences in expression, especially in non-reproductive tissues. The expression differences were overall more pronounced in females, in accordance with their greater phenotypic divergence in lifespan. Functional enrichment analysis revealed differences between E and L beetles in gene categories previously implicated in aging, such as mitochondrial function and defense response. The results show that divergent life history evolution can be associated with profound changes in gene expression that alter the transcriptome in a sex-specific way, highlighting the importance of understanding the mechanisms of aging in each sex.", "doi": "10.1093/gbe/evac177", "pmid": "36542472", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9830990"}, {"db": "pii", "key": "6948356"}], "notes": [], "created": "2023-12-01T12:26:26.019Z", "modified": "2024-07-01T06:04:47.982Z"}, {"entity": "publication", "iuid": "be695a433fa7423e9418d12e55b4d672", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be695a433fa7423e9418d12e55b4d672.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be695a433fa7423e9418d12e55b4d672"}}, "title": "Loss of Y in leukocytes as a risk factor for critical COVID-19 in men", "authors": [{"family": "Bruhn-Olszewska", "given": "Bo\u017cena", "initials": "B", "orcid": "0000-0003-2141-0247", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fa96509bbe94834858aee3c16d41b97.json"}}, {"family": "Davies", "given": "Hanna", "initials": "H", "orcid": "0000-0002-6289-3815", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d800ab99360483d8bd12ba4b386a4a4.json"}}, {"family": "Sarkisyan", "given": "Daniil", "initials": "D", "orcid": "0000-0002-2451-4386", "researcher": {"href": "https://publications.scilifelab.se/researcher/44fdd52fbf5d420396c87a31addea920.json"}}, {"family": "Juhas", "given": "Ulana", "initials": "U", "orcid": "0000-0001-8393-5845", "researcher": {"href": "https://publications.scilifelab.se/researcher/851c9b9c7ba943d6836633f8bd5003bd.json"}}, {"family": "Rychlicka-Buniowska", "given": "Edyta", "initials": "E", "orcid": "0000-0001-8050-2489", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b253253073749839c443de3003ecb89.json"}}, {"family": "W\u00f3jcik", "given": "Magdalena", "initials": "M", "orcid": "0000-0001-5475-8448", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbf367a185b347c6a9bf6b6f2adfe6e5.json"}}, {"family": "Horbacz", "given": "Monika", "initials": "M", "orcid": "0000-0003-1644-2957", "researcher": {"href": "https://publications.scilifelab.se/researcher/76c7f6d571214ca9a6940293c3dbc6c1.json"}}, {"family": "J\u0105kalski", "given": "Marcin", "initials": "M", "orcid": "0000-0002-5481-9148", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4411ec776b94c89b0444bd8d49672ca.json"}}, {"family": "Olszewski", "given": "Pawe\u0142", "initials": "P", "orcid": "0000-0002-2788-5254", "researcher": {"href": "https://publications.scilifelab.se/researcher/214b8864edb24164a1c9af68396603b9.json"}}, {"family": "Westholm", "given": "Jakub O", "initials": "JO", "orcid": "0000-0002-6849-6220", "researcher": {"href": "https://publications.scilifelab.se/researcher/161d8b5fb6734b33ad5f5590edbc0cff.json"}}, {"family": "Smialowska", "given": "Agata", "initials": "A"}, {"family": "Wierzba", "given": "Karol", "initials": "K", "orcid": "0000-0003-1257-4047", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddedb819ee5d4e33b0382e87e7369dec.json"}}, {"family": "Torinsson Naluai", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-0504-6492", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcf3474dc7054c598cbe3a195deb8a1b.json"}}, {"family": "Jern", "given": "Niklas", "initials": "N"}, {"family": "Andersson", "given": "Lars Magnus", "initials": "LM", "orcid": "0000-0002-9203-5969", "researcher": {"href": "https://publications.scilifelab.se/researcher/da6e24cc65a14537ad30353de972cd5f.json"}}, {"family": "J\u00e4rhult", "given": "Josef D", "initials": "JD", "orcid": "0000-0002-7075-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/2598129f86ee47ebafc696148f9da01f.json"}}, {"family": "Filipowicz", "given": "Natalia", "initials": "N", "orcid": "0000-0002-9673-2649", "researcher": {"href": "https://publications.scilifelab.se/researcher/153a4d73f8cb4ec68cedfd85556e383e.json"}}, {"family": "Tiensuu Janson", "given": "Eva", "initials": "E", "orcid": "0000-0002-1649-4880", "researcher": {"href": "https://publications.scilifelab.se/researcher/3838152188ee4e2580d139757ecd8df8.json"}}, {"family": "Rubertsson", "given": "Sten", "initials": "S"}, {"family": "Lipcsey", "given": "Mikl\u00f3s", "initials": "M", "orcid": "0000-0002-1976-4129", "researcher": {"href": "https://publications.scilifelab.se/researcher/81805f2324634628abefcf0ab6ce6a15.json"}}, {"family": "Gissl\u00e9n", "given": "Magnus", "initials": "M", "orcid": "0000-0002-2357-1020", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b50df8c8ecc45b89574dc76e244b07e.json"}}, {"family": "Hultstr\u00f6m", "given": "Michael", "initials": "M", "orcid": "0000-0003-4675-1099", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9a74d3380a24c31930e6e671e685b5b.json"}}, {"family": "Frithiof", "given": "Robert", "initials": "R", "orcid": "0000-0003-2278-7951", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fec11dd18f941b7842610ad14237a35.json"}}, {"family": "Dumanski", "given": "Jan P", "initials": "JP", "orcid": "0000-0002-1489-1452", "researcher": {"href": "https://publications.scilifelab.se/researcher/15b14282209342cfa9c82cdbf02999f6.json"}}], "type": "journal-article", "published": "2022-12-14", "journal": {"title": "Genome Med", "issn": "1756-994X", "issn-l": "1756-994X", "volume": "14", "issue": "1", "pages": "139"}, "abstract": "The COVID-19 pandemic, which has a prominent social and economic impact worldwide, shows a largely unexplained male bias for the severity and mortality of the disease. Loss of chromosome Y (LOY) is a risk factor candidate in COVID-19 due to its prior association with many chronic age-related diseases, and its impact on immune gene transcription.\n\nPublicly available scRNA-seq data of PBMC samples derived from male patients critically ill with COVID-19 were reanalyzed, and LOY status was added to the annotated cells. We further studied LOY in whole blood for 211 COVID-19 patients treated at intensive care units (ICU) from the first and second waves of the pandemic. Of these, 139 patients were subject to cell sorting for LOY analysis in granulocytes, low-density neutrophils (LDNs), monocytes, and PBMCs.\n\nReanalysis of available scRNA-seq data revealed LDNs and monocytes as the cell types most affected by LOY. Subsequently, DNA analysis indicated that 46%, 32%, and 29% of critically ill patients showed LOY above 5% cut-off in LDNs, granulocytes, and monocytes, respectively. Hence, the myeloid lineage that is crucial for the development of severe COVID-19 phenotype is affected by LOY. Moreover, LOY correlated with increasing WHO score (median difference 1.59%, 95% HDI 0.46% to 2.71%, p=0.025), death during ICU treatment (median difference 1.46%, 95% HDI 0.47% to 2.43%, p=0.0036), and history of vessel disease (median difference 2.16%, 95% HDI 0.74% to 3.7%, p=0.004), among other variables. In 16 recovered patients, sampled during ICU stay and 93-143 days later, LOY decreased significantly in whole blood and PBMCs. Furthermore, the number of LDNs at the recovery stage decreased dramatically (median difference 76.4 per 10,000 cell sorting events, 95% HDI 55.5 to 104, p=6e-11).\n\nWe present a link between LOY and an acute, life-threatening infectious disease. Furthermore, this study highlights LOY as the most prominent clonal mutation affecting the myeloid cell lineage during emergency myelopoiesis. The correlation between LOY level and COVID-19 severity might suggest that this mutation affects the functions of monocytes and neutrophils, which could have consequences for male innate immunity.", "doi": "10.1186/s13073-022-01144-5", "pmid": "36514076", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9747543"}, {"db": "pii", "key": "10.1186/s13073-022-01144-5"}], "notes": [], "created": "2022-12-20T08:30:45.356Z", "modified": "2023-06-19T09:07:39.861Z"}, {"entity": "publication", "iuid": "352bbc6455e4497cb527970199843717", "links": {"self": {"href": "https://publications.scilifelab.se/publication/352bbc6455e4497cb527970199843717.json"}, "display": {"href": "https://publications.scilifelab.se/publication/352bbc6455e4497cb527970199843717"}}, "title": "Plasma protein biomarker profiling reveals major differences between acute leukaemia, lymphoma patients and controls.", "authors": [{"family": "Abu Sabaa", "given": "Amal", "initials": "A"}, {"family": "Shen", "given": "Qiujin", "initials": "Q"}, {"family": "Lennmyr", "given": "Emma Bergfelt", "initials": "EB"}, {"family": "Enblad", "given": "Anna Pia", "initials": "AP"}, {"family": "Gammelg\u00e5rd", "given": "Gustav", "initials": "G"}, {"family": "Molin", "given": "Daniel", "initials": "D"}, {"family": "Hein", "given": "Anders", "initials": "A"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M"}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M"}, {"family": "Enblad", "given": "Gunilla", "initials": "G"}, {"family": "Eriksson", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2022-11-25", "journal": {"title": "N Biotechnol", "issn": "1876-4347", "volume": "71", "pages": "21-29", "issn-l": "1871-6784"}, "abstract": "Aiming to accommodate the unmet need for easily accessible biomarkers with a focus on biological differences between haematological diseases, the diagnostic value of plasma proteins in acute leukaemias and lymphomas was investigated. A multiplex proximity extension assay (PEA) was used to analyze 183 proteins in diagnostic plasma samples from 251 acute leukaemia and lymphoma patients and compared with samples from 60 healthy controls. Multivariate modelling using partial least square discriminant analysis revealed highly significant differences between distinct disease subgroups and controls. The model allowed explicit distinction between leukaemia and lymphoma, with few patients misclassified. Acute leukaemia samples had higher levels of proteins associated with haemostasis, inflammation, cell differentiation and cell-matrix integration, whereas lymphoma samples demonstrated higher levels of proteins known to be associated with tumour microenvironment and lymphoma dissemination. PEA technology can be used to screen for large number of plasma protein biomarkers in low \u00b5L sample volumes, enabling the distinction between controls, acute leukaemias and lymphomas. Plasma protein profiling could help gain insights into the pathophysiology of acute leukaemia and lymphoma and the technique may be a valuable tool in the diagnosis of these diseases.", "doi": "10.1016/j.nbt.2022.06.005", "pmid": "35779858", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Affinity Proteomics Uppsala": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1871-6784(22)00042-5"}], "notes": [], "created": "2022-11-24T15:04:46.925Z", "modified": "2022-12-02T08:48:01.227Z"}, {"entity": "publication", "iuid": "0f4c992adb014d0c962a7a62313aed71", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f4c992adb014d0c962a7a62313aed71.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f4c992adb014d0c962a7a62313aed71"}}, "title": "Choice of High-Throughput Proteomics Method Affects Data Integration with Transcriptomics and the Potential Use in Biomarker Discovery.", "authors": [{"family": "Mosquim Junior", "given": "Sergio", "initials": "S", "orcid": "0000-0002-1537-7252", "researcher": {"href": "https://publications.scilifelab.se/researcher/1354a13a0b2f4a35865224291239e730.json"}}, {"family": "Siino", "given": "Valentina", "initials": "V", "orcid": "0000-0002-0489-6380", "researcher": {"href": "https://publications.scilifelab.se/researcher/04ca620e18e14085be456f76eb429902.json"}}, {"family": "Ryd\u00e9n", "given": "Lisa", "initials": "L", "orcid": "0000-0001-7515-3130", "researcher": {"href": "https://publications.scilifelab.se/researcher/424bace557344431a47ffe5cdccbeb56.json"}}, {"family": "Vallon-Christersson", "given": "Johan", "initials": "J", "orcid": "0000-0002-2195-0385", "researcher": {"href": "https://publications.scilifelab.se/researcher/648fa1d04cb640858fe3534d04cd04d1.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b7add45d810457eb84a72aebbc7b82c.json"}}], "type": "journal article", "published": "2022-11-23", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "14", "issue": "23", "issn-l": "2072-6694"}, "abstract": "In recent years, several advances have been achieved in breast cancer (BC) classification and treatment. However, overdiagnosis, overtreatment, and recurrent disease are still significant causes of complication and death. Here, we present the development of a protocol aimed at parallel transcriptome and proteome analysis of BC tissue samples using mass spectrometry, via Data Dependent and Independent Acquisitions (DDA and DIA). Protein digestion was semi-automated and performed on flowthroughs after RNA extraction. Data for 116 samples were acquired in DDA and DIA modes and processed using MaxQuant, EncyclopeDIA, or DIA-NN. DIA-NN showed an increased number of identified proteins, reproducibility, and correlation with matching RNA-seq data, therefore representing the best alternative for this setup. Gene Set Enrichment Analysis pointed towards complementary information being found between transcriptomic and proteomic data. A decision tree model, designed to predict the intrinsic subtypes based on differentially abundant proteins across different conditions, selected protein groups that recapitulate important clinical features, such as estrogen receptor status, HER2 status, proliferation, and aggressiveness. Taken together, our results indicate that the proposed protocol performed well for the application. Additionally, the relevance of the selected proteins points to the possibility of using such data as a biomarker discovery tool for personalized medicine.", "doi": "10.3390/cancers14235761", "pmid": "36497242", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9736226"}, {"db": "pii", "key": "cancers14235761"}], "notes": [], "created": "2023-09-27T07:00:02.527Z", "modified": "2023-09-27T07:00:02.646Z"}, {"entity": "publication", "iuid": "5891893c3a104051b589084b98ee3003", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5891893c3a104051b589084b98ee3003.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5891893c3a104051b589084b98ee3003"}}, "title": "ID1 and CEBPA coordinate epidermal progenitor cell differentiation.", "authors": [{"family": "Kantzer", "given": "Christina Geraldine", "initials": "CG", "orcid": "0000-0002-4975-7579", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4ef0372d6b8415fb4ebc8ab4c2e24ff.json"}}, {"family": "Yang", "given": "Wei", "initials": "W"}, {"family": "Grommisch", "given": "David", "initials": "D", "orcid": "0000-0002-2666-1419", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba4e40cb43e64713b48caa02a0941d1a.json"}}, {"family": "Vikhe Patil", "given": "Kim", "initials": "K"}, {"family": "Mak", "given": "Kylie Hin-Man", "initials": "KH"}, {"family": "Shirokova", "given": "Vera", "initials": "V"}, {"family": "Genander", "given": "Maria", "initials": "M", "orcid": "0000-0002-2428-8040", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee0b27ddbb154eadbf3293d090720481.json"}}], "type": "journal article", "published": "2022-11-15", "journal": {"title": "Development", "issn": "1477-9129", "volume": "149", "issue": "22", "issn-l": "0950-1991"}, "abstract": "The regulatory circuits that coordinate epidermal differentiation during development are still not fully understood. Here, we report that the transcriptional regulator ID1 is enriched in mouse basal epidermal progenitor cells and find ID1 expression to be diminished upon differentiation. In utero silencing of Id1 impairs progenitor cell proliferation, leads to precocious delamination of targeted progenitor cells and enables differentiated keratinocytes to retain progenitor markers and characteristics. Transcriptional profiling suggests that ID1 acts by mediating adhesion to the basement membrane while inhibiting spinous layer differentiation. Co-immunoprecipitation reveals ID1 binding to transcriptional regulators of the class I bHLH family. We localize bHLH Tcf3, Tcf4 and Tcf12 to epidermal progenitor cells during epidermal stratification and establish TCF3 as a downstream effector of ID1-mediated epidermal proliferation. Finally, we identify crosstalk between CEBPA, a known mediator of epidermal differentiation, and Id1, and demonstrate that CEBPA antagonizes BMP-induced activation of Id1. Our work establishes ID1 as a key coordinator of epidermal development, acting to balance progenitor proliferation with differentiation and unveils how functional crosstalk between CEBPA and Id1 orchestrates epidermal lineage progression.", "doi": "10.1242/dev.201262", "pmid": "36330928", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9845743"}, {"db": "pii", "key": "282464"}], "notes": [], "created": "2023-11-16T12:38:08.748Z", "modified": "2023-11-16T12:38:08.820Z"}, {"entity": "publication", "iuid": "6be4e92973934cb69e13cdcf43dbd578", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6be4e92973934cb69e13cdcf43dbd578.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6be4e92973934cb69e13cdcf43dbd578"}}, "title": "Systems Biology in ELIXIR: modelling in the spotlight.", "authors": [{"family": "Martins Dos Santos", "given": "Vitor", "initials": "V"}, {"family": "Anton", "given": "Mihail", "initials": "M", "orcid": "0000-0002-7753-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a28ecc2261e436ea5884ada5e512aed.json"}}, {"family": "Szomolay", "given": "Barbara", "initials": "B"}, {"family": "Ostaszewski", "given": "Marek", "initials": "M"}, {"family": "Arts", "given": "Ilja", "initials": "I"}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Dominguez Del Angel", "given": "Victoria", "initials": "V", "orcid": "0000-0002-5514-6651", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a708fa6e9a44453b97cfc2089e06bec.json"}}, {"family": "Ferk", "given": "Polonca", "initials": "P"}, {"family": "Fey", "given": "Dirk", "initials": "D"}, {"family": "Goble", "given": "Carole", "initials": "C"}, {"family": "Golebiewski", "given": "Martin", "initials": "M", "orcid": "0000-0002-8683-7084", "researcher": {"href": "https://publications.scilifelab.se/researcher/5159dc6f9fa64c15b83ca6941cefc7b7.json"}}, {"family": "Gruden", "given": "Kristina", "initials": "K"}, {"family": "Heil", "given": "Katharina F", "initials": "KF", "orcid": "0000-0003-3341-3736", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3b2cbf1f0ed49faaf5dfd158da1a35e.json"}}, {"family": "Hermjakob", "given": "Henning", "initials": "H"}, {"family": "Kahlem", "given": "Pascal", "initials": "P", "orcid": "0000-0002-8810-444X", "researcher": {"href": "https://publications.scilifelab.se/researcher/135bc12706264a2abcca62c7eb690f87.json"}}, {"family": "Klapa", "given": "Maria I", "initials": "MI", "orcid": "0000-0002-2047-3185", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad30222c4c554a0881e3ee1d21f5fc87.json"}}, {"family": "Koehorst", "given": "Jasper", "initials": "J"}, {"family": "Kolodkin", "given": "Alexey", "initials": "A", "orcid": "0000-0002-7466-5027", "researcher": {"href": "https://publications.scilifelab.se/researcher/76faac66d6954e6d8d3ee709f1ae2999.json"}}, {"family": "Kutmon", "given": "Martina", "initials": "M", "orcid": "0000-0002-7699-8191", "researcher": {"href": "https://publications.scilifelab.se/researcher/f826bac4e2f04f18a225640a152da567.json"}}, {"family": "Lesko\u0161ek", "given": "Brane", "initials": "B"}, {"family": "Moretti", "given": "S\u00e9bastien", "initials": "S", "orcid": "0000-0003-3947-488X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d303d14d45a14a72bc7f8a9cc16ae964.json"}}, {"family": "M\u00fcller", "given": "Wolfgang", "initials": "W"}, {"family": "Pagni", "given": "Marco", "initials": "M"}, {"family": "Rezen", "given": "Tadeja", "initials": "T"}, {"family": "Rocha", "given": "Miguel", "initials": "M"}, {"family": "Rozman", "given": "Damjana", "initials": "D"}, {"family": "\u0160afr\u00e1nek", "given": "David", "initials": "D", "orcid": "0000-0002-0713-2431", "researcher": {"href": "https://publications.scilifelab.se/researcher/e679c1b8c368494a84b52bae36fefa7f.json"}}, {"family": "Sheriff", "given": "Rahuman S Malik", "initials": "RSM", "orcid": "0000-0003-0705-9809", "researcher": {"href": "https://publications.scilifelab.se/researcher/84d226b68a324e0289c466b6c932a048.json"}}, {"family": "Suarez Diez", "given": "Maria", "initials": "M", "orcid": "0000-0001-5845-146X", "researcher": {"href": "https://publications.scilifelab.se/researcher/023c84ba41c143d28dc00693731abeec.json"}}, {"family": "Van Steen", "given": "Kristel", "initials": "K"}, {"family": "Westerhoff", "given": "Hans V", "initials": "HV", "orcid": "0000-0002-0443-6114", "researcher": {"href": "https://publications.scilifelab.se/researcher/9899f237345c4a489ca21750977783f5.json"}}, {"family": "Wittig", "given": "Ulrike", "initials": "U", "orcid": "0000-0002-9077-5664", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a09cda9b5ad48b4a1743606ae9757e8.json"}}, {"family": "Wolstencroft", "given": "Katherine", "initials": "K", "orcid": "0000-0002-1279-5133", "researcher": {"href": "https://publications.scilifelab.se/researcher/6de31d88de1f486b9853fdad71e0428e.json"}}, {"family": "Zupanic", "given": "Anze", "initials": "A", "orcid": "0000-0003-3303-9086", "researcher": {"href": "https://publications.scilifelab.se/researcher/df0e3f62701448a8a212d49a363fee09.json"}}, {"family": "Evelo", "given": "Chris T", "initials": "CT", "orcid": "0000-0002-5301-3142", "researcher": {"href": "https://publications.scilifelab.se/researcher/5886980760ef4a79b98112a484619c81.json"}}, {"family": "Hancock", "given": "John M", "initials": "JM", "orcid": "0000-0003-2991-2217", "researcher": {"href": "https://publications.scilifelab.se/researcher/23a58deb7c574625bbdf1c7be2128027.json"}}], "type": "journal article", "published": "2022-11-07", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "11", "pages": "1265", "issn-l": "2046-1402"}, "abstract": "In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Community believes that the infrastructure aspects of systems biology - databases, (modelling) tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove key components of ELIXIR's future support of advanced biological applications and personalised medicine. By way of a series of meetings, the Community identified seven key areas for its future activities, reflecting both future needs and previous and current activities within ELIXIR Platforms and Communities. These are: overcoming barriers to the wider uptake of systems biology; linking new and existing data to systems biology models; interoperability of systems biology resources; further development and embedding of systems medicine; provisioning of modelling as a service; building and coordinating capacity building and training resources; and supporting industrial embedding of systems biology. A set of objectives for the Community has been identified under four main headline areas: Standardisation and Interoperability, Technology, Capacity Building and Training, and Industrial Embedding. These are grouped into short-term (3-year), mid-term (6-year) and long-term (10-year) objectives.", "doi": "10.12688/f1000research.126734.1", "pmid": "36742342", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9871403"}, {"db": "pii", "key": "ELIXIR-1265"}], "notes": [], "created": "2022-11-25T08:14:57.508Z", "modified": "2023-06-02T10:32:23.545Z"}, {"entity": "publication", "iuid": "5a7dbe2f2ad04caab77711a646a48243", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a7dbe2f2ad04caab77711a646a48243.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a7dbe2f2ad04caab77711a646a48243"}}, "title": "The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations.", "authors": [{"family": "Ament-Vel\u00e1squez", "given": "Sandra Lorena", "initials": "SL", "orcid": "0000-0003-3371-9292", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d54ef94f91c4c1c85d5dc3a846023e5.json"}}, {"family": "Gilchrist", "given": "Ciaran", "initials": "C", "orcid": "0000-0002-7639-6131", "researcher": {"href": "https://publications.scilifelab.se/researcher/44917102032e428998899b3e63e5c4df.json"}}, {"family": "R\u00eago", "given": "Alexandre", "initials": "A"}, {"family": "Bendixsen", "given": "Devin P", "initials": "DP", "orcid": "0000-0003-0831-7646", "researcher": {"href": "https://publications.scilifelab.se/researcher/533f0c534a214ee68a037b243a63a028.json"}}, {"family": "Brice", "given": "Claire", "initials": "C"}, {"family": "Grosse-Sommer", "given": "Julie Michelle", "initials": "JM"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Stelkens", "given": "Rike", "initials": "R", "orcid": "0000-0002-8530-0656", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8b3449c244a4c13b8610e401f4cbef4.json"}}], "type": "journal article", "published": "2022-11-03", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "39", "issue": "11", "pages": null}, "abstract": "Adaptation from standing genetic variation is an important process underlying evolution in natural populations, but we rarely get the opportunity to observe the dynamics of fitness and genomic changes in real time. Here, we used experimental evolution and Pool-Seq to track the phenotypic and genomic changes of genetically diverse asexual populations of the yeast Saccharomyces cerevisiae in four environments with different fitness costs. We found that populations rapidly and in parallel increased in fitness in stressful environments. In contrast, allele frequencies showed a range of trajectories, with some populations fixing all their ancestral variation in <30 generations and others maintaining diversity across hundreds of generations. We detected parallelism at the genomic level (involving genes, pathways, and aneuploidies) within and between environments, with idiosyncratic changes recurring in the environments with higher stress. In particular, we observed a tendency of becoming haploid-like in one environment, whereas the populations of another environment showed low overall parallelism driven by standing genetic variation despite high selective pressure. This work highlights the interplay between standing genetic variation and the influx of de novo mutations in populations adapting to a range of selective pressures with different underlying trait architectures, advancing our understanding of the constraints and drivers of adaptation.", "doi": "10.1093/molbev/msac242", "pmid": "36334099", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9703598"}, {"db": "pii", "key": "6806091"}], "notes": [], "created": "2022-11-25T07:56:20.931Z", "modified": "2024-01-16T13:48:34.514Z"}, {"entity": "publication", "iuid": "c6cb0a80038d48c69c3e38c25d0ed018", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6cb0a80038d48c69c3e38c25d0ed018.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6cb0a80038d48c69c3e38c25d0ed018"}}, "title": "Whole genome analyses based on single, field collected spores of the arbuscular mycorrhizal fungus Funneliformis geosporum.", "authors": [{"family": "Sahraei", "given": "Shadi Eshghi", "initials": "SE", "orcid": "0000-0003-4741-5871", "researcher": {"href": "https://publications.scilifelab.se/researcher/98f7d11029704e33b61a8c27daa54378.json"}}, {"family": "S\u00e1nchez-Garc\u00eda", "given": "Marisol", "initials": "M", "orcid": "0000-0002-0635-6281", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ccb3584fa144e178750ff2fc4666cfe.json"}}, {"family": "Montoliu-Nerin", "given": "Merce", "initials": "M", "orcid": "0000-0002-5200-0411", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f89e94a04c6429db7e706b4d8d6626a.json"}}, {"family": "Manyara", "given": "David", "initials": "D", "orcid": "0000-0002-8370-2651", "researcher": {"href": "https://publications.scilifelab.se/researcher/2132548af20445b2b0561fa38b8f8b89.json"}}, {"family": "Bergin", "given": "Claudia", "initials": "C", "orcid": "0000-0001-7960-1789", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdd58ab07d964bcfb865ce67f7826816.json"}}, {"family": "Rosendahl", "given": "S\u00f8ren", "initials": "S", "orcid": "0000-0001-5202-6585", "researcher": {"href": "https://publications.scilifelab.se/researcher/111116b3b09343f783385c30207fd9b3.json"}}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "Mycorrhiza", "issn": "1432-1890", "issn-l": "0940-6360", "volume": "32", "issue": "5-6", "pages": "361-371"}, "abstract": "Arbuscular mycorrhizal (AM) fungi are ubiquitous mutualistic symbionts of most terrestrial plants and many complete their lifecycles underground. Whole genome analysis of AM fungi has long been restricted to species and strains that can be maintained under controlled conditions that facilitate collection of biological samples. There is some evidence suggesting that AM fungi can adapt to culture resulting in phenotypic and possibly also genotypic changes in the fungi. In this study, we used field isolated spores of AM fungi and identified them as Funneliformis geosporum based on morphology and phylogenetic analyses. We separately assembled the genomes of two representative spores using DNA sequences of 19 and 22 individually amplified nuclei. The genomes were compared with previously published data from other members of Glomeraceae including two strains of F. mosseae. No significant differences were observed among the species in terms of gene content, while the single nucleotide polymorphism density was higher in the strains of F. geosporum than in the strains of F. mosseae. In this study, we demonstrate that it is possible to sequence and assemble genomes from AM fungal spores sampled in the field, which opens up the possibility to include uncultured AM fungi in phylogenomic and comparative genomic analysis and to study genomic variation in natural populations of these important plant symbionts.", "doi": "10.1007/s00572-022-01091-4", "pmid": "36161535", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Microbial Single Cell Genomics": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9560946"}, {"db": "pii", "key": "10.1007/s00572-022-01091-4"}], "notes": [], "created": "2022-11-29T12:15:19.004Z", "modified": "2024-01-16T13:48:34.535Z"}, {"entity": "publication", "iuid": "db2cb53665f444ec82e2dad906899885", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db2cb53665f444ec82e2dad906899885.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db2cb53665f444ec82e2dad906899885"}}, "title": "Translatome profiling in fatal familial insomnia implicates TOR signaling in somatostatin neurons.", "authors": [{"family": "Bauer", "given": "Susanne", "initials": "S", "orcid": "0000-0003-4731-5002", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b6d3b8355fa4f41b7015a8ffe8f398c.json"}}, {"family": "Dittrich", "given": "Lars", "initials": "L"}, {"family": "Kaczmarczyk", "given": "Lech", "initials": "L", "orcid": "0000-0003-2747-3134", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b192685d0c2438497741e66bfc183c9.json"}}, {"family": "Schleif", "given": "Melvin", "initials": "M"}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Jackson", "given": "Walker S", "initials": "WS", "orcid": "0000-0002-3003-5509", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f49c7978954d098514c5b1bfa9e34b.json"}}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "volume": "5", "issue": "11", "issn-l": "2575-1077"}, "abstract": "Selective neuronal vulnerability is common in neurodegenerative diseases but poorly understood. In genetic prion diseases, including fatal familial insomnia (FFI) and Creutzfeldt-Jakob disease (CJD), different mutations in the <i>Prnp<\/i> gene manifest as clinically and neuropathologically distinct diseases. Here we report with electroencephalography studies that theta waves are mildly increased in 21 mo old knock-in mice modeling FFI and CJD and that sleep is mildy affected in FFI mice. To define affected cell types, we analyzed cell type-specific translatomes from six neuron types of 9 mo old FFI and CJD mice. Somatostatin (SST) neurons responded the strongest in both diseases, with unexpectedly high overlap in genes and pathways. Functional analyses revealed up-regulation of neurodegenerative disease pathways and ribosome and mitochondria biogenesis, and down-regulation of synaptic function and small GTPase-mediated signaling in FFI, implicating down-regulation of mTOR signaling as the root of these changes. In contrast, responses in glutamatergic cerebellar neurons were disease-specific. The high similarity in SST neurons of FFI and CJD mice suggests that a common therapy may be beneficial for multiple genetic prion diseases.", "doi": "10.26508/lsa.202201530", "pmid": "36192034", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9531780"}, {"db": "pii", "key": "5/11/e202201530"}], "notes": [], "created": "2022-11-09T15:50:48.068Z", "modified": "2024-01-16T13:48:34.558Z"}, {"entity": "publication", "iuid": "cf165c58527e41439582a10d2cc5f063", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf165c58527e41439582a10d2cc5f063.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf165c58527e41439582a10d2cc5f063"}}, "title": "Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level.", "authors": [{"family": "Guti\u00e9rrez-Valencia", "given": "Juanita", "initials": "J"}, {"family": "Fracassetti", "given": "Marco", "initials": "M"}, {"family": "Berdan", "given": "Emma L", "initials": "EL"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Kutschera", "given": "Verena E", "initials": "VE"}, {"family": "Losvik", "given": "Aleksandra", "initials": "A"}, {"family": "D\u00e9samor\u00e9", "given": "Aur\u00e9lie", "initials": "A"}, {"family": "Hughes", "given": "P William", "initials": "PW"}, {"family": "Foroozani", "given": "Alireza", "initials": "A"}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Pesquet", "given": "Edouard", "initials": "E"}, {"family": "Abdelaziz", "given": "Mohamed", "initials": "M"}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Brennan", "given": "Adrian C", "initials": "AC"}, {"family": "Arroyo", "given": "Juan", "initials": "J"}, {"family": "Slotte", "given": "Tanja", "initials": "T"}], "type": "journal article", "published": "2022-10-24", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "issn-l": "0960-9822", "volume": "32", "issue": "20", "pages": "4360-4371.e6"}, "abstract": "Supergenes govern multi-trait-balanced polymorphisms in a wide range of systems; however, our understanding of their origins and evolution remains incomplete. The reciprocal placement of stigmas and anthers in pin and thrum floral morphs of distylous species constitutes an iconic example of a balanced polymorphism governed by a supergene, the distyly S-locus. Recent studies have shown that the Primula and Turnera distyly supergenes are both hemizygous in thrums, but it remains unknown whether hemizygosity is pervasive among distyly S-loci. As hemizygosity has major consequences for supergene evolution and loss, clarifying whether this genetic architecture is shared among distylous species is critical. Here, we have characterized the genetic architecture and evolution of the distyly supergene in Linum by generating a chromosome-level genome assembly of Linum tenue, followed by the identification of the S-locus using population genomic data. We show that hemizygosity and thrum-specific expression of S-linked genes, including a pistil-expressed candidate gene for style length, are major features of the Linum S-locus. Structural variation is likely instrumental for recombination suppression, and although the non-recombining dominant haplotype has accumulated transposable elements, S-linked genes are not under relaxed purifying selection. Our findings reveal remarkable convergence in the genetic architecture and evolution of independently derived distyly supergenes, provide a counterexample to classic inversion-based supergenes, and shed new light on the origin and maintenance of an iconic floral polymorphism.", "doi": "10.1016/j.cub.2022.08.042", "pmid": "36087578", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0960-9822(22)01364-1"}], "notes": [], "created": "2022-09-22T18:45:15.012Z", "modified": "2024-01-16T13:48:34.696Z"}, {"entity": "publication", "iuid": "b7699761f0324699b560a593b0122652", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7699761f0324699b560a593b0122652.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7699761f0324699b560a593b0122652"}}, "title": "Pediatric Hip Disease Increases the Risk for Opioid Use in Adulthood: Long-term Burden of Pain and Depression.", "authors": [{"family": "Wadstr\u00f6m", "given": "Miriam G", "initials": "MG"}, {"family": "Hailer", "given": "Yasmin D", "initials": "YD"}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "Pain Physician", "issn": "2150-1149", "volume": "25", "issue": "7", "pages": "E1153-E1160", "issn-l": null}, "abstract": "Legg-Calv\u00e9-Perthes disease (LCPD) and slipped capital femoral epiphysis (SCFE) can result in painful deformation of the hip joint with impaired range of motion and early development of secondary osteoarthritis. It has not been investigated whether having LCPD or SCFE is associated with increased use of pain or antidepressant drug prescriptions later in life.\n\nWith this study, we aimed to investigate if patients with a history of LCPD or SCFE have an increased risk of prescription analgesic or antidepressant drugs in adulthood compared with matched controls.\n\nThe included patients were identified by the Swedish Patient Register and matched for age, gender, and residency with 10 control individuals not exposed to any of the mentioned pediatric hip diseases, by the Swedish National Population Register.\n\nThis was a nationwide, registry-based cohort study which included 1,292 patients diagnosed with LCPD at age 2-15 years and 1,613 patients diagnosed with SCFE at age 5-16 years and > 17 years from 2005 through 2011.\n\nPrescription data of first-line analgesic drugs (acetaminophen, nonsteroidal anti-inflammatory drugs, and opioids), or first-line antidepressant drugs (selective serotonin reuptake inhibitors, serotonin-norepinephrine reuptake inhibitors, and tricyclic antidepressants) were derived from the Swedish Prescribed Drugs Register. Conditional logistic regression models were fitted to estimate the relative risk for the prescription in exposed compared with unexposed individuals. Adjustment was performed for gender and birth year.\n\nIn the group with an LCPD diagnosis, the adjusted odds ratio for analgesic prescriptions overall was 1.3 (95% CI, 1.2-1.5). For patients with an SCFE diagnosis, the adjusted odds ratio for analgesic prescriptions overall was 1.4 (95% CI, 1.3-1.6). Among patients with an LCPD diagnosis, the adjusted odds ratio for antidepressant prescriptions overall was 1.0 (95% CI, 0.8-1.2). For patients with an SCFE diagnosis, the adjusted odds ratio was 1.2 (95% CI, 1.1-1.4).\n\nAs with all register studies, there are known associated biases such as selection, detection, and observational bias as well as the uncertain quality of input data. Further, the Swedish Prescribed Drugs Register only includes drugs that were prescribed by a physician and dispensed at a pharmacy. This is also a factor that may lead to underestimating the use of acetaminophen and nonsteroidal anti-inflammatory drugs, as these drugs can be acquired \"over the counter.\"\n\nDuring childhood, patients with LCPD or SCFE seem to suffer long-term pain and have an increased risk of requiring analgesic medication in adulthood, including opioids. It is important to assess the causes, type, and severity of pain to optimize pain management to counteract possible overuse in these patients. Seemingly, patients with LCPD do not have an increased risk for antidepressant drug therapy in adulthood whereas we did see an increased risk for that in patients with previous SCFE compared with the general population.", "doi": null, "pmid": "36288602", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2023-11-16T12:16:40.911Z", "modified": "2024-01-19T11:57:19.656Z"}, {"entity": "publication", "iuid": "5ddeb520546645afb4117c5da734e00d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5ddeb520546645afb4117c5da734e00d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5ddeb520546645afb4117c5da734e00d"}}, "title": "Osteoclasts directly influence castration-resistant prostate cancer cells.", "authors": [{"family": "Huang", "given": "Junchi", "initials": "J"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Buckland", "given": "Robert", "initials": "R"}, {"family": "Josefsson", "given": "Andreas", "initials": "A"}, {"family": "Damber", "given": "Jan-Erik", "initials": "JE"}, {"family": "Wel\u00e9n", "given": "Karin", "initials": "K", "orcid": "0000-0003-2095-5333", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5cd5792c5094988a82ea9941fc29ace.json"}}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "Clin Exp Metastasis", "issn": "1573-7276", "volume": "39", "issue": "5", "pages": "801-814", "issn-l": null}, "abstract": "Metastasis to bone is the leading cause of death from prostate cancer. Interaction between tumor cells and bone cells can promote progression and influence tumor phenotype. It is known that prostate cancer cells support osteoclast differentiation, and degradation of bone matrix by osteoclasts releases growth factors stimulating tumor cell proliferation and invasion. In the present study osteolytic (PC-3) and osteoblastic (LNCaP-19) castration-resistant prostate cancer (CRPC) cells were co-cultured with mature osteoclasts or their precursor cells (RAW 264.7) to characterize direct effects of mature osteoclasts on CRPC cells. Osteoclasts increased proliferation and decrease apoptosis of CRPC cells as assessed with flow cytometry. RNA sequencing revealed that osteolytic CRPC cells were more responsive to osteoclast stimulation regarding gene expression, but the overall induced expression patterns were similar between the prostate cancer cell lines. Genes related to DNA repair were upregulated by osteoclasts, while genes related to endoplasmic reticulum stress-induced apoptosis and cholesterol synthesis were downregulated. The results of this study shows that osteoclasts directly influence CRPC cells, increasing proliferation, decreasing apoptosis, and affecting gene expression pathways that can affect sensitivity to DNA damage and endoplasmic reticulum function. This suggests targeting of osteoclasts to be a possible way to affect efficacy of other drugs by combination regimens in treating prostate cancer metastases.", "doi": "10.1007/s10585-022-10179-2", "pmid": "35971022", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9474581"}, {"db": "pii", "key": "10.1007/s10585-022-10179-2"}], "notes": [], "created": "2023-05-31T12:40:16.385Z", "modified": "2023-05-31T12:40:16.450Z"}, {"entity": "publication", "iuid": "f5a81fbb0cbc43fabca9d5298e78e612", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5a81fbb0cbc43fabca9d5298e78e612.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5a81fbb0cbc43fabca9d5298e78e612"}}, "title": "Synergistic Effects of Sanglifehrin-Based Cyclophilin Inhibitor NV651 with Cisplatin in Hepatocellular Carcinoma.", "authors": [{"family": "Sim\u00f3n Serrano", "given": "Sonia", "initials": "S", "orcid": "0000-0002-0166-0006", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e5c20f8789e40a299bfafa41129f999.json"}}, {"family": "Tavecchio", "given": "Michele", "initials": "M"}, {"family": "Mallik", "given": "Josef", "initials": "J"}, {"family": "Gr\u00f6nberg", "given": "Alvar", "initials": "A"}, {"family": "Elm\u00e9r", "given": "Eskil", "initials": "E", "orcid": "0000-0001-7901-1826", "researcher": {"href": "https://publications.scilifelab.se/researcher/8313ce5e20504a33822e0e4ff2faf46a.json"}}, {"family": "Kifagi", "given": "Chamseddine", "initials": "C", "orcid": "0000-0002-3744-5228", "researcher": {"href": "https://publications.scilifelab.se/researcher/47289b6fbb5740089077a49a9a9eb4e7.json"}}, {"family": "Gallay", "given": "Philippe", "initials": "P"}, {"family": "Hansson", "given": "Magnus Joakim", "initials": "MJ"}, {"family": "Massoumi", "given": "Ramin", "initials": "R", "orcid": "0000-0001-8875-6440", "researcher": {"href": "https://publications.scilifelab.se/researcher/c019a5eed3144760b8c55badc75280f7.json"}}], "type": "journal article", "published": "2022-09-20", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "14", "issue": "19", "pages": "4553", "issn-l": "2072-6694"}, "abstract": "Hepatocellular carcinoma (HCC), commonly diagnosed at an advanced stage, is the most common primary liver cancer. Owing to a lack of effective HCC treatments and the commonly acquired chemoresistance, novel therapies need to be investigated. Cyclophilins-intracellular proteins with peptidyl-prolyl isomerase activity-have been shown to play a key role in therapy resistance and cell proliferation. Here, we aimed to evaluate changes in the gene expression of HCC cells caused by cyclophilin inhibition in order to explore suitable combination treatment approaches, including the use of chemoagents, such as cisplatin. Our results show that the novel cyclophilin inhibitor NV651 decreases the expression of genes involved in several pathways related to the cancer cell cycle and DNA repair. We evaluated the potential synergistic effect of NV651 in combination with other treatments used against HCC in cisplatin-sensitive cells. NV651 showed a synergistic effect in inhibiting cell proliferation, with a significant increase in intrinsic apoptosis in combination with the DNA crosslinking agent cisplatin. This combination also affected cell cycle progression and reduced the capacity of the cell to repair DNA in comparison with a single treatment with cisplatin. Based on these results, we believe that the combination of cisplatin and NV651 may provide a novel approach to HCC treatment.", "doi": "10.3390/cancers14194553", "pmid": "36230472", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9559492"}, {"db": "pii", "key": "cancers14194553"}], "notes": [], "created": "2022-09-29T07:03:35.075Z", "modified": "2023-06-02T10:28:13.887Z"}, {"entity": "publication", "iuid": "fee6a328f53e4013a6ce31dfa9144540", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fee6a328f53e4013a6ce31dfa9144540.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fee6a328f53e4013a6ce31dfa9144540"}}, "title": "Congenital tremor and splay leg in piglets - insights into the virome, local cytokine response, and histology.", "authors": [{"family": "Stenberg", "given": "Hedvig", "initials": "H"}, {"family": "Hellman", "given": "Stina", "initials": "S"}, {"family": "Lindstr\u00f6m", "given": "Lisa", "initials": "L"}, {"family": "Jacobson", "given": "Magdalena", "initials": "M"}, {"family": "Fossum", "given": "Caroline", "initials": "C"}, {"family": "Hayer", "given": "Juliette", "initials": "J"}, {"family": "Malmberg", "given": "Maja", "initials": "M"}], "type": "journal article", "published": "2022-09-16", "journal": {"title": "BMC Vet Res", "issn": "1746-6148", "issn-l": null, "volume": "18", "issue": "1", "pages": "348"}, "abstract": "Atypical porcine pestivirus (APPV) is a neurotropic virus associated with congenital tremor type A-II. A few experimental studies also indicate an association between APPV and splay leg. The overarching aim of the present study was to provide insights into the virome, local cytokine response, and histology of the CNS in piglets with signs of congenital tremor or splay leg.\r\n\r\nCharacterization of the cytokine profile and virome of the brain in piglets with signs of congenital tremor revealed an APPV-associated upregulation of Stimulator of interferon genes (STING). The upregulation of STING was associated with an increased expression of the gene encoding IFN-\u03b1 but no differential expression was recorded for the genes encoding CXCL8, IFN-\u03b2, IFN-\u03b3, IL-1\u03b2, IL-6, or IL-10. No viral agents or cytokine upregulation could be detected in the spinal cord of piglets with signs of splay leg or in the brain of piglets without an APPV-infection. The histopathological examination showed no lesions in the CNS that could be attributed to the APPV-infection, as no difference between sick and healthy piglets could be seen.\r\n\r\nThe results from this study provide evidence of an APPV-induced antiviral cytokine response but found no lesions related to the infection nor any support for a common causative agent.", "doi": "10.1186/s12917-022-03443-w", "pmid": "36109741", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12917-022-03443-w"}, {"db": "pmc", "key": "PMC9479355"}], "notes": [], "created": "2022-09-23T08:16:31.989Z", "modified": "2024-01-16T13:48:35.004Z"}, {"entity": "publication", "iuid": "299d98ff9e534432952828bdd6f87512", "links": {"self": {"href": "https://publications.scilifelab.se/publication/299d98ff9e534432952828bdd6f87512.json"}, "display": {"href": "https://publications.scilifelab.se/publication/299d98ff9e534432952828bdd6f87512"}}, "title": "Sir2 and Reb1 antagonistically regulate nucleosome occupancy in subtelomeric X-elements and repress TERRAs by distinct mechanisms.", "authors": [{"family": "Bauer", "given": "Stefanie L", "initials": "SL", "orcid": "0000-0003-3870-7688", "researcher": {"href": "https://publications.scilifelab.se/researcher/2640af80f78b4595ab49ce93629e6f32.json"}}, {"family": "Grochalski", "given": "Thomas N T", "initials": "TNT"}, {"family": "Smialowska", "given": "Agata", "initials": "A"}, {"family": "\u00c5str\u00f6m", "given": "Stefan U", "initials": "SU", "orcid": "0000-0001-7721-6908", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f6ef7643731421b9821e208bc3e53bc.json"}}], "type": "journal article", "published": "2022-09-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "18", "issue": "9", "pages": "e1010419", "issn-l": "1553-7390"}, "abstract": "Telomere chromatin structure is pivotal for maintaining genome stability by regulating the binding of telomere-associated proteins and inhibiting the DNA damage response. In Saccharomyces cerevisiae, silent information regulator (Sir) proteins bind to terminal repeats and to subtelomeric X-elements, resulting in transcriptional silencing. Herein, we show that sir2 mutant strains display a specific loss of a nucleosome residing in the X-elements and that this deficiency is remarkably consistent between different telomeres. The X-elements contain several binding sites for the transcription factor Reb1 and we found that Sir2 and Reb1 compete for stabilizing/destabilizing this nucleosome, i.e. inactivation of Reb1 in a sir2 background reinstated the lost nucleosome. The telomeric-repeat-containing RNAs (TERRAs) originate from subtelomeric regions and extend into the terminal repeats. Both Sir2 and Reb1 repress TERRAs and in a sir2 reb1 double mutant, TERRA levels increased synergistically, showing that Sir2 and Reb1 act in different pathways for repressing TERRAs. We present evidence that Reb1 restricts TERRAs by terminating transcription. Mapping the 5'-ends of TERRAs from several telomeres revealed that the Sir2-stabilized nucleosome is the first nucleosome downstream from the transcriptional start site for TERRAs. Finally, moving an X-element to a euchromatic locus changed nucleosome occupancy and positioning, demonstrating that X-element nucleosome structure is dependent on the local telomere environment.", "doi": "10.1371/journal.pgen.1010419", "pmid": "36137093", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9531808"}, {"db": "pii", "key": "PGENETICS-D-22-00717"}], "notes": [], "created": "2022-11-24T11:52:24.784Z", "modified": "2022-11-24T11:52:24.839Z"}, {"entity": "publication", "iuid": "7152a9531a334b6f938c5bec186afe2b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7152a9531a334b6f938c5bec186afe2b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7152a9531a334b6f938c5bec186afe2b"}}, "title": "Plasma proteome profiling of healthy individuals across the life span in a Sicilian cohort with long-lived individuals.", "authors": [{"family": "Siino", "given": "Valentina", "initials": "V", "orcid": "0000-0002-0489-6380", "researcher": {"href": "https://publications.scilifelab.se/researcher/04ca620e18e14085be456f76eb429902.json"}}, {"family": "Ali", "given": "Ashfaq", "initials": "A", "orcid": "0000-0002-0164-2166", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0199dab5de9495baa7a4a3845209179.json"}}, {"family": "Accardi", "given": "Giulia", "initials": "G", "orcid": "0000-0003-3565-9529", "researcher": {"href": "https://publications.scilifelab.se/researcher/9eff3190fdae4350b84a770350a5166c.json"}}, {"family": "Aiello", "given": "Anna", "initials": "A", "orcid": "0000-0003-2593-3221", "researcher": {"href": "https://publications.scilifelab.se/researcher/e379a0ba210e4a0eadb997c857c3fc7b.json"}}, {"family": "Ligotti", "given": "Mattia E", "initials": "ME"}, {"family": "Mosquim Junior", "given": "Sergio", "initials": "S"}, {"family": "Candore", "given": "Giuseppina", "initials": "G", "orcid": "0000-0002-9966-934X", "researcher": {"href": "https://publications.scilifelab.se/researcher/71c386d9e1844064a99d596e443e4e7f.json"}}, {"family": "Caruso", "given": "Calogero", "initials": "C", "orcid": "0000-0001-8004-2363", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab49f2ed28ee4ec6a72a48e4077985a9.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b7add45d810457eb84a72aebbc7b82c.json"}}, {"family": "Vasto", "given": "Sonya", "initials": "S", "orcid": "0000-0002-6033-4745", "researcher": {"href": "https://publications.scilifelab.se/researcher/674c175d20da4428909e01f0b05badf9.json"}}], "type": "journal article", "published": "2022-09-00", "journal": {"title": "Aging Cell", "issn": "1474-9726", "volume": "21", "issue": "9", "pages": "e13684", "issn-l": "1474-9718"}, "abstract": "The study of healthy human aging is important for shedding light on the molecular mechanisms behind aging to promote well-being and to possibly predict and/or avoid the development of age-related disorders such as atherosclerosis and diabetes. Herein, we have employed an untargeted mass spectrometry-based approach to study age-related protein changes in a healthy Sicilian plasma cohort including long-lived individuals. This approach confirmed some of the previously known proteins correlated with age including fibulin-1, dystroglycan, and gamma-glutamyl hydrolase. Furthermore, our findings include novel proteins that correlate with age and/or with location and uric acid, which could represent a unique signature for healthy aging.", "doi": "10.1111/acel.13684", "pmid": "35932462", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9470904"}], "notes": [], "created": "2022-11-10T08:53:58.586Z", "modified": "2022-11-10T08:53:58.849Z"}, {"entity": "publication", "iuid": "c8fc3fc8849a44069ad6865663765a11", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c8fc3fc8849a44069ad6865663765a11.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c8fc3fc8849a44069ad6865663765a11"}}, "title": "Characterization of hemocytes and hematopoietic cells of a freshwater crayfish based on single-cell transcriptome analysis.", "authors": [{"family": "S\u00f6derh\u00e4ll", "given": "Irene", "initials": "I"}, {"family": "Fasterius", "given": "Erik", "initials": "E"}, {"family": "Ekblom", "given": "Charlotta", "initials": "C"}, {"family": "S\u00f6derh\u00e4ll", "given": "Kenneth", "initials": "K"}], "type": "journal article", "published": "2022-08-19", "journal": {"title": "iScience", "issn": "2589-0042", "issn-l": "2589-0042", "volume": "25", "issue": "8", "pages": "104850"}, "abstract": "Crustaceans constitute a species-rich and ecologically important animal group, and their circulating blood cells (hemocytes) are of critical importance in immunity as key players in pathogen recognition, phagocytosis, melanization, and antimicrobial defense. To gain a better understanding of the immune responses to different pathogens, it is crucial that we identify different hemocyte subpopulations with different functions and gain a better understanding of how these cells are formed. Here, we performed single-cell RNA sequencing of isolated hematopoietic tissue (HPT) cells and hemocytes from the crayfish Pacifastacus leniusculus to identify hitherto undescribed hemocyte types in the circulation and show that the circulating cells are more diversified than previously recognized. In addition, we discovered cell populations in the HPT with clear precursor characteristics as well as cells involved in iron homeostasis, representing a previously undiscovered cell type. These findings may improve our understanding of hematopoietic stem cell regulation in crustaceans and other animals.", "doi": "10.1016/j.isci.2022.104850", "pmid": "35996577", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Single cell": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9391574"}, {"db": "pii", "key": "S2589-0042(22)01122-1"}], "notes": [], "created": "2022-08-22T07:54:42.628Z", "modified": "2024-01-16T13:48:35.160Z"}, {"entity": "publication", "iuid": "034f6544dc3b4fbfb4aa2a0f67d8bcc3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/034f6544dc3b4fbfb4aa2a0f67d8bcc3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/034f6544dc3b4fbfb4aa2a0f67d8bcc3"}}, "title": "Human adaptation to arsenic in Bolivians living in the Andes.", "authors": [{"family": "De Loma", "given": "Jessica", "initials": "J"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Tirado", "given": "Noemi", "initials": "N"}, {"family": "Ascui", "given": "Franz", "initials": "F"}, {"family": "Vahter", "given": "Marie", "initials": "M"}, {"family": "Gardon", "given": "Jacques", "initials": "J"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM"}, {"family": "Broberg", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2022-08-00", "journal": {"title": "Chemosphere", "issn": "1879-1298", "volume": "301", "pages": "134764", "issn-l": "0045-6535"}, "abstract": "Humans living in the Andes Mountains have been historically exposed to arsenic from natural sources, including drinking water. Enzymatic methylation of arsenic allows it to be excreted more efficiently by the human body. Adaptation to high-arsenic environments via enhanced methylation and excretion of arsenic was first reported in indigenous women in the Argentinean Andes, but whether adaptation to arsenic is a general phenomenon across native populations from the Andes Mountains remains unclear. Therefore, we evaluated whether adaptation to arsenic has occurred in the Bolivian Andes by studying indigenous groups who belong to the Aymara-Quechua and Uru ethnicities and have lived in the Bolivian Andes for generations. Our population genetics methods, including genome-wide selection scans based on linkage disequilibrium patterns and allele frequency differences, in combination with targeted and whole-genome sequencing and genotype-phenotype association analyses, detected signatures of positive selection near the gene encoding arsenite methyltransferase (AS3MT), the main arsenic methylating enzyme. This was among the strongest selection signals (top 0.5% signals via locus-specific branch length and extended haplotype homozygosity tests) at a genome-wide level in the Bolivian study groups. We found a large haplotype block of 676 kb in the AS3MT region and identified candidate functional variants for further analysis. Moreover, our analyses revealed associations between AS3MT variants and the fraction of mono-methylated arsenic in urine and showed that the Bolivian study groups had the highest frequency of alleles associated with more efficient arsenic metabolism reported so far. Our data support the idea that arsenic exposure has been a driver for human adaptation to tolerate arsenic through more efficient arsenic detoxification in different Andean populations.", "doi": "10.1016/j.chemosphere.2022.134764", "pmid": "35490756", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Long read": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0045-6535(22)01257-7"}], "notes": [], "created": "2022-06-14T13:16:20.200Z", "modified": "2024-01-16T13:48:35.529Z"}, {"entity": "publication", "iuid": "64ad69b112e8486882a7f3720623a583", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64ad69b112e8486882a7f3720623a583.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64ad69b112e8486882a7f3720623a583"}}, "title": "Single-cell transcriptional pharmacodynamics of trifluridine in a tumor-immune model.", "authors": [{"family": "Selvin", "given": "Tove", "initials": "T"}, {"family": "Fasterius", "given": "Erik", "initials": "E"}, {"family": "Jarvius", "given": "Malin", "initials": "M"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Andersson", "given": "Claes R", "initials": "CR"}], "type": "journal article", "published": "2022-07-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "11960"}, "abstract": "Understanding the immunological effects of chemotherapy is of great importance, especially now that we have entered an era where ever-increasing pre-clinical and clinical efforts are put into combining chemotherapy and immunotherapy to combat cancer. Single-cell RNA sequencing (scRNA-seq) has proved to be a powerful technique with a broad range of applications, studies evaluating drug effects in co-cultures of tumor and immune cells are however scarce. We treated a co-culture comprised of human colorectal cancer (CRC) cells and peripheral blood mononuclear cells (PBMCs) with the nucleoside analogue trifluridine (FTD) and used scRNA-seq to analyze posttreatment gene expression profiles in thousands of individual cancer and immune cells concurrently. ScRNA-seq recapitulated major mechanisms of action previously described for FTD and provided new insight into possible treatment-induced effects on T-cell mediated antitumor responses.", "doi": "10.1038/s41598-022-16077-7", "pmid": "35831404", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Single cell": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9279337"}, {"db": "pii", "key": "10.1038/s41598-022-16077-7"}], "notes": [], "created": "2022-08-22T07:53:44.772Z", "modified": "2024-01-16T13:48:35.689Z"}, {"entity": "publication", "iuid": "52d17bcd67b34305a5fe00573dccf416", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52d17bcd67b34305a5fe00573dccf416.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52d17bcd67b34305a5fe00573dccf416"}}, "title": "Genomic dynamics of brown trout populations released to a novel environment.", "authors": [{"family": "Kurland", "given": "Sara", "initials": "S", "orcid": "0000-0002-5370-1236", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdfc16fe9c7c4065b3e3d3f6877424f7.json"}}, {"family": "Rafati", "given": "Nima", "initials": "N", "orcid": "0000-0002-3687-9745", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b5c32bab72f430a80485c0312ca0e21.json"}}, {"family": "Ryman", "given": "Nils", "initials": "N", "orcid": "0000-0003-3342-8479", "researcher": {"href": "https://publications.scilifelab.se/researcher/97201873ea354e959e294d8d2d69be13.json"}}, {"family": "Laikre", "given": "Linda", "initials": "L", "orcid": "0000-0001-9286-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7c7ebbb5d7a4af582746b6ab2c2d132.json"}}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "issn-l": "2045-7758", "volume": "12", "issue": "7", "pages": "e9050"}, "abstract": "Population translocations occur for a variety of reasons, from displacement due to climate change to human-induced transfers. Such actions have adverse effects on genetic variation and understanding their microevolutionary consequences requires monitoring. Here, we return to an experimental release of brown trout (Salmo trutta) in order to monitor the genomic effects of population translocations. In 1979, fish from each of two genetically (F ST = 0.16) and ecologically separate populations were simultaneously released, at one point in time, to a lake system previously void of brown trout. Here, whole-genome sequencing of pooled DNA (Pool-seq) is used to characterize diversity within and divergence between the introduced populations and fish inhabiting two lakes downstream of the release sites, sampled 30 years later (c. 5 generations). Present results suggest that while extensive hybridization has occurred, the two introduced populations are unequally represented in the lakes downstream of the release sites. One population, which is ecologically resident in its original habitat, mainly contributes to the lake closest to the release site. The other population, migratory in its natal habitat, is genetically more represented in the lake further downstream. Genomic regions putatively under directional selection in the new habitat are identified, where allele frequencies in both established populations are more similar to the introduced population stemming from a resident population than the migratory one. Results suggest that the microevolutionary consequences of population translocations, for example, hybridization and adaptation, can be rapid and that Pool-seq can be used as an initial tool to monitor genome-wide effects.", "doi": "10.1002/ece3.9050", "pmid": "35813906", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9251865"}, {"db": "pii", "key": "ECE39050"}], "notes": [], "created": "2022-08-01T12:29:56.905Z", "modified": "2024-01-16T13:48:36.012Z"}, {"entity": "publication", "iuid": "e6d9c64d82f3471c902b98f30cac0cba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e6d9c64d82f3471c902b98f30cac0cba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e6d9c64d82f3471c902b98f30cac0cba"}}, "title": "\ufeffEvidence for further non-coding RNA genes in the fungal rDNA region.", "authors": [{"family": "Rosenblad", "given": "Magnus Alm", "initials": "MA", "orcid": "0000-0002-4077-7821", "researcher": {"href": "https://publications.scilifelab.se/researcher/1db3e7106016494bb4365e099a8493ef.json"}}, {"family": "Larsson", "given": "Ellen", "initials": "E", "orcid": "0000-0003-4308-4972", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff2004120e9d46ea80f5a4cfc630ffdb.json"}}, {"family": "Walker", "given": "Arttapon", "initials": "A", "orcid": "0000-0002-3855-4522", "researcher": {"href": "https://publications.scilifelab.se/researcher/7fee6666dd05402b98a8cffd86a939ec.json"}}, {"family": "Thongklang", "given": "Naritsada", "initials": "N", "orcid": "0000-0001-9337-5001", "researcher": {"href": "https://publications.scilifelab.se/researcher/df8dcef5b3314d71abb6ccb60dce5dc7.json"}}, {"family": "Wurzbacher", "given": "Christian", "initials": "C", "orcid": "0000-0001-7418-0831", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fed784d185749498b07f7458c9ccfb6.json"}}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH", "orcid": "0000-0002-8052-0107", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f74b9c6c3d4e749adacffa0efb80b2.json"}}], "type": "journal article", "published": "2022-06-30", "journal": {"title": "MycoKeys", "issn": "1314-4049", "volume": "90", "pages": "203-213", "issn-l": null}, "abstract": "Non-coding RNA (ncRNA) genes play important, but incompletely understood, roles in various cellular processes, notably translation and gene regulation. A recent report on the detection of the ncRNA Signal Recognition Particle gene in the nuclear ribosomal internal transcribed spacer region of several species of three genera of ectomycorrhizal basidiomycetes prompted a more thorough bioinformatics search for additional ncRNA genes in the full fungal ribosomal operon. This study reports on the detection of three ncRNA genes hitherto not known from the fungal ribosomal region: nuclear RNase P RNA, RNase MRP RNA, and a possible snoRNA U14 in a total of five species of Auricularia and Inocybe. We verified their presence through resequencing of independent specimens. Two completed Auricularia genomes were found to lack these ncRNAs elsewhere than in the ribosomal operon, suggesting that these are functional genes. It seems clear that ncRNA genes play a larger role in fungal ribosomal genetics than hitherto thought.", "doi": "10.3897/mycokeys.90.84866", "pmid": "36760425", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9849065"}, {"db": "pii", "key": "84866"}], "notes": [], "created": "2022-08-26T08:39:52.764Z", "modified": "2023-06-02T10:27:22.383Z"}, {"entity": "publication", "iuid": "060874a4da484eb1bb146a7d3c2a60be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/060874a4da484eb1bb146a7d3c2a60be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/060874a4da484eb1bb146a7d3c2a60be"}}, "title": "MYCN induces cell-specific tumorigenic growth in RB1-proficient human retinal organoid and chicken retina models of retinoblastoma.", "authors": [{"family": "Blixt", "given": "Maria K E", "initials": "MKE"}, {"family": "Hellsand", "given": "Minas", "initials": "M", "orcid": "0000-0002-1459-0377", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa1e2f60d8c4fcd97c54b23246f55f2.json"}}, {"family": "Konjusha", "given": "Dardan", "initials": "D", "orcid": "0000-0002-6959-8376", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfa3697dd35c422a993a87be8d50c40b.json"}}, {"family": "Zhang", "given": "Hanzhao", "initials": "H"}, {"family": "Stenfelt", "given": "Sonya", "initials": "S"}, {"family": "\u00c5kesson", "given": "Mikael", "initials": "M"}, {"family": "Rafati", "given": "Nima", "initials": "N", "orcid": "0000-0002-3687-9745", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b5c32bab72f430a80485c0312ca0e21.json"}}, {"family": "Tararuk", "given": "Tatsiana", "initials": "T"}, {"family": "St\u00e5lhammar", "given": "Gustav", "initials": "G"}, {"family": "All-Eriksson", "given": "Charlotta", "initials": "C"}, {"family": "Ring", "given": "Henrik", "initials": "H"}, {"family": "Hallb\u00f6\u00f6k", "given": "Finn", "initials": "F", "orcid": "0000-0001-7552-187X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fd6bad55b67431c82e2e54e5b007917.json"}}], "type": "journal article", "published": "2022-06-21", "journal": {"title": "Oncogenesis", "issn": "2157-9024", "issn-l": null, "volume": "11", "issue": "1", "pages": "34"}, "abstract": "Retinoblastoma is a rare, intraocular paediatric cancer that originates in the neural retina and is most frequently caused by bi-allelic loss of RB1 gene function. Other oncogenic mutations, such as amplification and increased expression of the MYCN gene, have been found even with proficient RB1 function. In this study, we investigated whether MYCN over-expression can drive carcinogenesis independently of RB1 loss-of-function mutations. The aim was to elucidate the events that result in carcinogenesis and identify the cancer cell-of-origin. We used the chicken retina, a well-established model for studying retinal neurogenesis, and established human embryonic stem cell-derived retinal organoids as model systems. We over-expressed MYCN by electroporation of piggyBac genome-integrating expression vectors. We found that over-expression of MYCN induced tumorigenic growth with high frequency in RB1-proficient chicken retinas and human organoids. In both systems, the tumorigenic cells expressed markers for undifferentiated cone photoreceptor/horizontal cell progenitors. The over-expression resulted in metastatic retinoblastoma within 7-9 weeks in chicken. Cells expressing MYCN could be grown in vitro and, when orthotopically injected, formed tumours that infiltrated the sclera and optic nerve and expressed markers for cone progenitors. Investigation of the tumour cell phenotype determined that the potential for neoplastic growth was embryonic stage-dependent and featured a cell-specific resistance to apoptosis in the cone/horizontal cell lineage, but not in ganglion or amacrine cells. We conclude that MYCN over-expression is sufficient to drive tumorigenesis and that a cell-specific resistance to apoptosis in the cone/horizontal cell lineage mediates the cancer phenotype.", "doi": "10.1038/s41389-022-00409-3", "pmid": "35729105", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9213451"}, {"db": "pii", "key": "10.1038/s41389-022-00409-3"}], "notes": [], "created": "2022-11-09T15:38:35.302Z", "modified": "2024-01-16T13:48:36.126Z"}, {"entity": "publication", "iuid": "1abb2cd01b39416f914ab34e8dd7e53b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1abb2cd01b39416f914ab34e8dd7e53b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1abb2cd01b39416f914ab34e8dd7e53b"}}, "title": "Reply to Carlos G. Wambier and Gerard J. Nau's Letter to the Editor re: Karin Wel\u00e9n, Ebba Rosendal, Magnus Gissl\u00e9n, et al. A Phase 2 Trial of the Effect of Antiandrogen Therapy on COVID-19 Outcome: No Evidence of Benefit, Supported by Epidemiology and In Vitro Data. Eur Urol. 2022;81:285-93. Positive Effects of Enzalutamide for Hospitalized COVID-19 Patients: Still No Positive Effect of Enzalutamide for Hospitalized COVID-19 Patients.", "authors": [{"family": "Wel\u00e9n", "given": "Karin", "initials": "K"}, {"family": "Rosendal", "given": "Ebba", "initials": "E"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Oh", "given": "William K", "initials": "WK"}, {"family": "Gissl\u00e9n", "given": "Magnus", "initials": "M"}, {"family": "Ahlm", "given": "Clas", "initials": "C"}, {"family": "Connolly", "given": "Anne-Marie Fors", "initials": "AF"}, {"family": "\u00d6verby", "given": "Anna K", "initials": "AK"}, {"family": "Josefsson", "given": "Andreas", "initials": "A"}], "type": "clinical trial, phase ii", "published": "2022-06-00", "journal": {"title": "Eur. Urol.", "issn": "1873-7560", "issn-l": "0302-2838", "volume": "81", "issue": "6", "pages": "e143-e144"}, "abstract": null, "doi": "10.1016/j.eururo.2022.02.016", "pmid": "35248411", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8864103"}, {"db": "pii", "key": "S0302-2838(22)01659-1"}], "notes": [], "created": "2023-11-16T12:12:11.299Z", "modified": "2023-11-16T12:12:31.136Z"}, {"entity": "publication", "iuid": "bc12467f5df540deb9a014812f7caf7d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bc12467f5df540deb9a014812f7caf7d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bc12467f5df540deb9a014812f7caf7d"}}, "title": "Inflammation and Interferon Signatures in Peripheral B-Lymphocytes and Sera of Individuals With Fibromyalgia.", "authors": [{"family": "Fineschi", "given": "Serena", "initials": "S"}, {"family": "Klar", "given": "Joakim", "initials": "J"}, {"family": "Gustafsson", "given": "Kristin Ayoola", "initials": "KA"}, {"family": "Jonsson", "given": "Kent", "initials": "K"}, {"family": "Karlsson", "given": "Bo", "initials": "B"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2022-05-26", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "13", "pages": "874490", "issn-l": "1664-3224"}, "abstract": "Fibromyalgia (FM) is an idiopathic chronic disease characterized by widespread musculoskeletal pain, hyperalgesia and allodynia, often accompanied by fatigue, cognitive dysfunction and other symptoms. Autoimmunity and neuroinflammatory mechanisms have been suggested to play important roles in the pathophysiology of FM supported by recently identified interferon signatures in affected individuals. However, the contribution of different components in the immune system, such as the B-lymphocytes, in the progression to FM are yet unknown. Furthermore, there is a great need for biomarkers that may improve diagnostics of FM. Herein, we investigated the gene expression profile in peripheral B-cells, as well as a panel of inflammatory serum proteins, in 30 FM patients and 23 healthy matched control individuals. RNA sequence analysis revealed 60 differentially expressed genes when comparing the two groups. The group of FM patients showed increased expression of twenty-five interferon-regulated genes, such as S100A8 and S100A9, VCAM, CD163, SERPINA1, ANXA1, and an increased interferon score. Furthermore, FM was associated with elevated levels of 19 inflammatory serum proteins, such as IL8, AXIN1, SIRT2 and STAMBP, that correlated with the FM severity score. Together, the results shows that FM is associated with an interferon signature in B-cells and increased levels of a set of inflammatory serum proteins. Our findings bring further support for immune activation in the pathogenesis of FM and highlight candidate biomarkers for diagnosis and intervention in the management of FM.", "doi": "10.3389/fimmu.2022.874490", "pmid": "35693781", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9177944"}], "notes": [], "created": "2022-06-13T14:53:56.387Z", "modified": "2024-01-16T13:48:36.443Z"}, {"entity": "publication", "iuid": "0e1585b638064c99b51f7e0e203b34c1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e1585b638064c99b51f7e0e203b34c1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e1585b638064c99b51f7e0e203b34c1"}}, "title": "The impact of digital media on children's intelligence while controlling for genetic differences in cognition and socioeconomic background.", "authors": [{"family": "Sauce", "given": "Bruno", "initials": "B"}, {"family": "Liebherr", "given": "Magnus", "initials": "M"}, {"family": "Judd", "given": "Nicholas", "initials": "N"}, {"family": "Klingberg", "given": "Torkel", "initials": "T"}], "type": "journal article", "published": "2022-05-11", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "7720", "issn-l": "2045-2322"}, "abstract": "Digital media defines modern childhood, but its cognitive effects are unclear and hotly debated. We believe that studies with genetic data could clarify causal claims and correct for the typically unaccounted role of genetic predispositions. Here, we estimated the impact of different types of screen time (watching, socializing, or gaming) on children's intelligence while controlling for the confounding effects of genetic differences in cognition and socioeconomic status. We analyzed 9855 children from the USA who were part of the ABCD dataset with measures of intelligence at baseline (ages 9-10) and after two years. At baseline, time watching (r = - 0.12) and socializing (r = - 0.10) were negatively correlated with intelligence, while gaming did not correlate. After two years, gaming positively impacted intelligence (standardized \u03b2 = + 0.17), but socializing had no effect. This is consistent with cognitive benefits documented in experimental studies on video gaming. Unexpectedly, watching videos also benefited intelligence (standardized \u03b2 = + 0.12), contrary to prior research on the effect of watching TV. Although, in a posthoc analysis, this was not significant if parental education (instead of SES) was controlled for. Broadly, our results are in line with research on the malleability of cognitive abilities from environmental factors, such as cognitive training and the Flynn effect.", "doi": "10.1038/s41598-022-11341-2", "pmid": "35545630", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9095723"}, {"db": "pii", "key": "10.1038/s41598-022-11341-2"}], "notes": [], "created": "2022-11-25T08:08:47.964Z", "modified": "2022-11-25T08:08:47.967Z"}, {"entity": "publication", "iuid": "9c25f649010d4c10b0c89f067f250b61", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c25f649010d4c10b0c89f067f250b61.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c25f649010d4c10b0c89f067f250b61"}}, "title": "Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability.", "authors": [{"family": "Kierczak", "given": "Marcin", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e.json"}}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "H\u00f6glund", "given": "Julia", "initials": "J", "orcid": "0000-0001-8061-3947", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b02049b625d47a69324be23e35f5b58.json"}}, {"family": "Gourl\u00e9", "given": "Hadrien", "initials": "H", "orcid": "0000-0001-9807-1082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4143a879fa2043e7873be9e2aa72d051.json"}}, {"family": "Lo Faro", "given": "Valeria", "initials": "V", "orcid": "0000-0003-4931-7327", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e77657632e1469d9f0382673f54d071.json"}}, {"family": "Schmitz", "given": "Daniel", "initials": "D", "orcid": "0000-0003-4480-891X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b1d0c4505854c7d9ab7a2ed3116b7ae.json"}}, {"family": "Ek", "given": "Weronica E", "initials": "WE", "orcid": "0000-0003-2194-496X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7398a2bfa9154e15a4295828bc0f5bb8.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "Enroth", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5056-9137", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bb97ef16ee49f3ae0c7ea0495fd971.json"}}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Karlsson", "given": "Torgny", "initials": "T", "orcid": "0000-0001-8095-6149", "researcher": {"href": "https://publications.scilifelab.se/researcher/691d6823b8e04c5abf1613513da32b08.json"}}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-2915-4498", "researcher": {"href": "https://publications.scilifelab.se/researcher/76265c54961046e99bdb0439f9ae1d34.json"}}], "type": "journal article", "published": "2022-05-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "2532"}, "abstract": "Despite the success of genome-wide association studies, much of the genetic contribution to complex traits remains unexplained. Here, we analyse high coverage whole-genome sequencing data, to evaluate the contribution of rare genetic variants to 414 plasma proteins. The frequency distribution of genetic variants is skewed towards the rare spectrum, and damaging variants are more often rare. We estimate that less than 4.3% of the narrow-sense heritability is expected to be explained by rare variants in our cohort. Using a gene-based approach, we identify Cis-associations for 237 of the proteins, which is slightly more compared to a GWAS (N = 213), and we identify 34 associated loci in Trans. Several associations are driven by rare variants, which have larger effects, on average. We therefore conclude that rare variants could be of importance for precision medicine applications, but have a more limited contribution to the missing heritability of complex diseases.", "doi": "10.1038/s41467-022-30208-8", "pmid": "35534486", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9085767"}, {"db": "pii", "key": "10.1038/s41467-022-30208-8"}], "notes": [], "created": "2022-06-10T08:49:57.584Z", "modified": "2024-01-16T13:48:36.679Z"}, {"entity": "publication", "iuid": "370814a7c3394127aa1626b532df0e55", "links": {"self": {"href": "https://publications.scilifelab.se/publication/370814a7c3394127aa1626b532df0e55.json"}, "display": {"href": "https://publications.scilifelab.se/publication/370814a7c3394127aa1626b532df0e55"}}, "title": "Combined Transcriptomic and Protein Array Cytokine Profiling of Human Stem Cells from Dental Apical Papilla Modulated by Oral Bacteria.", "authors": [{"family": "Zymovets", "given": "Valeriia", "initials": "V"}, {"family": "Razghonova", "given": "Yelyzaveta", "initials": "Y"}, {"family": "Rakhimova", "given": "Olena", "initials": "O", "orcid": "0000-0002-3536-4467", "researcher": {"href": "https://publications.scilifelab.se/researcher/727f418f4ea24859ba4bf0e4bdf1f64c.json"}}, {"family": "Aripaka", "given": "Karthik", "initials": "K", "orcid": "0000-0001-5071-6187", "researcher": {"href": "https://publications.scilifelab.se/researcher/2622fdbe964f4f99810cdc20c67a9fe0.json"}}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L", "orcid": "0000-0001-9751-5745", "researcher": {"href": "https://publications.scilifelab.se/researcher/000321fd81b9457db66140246bbd9066.json"}}, {"family": "Kelk", "given": "Peyman", "initials": "P"}, {"family": "Landstr\u00f6m", "given": "Mar\u00e9ne", "initials": "M", "orcid": "0000-0001-6737-7230", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2f02fcfb1c1497d81a6f343bc0e6928.json"}}, {"family": "Romani Vestman", "given": "Nelly", "initials": "N", "orcid": "0000-0002-5674-8179", "researcher": {"href": "https://publications.scilifelab.se/researcher/3273e2c1a9cc4af699a0c61d2b52077a.json"}}], "type": "journal article", "published": "2022-05-03", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "23", "issue": "9", "pages": "5098", "issn-l": null}, "abstract": "Stem cells from the apical papilla (SCAP) are a promising resource for use in regenerative endodontic treatment (RET) that may be adversely affected by oral bacteria, which in turn can exert an effect on the success of RET. Our work aims to study the cytokine profile of SCAP upon exposure to oral bacteria and their supernatants-Fusobacterium nucleatum and Enterococcus faecalis-as well as to establish their effect on the osteogenic and immunogenic potentials of SCAP. Further, we target the presence of key proteins of the Wnt/\u03b2-Catenin, TGF-\u03b2, and NF-\u03baB signaling pathways, which play a crucial role in adult osteogenic differentiation of mesenchymal stem cells, using the Western blot (WB) technique. The membrane-based sandwich immunoassay and transcriptomic analysis showed that, under the influence of F. nucleatum (both bacteria and supernatant), the production of pro-inflammatory cytokines IL-6, IL-8, and MCP-1 occurred, which was also confirmed at the mRNA level. Conversely, E. faecalis reduced the secretion of the aforementioned cytokines at both mRNA and protein levels. WB analysis showed that SCAP co-cultivation with E. faecalis led to a decrease in the level of the key proteins of the Wnt/\u03b2-Catenin and NF-\u03baB signaling pathways: \u03b2-Catenin (p = 0.0068 *), LRP-5 (p = 0.0059 **), and LRP-6 (p = 0.0329 *), as well as NF-kB (p = 0.0034 **) and TRAF6 (p = 0.0285 *). These results suggest that oral bacteria can up- and downregulate the immune and inflammatory responses of SCAP, as well as influence the osteogenic potential of SCAP, which may negatively regulate the success of RET.", "doi": "10.3390/ijms23095098", "pmid": "35563488", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9103834"}, {"db": "pii", "key": "ijms23095098"}], "notes": [], "created": "2022-05-09T09:39:42.630Z", "modified": "2024-01-16T13:48:36.757Z"}, {"entity": "publication", "iuid": "e43fbc284d1246c1a9c5d431885a3a6b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e43fbc284d1246c1a9c5d431885a3a6b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e43fbc284d1246c1a9c5d431885a3a6b"}}, "title": "Re: Chen Dong, Sung-Lang Chen, and Wen-Wei Sung's Letter to the Editor re: Karin Wel\u00e9n, Ebba Rosendal, Magnus Gissl\u00e9n, et al. A Phase 2 Trial of the Effect of Antiandrogen Therapy on COVID-19 Outcome: No Evidence of Benefit, Supported by Epidemiology and In Vitro Data. Eur Urol. 2022;81:285-93.", "authors": [{"family": "Welen", "given": "Karin", "initials": "K"}, {"family": "Rosendal", "given": "Ebba", "initials": "E"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Fors Connolly", "given": "Anne-Marie", "initials": "AM"}, {"family": "\u00d6verby", "given": "Anna K", "initials": "AK"}, {"family": "Josefsson", "given": "Andreas", "initials": "A"}], "type": "letter", "published": "2022-05-00", "journal": {"title": "Eur. Urol.", "issn": "1873-7560", "volume": "81", "issue": "5", "pages": "e124-e125", "issn-l": "0302-2838"}, "abstract": null, "doi": "10.1016/j.eururo.2022.02.001", "pmid": "35168845", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8837902"}, {"db": "pii", "key": "S0302-2838(22)01605-0"}], "notes": [], "created": "2023-11-16T12:11:34.295Z", "modified": "2023-11-16T12:11:34.300Z"}, {"entity": "publication", "iuid": "a0a0ece375d24f3fafa2a00b725911ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a0a0ece375d24f3fafa2a00b725911ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a0a0ece375d24f3fafa2a00b725911ff"}}, "title": "Multi-omics analysis of the cervical epithelial integrity of women using depot medroxyprogesterone acetate.", "authors": [{"family": "Bradley", "given": "Frideborg", "initials": "F", "orcid": "0000-0003-3006-7284", "researcher": {"href": "https://publications.scilifelab.se/researcher/d51eaeb949e94bd39ab3605d495dc647.json"}}, {"family": "Franz\u00e9n Boger", "given": "Mathias", "initials": "M"}, {"family": "Kaldhusdal", "given": "Vilde", "initials": "V"}, {"family": "\u00c5hlberg", "given": "Alexandra", "initials": "A"}, {"family": "Edfeldt", "given": "Gabriella", "initials": "G"}, {"family": "Lajoie", "given": "Julie", "initials": "J"}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Omollo", "given": "Kenneth", "initials": "K"}, {"family": "Damdimopoulos", "given": "Anastasios", "initials": "A"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Oyugi", "given": "Julius", "initials": "J"}, {"family": "Kimani", "given": "Joshua", "initials": "J"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Fowke", "given": "Keith", "initials": "K"}, {"family": "Tjernlund", "given": "Annelie", "initials": "A"}, {"family": "Broliden", "given": "Kristina", "initials": "K", "orcid": "0000-0003-2224-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/95346da4e5984d48bbb50032797155e5.json"}}], "type": "journal article", "published": "2022-05-00", "journal": {"title": "PLoS Pathog.", "issn": "1553-7374", "volume": "18", "issue": "5", "pages": "e1010494", "issn-l": "1553-7366"}, "abstract": "Depot medroxyprogesterone acetate (DMPA) is an injectable hormonal contraceptive used by millions of women worldwide. However, experimental studies have associated DMPA use with genital epithelial barrier disruption and mucosal influx of human immunodeficiency virus (HIV) target cells. We explored the underlying molecular mechanisms of these findings. Ectocervical biopsies and cervicovaginal lavage (CVL) specimens were collected from HIV-seronegative Kenyan sex workers using DMPA (n = 32) or regularly cycling controls (n = 64). Tissue samples were assessed by RNA-sequencing and quantitative imaging analysis, whereas protein levels were measured in CVL samples. The results suggested a DMPA-associated upregulation of genes involved in immune regulation, including genes associated with cytokine-mediated signaling and neutrophil-mediated immunity. A transcription factor analysis further revealed DMPA-associated upregulation of RELA and NFKB1 which are involved in several immune activation pathways. Several genes significantly downregulated in the DMPA versus the control group were involved in epithelial structure and function, including genes encoding keratins, small proline-rich proteins, and cell-cell adhesion proteins. Pathway analyses indicated DMPA use was associated with immune activation and suppression of epithelium development, including keratinization and cornification processes. The cervicovaginal microbiome composition (Lactobacillus dominant and non-Lactobacillus dominant) had no overall interactional impact on the DMPA associated tissue gene expression. Imaging analysis verified that DMPA use was associated with an impaired epithelial layer as illustrated by staining for the selected epithelial junction proteins E-cadherin, desmoglein-1 and claudin-1. Additional staining for CD4+ cells revealed a more superficial location of these cells in the ectocervical epithelium of DMPA users versus controls. Altered protein levels of SERPINB1 and ITIH2 were further observed in the DMPA group. Identification of specific impaired epithelial barrier structures at the gene expression level, which were verified at the functional level by tissue imaging analysis, illustrates mechanisms by which DMPA adversely may affect the integrity of the genital mucosa.", "doi": "10.1371/journal.ppat.1010494", "pmid": "35533147", "labels": {"BioImage Informatics": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9119532"}, {"db": "pii", "key": "PPATHOGENS-D-21-02612"}], "notes": [], "created": "2022-08-30T13:46:44.982Z", "modified": "2022-12-07T11:49:48.217Z"}, {"entity": "publication", "iuid": "4ffe9e31ba3e4dca84a065bd8a0d8062", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ffe9e31ba3e4dca84a065bd8a0d8062.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ffe9e31ba3e4dca84a065bd8a0d8062"}}, "title": "Microbial functional genes influenced by short-term experimental drought across European agricultural fields", "authors": [{"family": "Kozjek", "given": "Katja", "initials": "K", "orcid": "0000-0001-9381-7447", "researcher": {"href": "https://publications.scilifelab.se/researcher/89d979db71154d31af52f3e739a538a1.json"}}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L", "orcid": "0000-0001-9751-5745", "researcher": {"href": "https://publications.scilifelab.se/researcher/000321fd81b9457db66140246bbd9066.json"}}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Hedlund", "given": "Katarina", "initials": "K"}], "type": "journal-article", "published": "2022-05-00", "journal": {"title": "Soil Biology and Biochemistry", "issn": "0038-0717", "volume": "168", "pages": "108650", "issn-l": null}, "abstract": null, "doi": "10.1016/j.soilbio.2022.108650", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2022-11-25T08:15:49.438Z", "modified": "2024-01-16T13:48:36.801Z"}, {"entity": "publication", "iuid": "651395720d3344fa8938a31e17c0c548", "links": {"self": {"href": "https://publications.scilifelab.se/publication/651395720d3344fa8938a31e17c0c548.json"}, "display": {"href": "https://publications.scilifelab.se/publication/651395720d3344fa8938a31e17c0c548"}}, "title": "A starch- and sucrose-reduced dietary intervention in irritable bowel syndrome patients produced a shift in gut microbiota composition along with changes in phylum, genus, and amplicon sequence variant abundances, without affecting the micro-RNA levels.", "authors": [{"family": "Nilholm", "given": "Clara", "initials": "C"}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L"}, {"family": "Roth", "given": "Bodil", "initials": "B"}, {"family": "D'Amato", "given": "Mauro", "initials": "M"}, {"family": "Ohlsson", "given": "Bodil", "initials": "B", "orcid": "0000-0002-9142-5244", "researcher": {"href": "https://publications.scilifelab.se/researcher/d61d0a97d7df49e5856419fc06769c23.json"}}], "type": "journal article", "published": "2022-05-00", "journal": {"title": "United European Gastroenterol J", "issn": "2050-6414", "volume": "10", "issue": "4", "pages": "363-375", "issn-l": null}, "abstract": "A randomized clinical trial with a starch- and sucrose-reduced diet (SSRD) in irritable bowel syndrome (IBS) patients has shown clear improvement of participants' symptoms. The present study aimed to explore the effects of the SSRD on the gut microbiota and circulating micro-RNA in relation to nutrient intake and gastrointestinal symptoms.\n\nIBS patients were randomized to a 4-week SSRD intervention (n = 80) or control group (n = 25); habitual diet). At baseline and 4 weeks, blood and fecal samples, 4 day-dietary records, and symptom questionnaires were collected, that is, Rome IV questionnaires, IBS-symptom severity score (IBS-SSS) and visual analog scale for IBS (VAS-IBS). Micro-RNA was analyzed in blood and microbiota in faeces by 16S rRNA from regions V1-V2.\n\nThe alpha diversity was unaffected, whereas beta diversity was decreased (p < 0.001) along with increased abundance of Proteobacteria (p = 0.0036) and decreased abundance of Bacteroidetes phyla (p < 0.001) in the intervention group at 4 weeks. Few changes were noted in the controls. The shift in beta diversity and phyla abundance correlated with decreased intakes of carbohydrates, disaccharides, and starch and increased fat and protein intakes. Proteobacteria abundance also correlated positively (R2 = 0.07, p = 0.0016), and Bacteroidetes negatively (R2 = 0.07, p = 0.0017), with reduced total IBS-SSS. Specific genera, for example, Eubacterium eligens, Lachnospiraceae UCG-001, Victivallis, and Lachnospira increased significantly in the intervention group (p < 0.001 for all), whereas Marvinbryantia, DTU089 (Ruminoccocaceae family), Enterorhabdus, and Olsenella decreased, together with changes in amplicon sequence variant (ASV) levels. Modest changes of genus and ASV abundance were observed in the control group. No changes were observed in micro-RNA expression in either group.\n\nThe SSRD induced a shift in beta diversity along with several bacteria at different levels, associated with changes in nutrient intakes and reduced gastrointestinal symptoms. No corresponding changes were observed in the control group. Neither the nutrient intake nor the microbiota changes affected micro-RNA expression. The study was registered at ClinicalTrials.gov data base (NCT03306381).", "doi": "10.1002/ueg2.12227", "pmid": "35484927", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9103372"}, {"db": "ClinicalTrials.gov", "key": "NCT03306381"}], "notes": [], "created": "2022-05-09T09:39:01.304Z", "modified": "2024-01-16T13:48:36.858Z"}, {"entity": "publication", "iuid": "4dccb5a262a34109b4a7765cc807349f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4dccb5a262a34109b4a7765cc807349f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4dccb5a262a34109b4a7765cc807349f"}}, "title": "The Carniolan Honeybee from Slovenia-A Complete and Annotated Mitochondrial Genome with Comparisons to Closely Related Apis mellifera Subspecies.", "authors": [{"family": "Mo\u0161kri\u010d", "given": "Ajda", "initials": "A", "orcid": "0000-0001-7517-293X", "researcher": {"href": "https://publications.scilifelab.se/researcher/02163129a89143cdaeb61e7b7656ca60.json"}}, {"family": "Marin\u010d", "given": "Andra\u017e", "initials": "A"}, {"family": "Ferk", "given": "Polonca", "initials": "P", "orcid": "0000-0002-4541-3648", "researcher": {"href": "https://publications.scilifelab.se/researcher/975dc1d760854f7e98262a92ac7bdcc6.json"}}, {"family": "Lesko\u0161ek", "given": "Brane", "initials": "B"}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "MB"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Soler", "given": "Lucile", "initials": "L", "orcid": "0000-0002-0121-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/f701059f90fe4c7c9b969079e74aac57.json"}}, {"family": "Pre\u0161ern", "given": "Janez", "initials": "J", "orcid": "0000-0003-2479-6106", "researcher": {"href": "https://publications.scilifelab.se/researcher/b736d51a725343fba00c2c8871097158.json"}}], "type": "journal article", "published": "2022-04-22", "journal": {"title": "Insects", "issn": "2075-4450", "volume": "13", "issue": "5", "pages": "403", "issn-l": null}, "abstract": "The complete mitochondrial genome of the Carniolan honeybee (Apis mellifera carnica) from Slovenia, a homeland of this subspecies, was acquired in two contigs from WGS data and annotated. The newly obtained mitochondrial genome is a circular closed loop of 16,447 bp. It comprises 37 genes (13 protein coding genes, 22 tRNA genes, and 2 rRNA genes) and an AT-rich control region. The order of the tRNA genes resembles the order characteristic of A. mellifera. The mitogenomic sequence of A. m. carnica from Slovenia contains 44 uniquely coded sites in comparison to the closely related subspecies A. m. ligustica and to A. m. carnica from Austria. Furthermore, 24 differences were recognised in comparison between A. m. carnica and A. m. ligustica subspecies. Among them, there are three SNPs that affect translation in the nd2, nd4, and cox2 genes, respectively. The phylogenetic placement of A. m. carnica from Slovenia within C lineage deviates from the expected position and changes the perspective on relationship between C and O lineages. The results of this study represent a valuable addition to the information available in the phylogenomic studies of A. mellifera-a pollinator species of worldwide importance. Such genomic information is essential for this local subspecies' conservation and preservation as well as its breeding and selection.", "doi": "10.3390/insects13050403", "pmid": "35621738", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9146700"}, {"db": "pii", "key": "insects13050403"}], "notes": [], "created": "2022-05-24T11:31:50.168Z", "modified": "2024-01-16T13:48:36.990Z"}, {"entity": "publication", "iuid": "595bc0af097f4c82b88f2b3184d72f42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/595bc0af097f4c82b88f2b3184d72f42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/595bc0af097f4c82b88f2b3184d72f42"}}, "title": "Weakened resilience of benthic microbial communities in the face of climate change", "authors": [{"family": "Seidel", "given": "Laura", "initials": "L", "orcid": "0000-0002-2620-914X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0923436cd0a42cea933771b57ae8c94.json"}}, {"family": "Ketzer", "given": "Marcelo", "initials": "M", "orcid": "0000-0003-4796-8177", "researcher": {"href": "https://publications.scilifelab.se/researcher/5224e1bded3a4866802b863ed32cb10e.json"}}, {"family": "Broman", "given": "Elias", "initials": "E", "orcid": "0000-0001-9005-5168", "researcher": {"href": "https://publications.scilifelab.se/researcher/63826da04a1f4f80bc3229df12bac9b7.json"}}, {"family": "Shahabi-Ghahfarokhi", "given": "Sina", "initials": "S"}, {"family": "Rahmati-Abkenar", "given": "Mahboubeh", "initials": "M", "orcid": "0000-0002-3193-9331", "researcher": {"href": "https://publications.scilifelab.se/researcher/f64c520b937a4871ba129141b01042b9.json"}}, {"family": "Turner", "given": "Stephanie", "initials": "S"}, {"family": "St\u00e5hle", "given": "Magnus", "initials": "M"}, {"family": "Bergstr\u00f6m", "given": "Kristofer", "initials": "K"}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L", "orcid": "0000-0001-9751-5745", "researcher": {"href": "https://publications.scilifelab.se/researcher/000321fd81b9457db66140246bbd9066.json"}}, {"family": "Ali", "given": "Ashfaq", "initials": "A"}, {"family": "Forsman", "given": "Anders", "initials": "A", "orcid": "0000-0001-9598-7618", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a605b671cd3414d9c75c2408b74d3de.json"}}, {"family": "Hylander", "given": "Samuel", "initials": "S", "orcid": "0000-0002-3740-5998", "researcher": {"href": "https://publications.scilifelab.se/researcher/47f71565ec50426e9d4893a5335e5fa3.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal-article", "published": "2022-03-08", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "issn-l": null, "volume": "2", "issue": "1", "pages": null}, "abstract": null, "doi": "10.1038/s43705-022-00104-9", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2022-03-28T08:58:38.250Z", "modified": "2024-01-16T13:48:37.272Z"}, {"entity": "publication", "iuid": "3c91f8a634fa4acda7402751635c19b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3c91f8a634fa4acda7402751635c19b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3c91f8a634fa4acda7402751635c19b8"}}, "title": "Hypoxia induces radioresistance, epithelial\u2011mesenchymal transition, cancer stem cell\u2011like phenotype and changes in genes possessing multiple biological functions in head and neck squamous cell carcinoma.", "authors": [{"family": "Wiechec", "given": "Emilia", "initials": "E"}, {"family": "Matic", "given": "Natasa", "initials": "N"}, {"family": "Ali", "given": "Ashfaq", "initials": "A"}, {"family": "Roberg", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "Oncol. Rep.", "issn": "1791-2431", "volume": "47", "issue": "3", "issn-l": "1021-335X"}, "abstract": "Hypoxia has been linked with increased resistance to treatment in various solid tumors, including head and neck squamous cell carcinoma (HNSCC). The aim of the present study was to identify genes involved in hypoxia\u2011mediated responses to radiotherapy in HNSCC. A total of three HNSCC cell lines with an epithelial phenotype were selected for this study and cultured under normoxic (21% O2) or hypoxic (1% O2) conditions. The sensitivity of the HNSCC cells to radiotherapy was assessed by a crystal violet assay. Western blotting (for protein expression), cDNA microarrays and reverse transcription\u2011quantitative PCR (for gene expression) were also applied. Small interfering RNA silencing was used to knock down target genes. The results revealed that hypoxia negatively affected the response of HNSCC cells to radiotherapy. Of note, increased levels of N\u2011cadherin, vimentin and fibronectin, as well as stem cell\u2011associated transcription factors, were observed under hypoxia. The microarray analysis revealed a number of hypoxia\u2011regulated genes that were involved in multiple biological functions. However, downregulation of hypoxia\u2011regulated genes did not affect sensitivity to radiotherapy of the investigated cell lines. Taken together, the present findings indicated several important pathways and genes that were involved in hypoxia and radiotherapy resistance. It is hypothesized that panels of reported hypoxia\u2011regulated genes may be useful for the prediction of radiotherapy responses in patients with HNSCC.", "doi": "10.3892/or.2022.8269", "pmid": "35059742", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8808704"}, {"db": "pii", "key": "58"}], "notes": [], "created": "2022-11-24T15:00:08.554Z", "modified": "2022-11-24T15:00:08.562Z"}, {"entity": "publication", "iuid": "436dafbcf3644397a7fb3f855f9e961a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/436dafbcf3644397a7fb3f855f9e961a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/436dafbcf3644397a7fb3f855f9e961a"}}, "title": "Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long-read metabarcoding.", "authors": [{"family": "Eshghi Sahraei", "given": "Shadi", "initials": "S", "orcid": "0000-0003-4741-5871", "researcher": {"href": "https://publications.scilifelab.se/researcher/98f7d11029704e33b61a8c27daa54378.json"}}, {"family": "Furneaux", "given": "Brendan", "initials": "B", "orcid": "0000-0003-3522-7363", "researcher": {"href": "https://publications.scilifelab.se/researcher/df196c994b3c4086b4f94eacf4e57239.json"}}, {"family": "Kluting", "given": "Kerri", "initials": "K", "orcid": "0000-0002-2328-8081", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc941190363e475e818618f5ede34218.json"}}, {"family": "Zakieh", "given": "Mustafa", "initials": "M"}, {"family": "Rydin", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0002-7582-3998", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee9ea3f8490b43128a5710c693855584.json"}}, {"family": "Hytteborn", "given": "H\u00e5kan", "initials": "H"}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "12", "issue": "3", "pages": "e8676", "issn-l": "2045-7758"}, "abstract": "Long amplicon metabarcoding has opened the door for phylogenetic analysis of the largely unknown communities of microeukaryotes in soil. Here, we amplified and sequenced the ITS and LSU regions of the rDNA operon (around 1500 bp) from grassland soils using PacBio SMRT sequencing. We tested how three different methods for generation of operational taxonomic units (OTUs) effected estimated richness and identified taxa, and how well large-scale ecological patterns associated with shifting environmental conditions were recovered in data from the three methods. The field site at Kungs\u00e4ngen Nature Reserve has drawn frequent visitors since Linnaeus's time, and its species rich vegetation includes the largest population of Fritillaria meleagris in Sweden. To test the effect of different OTU generation methods, we sampled soils across an abrupt moisture transition that divides the meadow community into a Carex acuta dominated plant community with low species richness in the wetter part, which is visually distinct from the mesic-dry part that has a species rich grass-dominated plant community including a high frequency of F. meleagris. We used the moisture and plant community transition as a framework to investigate how detected belowground microeukaryotic community composition was influenced by OTU generation methods. Soil communities in both moisture regimes were dominated by protists, a large fraction of which were taxonomically assigned to Ciliophora (Alveolata) while 30%-40% of all reads were assigned to kingdom Fungi. Ecological patterns were consistently recovered irrespective of OTU generation method used. However, different methods strongly affect richness estimates and the taxonomic and phylogenetic resolution of the characterized community with implications for how well members of the microeukaryotic communities can be recognized in the data.", "doi": "10.1002/ece3.8676", "pmid": "35342585", "labels": {"NGI Long read": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8928899"}, {"db": "pii", "key": "ECE38676"}], "notes": [], "created": "2022-03-29T04:46:34.688Z", "modified": "2024-01-16T13:48:37.364Z"}, {"entity": "publication", "iuid": "688998759da24819bb8ca791b299f124", "links": {"self": {"href": "https://publications.scilifelab.se/publication/688998759da24819bb8ca791b299f124.json"}, "display": {"href": "https://publications.scilifelab.se/publication/688998759da24819bb8ca791b299f124"}}, "title": "Similar risk of cancer in patients younger than 55 years with or without a total hip arthroplasty (THA): a population- based cohort study on 18,771 exposed to THA and 87,683 controls.", "authors": [{"family": "Hailer", "given": "Yasmin D", "initials": "YD"}, {"family": "K\u00e4rrholm", "given": "Johan", "initials": "J"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Holmberg", "given": "Lars", "initials": "L"}, {"family": "Hailer", "given": "Nils P", "initials": "NP"}], "type": "journal article", "published": "2022-02-08", "journal": {"title": "Acta Orthop", "issn": "1745-3682", "volume": "93", "pages": "317-326", "issn-l": null}, "abstract": "Concerns related to a potentially increased risk of cancer after total hip arthroplasty (THA) have frequently surfaced, especially since the novel EU medical device regulation classified cobalt as carcinogenic. We assessed the risk of cancer after THA in a nationwide cohort of patients younger than 55 years at surgery.\n\nIn this population-based longitudinal cohort study, 18,771 individuals exposed to THA were identified in the Swedish Hip Arthroplasty Registry (SHAR) and compared with 87,683 unexposed individuals who were matched by age, sex, and residence. Diagnoses, socioeconomic background, and dates of death were obtained from the Swedish Cancer Register, the National Patient Register, and Statistics Sweden. Primary outcome was the adjusted risk of any cancer after the first THA; secondary outcomes were specific cancer forms.\n\nWe found no enhanced adjusted risk of developing any cancer, either in exposed females compared with unexposed females (hazard ratio [HR] 1.1, 95% confidence interval [CI] 0.95-1.2), or in exposed males (HR 1.1, CI 0.99-1.2). When analysing specific cancers, increased adjusted risks were found for thyroid and pancreas cancer in exposed females, and for cancer of the stomach, skin melanoma, and prostate cancer in exposed males.\n\nThis study indicates that there is no statistically significant increased overall risk of cancer in young THA-exposed patients. The potentially slightly enhanced risk for specific cancers may be due to residual confounding resulting from risk factors not accounted for and merits further investigation.", "doi": "10.2340/17453674.2022.2044", "pmid": "35138409", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8826686"}], "notes": [], "created": "2023-11-16T12:15:22.844Z", "modified": "2023-11-16T12:15:22.847Z"}, {"entity": "publication", "iuid": "d5c0c16b13b14f5e88c23efe7344bee1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d5c0c16b13b14f5e88c23efe7344bee1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d5c0c16b13b14f5e88c23efe7344bee1"}}, "title": "Clinical and biological relevance of the transcriptomic-based prostate cancer metastasis subtypes MetA-C.", "authors": [{"family": "Thysell", "given": "Elin", "initials": "E"}, {"family": "K\u00f6hn", "given": "Linda", "initials": "L"}, {"family": "Semenas", "given": "Julius", "initials": "J", "orcid": "0000-0001-5394-7239", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0402a104066426dbeb5108ac120a46f.json"}}, {"family": "J\u00e4remo", "given": "Helena", "initials": "H"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Lundholm", "given": "Marie", "initials": "M"}, {"family": "Thellenberg Karlsson", "given": "Camilla", "initials": "C"}, {"family": "Damber", "given": "Jan-Erik", "initials": "JE"}, {"family": "Widmark", "given": "Anders", "initials": "A"}, {"family": "Crnalic", "given": "Sead", "initials": "S"}, {"family": "Josefsson", "given": "Andreas", "initials": "A"}, {"family": "Wel\u00e9n", "given": "Karin", "initials": "K"}, {"family": "Nilsson", "given": "Rolf J A", "initials": "RJA"}, {"family": "Bergh", "given": "Anders", "initials": "A"}, {"family": "Wikstr\u00f6m", "given": "Pernilla", "initials": "P", "orcid": "0000-0002-6347-1999", "researcher": {"href": "https://publications.scilifelab.se/researcher/66e1e640e83948a4a3f8a1ddd49bd953.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "issn-l": "1574-7891", "volume": "16", "issue": "4", "pages": "846-859"}, "abstract": "To improve treatment of metastatic prostate cancer, the biology of metastases needs to be understood. We recently described three subtypes of prostate cancer bone metastases (MetA-C), based on differential gene expression. The aim of this study was to verify the clinical relevance of these subtypes and to explore their biology and relations to genetic drivers. Freshly-frozen metastasis samples were obtained as hormone-naive (n = 17), short-term castrated (n = 21), or castration-resistant (n = 65) from a total of 67 patients. Previously published sequencing data from 573 metastasis samples were also analyzed. Through transcriptome profiling and sample classification based on a set of predefined MetA-C-differentiating genes, we found that most metastases were heterogeneous for the MetA-C subtypes. Overall, MetA was the most common subtype, while MetB was significantly enriched in castration-resistant samples and in liver metastases, and consistently associated with poor prognosis. By gene set enrichment analysis, the phenotype of MetA was described by high androgen response, protein secretion and adipogenesis, MetB by high cell cycle activity and DNA repair, and MetC by epithelial-to-mesenchymal transition and inflammation. The MetB subtype demonstrated single nucleotide variants of RB transcriptional corepressor 1 (RB1) and loss of 21 genes at chromosome 13, including RB1, but provided independent prognostic value to those genetic aberrations. In conclusion, a distinct set of gene transcripts can be used to classify prostate cancer metastases into the subtypes MetA-C. The MetA-C subtypes show diverse biology, organ tropism, and prognosis. The MetA-C classification may be used independently, or in combination with genetic markers, primarily to identify MetB patients in need of complementary therapy to conventional androgen receptor-targeting treatments.", "doi": "10.1002/1878-0261.13158", "pmid": "34889043", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Clinical Genomics Ume\u00e5": "Service", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8847984"}], "notes": [], "created": "2022-01-11T07:51:15.811Z", "modified": "2022-12-05T11:19:52.667Z"}, {"entity": "publication", "iuid": "77a6fcbf80d74953b0f9c1b7234a221d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/77a6fcbf80d74953b0f9c1b7234a221d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/77a6fcbf80d74953b0f9c1b7234a221d"}}, "title": "Whole-Exome Sequencing of HPV Positive Tonsillar and Base of Tongue Squamous Cell Carcinomas Reveals a Global Mutational Pattern along with Relapse-Specific Somatic Variants.", "authors": [{"family": "\u00c4hrlund-Richter", "given": "Andreas", "initials": "A"}, {"family": "Holzhauser", "given": "Stefan", "initials": "S"}, {"family": "Dalianis", "given": "Tina", "initials": "T"}, {"family": "N\u00e4sman", "given": "Anders", "initials": "A", "orcid": "0000-0003-4602-4297", "researcher": {"href": "https://publications.scilifelab.se/researcher/368352486dc54915b6873ad1aae59ea2.json"}}, {"family": "Mints", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2021-12-24", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "14", "issue": "1", "issn-l": "2072-6694"}, "abstract": "To identify predictive/targetable markers in human papillomavirus positive (HPV+) tonsillar and base of tongue cancer (TSCC/BOTSCC), whole-exome sequencing (WES) of tumours of patients with/without recurrence was performed. Forty primary tumours and adjacent normal tissue were separated by micro-dissection from formalin-fixed paraffin-embedded tissue from patients treated with curative intent 2000-2014 at Karolinska University Hospital. Successful sequencing was obtained in primary tumours of 18 patients without and primaries of 17 with local or distant recurrence, as well as in 10 corresponding recurrences (i.e., five local relapses and five distant metastases) from these 17 patients. One variant-a high-impact deletion in the CDC27 gene-was observed only in primaries of 5/17 patients that had a recurrence after full treatment but in none of those without recurrence. In addition, 3 variants and 26 mutated genes, including CDC27, BCLAF1 and AQP7, were present in at least 30% of all primary tumours independent of prognosis. To conclude, a CDC27 deletion was specific and found in ~30% of samples from patients with a local relapse/distant metastasis and could, therefore, potentially be a prospective marker to predict prognosis. Commonly mutated genes, such as BCLAF1, should be further studied in the context of targeted therapy.", "doi": "10.3390/cancers14010077", "pmid": "35008243", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "cancers14010077"}, {"db": "pmc", "key": "PMC8750256"}], "notes": [], "created": "2022-01-17T08:37:22.165Z", "modified": "2022-01-17T08:37:22.180Z"}, {"entity": "publication", "iuid": "fd32a79bac2c4dec8dc43e60bcd060f0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd32a79bac2c4dec8dc43e60bcd060f0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd32a79bac2c4dec8dc43e60bcd060f0"}}, "title": "Immune-Proteome Profiling in Classical Hodgkin Lymphoma Tumor Diagnostic Tissue.", "authors": [{"family": "Gholiha", "given": "Alex Reza", "initials": "AR", "orcid": "0000-0002-3393-1106", "researcher": {"href": "https://publications.scilifelab.se/researcher/727d46bb6742412aacdf87a38957b3e9.json"}}, {"family": "Hollander", "given": "Peter", "initials": "P", "orcid": "0000-0002-0226-5681", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1c6693d3ede463eb78e6da010db601f.json"}}, {"family": "L\u00f6f", "given": "Liza", "initials": "L"}, {"family": "Larsson", "given": "Anders", "initials": "A", "orcid": "0000-0003-3161-0402", "researcher": {"href": "https://publications.scilifelab.se/researcher/2276de26382b402aa384ac231f30f156.json"}}, {"family": "Hashemi", "given": "Jamileh", "initials": "J"}, {"family": "Ulfstedt", "given": "Johan Mattsson", "initials": "JM", "orcid": "0000-0003-0682-7394", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97878de79294d14b317f56f7bbf774c.json"}}, {"family": "Molin", "given": "Daniel", "initials": "D"}, {"family": "Amini", "given": "Rose-Marie", "initials": "RM"}, {"family": "Freyhult", "given": "Eva", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M"}, {"family": "Enblad", "given": "Gunilla", "initials": "G"}], "type": "journal article", "published": "2021-12-21", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "14", "issue": "1", "pages": "9", "issn-l": "2072-6694"}, "abstract": "In classical Hodgkin Lymphoma (cHL), immunoediting via protein signaling is key to evading tumor surveillance. We aimed to identify immune-related proteins that distinguish diagnostic cHL tissues (=diagnostic tumor lysates, n = 27) from control tissues (reactive lymph node lysates, n = 30). Further, we correlated our findings with the proteome plasma profile between cHL patients (n = 26) and healthy controls (n = 27). We used the proximity extension assay (PEA) with the OlinkTM multiplex Immuno-Oncology panel, consisting of 92 proteins. Univariate, multivariate-adjusted analysis and Benjamini-Hochberg's false discovery testing (=Padj) were performed to detect significant discrepancies. Proteins distinguishing cHL cases from controls were more numerous in plasma (30 proteins) than tissue (17 proteins), all Padj < 0.05. Eight of the identified proteins in cHL tissue (PD-L1, IL-6, CCL17, CCL3, IL-13, MMP12, TNFRS4, and LAG3) were elevated in both cHL tissues and cHL plasma compared with control samples. Six proteins distinguishing cHL tissues from controls tissues were significantly correlated to PD-L1 expression in cHL tissue (IL-6, MCP-2, CCL3, CCL4, GZMB, and IFN-gamma, all p \u22640.05). In conclusion, this study introduces a distinguishing proteomic profile in cHL tissue and potential immune-related markers of pathophysiological relevance.", "doi": "10.3390/cancers14010009", "pmid": "35008176", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "cancers14010009"}, {"db": "pmc", "key": "PMC8750205"}], "notes": [], "created": "2022-01-11T07:52:22.416Z", "modified": "2022-11-21T15:22:11.449Z"}, {"entity": "publication", "iuid": "c9e68c660100430f9245ba4d70b9595f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9e68c660100430f9245ba4d70b9595f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9e68c660100430f9245ba4d70b9595f"}}, "title": "A Phase 2 Trial of the Effect of Antiandrogen Therapy on COVID-19 Outcome: No Evidence of Benefit, Supported by Epidemiology and In Vitro Data.", "authors": [{"family": "Wel\u00e9n", "given": "Karin", "initials": "K"}, {"family": "Rosendal", "given": "Ebba", "initials": "E"}, {"family": "Gissl\u00e9n", "given": "Magnus", "initials": "M"}, {"family": "Lenman", "given": "Annasara", "initials": "A"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Fonseca-Rodr\u00edguez", "given": "Osvaldo", "initials": "O"}, {"family": "Bremell", "given": "Daniel", "initials": "D"}, {"family": "Stranne", "given": "Johan", "initials": "J"}, {"family": "Balkhed", "given": "\u00c5se \u00d6stholm", "initials": "\u00c5\u00d6"}, {"family": "Niward", "given": "Katarina", "initials": "K"}, {"family": "Repo", "given": "Johanna", "initials": "J"}, {"family": "Robinsson", "given": "David", "initials": "D"}, {"family": "Henningsson", "given": "Anna J", "initials": "AJ"}, {"family": "Styrke", "given": "Johan", "initials": "J"}, {"family": "Angelin", "given": "Martin", "initials": "M"}, {"family": "Lindquist", "given": "Elisabeth", "initials": "E"}, {"family": "Allard", "given": "Annika", "initials": "A"}, {"family": "Becker", "given": "Miriam", "initials": "M"}, {"family": "Rudolfsson", "given": "Stina", "initials": "S"}, {"family": "Buckland", "given": "Robert", "initials": "R"}, {"family": "Carlsson", "given": "Camilla Thellenberg", "initials": "CT"}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"family": "Nilsson", "given": "Anna C", "initials": "AC"}, {"family": "Ahlm", "given": "Clas", "initials": "C"}, {"family": "Connolly", "given": "Anne-Marie Fors", "initials": "AF"}, {"family": "\u00d6verby", "given": "Anna K", "initials": "AK"}, {"family": "Josefsson", "given": "Andreas", "initials": "A"}], "type": "journal article", "published": "2021-12-15", "journal": {"title": "Eur. Urol.", "issn": "1873-7560", "issn-l": "0302-2838"}, "abstract": "Men are more severely affected by COVID-19. Testosterone may influence SARS-CoV-2 infection and the immune response.\n\nTo clinically, epidemiologically, and experimentally evaluate the effect of antiandrogens on SARS-CoV-2 infection.\n\nA randomized phase 2 clinical trial (COVIDENZA) enrolled 42 hospitalized COVID-19 patients before safety evaluation. We also conducted a population-based retrospective study of 7894 SARS-CoV-2-positive prostate cancer patients and an experimental study using an air-liquid interface three-dimensional culture model of primary lung cells.\n\nIn COVIDENZA, patients were randomized 2:1 to 5 d of enzalutamide or standard of care.\n\nThe primary outcomes in COVIDENZA were the time to mechanical ventilation or discharge from hospital. The population-based study investigated risk of hospitalization, intensive care, and death from COVID-19 after androgen inhibition.\n\nEnzalutamide-treated patients required longer hospitalization (hazard ratio [HR] for discharge from hospital 0.43, 95% confidence interval [CI] 0.20-0.93) and the trial was terminated early. In the epidemiological study, no preventive effects were observed. The frail population of patients treated with androgen deprivation therapy (ADT) in combination with abiraterone acetate or enzalutamide had a higher risk of dying from COVID-19 (HR 2.51, 95% CI 1.52-4.16). In vitro data showed no effect of enzalutamide on virus replication. The epidemiological study has limitations that include residual confounders.\n\nThe results do not support a therapeutic effect of enzalutamide or preventive effects of bicalutamide or ADT in COVID-19. Thus, these antiandrogens should not be used for hospitalized COVID-19 patients or as prevention for COVID-19. Further research on these therapeutics in this setting are not warranted.\n\nWe studied whether inhibition of testosterone could diminish COVID-19 symptoms. We found no evidence of an effect in a clinical study or in epidemiological or experimental investigations. We conclude that androgen inhibition should not be used for prevention or treatment of COVID-19.", "doi": "10.1016/j.eururo.2021.12.013", "pmid": "34980495", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0302-2838(21)02224-7"}, {"db": "pmc", "key": "PMC8673828"}], "notes": [], "created": "2022-01-11T07:51:51.302Z", "modified": "2022-01-11T07:51:51.316Z"}, {"entity": "publication", "iuid": "c36cf52bd4aa40a8adcb11c537f1ad8e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c36cf52bd4aa40a8adcb11c537f1ad8e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c36cf52bd4aa40a8adcb11c537f1ad8e"}}, "title": "Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR", "authors": [{"family": "Waterhouse", "given": "Robert M", "initials": "RM"}, {"family": "Adam-Blondon", "given": "Anne Fran\u00e7oise", "initials": "AF"}, {"family": "Agosti", "given": "Donat", "initials": "D"}, {"family": "Baldrian", "given": "Petr", "initials": "P"}, {"family": "Balech", "given": "Bachir", "initials": "B", "orcid": "0000-0002-4419-0729", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d508b8520c9466c9884ccf9b7aa84a8.json"}}, {"family": "Corre", "given": "Erwan", "initials": "E"}, {"family": "Davey", "given": "Robert P", "initials": "RP", "orcid": "0000-0002-5589-7754", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cf570bbd5ba4a22a1eae398748c3087.json"}}, {"family": "Lantz", "given": "Henrik", "initials": "H", "orcid": "0000-0003-2419-0075", "researcher": {"href": "https://publications.scilifelab.se/researcher/85fa15d934214e00bb7818b865c4d754.json"}}, {"family": "Pesole", "given": "Graziano", "initials": "G", "orcid": "0000-0003-3663-0859", "researcher": {"href": "https://publications.scilifelab.se/researcher/5478d454fcd345deaab9863c5476ac2b.json"}}, {"family": "Quast", "given": "Christian", "initials": "C"}, {"family": "Gl\u00f6ckner", "given": "Frank Oliver", "initials": "FO", "orcid": "0000-0001-8528-9023", "researcher": {"href": "https://publications.scilifelab.se/researcher/67f068164c1c40c28b8f46c470c5c0c5.json"}}, {"family": "Raes", "given": "Niels", "initials": "N", "orcid": "0000-0002-4329-4892", "researcher": {"href": "https://publications.scilifelab.se/researcher/29ec7cb00a8945b38b945688b9b15df3.json"}}, {"family": "Sandionigi", "given": "Anna", "initials": "A"}, {"family": "Santamaria", "given": "Monica", "initials": "M", "orcid": "0000-0002-5257-0027", "researcher": {"href": "https://publications.scilifelab.se/researcher/22c839e85d76419e85deb4c9872ef99f.json"}}, {"family": "Addink", "given": "Wouter", "initials": "W"}, {"family": "Vohradsky", "given": "Jiri", "initials": "J"}, {"family": "Nunes-Jorge", "given": "Amandine", "initials": "A"}, {"family": "Willassen", "given": "Nils Peder", "initials": "NP"}, {"family": "Lanfear", "given": "Jerry", "initials": "J", "orcid": "0000-0002-8007-5568", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fbbf24c85954f5c9a30c462324b5879.json"}}], "type": "journal-article", "published": "2021-12-03", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "10", "pages": "1238", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.73825.1", "pmid": null, "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-12-09T09:31:03.057Z", "modified": "2022-01-03T10:02:39.189Z"}, {"entity": "publication", "iuid": "1d95029adc794903bf11503ddeab9127", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d95029adc794903bf11503ddeab9127.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d95029adc794903bf11503ddeab9127"}}, "title": "Insights into the changes in the proteome of Alzheimer disease elucidated by a meta-analysis.", "authors": [{"family": "Haytural", "given": "Hazal", "initials": "H", "orcid": "0000-0002-6805-6989", "researcher": {"href": "https://publications.scilifelab.se/researcher/863ccd2db6794dff8e36a313075e4ea2.json"}}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Schedin-Weiss", "given": "Sophia", "initials": "S"}, {"family": "Bereczki", "given": "Erika", "initials": "E"}, {"family": "Rezeli", "given": "Melinda", "initials": "M"}, {"family": "Unwin", "given": "Richard D", "initials": "RD"}, {"family": "Wang", "given": "Xusheng", "initials": "X"}, {"family": "Dammer", "given": "Eric B", "initials": "EB", "orcid": "0000-0003-2947-7606", "researcher": {"href": "https://publications.scilifelab.se/researcher/026547f280c8451586bf92ab028090f7.json"}}, {"family": "Johnson", "given": "Erik C B", "initials": "ECB"}, {"family": "Seyfried", "given": "Nicholas T", "initials": "NT", "orcid": "0000-0002-4507-624X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c940f8678724c38b1c6e98ea1b335e4.json"}}, {"family": "Winblad", "given": "Bengt", "initials": "B", "orcid": "0000-0002-0011-1179", "researcher": {"href": "https://publications.scilifelab.se/researcher/73185a13ca474153b66415e6a2dfff0f.json"}}, {"family": "Tijms", "given": "Betty M", "initials": "BM", "orcid": "0000-0002-2612-1797", "researcher": {"href": "https://publications.scilifelab.se/researcher/74734f1c78e840b0aaadd74cc2c1ae9f.json"}}, {"family": "Visser", "given": "Pieter Jelle", "initials": "PJ"}, {"family": "Frykman", "given": "Susanne", "initials": "S"}, {"family": "Tjernberg", "given": "Lars O", "initials": "LO", "orcid": "0000-0001-6889-4950", "researcher": {"href": "https://publications.scilifelab.se/researcher/35d7bd25361f4e08a7223926311b399a.json"}}], "type": "journal article", "published": "2021-12-03", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "8", "issue": "1", "pages": "312", "issn-l": "2052-4463"}, "abstract": "Mass spectrometry (MS)-based proteomics is a powerful tool to explore pathogenic changes of a disease in an unbiased manner and has been used extensively in Alzheimer disease (AD) research. Here, by performing a meta-analysis of high-quality proteomic studies, we address which pathological changes are observed consistently and therefore most likely are of great importance for AD pathogenesis. We retrieved datasets, comprising a total of 21,588 distinct proteins identified across 857 postmortem human samples, from ten studies using labeled or label-free MS approaches. Our meta-analysis findings showed significant alterations of 757 and 1,195 proteins in AD in the labeled and label-free datasets, respectively. Only 33 proteins, some of which were associated with synaptic signaling, had the same directional change across the individual studies. However, despite alterations in individual proteins being different between the labeled and the label-free datasets, several pathways related to synaptic signaling, oxidative phosphorylation, immune response and extracellular matrix were commonly dysregulated in AD. These pathways represent robust changes in the human AD brain and warrant further investigation.", "doi": "10.1038/s41597-021-01090-8", "pmid": "34862388", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41597-021-01090-8"}, {"db": "pmc", "key": "PMC8642431"}], "notes": [], "created": "2021-12-06T08:17:14.664Z", "modified": "2024-01-16T13:48:38.002Z"}, {"entity": "publication", "iuid": "0d3c758a29a144ae98a4c7540982c2fc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d3c758a29a144ae98a4c7540982c2fc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d3c758a29a144ae98a4c7540982c2fc"}}, "title": "Long-term agricultural management impacts arbuscular mycorrhizal fungi more than short-term experimental drought", "authors": [{"family": "Kozjek", "given": "Katja", "initials": "K"}, {"family": "Kundel", "given": "Dominika", "initials": "D"}, {"family": "Kushwaha", "given": "Sandeep K", "initials": "SK"}, {"family": "Olsson", "given": "P\u00e5l Axel", "initials": "PA"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Fliessbach", "given": "Andreas", "initials": "A"}, {"family": "Birkhofer", "given": "Klaus", "initials": "K"}, {"family": "Hedlund", "given": "Katarina", "initials": "K"}], "type": "journal-article", "published": "2021-12-00", "journal": {"title": "Applied Soil Ecology", "issn": "0929-1393", "issn-l": null, "volume": "168", "issue": null, "pages": "104140"}, "abstract": null, "doi": "10.1016/j.apsoil.2021.104140", "pmid": null, "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-08-05T12:10:35.123Z", "modified": "2024-01-16T13:48:38.039Z"}, {"entity": "publication", "iuid": "0b34b7db41124b8eb5f36bf6e8077154", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b34b7db41124b8eb5f36bf6e8077154.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b34b7db41124b8eb5f36bf6e8077154"}}, "title": "Palmdelphin Regulates Nuclear Resilience to Mechanical Stress in the Endothelium.", "authors": [{"family": "S\u00e1inz-Jaspeado", "given": "Miguel", "initials": "M"}, {"family": "Smith", "given": "Ross O", "initials": "RO", "orcid": "0000-0003-4239-3204", "researcher": {"href": "https://publications.scilifelab.se/researcher/a464f28ad47c4706a08645b9616198b7.json"}}, {"family": "Plunde", "given": "Oscar", "initials": "O"}, {"family": "Pawelzik", "given": "Sven-Christian", "initials": "SC"}, {"family": "Jin", "given": "Yi", "initials": "Y", "orcid": "0000-0001-9704-973X", "researcher": {"href": "https://publications.scilifelab.se/researcher/deff30d686dd469f907bc80b8f628390.json"}}, {"family": "Nordling", "given": "Sofia", "initials": "S"}, {"family": "Ding", "given": "Yindi", "initials": "Y", "orcid": "0000-0003-4672-7611", "researcher": {"href": "https://publications.scilifelab.se/researcher/cda52c187d0e49f4b1f09b76bbfa0202.json"}}, {"family": "Aspenstr\u00f6m", "given": "Pontus", "initials": "P"}, {"family": "Hedlund", "given": "Marie", "initials": "M"}, {"family": "Bastianello", "given": "Giulia", "initials": "G"}, {"family": "Ascione", "given": "Flora", "initials": "F"}, {"family": "Li", "given": "Qingsen", "initials": "Q"}, {"family": "Demir", "given": "Cansaran Saygili", "initials": "CS"}, {"family": "Fernando", "given": "Dinesh", "initials": "D", "orcid": "0000-0003-2487-0599", "researcher": {"href": "https://publications.scilifelab.se/researcher/85093375f68a4e70912f07bb5c05ad48.json"}}, {"family": "Daniel", "given": "Geoffrey", "initials": "G", "orcid": "0000-0002-8886-1942", "researcher": {"href": "https://publications.scilifelab.se/researcher/628aeb01d86b47c1b09e2d070356dde8.json"}}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Kroon", "given": "Jeffrey", "initials": "J", "orcid": "0000-0001-9983-6614", "researcher": {"href": "https://publications.scilifelab.se/researcher/df348c68131743d1a78d5058aacd20b4.json"}}, {"family": "Foiani", "given": "Marco", "initials": "M"}, {"family": "Petrova", "given": "Tatiana V", "initials": "TV"}, {"family": "Kilimann", "given": "Manfred W", "initials": "MW"}, {"family": "B\u00e4ck", "given": "Magnus", "initials": "M", "orcid": "0000-0003-0853-5141", "researcher": {"href": "https://publications.scilifelab.se/researcher/2208efeca524405f8162841b2d2e5910.json"}}, {"family": "Claesson-Welsh", "given": "Lena", "initials": "L", "orcid": "0000-0003-4275-2000", "researcher": {"href": "https://publications.scilifelab.se/researcher/647e2a349efd4e11827209883e86079b.json"}}], "type": "journal article", "published": "2021-11-16", "journal": {"title": "Circulation", "issn": "1524-4539", "issn-l": "0009-7322", "volume": "144", "issue": "20", "pages": "1629-1645"}, "abstract": "PALMD (palmdelphin) belongs to the family of paralemmin proteins implicated in cytoskeletal regulation. Single nucleotide polymorphisms in the PALMD locus that result in reduced expression are strong risk factors for development of calcific aortic valve stenosis and predict severity of the disease.\n\nImmunodetection and public database screening showed dominant expression of PALMD in endothelial cells (ECs) in brain and cardiovascular tissues including aortic valves. Mass spectrometry, coimmunoprecipitation, and immunofluorescent staining allowed identification of PALMD partners. The consequence of loss of PALMD expression was assessed in small interferring RNA-treated EC cultures, knockout mice, and human valve samples. RNA sequencing of ECs and transcript arrays on valve samples from an aortic valve study cohort including patients with the single nucleotide polymorphism rs7543130 informed about gene regulatory changes.\n\nECs express the cytosolic PALMD-KKVI splice variant, which associated with RANGAP1 (RAN GTP hydrolyase activating protein 1). RANGAP1 regulates the activity of the GTPase RAN and thereby nucleocytoplasmic shuttling via XPO1 (Exportin1). Reduced PALMD expression resulted in subcellular relocalization of RANGAP1 and XPO1, and nuclear arrest of the XPO1 cargoes p53 and p21. This indicates an important role for PALMD in nucleocytoplasmic transport and consequently in gene regulation because of the effect on localization of transcriptional regulators. Changes in EC responsiveness on loss of PALMD expression included failure to form a perinuclear actin cap when exposed to flow, indicating lack of protection against mechanical stress. Loss of the actin cap correlated with misalignment of the nuclear long axis relative to the cell body, observed in PALMD-deficient ECs, Palmd mouse aorta, and human aortic valve samples derived from patients with calcific aortic valve stenosis. In agreement with these changes in EC behavior, gene ontology analysis showed enrichment of nuclear- and cytoskeleton-related terms in -/-PALMD-silenced ECs.\n\nWe identify RANGAP1 as a PALMD partner in ECs. Disrupting the PALMD/RANGAP1 complex alters the subcellular localization of RANGAP1 and XPO1, and leads to nuclear arrest of the XPO1 cargoes p53 and p21, accompanied by gene regulatory changes and loss of actin-dependent nuclear resilience. Combined, these consequences of reduced PALMD expression provide a mechanistic underpinning for PALMD's contribution to calcific aortic valve stenosis pathology.", "doi": "10.1161/CIRCULATIONAHA.121.054182", "pmid": "34636652", "labels": {"Global Proteomics and Proteogenomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8589083"}], "notes": [], "created": "2022-03-29T10:27:37.036Z", "modified": "2023-11-16T12:06:34.222Z"}, {"entity": "publication", "iuid": "5f02577a971e4e6dac88cd3ce52c6a33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f02577a971e4e6dac88cd3ce52c6a33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f02577a971e4e6dac88cd3ce52c6a33"}}, "title": "Identification and characterization of distinct cell cycle stages in cardiomyocytes using the FUCCI transgenic system.", "authors": [{"family": "Baniol", "given": "Marion", "initials": "M"}, {"family": "Murganti", "given": "Francesca", "initials": "F"}, {"family": "Smialowska", "given": "Agata", "initials": "A"}, {"family": "Panula", "given": "Joni", "initials": "J"}, {"family": "L\u00e1z\u00e1r", "given": "Enik\u0151", "initials": "E"}, {"family": "Brockman", "given": "Viveka", "initials": "V"}, {"family": "Giatrellis", "given": "Sarantis", "initials": "S"}, {"family": "Derks", "given": "Wouter", "initials": "W"}, {"family": "Bergmann", "given": "Olaf", "initials": "O"}], "type": "journal article", "published": "2021-11-15", "journal": {"title": "Exp. Cell Res.", "issn": "1090-2422", "volume": "408", "issue": "2", "pages": "112880", "issn-l": "0014-4827"}, "abstract": "Understanding the regulatory mechanism by which cardiomyocyte proliferation transitions to endoreplication and cell cycle arrest during the neonatal period is crucial for identifying proproliferative factors and developing regenerative therapies. We used a transgenic mouse model based on the fluorescent ubiquitination-based cell cycle indicator (FUCCI) system to isolate and characterize cycling cardiomyocytes at different cell cycle stages at a single-cell resolution. Single-cell transcriptome analysis of cycling and noncycling cardiomyocytes was performed at postnatal days 0 (P0) and 7 (P7). The FUCCI system proved to be efficient for the identification of cycling cardiomyocytes with the highest mitotic activity at birth, followed by a gradual decline in the number of cycling and mitotic cardiomyocytes during the neonatal period. Cardiomyocytes showed premature cell cycle exit at G1/S shortly after birth and delayed G1/S progression during endoreplication at P7. Single-cell RNA-seq confirmed previously described signaling pathways involved in cardiomyocyte proliferation (Erbb2 and Hippo/YAP), and maturation-related transcriptional changes during postnatal development, including the metabolic switch from glycolysis to fatty acid oxidation in cardiomyocytes. Importantly, we generated transcriptional profiles specific to cell division and endoreplication in cardiomyocytes at different developmental stages that may facilitate the identification of genes important for adult cardiomyocyte proliferation and heart regeneration. In conclusion, the FUCCI mouse provides a valuable system to study cardiomyocyte cell cycle activity at single cell resolution that can help to decipher the switch from cardiomyocyte proliferation to endoreplication, and to revert this process to facilitate endogenous repair.", "doi": "10.1016/j.yexcr.2021.112880", "pmid": "34655601", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0014-4827(21)00434-1"}], "notes": [], "created": "2021-12-02T13:58:32.464Z", "modified": "2024-01-16T13:48:38.129Z"}, {"entity": "publication", "iuid": "b452ba831ed844649437c1c74c9fc32a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b452ba831ed844649437c1c74c9fc32a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b452ba831ed844649437c1c74c9fc32a"}}, "title": "Leaf Apoplast of Field-Grown Potato Analyzed by Quantitative Proteomics and Activity-Based Protein Profiling.", "authors": [{"family": "Abreha", "given": "Kibrom B", "initials": "KB", "orcid": "0000-0001-8084-8340", "researcher": {"href": "https://publications.scilifelab.se/researcher/eebbd2766e6d4c38bbb6284dd310f6df.json"}}, {"family": "Alexandersson", "given": "Erik", "initials": "E", "orcid": "0000-0001-6320-2492", "researcher": {"href": "https://publications.scilifelab.se/researcher/eae8dc98de79429495f0a1727a342e9f.json"}}, {"family": "Resj\u00f6", "given": "Svante", "initials": "S"}, {"family": "Lankinen", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Sueldo", "given": "Daniela", "initials": "D"}, {"family": "Kaschani", "given": "Farnusch", "initials": "F"}, {"family": "Kaiser", "given": "Markus", "initials": "M"}, {"family": "van der Hoorn", "given": "Renier A L", "initials": "RAL"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b7add45d810457eb84a72aebbc7b82c.json"}}, {"family": "Andreasson", "given": "Erik", "initials": "E", "orcid": "0000-0003-0666-7204", "researcher": {"href": "https://publications.scilifelab.se/researcher/664a0be84db14b80a717edec6cab5dda.json"}}], "type": "journal article", "published": "2021-11-06", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "22", "issue": "21", "issn-l": null}, "abstract": "Multiple biotic and abiotic stresses challenge plants growing in agricultural fields. Most molecular studies have aimed to understand plant responses to challenges under controlled conditions. However, studies on field-grown plants are scarce, limiting application of the findings in agricultural conditions. In this study, we investigated the composition of apoplastic proteomes of potato cultivar Bintje grown under field conditions, i.e., two field sites in June-August across two years and fungicide treated and untreated, using quantitative proteomics, as well as its activity using activity-based protein profiling (ABPP). Samples were clustered and some proteins showed significant intensity and activity differences, based on their field site and sampling time (June-August), indicating differential regulation of certain proteins in response to environmental or developmental factors. Peroxidases, class II chitinases, pectinesterases, and osmotins were among the proteins more abundant later in the growing season (July-August) as compared to early in the season (June). We did not detect significant differences between fungicide Shirlan treated and untreated field samples in two growing seasons. Using ABPP, we showed differential activity of serine hydrolases and \u03b2-glycosidases under greenhouse and field conditions and across a growing season. Furthermore, the activity of serine hydrolases and \u03b2-glycosidases, including proteins related to biotic stress tolerance, decreased as the season progressed. The generated proteomics data would facilitate further studies aiming at understanding mechanisms of molecular plant physiology in agricultural fields and help applying effective strategies to mitigate biotic and abiotic stresses.", "doi": "10.3390/ijms222112033", "pmid": "34769464", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ijms222112033"}, {"db": "pmc", "key": "PMC8584485"}], "notes": [], "created": "2021-12-02T14:03:05.767Z", "modified": "2021-12-02T14:03:05.904Z"}, {"entity": "publication", "iuid": "92916c7849ec4651b0b9ec3d10f0581a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92916c7849ec4651b0b9ec3d10f0581a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92916c7849ec4651b0b9ec3d10f0581a"}}, "title": "Tonsillar Cancer with High CD8+ T-Cell Infiltration Features Increased Levels of Dendritic Cells and Transcriptional Regulation Associated with an Inflamed Tumor Microenvironment.", "authors": [{"family": "Jimenez", "given": "David Gomez", "initials": "DG"}, {"family": "Sobti", "given": "Aastha", "initials": "A"}, {"family": "Askmyr", "given": "David", "initials": "D", "orcid": "0000-0003-1312-8524", "researcher": {"href": "https://publications.scilifelab.se/researcher/0249a39d931d4f5198312aa3125a105d.json"}}, {"family": "Sakellariou", "given": "Christina", "initials": "C"}, {"family": "Santos", "given": "Sofia Carreira", "initials": "SC"}, {"family": "Swoboda", "given": "Sabine", "initials": "S"}, {"family": "Forslund", "given": "Ola", "initials": "O"}, {"family": "Greiff", "given": "Lennart", "initials": "L"}, {"family": "Lindstedt", "given": "Malin", "initials": "M"}], "type": "journal article", "published": "2021-10-25", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "13", "issue": "21", "issn-l": "2072-6694"}, "abstract": "Human papillomavirus (HPV) is the main causal agent of tonsillar cancer (TC) and HPV+ TC has a favorable prognosis compared to HPV- disease. In this study, we examined aspects of the tumor microenvironment of TC, focusing on T-cells, dendritic cells (DC), and macrophages. Fresh biopsies of TC and the contralateral healthy tonsil (HT) were obtained from 20 patients, analyzed by multiparameter flow cytometry, and assessed against a detailed HPV-status. Additionally, RNA-sequencing data from 38 TC samples available in the public database, The Cancer Genome Atlas (TCGA), were explored, focusing on the same leukocyte populations. HPV+ TC featured increased levels of CD8+ T-cells and antigen-presenting cells (cf. HPV- TC and HT, respectively). In HPV+ TC, CD8+ T-cell frequencies correlated to DC levels independently of tumor stage, HPV 16 copy number, and E7 oncogene expression as well as frequencies of other leukocytes. Similarly, RNA sequencing data were explored by dividing the HPV+ TCs according to predefined CD8+ T-cell scores in silico. Higher levels of genes expressed by antigen-presenting cells and effector T-cells, such as immune checkpoints and cytokines, were detected in the CD8HIGH HPV+ TC samples (cf. CD8LOW HPV+ TC). In conclusion, CD8HIGH HPV+ TC displays a unique inflammatory profile associated with increased effector T-cell functions and the presence of antigen-presenting cells in the tumor microenvironment. Further studies are warranted to assess if this information can be used on an individual basis to aid in prognosis and treatment decisions.", "doi": "10.3390/cancers13215341", "pmid": "34771506", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "cancers13215341"}, {"db": "pmc", "key": "PMC8582523"}], "notes": [], "created": "2021-12-02T13:59:26.828Z", "modified": "2021-12-02T13:59:26.872Z"}, {"entity": "publication", "iuid": "5584e86c855f43819255fd1c8610c93a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5584e86c855f43819255fd1c8610c93a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5584e86c855f43819255fd1c8610c93a"}}, "title": "Whole-genome Sequencing of Follicular Thyroid Carcinomas Reveal Recurrent Mutations in MicroRNA Processing Subunit DGCR8.", "authors": [{"family": "Paulsson", "given": "Johan O", "initials": "JO", "orcid": "0000-0003-0390-6740", "researcher": {"href": "https://publications.scilifelab.se/researcher/762d22bad5b7462dbba2a87c9b3221a0.json"}}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "DiLorenzo", "given": "Sebastian", "initials": "S"}, {"family": "Chen", "given": "Yi", "initials": "Y"}, {"family": "Haglund", "given": "Felix", "initials": "F"}, {"family": "Zedenius", "given": "Jan", "initials": "J"}, {"family": "Juhlin", "given": "C Christofer", "initials": "CC", "orcid": "0000-0002-5945-9081", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb660e24421749d4acaaf6e9a90042f8.json"}}], "type": "journal article", "published": "2021-10-21", "journal": {"title": "J. Clin. Endocrinol. Metab.", "issn": "1945-7197", "issn-l": "0021-972X", "volume": "106", "issue": "11", "pages": "3265-3282"}, "abstract": "The genomic and transcriptomic landscape of widely invasive follicular thyroid carcinomas (wiFTCs) and H\u00fcrthle cell carcinoma (HCC) are poorly characterized, and subsets of these tumors lack information on genetic driver events.\n\nThe aim of this study was to bridge this gap.\n\nWe performed whole-genome and RNA sequencing and subsequent bioinformatic analyses of 11 wiFTCs and 2 HCCs with a particularly poor prognosis, and matched normal tissue.\n\nAll wiFTCs exhibited one or several mutations in established thyroid cancer genes, including TERT (n = 4), NRAS (n = 3), HRAS, KRAS, AKT, PTEN, PIK3CA, MUTYH, TSHR, and MEN1 (n = 1 each). MutSig2CV analysis revealed recurrent somatic mutations in FAM72D (n = 3, in 2 wiFTCs and in a single HCC), TP53 (n = 3, in 2 wiFTCs and a single HCC), and EIF1AX (n = 3), with DGCR8 (n = 2) as borderline significant. The DGCR8 mutations were recurrent p.E518K missense alterations, known to cause familial multinodular goiter via disruption of microRNA (miRNA) processing. Expression analyses showed reduced DGCR8 messenger RNA expression in FTCs in general, and the 2 DGCR8 mutants displayed a distinct miRNA profile compared to DGCR8 wild-types. Copy number analyses revealed recurrent gains on chromosomes 4, 6, and 10, and fusion gene analyses revealed 27 high-quality events. Both HCCs displayed hyperploidy, which was fairly unusual in the FTC cohort. Based on the transcriptome data, tumors amassed in 2 principal clusters.\n\nWe describe the genomic and transcriptomic landscape in wiFTCs and HCCs and identify novel recurrent mutations and copy number alterations with possible driver properties and lay the foundation for future studies.", "doi": "10.1210/clinem/dgab471", "pmid": "34171097", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6309631"}, {"db": "pmc", "key": "PMC8530729"}], "notes": [], "created": "2021-12-02T14:30:01.594Z", "modified": "2024-01-16T13:48:38.199Z"}, {"entity": "publication", "iuid": "905b33ff17fa45b69f16c281ae963e70", "links": {"self": {"href": "https://publications.scilifelab.se/publication/905b33ff17fa45b69f16c281ae963e70.json"}, "display": {"href": "https://publications.scilifelab.se/publication/905b33ff17fa45b69f16c281ae963e70"}}, "title": "Composition and Seasonality of Membrane Transporters in Marine Picoplankton.", "authors": [{"family": "Hagstr\u00f6m", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Zweifel", "given": "Ulla Li", "initials": "UL"}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Osbeck", "given": "Christofer M G", "initials": "CMG"}, {"family": "Bunse", "given": "Carina", "initials": "C"}, {"family": "Sj\u00f6stedt", "given": "Johanna", "initials": "J"}, {"family": "M\u00fcller-Karulis", "given": "B\u00e4rbel", "initials": "B"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}], "type": "journal article", "published": "2021-09-28", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "12", "pages": "714732", "issn-l": "1664-302X"}, "abstract": "In this study, we examined transporter genes in metagenomic and metatranscriptomic data from a time-series survey in the temperate marine environment of the Baltic Sea. We analyzed the abundance and taxonomic distribution of transporters in the 3\u03bcm-0.2\u03bcm size fraction comprising prokaryotes and some picoeukaryotes. The presence of specific transporter traits was shown to be guiding the succession of these microorganisms. A limited number of taxa were associated with the dominant transporter proteins that were identified for the nine key substrate categories for microbial growth. Throughout the year, the microbial taxa at the level of order showed highly similar patterns in terms of transporter traits. The distribution of transporters stayed the same, irrespective of the abundance of each taxon. This would suggest that the distribution pattern of transporters depends on the bacterial groups being dominant at a given time of the year. Also, we find notable numbers of secretion proteins that may allow marine bacteria to infect and kill prey organisms thus releasing nutrients. Finally, we demonstrate that transporter proteins may provide clues to the relative importance of biogeochemical processes, and we suggest that virtual transporter functionalities may become important components in future population dynamics models.", "doi": "10.3389/fmicb.2021.714732", "pmid": "34650527", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8507841"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.4508144.v2"}], "notes": [], "created": "2021-12-06T13:49:16.062Z", "modified": "2024-01-16T13:48:38.439Z"}, {"entity": "publication", "iuid": "1fafeea0c1fc4b21b45c073667f92be3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fafeea0c1fc4b21b45c073667f92be3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fafeea0c1fc4b21b45c073667f92be3"}}, "title": "Avian neo-sex chromosomes reveal dynamics of recombination suppression and W degeneration.", "authors": [{"family": "Sigeman", "given": "Hanna", "initials": "H", "orcid": "0000-0002-1457-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/f75fea472d1d495a92228c50bd63891e.json"}}, {"family": "Strandh", "given": "Maria", "initials": "M"}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E"}, {"family": "Kutschera", "given": "Verena E", "initials": "VE"}, {"family": "Ponnikas", "given": "Suvi", "initials": "S"}, {"family": "Zhang", "given": "Hongkai", "initials": "H"}, {"family": "Lundberg", "given": "Max", "initials": "M"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Tarka", "given": "Maja", "initials": "M"}, {"family": "Hasselquist", "given": "Dennis", "initials": "D"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Westerdahl", "given": "Helena", "initials": "H"}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2021-09-20", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "38", "issue": "12", "pages": "5275-5291"}, "abstract": "How the avian sex chromosomes first evolved from autosomes remains elusive as 100 million years (Myr) of divergence and degeneration obscure their evolutionary history. The Sylvioidea group of songbirds is interesting for understanding avian sex chromosome evolution because a chromosome fusion event \u223c24 Myr ago formed \"neo-sex chromosomes\" consisting of an added (new) and an ancestral (old) part. Here, we report the complete female genome (ZW) of one Sylvioidea species, the great reed warbler (Acrocephalus arundinaceus). Our long-read assembly shows that the added region has been translocated to both Z and W, and while the added-Z has remained its gene order the added-W part has been heavily rearranged. Phylogenetic analyses show that recombination between the homologous added-Z and -W regions continued after the fusion event, and that recombination suppression across this region took several million years to be completed. Moreover, recombination suppression was initiated across multiple positions over the added-Z, which is not consistent with a simple linear progression starting from the fusion point. As expected following recombination suppression, the added-W show signs of degeneration including repeat accumulation and gene loss. Finally, we present evidence for non-random maintenance of slowly evolving and dosage-sensitive genes on both ancestral- and added-W, a process causing correlated evolution among orthologous genes across broad taxonomic groups, regardless of sex-linkage.", "doi": "10.1093/molbev/msab277", "pmid": "34542640", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6372697"}], "notes": [], "created": "2021-10-29T14:04:51.682Z", "modified": "2024-01-16T13:48:38.463Z"}, {"entity": "publication", "iuid": "3f41da8f8fce4eea80f6148233aa9ae8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f41da8f8fce4eea80f6148233aa9ae8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f41da8f8fce4eea80f6148233aa9ae8"}}, "title": "Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs.", "authors": [{"family": "Chase", "given": "Madeline A", "initials": "MA", "orcid": "0000-0002-7916-3560", "researcher": {"href": "https://publications.scilifelab.se/researcher/3053121df4b64418bc1dcc2d7e50d87c.json"}}, {"family": "Ellegren", "given": "Hans", "initials": "H"}, {"family": "Mugal", "given": "Carina F", "initials": "CF"}], "type": "journal article", "published": "2021-09-00", "journal": {"title": "Evolution", "issn": "1558-5646", "issn-l": "0014-3820", "volume": "75", "issue": "9", "pages": "2179-2196"}, "abstract": "A current debate within population genomics surrounds the relevance of patterns of genomic differentiation between closely related species for our understanding of adaptation and speciation. Mounting evidence across many taxa suggests that the same genomic regions repeatedly develop elevated differentiation in independent species pairs. These regions often coincide with high gene density and/or low recombination, leading to the hypothesis that the genomic differentiation landscape mostly reflects a history of background selection, and reveals little about adaptation or speciation. A comparative genomics approach with multiple independent species pairs at a timescale where gene flow and ILS are negligible permits investigating whether different evolutionary processes are responsible for generating lineage-specific versus shared patterns of species differentiation. We use whole-genome resequencing data of 195 individuals from four Ficedula flycatcher species comprising two independent species pairs: collared and pied flycatchers, and red-breasted and taiga flycatchers. We found that both shared and lineage-specific FST peaks could partially be explained by selective sweeps, with recurrent selection likely to underlie shared signatures of selection, whereas indirect evidence supports a role of recombination landscape evolution in driving lineage-specific signatures of selection. This work therefore provides evidence for an interplay of positive selection and recombination to genomic landscape evolution.", "doi": "10.1111/evo.14234", "pmid": "33851440", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "Dryad", "key": "10.5061/dryad.n2z34tmw6"}], "notes": [], "created": "2021-12-02T14:05:48.724Z", "modified": "2024-01-16T13:48:38.584Z"}, {"entity": "publication", "iuid": "7cf7dd6ca7064c6085e07d7f075696cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7cf7dd6ca7064c6085e07d7f075696cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7cf7dd6ca7064c6085e07d7f075696cd"}}, "title": "Drought legacy affects microbial community trait distributions related to moisture along a savannah grassland precipitation gradient", "authors": [{"family": "Leizeaga", "given": "Ainara", "initials": "A", "orcid": "0000-0003-4014-7464", "researcher": {"href": "https://publications.scilifelab.se/researcher/06c08f400a14454794070896fbae6bcd.json"}}, {"family": "Hicks", "given": "Lettice C", "initials": "LC", "orcid": "0000-0002-0265-3887", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ff3a631e45348c0b9d5c4b7cae04b56.json"}}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L", "orcid": "0000-0001-9751-5745", "researcher": {"href": "https://publications.scilifelab.se/researcher/000321fd81b9457db66140246bbd9066.json"}}, {"family": "Hawkes", "given": "Christine V", "initials": "CV"}, {"family": "Rousk", "given": "Johannes", "initials": "J", "orcid": "0000-0002-4985-7262", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6db580d025a4e3aa97784ebef5edb4f.json"}}], "type": "journal-article", "published": "2021-09-00", "journal": {"title": "J Ecol", "issn": "0022-0477", "volume": "109", "issue": "9", "pages": "3195-3210", "issn-l": null}, "abstract": null, "doi": "10.1111/1365-2745.13550", "pmid": null, "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2020-11-05T12:28:49.043Z", "modified": "2024-01-16T13:48:38.609Z"}, {"entity": "publication", "iuid": "733f4ec1bbe6450aac67c199b68f52b4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/733f4ec1bbe6450aac67c199b68f52b4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/733f4ec1bbe6450aac67c199b68f52b4"}}, "title": "Calcium and pH interaction limits bloom formation and expansion of a nuisance microalga", "authors": [{"family": "Gollnisch", "given": "Raphael", "initials": "R", "orcid": "0000-0001-6177-8877", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f78f6e8cacf4eba9104fbfd2ab26f66.json"}}, {"family": "Alling", "given": "Teodor", "initials": "T"}, {"family": "Stockenreiter", "given": "Maria", "initials": "M", "orcid": "0000-0001-7380-071X", "researcher": {"href": "https://publications.scilifelab.se/researcher/206b35b665ef46db8f72db684eed1646.json"}}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Grabowska", "given": "Magdalena", "initials": "M"}, {"family": "Rengefors", "given": "Karin", "initials": "K"}], "type": "journal-article", "published": "2021-09-00", "journal": {"title": "Limnol Oceanogr", "issn": "0024-3590", "volume": "66", "issue": "9", "pages": "3523-3534", "issn-l": null}, "abstract": null, "doi": "10.1002/lno.11896", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-12-10T09:49:09.482Z", "modified": "2022-01-03T10:04:02.179Z"}, {"entity": "publication", "iuid": "d113d0c37b074a75b7a8dfb5c565524f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d113d0c37b074a75b7a8dfb5c565524f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d113d0c37b074a75b7a8dfb5c565524f"}}, "title": "Amnion signals are essential for mesoderm formation in primates.", "authors": [{"family": "Yang", "given": "Ran", "initials": "R"}, {"family": "Goedel", "given": "Alexander", "initials": "A", "orcid": "0000-0002-5980-2257", "researcher": {"href": "https://publications.scilifelab.se/researcher/866e8580c3d8462da0f3ee3b8909ea6f.json"}}, {"family": "Kang", "given": "Yu", "initials": "Y"}, {"family": "Si", "given": "Chenyang", "initials": "C"}, {"family": "Chu", "given": "Chu", "initials": "C"}, {"family": "Zheng", "given": "Yi", "initials": "Y"}, {"family": "Chen", "given": "Zhenzhen", "initials": "Z"}, {"family": "Gruber", "given": "Peter J", "initials": "PJ", "orcid": "0000-0002-7356-905X", "researcher": {"href": "https://publications.scilifelab.se/researcher/623bc96d071d410c8199b178a1e31808.json"}}, {"family": "Xiao", "given": "Yao", "initials": "Y"}, {"family": "Zhou", "given": "Chikai", "initials": "C", "orcid": "0000-0001-9653-3466", "researcher": {"href": "https://publications.scilifelab.se/researcher/05559fcfc7724eb1bf06305a907b58d4.json"}}, {"family": "Witman", "given": "Nevin", "initials": "N"}, {"family": "Eroglu", "given": "Elif", "initials": "E"}, {"family": "Leung", "given": "Chuen-Yan", "initials": "CY"}, {"family": "Chen", "given": "Yongchang", "initials": "Y"}, {"family": "Fu", "given": "Jianping", "initials": "J", "orcid": "0000-0001-9629-6739", "researcher": {"href": "https://publications.scilifelab.se/researcher/127bba88c5534146ae9ba1b10929bb4b.json"}}, {"family": "Ji", "given": "Weizhi", "initials": "W", "orcid": "0000-0003-2550-4224", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e1228641df34f3fa2f8b961d414233b.json"}}, {"family": "Lanner", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-2771-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba53ce48a35d413eb86cd104488ce669.json"}}, {"family": "Niu", "given": "Yuyu", "initials": "Y"}, {"family": "Chien", "given": "Kenneth R", "initials": "KR", "orcid": "0000-0002-2759-8378", "researcher": {"href": "https://publications.scilifelab.se/researcher/971382878b474966bbe58acaa1585999.json"}}], "type": "journal article", "published": "2021-08-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "5126", "issn-l": "2041-1723"}, "abstract": "Embryonic development is largely conserved among mammals. However, certain genes show divergent functions. By generating a transcriptional atlas containing >30,000 cells from post-implantation non-human primate embryos, we uncover that ISL1, a gene with a well-established role in cardiogenesis, controls a gene regulatory network in primate amnion. CRISPR/Cas9-targeting of ISL1 results in non-human primate embryos which do not yield viable offspring, demonstrating that ISL1 is critically required in primate embryogenesis. On a cellular level, mutant ISL1 embryos display a failure in mesoderm formation due to reduced BMP4 signaling from the amnion. Via loss of function and rescue studies in human embryonic stem cells we confirm a similar role of ISL1 in human in vitro derived amnion. This study highlights the importance of the amnion as a signaling center during primate mesoderm formation and demonstrates the potential of in vitro primate model systems to dissect the genetics of early human embryonic development.", "doi": "10.1038/s41467-021-25186-2", "pmid": "34446705", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8390679"}, {"db": "pii", "key": "10.1038/s41467-021-25186-2"}], "notes": [], "created": "2021-08-30T07:44:40.804Z", "modified": "2024-01-16T13:48:38.655Z"}, {"entity": "publication", "iuid": "4adf66bcf02144de8e00d95337520efa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4adf66bcf02144de8e00d95337520efa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4adf66bcf02144de8e00d95337520efa"}}, "title": "Genome assemblies of three closely related leaf beetle species (Galerucella spp.).", "authors": [{"family": "Yang", "given": "Xuyue", "initials": "X", "orcid": "0000-0003-2084-1651", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0959fee187345d497cec63bce88d136.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Hamb\u00e4ck", "given": "Peter A", "initials": "PA"}], "type": "journal article", "published": "2021-08-07", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "volume": "11", "issue": "8", "issn-l": "2160-1836"}, "abstract": "Galerucella (Coleoptera: Chrysomelidae) is a leaf beetle genus that has been extensively used for ecological and evolutionary studies. It has also been used as biological control agent against invading purple loosestrife in North America, with large effects on biodiversity. Here, we report genome assembly and annotation of three closely related Galerucella species: G. calmariensis, G. pusilla, and G. tenella. The three assemblies have a genome size ranging from 460 to 588 Mbp, with N50 from 31,588 to 79,674 kbp, containing 29,202 to 40,929 scaffolds. Using an ab initio evidence-driven approach, 30,302 to 33,794 protein-coding genes were identified and functionally annotated. These draft genomes will contribute to the understanding of host-parasitoid interactions, evolutionary comparisons of leaf beetle species and future population genomics studies.", "doi": "10.1093/g3journal/jkab214", "pmid": "34849825", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6307723"}, {"db": "pmc", "key": "PMC8496278"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.5470650"}], "notes": [], "created": "2021-12-10T09:54:47.125Z", "modified": "2024-01-16T13:48:38.816Z"}, {"entity": "publication", "iuid": "03a43d038b744f0887c31cc6c641bec2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/03a43d038b744f0887c31cc6c641bec2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/03a43d038b744f0887c31cc6c641bec2"}}, "title": "High-Resolution Proteomic Profiling Shows Sexual Dimorphism in Zebrafish Heart-Associated Proteins.", "authors": [{"family": "Niksirat", "given": "Hamid", "initials": "H", "orcid": "0000-0003-3782-4954", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7d5fa5b680a4470a1babd21c7d386f9.json"}}, {"family": "Siino", "given": "Valentina", "initials": "V"}, {"family": "Steinbach", "given": "Christoph", "initials": "C"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b7add45d810457eb84a72aebbc7b82c.json"}}], "type": "journal article", "published": "2021-08-06", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "20", "issue": "8", "pages": "4075-4088", "issn-l": "1535-3893"}, "abstract": "Understanding the molecular basis of sexual dimorphism in the cardiovascular system may contribute to the improvement of the outcome in biological, pharmacological, and toxicological studies as well as on the development of sex-based drugs and therapeutic approaches. Label-free protein quantification using high-resolution mass spectrometry was applied to detect sex-based proteome differences in the heart of zebrafish Danio rerio. Out of almost 3000 unique identified proteins in the heart, 79 showed significant abundance differences between male and female fish. The functional differences were mapped using enrichment analyses. Our results suggest that a large amount of materials needed for reproduction (e.g., sugars, lipids, proteins, etc.) may impose extra pressure on blood, vessels, and heart on their way toward the ovaries. In the present study, the female's heart shows a clear sexual dimorphism by changing abundance levels of numerous proteins, which could be a way to safely overcome material-induced elevated pressures. These proteins belong to the immune system, oxidative stress response, drug metabolization, detoxification, energy, metabolism, and so on. In conclusion, we showed that sex can induce dimorphism at the molecular level in nonsexual organs such as heart and must be considered as an important factor in cardiovascular research. Data are available via ProteomeXchange with identifier PXD023506.", "doi": "10.1021/acs.jproteome.1c00387", "pmid": "34185526", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-12-02T14:02:35.214Z", "modified": "2021-12-02T14:02:35.299Z"}, {"entity": "publication", "iuid": "02764c416c9248f5bf9c7f345484968c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02764c416c9248f5bf9c7f345484968c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02764c416c9248f5bf9c7f345484968c"}}, "title": "Shifts in gene expression variability in the blood-stage of Plasmodium relictum.", "authors": [{"family": "Kalbskopf", "given": "Victor", "initials": "V"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Valki\u016bnas", "given": "Gediminas", "initials": "G"}, {"family": "Palinauskas", "given": "Vaidas", "initials": "V"}, {"family": "Hellgren", "given": "Olof", "initials": "O"}], "type": "journal article", "published": "2021-08-05", "journal": {"title": "Gene", "issn": "1879-0038", "volume": "792", "pages": "145723", "issn-l": "0378-1119"}, "abstract": "Avian malaria is a common and widespread disease of birds caused by a diverse group of pathogens of the genera Plasmodium. We investigated the transcriptomal profiles of one of the most common species, Plasmodium relictum, lineage SGS1, at multiple timepoints during the blood stages of the infection under experimental settings. The parasite showed well separated overall transcriptome profiles between day 8 and 20 after the infection, shown by well separated PCA profiles. Moreover, gene expression becomes more heterogenous within the experimental group late in the infection, either due to adaptations to individual differences between the experimental hosts, or due to desynchronisation of the life-cycle of the parasite. Overall, this study shows how the avian malaria system can be used to study gene expression of the avian Plasmodium parasite under controlled experimental settings, thus allowing for future comparative analysis of gene responses of parasite with different life-history traits and host effects.", "doi": "10.1016/j.gene.2021.145723", "pmid": "34019936", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0378-1119(21)00317-6"}], "notes": [], "created": "2021-12-10T09:49:48.343Z", "modified": "2021-12-10T09:49:48.355Z"}, {"entity": "publication", "iuid": "58eb7a843c0344258c15ea9349bdbe5a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58eb7a843c0344258c15ea9349bdbe5a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58eb7a843c0344258c15ea9349bdbe5a"}}, "title": "Single-cell multimodal analysis in a case with reduced penetrance of Progranulin-Frontotemporal Dementia.", "authors": [{"family": "Natarajan", "given": "Karthick", "initials": "K", "orcid": "0000-0001-5335-875X", "researcher": {"href": "https://publications.scilifelab.se/researcher/389c50cf68cc43c2bd154addeafe768a.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Hammond", "given": "Maria", "initials": "M"}, {"family": "Laffita-Mesa", "given": "Jos\u00e9 Miguel", "initials": "JM"}, {"family": "Patra", "given": "Kalicharan", "initials": "K"}, {"family": "Khoshnood", "given": "Behzad", "initials": "B"}, {"family": "\u00d6ijerstedt", "given": "Linn", "initials": "L"}, {"family": "Graff", "given": "Caroline", "initials": "C"}], "type": "journal article", "published": "2021-08-03", "journal": {"title": "Acta Neuropathol Commun", "issn": "2051-5960", "issn-l": "2051-5960", "volume": "9", "issue": "1", "pages": "132"}, "abstract": "We identified an autosomal dominant progranulin mutation carrier without symptoms of dementia in her lifetime (Reduced Penetrance Mutation Carrier, RedPenMC). This resistance to develop expected pathology presents a unique opportunity to interrogate neurodegenerative mechanisms. We performed multimodal single-nuclei analyses of post-mortem frontal cortex from RedPenMC, including transcriptomics and global levels of chromatin marks. RedPenMC had an increased ratio of GRN-expressing microglia, higher levels of activating histone mark H3k4me3 in microglia and lower levels of the repressive chromatin marks H3k9me1 and H3k9me3 in the frontal cortex than her affected mutation carrier son and evidence of higher protein levels of progranulin in both plasma and brain homogenates. Although the study is limited to one case, the results support that restoring brain progranulin levels may be sufficient to escape neurodegeneration and FTD. In addition to previously identified modifier genes, it is possible that epigenetic marks may contribute to the increased progranulin expression in cases of reduced penetrance. These findings may stimulate similar follow-up studies and new therapeutic approaches.", "doi": "10.1186/s40478-021-01234-2", "pmid": "34344473", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Affinity Proteomics Uppsala": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s40478-021-01234-2"}, {"db": "pmc", "key": "PMC8336016"}], "notes": [], "created": "2021-08-25T09:08:35.655Z", "modified": "2024-01-16T13:48:38.876Z"}, {"entity": "publication", "iuid": "32abd265731b436a8ebb2698a1d8ab40", "links": {"self": {"href": "https://publications.scilifelab.se/publication/32abd265731b436a8ebb2698a1d8ab40.json"}, "display": {"href": "https://publications.scilifelab.se/publication/32abd265731b436a8ebb2698a1d8ab40"}}, "title": "The enigmatic RNase MRP of kinetoplastids.", "authors": [{"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "L\u00f3pez", "given": "Marcela D\u00e1vila", "initials": "MD"}, {"family": "Samuelsson", "given": "Tore", "initials": "T"}], "type": "journal article", "published": "2021-07-25", "journal": {"title": "RNA Biol", "issn": "1555-8584", "issn-l": "1547-6286", "volume": null, "issue": null, "pages": "1-9"}, "abstract": "The ribonucleoprotein RNase MRP is responsible for the processing of ribosomal RNA precursors. It is found in virtually all eukaryotes that have been examined. In the Euglenozoa, including the genera Euglena, Diplonema and kinetoplastids, MRP RNA and protein subunits have so far escaped detection using bioinformatic methods. However, we now demonstrate that the RNA component is widespread among the Euglenozoa and that these RNAs have secondary structures that conform to the structure of all other phylogenetic groups. In Euglena, we identified the same set of P/MRP protein subunits as in many other protists. However, we failed to identify any of these proteins in the kinetoplastids. This finding poses interesting questions regarding the structure and function of RNase MRP in these species.", "doi": "10.1080/15476286.2021.1952758", "pmid": "34308760", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-08-10T09:28:29.464Z", "modified": "2021-11-10T12:23:14.389Z"}, {"entity": "publication", "iuid": "a3a1f68ac3254552807509697dc8a4dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3a1f68ac3254552807509697dc8a4dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3a1f68ac3254552807509697dc8a4dd"}}, "title": "Gene regulation of the avian malaria parasite Plasmodium relictum, during the different stages within the mosquito vector.", "authors": [{"family": "Sekar", "given": "Vaishnovi", "initials": "V"}, {"family": "Rivero", "given": "Ana", "initials": "A"}, {"family": "Pigeault", "given": "Romain", "initials": "R"}, {"family": "Gandon", "given": "Sylvain", "initials": "S"}, {"family": "Drews", "given": "Anna", "initials": "A"}, {"family": "Ahren", "given": "Dag", "initials": "D"}, {"family": "Hellgren", "given": "Olof", "initials": "O"}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Genomics", "issn": "1089-8646", "volume": "113", "issue": "4", "pages": "2327-2337", "issn-l": "0888-7543"}, "abstract": "The malaria parasite Plasmodium relictum is one of the most widespread species of avian malaria. As in the case of its human counterparts, bird Plasmodium undergoes a complex life cycle infecting two hosts: the arthropod vector and the vertebrate host. In this study, we examined transcriptomes of P. relictum (SGS1) during crucial timepoints within its vector, Culex pipiens quinquefasciatus. Differential gene-expression analyses identified genes linked to the parasites life-stages at: i) a few minutes after the blood meal is ingested, ii) during peak oocyst production phase, iii) during peak sporozoite phase and iv) during the late-stages of the infection. A large amount of genes coding for functions linked to host-immune invasion and multifunctional genes was active throughout the infection cycle. One gene associated with a conserved Plasmodium membrane protein with unknown function was upregulated throughout the parasite development in the vector, suggesting an important role in the successful completion of the sporogonic cycle. Gene expression analysis further identified genes, with unknown functions to be significantly differentially expressed during the infection in the vector as well as upregulation of reticulocyte-binding proteins, which raises the possibility of the multifunctionality of these RBPs. We establish the existence of highly stage-specific pathways being overexpressed during the infection. This first study of gene-expression of a non-human Plasmodium species in its vector provides a comprehensive insight into the molecular mechanisms of the common avian malaria parasite P. relictum and provides essential information on the evolutionary diversity in gene regulation of the Plasmodium's vector stages.", "doi": "10.1016/j.ygeno.2021.05.021", "pmid": "34023365", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0888-7543(21)00194-4"}], "notes": [], "created": "2021-12-10T09:50:26.097Z", "modified": "2021-12-10T09:50:26.102Z"}, {"entity": "publication", "iuid": "83d87735b99145889c0e1ebe02901133", "links": {"self": {"href": "https://publications.scilifelab.se/publication/83d87735b99145889c0e1ebe02901133.json"}, "display": {"href": "https://publications.scilifelab.se/publication/83d87735b99145889c0e1ebe02901133"}}, "title": "Bifidobacteria-mediated immune system imprinting early in life", "authors": [{"family": "Henrick", "given": "Bethany M", "initials": "BM"}, {"family": "Rodriguez", "given": "Lucie", "initials": "L"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T"}, {"family": "Pou", "given": "Christian", "initials": "C"}, {"family": "Henckel", "given": "Ewa", "initials": "E"}, {"family": "Arzoomand", "given": "Aron", "initials": "A"}, {"family": "Olin", "given": "Axel", "initials": "A"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "Mikes", "given": "Jaromir", "initials": "J"}, {"family": "Tan", "given": "Ziyang", "initials": "Z"}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Ehrlich", "given": "Amy M", "initials": "AM"}, {"family": "Bernhardsson", "given": "Anna Karin", "initials": "AK"}, {"family": "Mugabo", "given": "Constantin Habimana", "initials": "CH"}, {"family": "Ambrosiani", "given": "Ylva", "initials": "Y"}, {"family": "Gustafsson", "given": "Anna", "initials": "A"}, {"family": "Chew", "given": "Stephanie", "initials": "S"}, {"family": "Brown", "given": "Heather K", "initials": "HK"}, {"family": "Prambs", "given": "Johann", "initials": "J"}, {"family": "Bohlin", "given": "Kajsa", "initials": "K"}, {"family": "Mitchell", "given": "Ryan D", "initials": "RD"}, {"family": "Underwood", "given": "Mark A", "initials": "MA"}, {"family": "Smilowitz", "given": "Jennifer T", "initials": "JT"}, {"family": "German", "given": "J Bruce", "initials": "JB"}, {"family": "Frese", "given": "Steven A", "initials": "SA"}, {"family": "Brodin", "given": "Petter", "initials": "P"}], "type": "journal-article", "published": "2021-07-00", "journal": {"title": "Cell", "issn": "0092-8674", "issn-l": null, "volume": "184", "issue": "15", "pages": "3884-3898.e11"}, "abstract": "Immune-microbe interactions early in life influence the risk of allergies, asthma, and other inflammatory diseases. Breastfeeding guides healthier immune-microbe relationships by providing nutrients to specialized microbes that in turn benefit the host's immune system. Such bacteria have co-evolved with humans but are now increasingly rare in modern societies. Here we show that a lack of bifidobacteria, and in particular depletion of genes required for human milk oligosaccharide (HMO) utilization from the metagenome, is associated with systemic inflammation and immune dysregulation early in life. In breastfed infants given Bifidobacterium infantis EVC001, which expresses all HMO-utilization genes, intestinal T helper 2 (Th2) and Th17 cytokines were silenced and interferon \u03b2 (IFN\u03b2) was induced. Fecal water from EVC001-supplemented infants contains abundant indolelactate and B. infantis-derived indole-3-lactic acid (ILA) upregulated immunoregulatory galectin-1 in Th2 and Th17 cells during polarization, providing a functional link between beneficial microbes and immunoregulation during the first months of life.", "doi": "10.1016/j.cell.2021.05.030", "pmid": "34143954", "labels": {"Cellular Immunomonitoring": "Technology development", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Affinity Proteomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(21)00660-7"}], "notes": [], "created": "2021-11-24T09:22:22.336Z", "modified": "2024-01-16T13:48:39.293Z"}, {"entity": "publication", "iuid": "cb924dd69d9a4420b002941f568ddb57", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb924dd69d9a4420b002941f568ddb57.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb924dd69d9a4420b002941f568ddb57"}}, "title": "Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy.", "authors": [{"family": "Bai", "given": "Xiangning", "initials": "X"}, {"family": "Narayanan", "given": "Aswathy", "initials": "A"}, {"family": "Nowak", "given": "Piotr", "initials": "P"}, {"family": "Ray", "given": "Shilpa", "initials": "S"}, {"family": "Neogi", "given": "Ujjwal", "initials": "U"}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2021-06-25", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "12", "pages": "667718", "issn-l": "1664-302X"}, "abstract": "Gut microbiome plays a significant role in HIV-1 immunopathogenesis and HIV-1-associated complications. Previous studies have mostly been based on 16S rRNA gene sequencing, which is limited in taxonomic resolution at the genus level and inferred functionality. Herein, we performed a deep shotgun metagenomics study with the aim to obtain a more precise landscape of gut microbiome dysbiosis in HIV-1 infection. A reduced tendency of alpha diversity and significantly higher beta diversity were found in HIV-1-infected individuals on antiretroviral therapy (ART) compared to HIV-1-negative controls. Several species, such as Streptococcus anginosus, Actinomyces odontolyticus, and Rothia mucilaginosa, were significantly enriched in the HIV-1-ART group. Correlations were observed between the degree of immunodeficiency and gut microbiome in terms of microbiota composition and metabolic pathways. Furthermore, microbial shift in HIV-1-infected individuals was found to be associated with changes in microbial virulome and resistome. From the perspective of methodological evaluations, our study showed that different DNA extraction protocols significantly affect the genomic DNA quantity and quality. Moreover, whole metagenome sequencing depth affects critically the recovery of microbial genes, including virulome and resistome, while less than 5 million reads per sample is sufficient for taxonomy profiling in human fecal metagenomic samples. These findings advance our understanding of human gut microbiome and their potential associations with HIV-1 infection. The methodological assessment assists in future study design to accurately assess human gut microbiome.", "doi": "10.3389/fmicb.2021.667718", "pmid": "34248876", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8267369"}], "notes": [], "created": "2021-06-28T08:00:15.729Z", "modified": "2024-01-16T13:48:39.430Z"}, {"entity": "publication", "iuid": "28b16b8dfd734823b09881b88015de95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/28b16b8dfd734823b09881b88015de95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/28b16b8dfd734823b09881b88015de95"}}, "title": "Methods to Identify and Study the Evolution of Pseudogenes Using a Phylogenetic Approach.", "authors": [{"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Pontarotti", "given": "Pierre", "initials": "P"}], "type": "journal article", "published": "2021-06-25", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "volume": "2324", "pages": "21-34", "issn-l": "1064-3745"}, "abstract": "The discovery that pseudogenes are involved in important biological processes has excited enthusiasm and increased the research interest on them. An accurate detection and analysis of pseudogenes can be achieved using comparative methods, but only the use of phylogenetic tools can provide accurate information about their birth, their evolution and their death, hence about the impact that they have on genes and genomes. Here, phylogenetic methods that allow for studying pseudogene history are described.", "doi": "10.1007/978-1-0716-1503-4_2", "pmid": "34165706", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-12-10T09:55:35.691Z", "modified": "2021-12-10T09:55:35.696Z"}, {"entity": "publication", "iuid": "e0711f8e6d244b13b40907137a87996f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0711f8e6d244b13b40907137a87996f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0711f8e6d244b13b40907137a87996f"}}, "title": "Toll-like receptor 4 methylation grade is linked to depressive symptom severity.", "authors": [{"family": "Rasmusson", "given": "Annica J", "initials": "AJ", "orcid": "0000-0002-7228-7755", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ef833f6dd204c189586fba5c33d1d58.json"}}, {"family": "Gallwitz", "given": "Maike", "initials": "M"}, {"family": "Soltanabadi", "given": "Bardia", "initials": "B", "orcid": "0000-0003-4827-5268", "researcher": {"href": "https://publications.scilifelab.se/researcher/5018ceb09cc8462bb8df7b6cad75d615.json"}}, {"family": "Ciuculete", "given": "Diana M", "initials": "DM"}, {"family": "Mengel-From", "given": "Jonas", "initials": "J"}, {"family": "Christensen", "given": "Kaare", "initials": "K", "orcid": "0000-0002-5429-5292", "researcher": {"href": "https://publications.scilifelab.se/researcher/e79ea43d09544efc95351b52ac682910.json"}}, {"family": "Nygaard", "given": "Marianne", "initials": "M", "orcid": "0000-0003-0703-2665", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d68eda16735460d81993dc39006d5a5.json"}}, {"family": "Soerensen", "given": "Mette", "initials": "M", "orcid": "0000-0001-5268-3366", "researcher": {"href": "https://publications.scilifelab.se/researcher/712cb1928fdf429ca777a8209b31090d.json"}}, {"family": "Bostr\u00f6m", "given": "Adrian E", "initials": "AE"}, {"family": "Fredriksson", "given": "Robert", "initials": "R"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Mwinyi", "given": "Jessica", "initials": "J"}, {"family": "Czamara", "given": "Darina", "initials": "D", "orcid": "0000-0001-7381-904X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e9a8a7d605d4f63a311fc8a211422a6.json"}}, {"family": "Binder", "given": "Elisabeth B", "initials": "EB", "orcid": "0000-0001-7088-6618", "researcher": {"href": "https://publications.scilifelab.se/researcher/0cfb2bf09e9d49ad922bb5c3c252c716.json"}}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}, {"family": "Cunningham", "given": "Janet L", "initials": "JL", "orcid": "0000-0001-7876-7779", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ab30dd6c6874bc7a227a8699c4a7085.json"}}], "type": "journal article", "published": "2021-06-24", "journal": {"title": "Transl Psychiatry", "issn": "2158-3188", "issn-l": "2158-3188", "volume": "11", "issue": "1", "pages": "371"}, "abstract": "This study explores potential associations between the methylation of promoter-associated CpG sites of the toll-like receptor (TLR)-family, plasma levels of pro-inflammatory proteins and depressive symptoms in young female psychiatric patients. Ratings of depressive symptoms and blood samples were obtained from 92 young women seeking psychiatric care. Methylation of 32 promoter-associated CpG sites in TLR1 to TLR10 was analysed using the Illumina Infinium Methylation EPIC BeadChip. Expression levels of 91 inflammatory proteins were determined by proximity extension assay. Statistical correlations between depressive state, TLR1-10 methylation and inflammatory proteins were investigated. Four additional cohorts were studied to evaluate the generalizability of the findings. In the discovery cohort, methylation grade of cg05429895 (TLR4) in blood was inversely correlated with depressive symptoms score in young adults. After correction for multiple testing, plasma levels of macrophage inflammatory protein 1\u03b2 (MIP-1\u03b2/CCL4) were associated with both TLR4 methylation and depressive symptom severity. A similar inverse association between TLR4 methylation in blood and affective symptoms score was also found in a cohort of 148 both males and females (<40 years of age) from the Danish Twin Registry. These findings were not, however, replicated in three other external cohorts; which differed from the first two cohorts by a higher age and mixed ethnicities, thus limiting the generalizability of our findings. However, TLR4 methylation inversely correlated with TLR4 mRNA expression in the Danish Twin Study indicating a functional significance of methylation at this particular CpG. Higher depression scores in young Scandinavian adults was associated with decreased methylation of TLR4 in blood.", "doi": "10.1038/s41398-021-01481-w", "pmid": "34226490", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Affinity Proteomics Uppsala": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8257733"}, {"db": "pii", "key": "10.1038/s41398-021-01481-w"}], "notes": [], "created": "2021-08-19T13:41:38.152Z", "modified": "2024-01-16T13:48:39.445Z"}, {"entity": "publication", "iuid": "f470c71971e84209bc3eef845edc1f9f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f470c71971e84209bc3eef845edc1f9f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f470c71971e84209bc3eef845edc1f9f"}}, "title": "Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa.", "authors": [{"family": "Meidl", "given": "Peter", "initials": "P"}, {"family": "Furneaux", "given": "Brendan", "initials": "B", "orcid": "0000-0003-3522-7363", "researcher": {"href": "https://publications.scilifelab.se/researcher/df196c994b3c4086b4f94eacf4e57239.json"}}, {"family": "Tchan", "given": "Kassim I", "initials": "KI"}, {"family": "Kluting", "given": "Kerri", "initials": "K"}, {"family": "Ryberg", "given": "Martin", "initials": "M", "orcid": "0000-0002-6795-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0a8578a1ace4105be91ec8116c84365.json"}}, {"family": "Guissou", "given": "Marie-Laure", "initials": "ML"}, {"family": "Soro", "given": "Bakary", "initials": "B"}, {"family": "Traor\u00e9", "given": "A\u00efssata", "initials": "A"}, {"family": "Konomou", "given": "Gbamon", "initials": "G"}, {"family": "Yorou", "given": "Nourou S", "initials": "NS", "orcid": "0000-0001-6997-811X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a56781052962486cb78d1b4462a52fcb.json"}}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}}], "type": "journal article", "published": "2021-06-11", "journal": {"title": "MycoKeys", "issn": "1314-4049", "volume": "81", "pages": "45-68", "issn-l": null}, "abstract": "Forests and woodlands in the West African Guineo-Sudanian transition zone contain many tree species that form symbiotic interactions with ectomycorrhizal (ECM) fungi. These fungi facilitate plant growth by increasing nutrient and water uptake and include many fruiting body-forming fungi, including some edible mushrooms. Despite their importance for ecosystem functioning and anthropogenic use, diversity and distribution of ECM fungi is severely under-documented in West Africa. We conducted a broad regional sampling across five West African countries using soil eDNA to characterize the ECM as well as the total soil fungal community in gallery forests and savanna woodlands dominated by ECM host tree species. We subsequently sequenced the entire ITS region and much of the LSU region to infer a phylogeny for all detected soil fungal species. Utilizing a long read sequencing approach allows for higher taxonomic resolution by using the full ITS region, while the highly conserved LSU gene allows for a more accurate higher-level assignment of species hypotheses, including species without ITS-based taxonomy assignments. We detect no overall difference in species richness between gallery forests and woodlands. However, additional gallery forest plots and more samples per plot would have been needed to firmly conclude this pattern. Based on both abundance and richness, species from the families Russulaceae and Inocybaceae dominate the ECM fungal soil communities across both vegetation types. The community structure of both total soil fungi and ECM fungi was significantly influenced by vegetation types and showed strong correlation within plots. However, we found no significant difference in fungal community structure between samples collected adjacent to different host tree species within each plot. We conclude that within plots, the fungal community is structured more by the overall ECM host plant community than by the species of the individual host tree that each sample was collected from.", "doi": "10.3897/mycokeys.81.66249", "pmid": "34475800", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8390883"}, {"db": "pii", "key": "66249"}], "notes": [], "created": "2022-11-24T15:07:20.969Z", "modified": "2022-11-24T15:07:21.002Z"}, {"entity": "publication", "iuid": "0afde3308313428ca7afd4c0f04897d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0afde3308313428ca7afd4c0f04897d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0afde3308313428ca7afd4c0f04897d1"}}, "title": "Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172.", "authors": [{"family": "T\u00f5lgo", "given": "Monika", "initials": "M"}, {"family": "H\u00fcttner", "given": "Silvia", "initials": "S"}, {"family": "Rugbjerg", "given": "Peter", "initials": "P"}, {"family": "Thuy", "given": "Nguyen Thanh", "initials": "NT"}, {"family": "Thanh", "given": "Vu Nguyen", "initials": "VN"}, {"family": "Larsbrink", "given": "Johan", "initials": "J"}, {"family": "Olsson", "given": "Lisbeth", "initials": "L", "orcid": "0000-0002-0827-5442", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fa7036912fb4073be4a4365937f2232.json"}}], "type": "journal article", "published": "2021-06-03", "journal": {"title": "Biotechnol Biofuels", "issn": "1754-6834", "volume": "14", "issue": "1", "pages": "131", "issn-l": "1754-6834"}, "abstract": "Biomass-degrading enzymes with improved activity and stability can increase substrate saccharification and make biorefineries economically feasible. Filamentous fungi are a rich source of carbohydrate-active enzymes (CAZymes) for biomass degradation. The newly isolated LPH172 strain of the thermophilic Ascomycete Thielavia terrestris has been shown to possess high xylanase and cellulase activities and tolerate low pH and high temperatures. Here, we aimed to illuminate the lignocellulose-degrading machinery and novel carbohydrate-active enzymes in LPH172 in detail.\n\nWe sequenced and analyzed the 36.6-Mb genome and transcriptome of LPH172 during growth on glucose, cellulose, rice straw, and beechwood xylan. 10,128 predicted genes were found in total, which included 411 CAZy domains. Compared to other fungi, auxiliary activity (AA) domains were particularly enriched. A higher GC content was found in coding sequences compared to the overall genome, as well as a high GC3 content, which is hypothesized to contribute to thermophilicity. Primarily auxiliary activity (AA) family 9 lytic polysaccharide monooxygenase (LPMO) and glycoside hydrolase (GH) family 7 glucanase encoding genes were upregulated when LPH172 was cultivated on cellulosic substrates. Conventional hemicellulose encoding genes (GH10, GH11 and various CEs), as well as AA9 LPMOs, were upregulated when LPH172 was cultivated on xylan. The observed co-expression and co-upregulation of genes encoding AA9 LPMOs, other AA CAZymes, and (hemi)cellulases point to a complex and nuanced degradation strategy.\n\nOur analysis of the genome and transcriptome of T. terrestris LPH172 elucidates the enzyme arsenal that the fungus uses to degrade lignocellulosic substrates. The study provides the basis for future characterization of potential new enzymes for industrial biomass saccharification.", "doi": "10.1186/s13068-021-01975-1", "pmid": "34082802", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13068-021-01975-1"}, {"db": "pmc", "key": "PMC8176577"}], "notes": [], "created": "2021-12-10T09:56:25.041Z", "modified": "2021-12-10T09:56:25.065Z"}, {"entity": "publication", "iuid": "10c3760aaf154862956bca5a07c09c65", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10c3760aaf154862956bca5a07c09c65.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10c3760aaf154862956bca5a07c09c65"}}, "title": "Large-scale identification of protein histidine methylation in human cells.", "authors": [{"family": "Kapell", "given": "Sebastian", "initials": "S"}, {"family": "Jakobsson", "given": "Magnus E", "initials": "ME", "orcid": "0000-0002-4259-4180", "researcher": {"href": "https://publications.scilifelab.se/researcher/e576d596ae3144bb8e4c92911c12f8a3.json"}}], "type": "journal article", "published": "2021-06-00", "journal": {"title": "NAR Genom Bioinform", "issn": "2631-9268", "volume": "3", "issue": "2", "pages": "lqab045", "issn-l": null}, "abstract": "Methylation can occur on histidine, lysine and arginine residues in proteins and often serves a regulatory function. Histidine methylation has recently attracted attention through the discovery of the human histidine methyltransferase enzymes SETD3 and METTL9. There are currently no methods to enrich histidine methylated peptides for mass spectrometry analysis and large-scale studies of the modification are hitherto absent. Here, we query ultra-comprehensive human proteome datasets to generate a resource of histidine methylation sites. In HeLa cells alone, we report 299 histidine methylation sites as well as 895 lysine methylation events. We use this resource to explore the frequency, localization, targeted domains, protein types and sequence requirements of histidine methylation and benchmark all analyses to methylation events on lysine and arginine. Our results demonstrate that histidine methylation is widespread in human cells and tissues and that the modification is over-represented in regions of mono-spaced histidine repeats. We also report colocalization of the modification with functionally important phosphorylation sites and disease associated mutations to identify regions of likely regulatory and functional importance. Taken together, we here report a system level analysis of human histidine methylation and our results represent a comprehensive resource enabling targeted studies of individual histidine methylation events.", "doi": "10.1093/nargab/lqab045", "pmid": "34046594", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "lqab045"}, {"db": "pmc", "key": "PMC8140740"}], "notes": [], "created": "2021-06-03T12:45:21.271Z", "modified": "2024-01-16T13:48:39.594Z"}, {"entity": "publication", "iuid": "37a57995a5b84f1da07545fd29e58163", "links": {"self": {"href": "https://publications.scilifelab.se/publication/37a57995a5b84f1da07545fd29e58163.json"}, "display": {"href": "https://publications.scilifelab.se/publication/37a57995a5b84f1da07545fd29e58163"}}, "title": "Identification of Candidate Protein Biomarkers for CIN2+ Lesions from Self-Sampled, Dried Cervico-Vaginal Fluid Using LC-MS/MS.", "authors": [{"family": "Guti\u00e9rrez", "given": "Ariadna Lara", "initials": "AL", "orcid": "0000-0003-3584-0627", "researcher": {"href": "https://publications.scilifelab.se/researcher/76b18f907c414f258383f9fde9798a75.json"}}, {"family": "Lindberg", "given": "Julia Hedlund", "initials": "JH"}, {"family": "Shevchenko", "given": "Ganna", "initials": "G"}, {"family": "Gustavsson", "given": "Inger", "initials": "I"}, {"family": "Bergquist", "given": "Jonas", "initials": "J", "orcid": "0000-0002-4597-041X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d745034529f3423abbea230b4e586d20.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Enroth", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5056-9137", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bb97ef16ee49f3ae0c7ea0495fd971.json"}}], "type": "journal article", "published": "2021-05-25", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "13", "issue": "11", "issn-l": "2072-6694"}, "abstract": "Molecular screening programs for cervical cancer detect the presence of human papilloma virus (HPV) in cell material or vaginal fluids. Persistent infection with high-risk HPV is a necessary pre-requisite, but the majority of infections do not lead to pathological states. Additional biomarkers are needed to increase the specificity of the molecular tests. Here, we have investigated the possibility of detecting protein biomarkers using mass spectrometry from dried self-sampled cervico-vaginal fluid deposited on FTA cards. We found significant intra-individual correlations (p < 2.2 \u00d7 10-16), although heterogenous protein profiles were obtained between individuals. Out of 3699 proteins found in total, 169 were detected in at least 95% of the samples. Using a discovery/replication design, 18 proteins were found to be significant in the discovery cohort, with higher values in those cases compared to controls. All of these were found to also have higher levels among the cases in the replication cohort, with one protein (DEAD-Box Helicase) remaining statistically significant. Finally, a predictive 7-protein multivariate model was developed with a sensitivity and specificity of 0.90 and 0.55, respectively. Our results demonstrate that robust measurements of protein biomarkers can be obtained from self-sampled dried CVF and that these could be used to predict cervical cancer pre-stages.", "doi": "10.3390/cancers13112592", "pmid": "34070587", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8198222"}, {"db": "pii", "key": "cancers13112592"}], "notes": [], "created": "2025-11-21T13:13:36.269Z", "modified": "2025-11-21T13:13:36.473Z"}, {"entity": "publication", "iuid": "ff762513ebb04c45bf11963125687232", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff762513ebb04c45bf11963125687232.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff762513ebb04c45bf11963125687232"}}, "title": "Stromal Heterogeneity in the Human Proliferative Endometrium-A Single-Cell RNA Sequencing Study.", "authors": [{"family": "Queckb\u00f6rner", "given": "Suzanna", "initials": "S"}, {"family": "von Grothusen", "given": "Carolina", "initials": "C", "orcid": "0000-0002-1508-8952", "researcher": {"href": "https://publications.scilifelab.se/researcher/d114195666f34b3ab78b054a13ceede1.json"}}, {"family": "Boggavarapu", "given": "Nageswara Rao", "initials": "NR"}, {"family": "Francis", "given": "Roy Mathew", "initials": "RM"}, {"family": "Davies", "given": "Lindsay C", "initials": "LC"}, {"family": "Gemzell-Danielsson", "given": "Kristina", "initials": "K", "orcid": "0000-0001-6516-1444", "researcher": {"href": "https://publications.scilifelab.se/researcher/44544a9f401c4db8a5cbdeca3d31e4b2.json"}}], "type": "journal article", "published": "2021-05-22", "journal": {"title": "J Pers Med", "issn": "2075-4426", "volume": "11", "issue": "6", "issn-l": null}, "abstract": "The endometrium undergoes regular regeneration and stromal proliferation as part of the normal menstrual cycle. To better understand cellular interactions driving the mechanisms in endometrial regeneration we employed single-cell RNA sequencing. Endometrial biopsies were obtained during the proliferative phase of the menstrual cycle from healthy fertile women and processed to single-cell suspensions which were submitted for sequencing. In addition to known endometrial cell types, bioinformatic analysis revealed multiple stromal populations suggestive of specific stromal niches with the ability to control inflammation and extracellular matrix composition. Ten different stromal cells and two pericyte subsets were identified. Applying different R packages (Seurat, SingleR, Velocyto) we established cell cluster diversity and cell lineage/trajectory, while using external data to validate our findings. By understanding healthy regeneration in the described stromal compartments, we aim to identify points of further investigation and possible targets for novel therapy development for benign gynecological disorders affecting endometrial regeneration and proliferation such as endometriosis and Asherman's syndrome.", "doi": "10.3390/jpm11060448", "pmid": "34067358", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "jpm11060448"}, {"db": "pmc", "key": "PMC8224746"}], "notes": [], "created": "2021-12-02T13:20:38.533Z", "modified": "2024-01-16T13:48:39.689Z"}, {"entity": "publication", "iuid": "b45c93184c244e1aa85993dd4a85d654", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b45c93184c244e1aa85993dd4a85d654.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b45c93184c244e1aa85993dd4a85d654"}}, "title": "Virus Diversity and Loads in Crickets Reared for Feed: Implications for Husbandry.", "authors": [{"family": "de Miranda", "given": "Joachim R", "initials": "JR"}, {"family": "Granberg", "given": "Fredrik", "initials": "F"}, {"family": "Low", "given": "Matthew", "initials": "M"}, {"family": "Onorati", "given": "Piero", "initials": "P"}, {"family": "Semberg", "given": "Emilia", "initials": "E"}, {"family": "Jansson", "given": "Anna", "initials": "A"}, {"family": "Berggren", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2021-05-20", "journal": {"title": "Front Vet Sci", "issn": "2297-1769", "volume": "8", "pages": "642085", "issn-l": null}, "abstract": "Insects generally have high reproductive rates leading to rapid population growth and high local densities; ideal conditions for disease epidemics. The parasites and diseases that naturally regulate wild insect populations can also impact when these insects are produced commercially, on farms. While insects produced for human or animal consumption are often reared under high density conditions, very little is known about the microbes associated with these insects, particularly those with pathogenic potential. In this study we used both target-free and targeted screening approaches to explore the virome of two cricket species commonly reared for feed and food, Acheta domesticus and Gryllus bimaculatus. The target-free screening of DNA and RNA from a single A. domesticus frass sample revealed that only 1% of the nucleic acid reads belonged to viruses, including known cricket, insect, bacterial and plant pathogens, as well as a diverse selection of novel viruses. The targeted screening revealed relatively high levels of Acheta domesticus densovirus, invertebrate iridovirus 6 and a novel iflavirus, as well as low levels of Acheta domesticus volvovirus, in insect and frass samples from several retailers. Our findings highlight the value of multiple screening approaches for a comprehensive and robust cricket disease monitoring and management strategy. This will become particularly relevant as-and-when cricket rearing facilities scale up and transform from producing insects for animal feed to producing insects for human consumption.", "doi": "10.3389/fvets.2021.642085", "pmid": "34095270", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8173086"}], "notes": [], "created": "2021-12-02T14:25:38.345Z", "modified": "2024-01-16T13:48:39.696Z"}, {"entity": "publication", "iuid": "0e37ae638f8a41589a54a60d69ead29f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e37ae638f8a41589a54a60d69ead29f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e37ae638f8a41589a54a60d69ead29f"}}, "title": "Continent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe.", "authors": [{"family": "Salm\u00f3n", "given": "Pablo", "initials": "P", "orcid": "0000-0001-9718-6611", "researcher": {"href": "https://publications.scilifelab.se/researcher/b60bfa8b60174680a1546f283c2ccbc1.json"}}, {"family": "Jacobs", "given": "Arne", "initials": "A", "orcid": "0000-0001-7635-5447", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c375694c76e48279bdc6e7dcc2808a6.json"}}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Biard", "given": "Clotilde", "initials": "C", "orcid": "0000-0001-7474-5345", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f2845cc669e41f38f4abc7be2d749c2.json"}}, {"family": "Dingemanse", "given": "Niels J", "initials": "NJ", "orcid": "0000-0003-3320-0861", "researcher": {"href": "https://publications.scilifelab.se/researcher/364e2f2173244470bc7f9c1feff13bc9.json"}}, {"family": "Dominoni", "given": "Davide M", "initials": "DM", "orcid": "0000-0003-2063-9955", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5c5e5b23a174cecb550e7a68cd0b0d7.json"}}, {"family": "Helm", "given": "Barbara", "initials": "B", "orcid": "0000-0002-6648-1463", "researcher": {"href": "https://publications.scilifelab.se/researcher/54eeba33656a4e44a2a8281b9a1d9c6d.json"}}, {"family": "Lundberg", "given": "Max", "initials": "M"}, {"family": "Senar", "given": "Juan Carlos", "initials": "JC", "orcid": "0000-0001-9955-3892", "researcher": {"href": "https://publications.scilifelab.se/researcher/9acb6c1702bf4ce88d24eb8a35b39ae3.json"}}, {"family": "Sprau", "given": "Philipp", "initials": "P"}, {"family": "Visser", "given": "Marcel E", "initials": "ME", "orcid": "0000-0002-1456-1939", "researcher": {"href": "https://publications.scilifelab.se/researcher/87e0c4d6e845447ab627a26c7d12d989.json"}}, {"family": "Isaksson", "given": "Caroline", "initials": "C", "orcid": "0000-0002-6889-1386", "researcher": {"href": "https://publications.scilifelab.se/researcher/30ddbca044f64cb1b1feef58baf539ba.json"}}], "type": "journal article", "published": "2021-05-20", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "2983", "issn-l": "2041-1723"}, "abstract": "Urbanisation is increasing worldwide, and there is now ample evidence of phenotypic changes in wild organisms in response to this novel environment. Yet, the genetic changes and genomic architecture underlying these adaptations are poorly understood. Here, we genotype 192 great tits (Parus major) from nine European cities, each paired with an adjacent rural site, to address this major knowledge gap in our understanding of wildlife urban adaptation. We find that a combination of polygenic allele frequency shifts and recurrent selective sweeps are associated with the adaptation of great tits to urban environments. While haplotypes under selection are rarely shared across urban populations, selective sweeps occur within the same genes, mostly linked to neural function and development. Collectively, we show that urban adaptation in a widespread songbird occurs through unique and shared selective sweeps in a core-set of behaviour-linked genes.", "doi": "10.1038/s41467-021-23027-w", "pmid": "34016968", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-23027-w"}, {"db": "pmc", "key": "PMC8137928"}], "notes": [], "created": "2021-12-10T09:50:47.664Z", "modified": "2021-12-10T09:50:47.897Z"}, {"entity": "publication", "iuid": "e11abdff9c1e4dc2bb809825671d8520", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e11abdff9c1e4dc2bb809825671d8520.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e11abdff9c1e4dc2bb809825671d8520"}}, "title": "Pulmonary fibrosis in relation to genetic loci in an inception cohort of patients with early rheumatoid arthritis from northern Sweden.", "authors": [{"family": "J\u00f6nsson", "given": "Elias", "initials": "E"}, {"family": "Ljung", "given": "Lotta", "initials": "L", "orcid": "0000-0001-8999-0925", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad0a3f26e6a64fa9b42d4c4dbcd9a2f6.json"}}, {"family": "Norrman", "given": "Eva", "initials": "E"}, {"family": "Freyhult", "given": "Eva", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "\u00c4rlestig", "given": "Lisbeth", "initials": "L", "orcid": "0000-0003-3965-9403", "researcher": {"href": "https://publications.scilifelab.se/researcher/a567edc80e1b476385b9bc2d3c3994f2.json"}}, {"family": "Dahlqvist", "given": "Johanna", "initials": "J", "orcid": "0000-0002-6283-644X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fb2ab2d83b6437f9918f330e5fb81b2.json"}}, {"family": "Dahlqvist", "given": "Solbritt Rantap\u00e4\u00e4", "initials": "SR", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}], "type": "journal article", "published": "2021-05-16", "journal": {"title": "Rheumatology (Oxford)", "issn": "1462-0332", "issn-l": "1462-0324", "volume": null, "issue": null, "pages": null}, "abstract": "Pulmonary manifestations in rheumatoid arthritis (RA) are common comorbidities. Interstitial lung disease (ILD), both idiopathic and in RA has been associated with several genetic variants. We assessed pulmonary fibrosis (PF) in an inception cohort of RA patients in relation to genetic variants and disease-related factors.\n\n1466 early RA patients were consecutively included and followed prospectively from index date until death or December 31, 2016. Clinical, and laboratory data and treatment were continuously registered according to Swedish Rheumatology quality register. DNA was available from 1184 patients and 571 151 genome-wide-single-nucleotide polymorphism were analysed (GSA, Illumina, deCode, Island). Thirteen identified genetic variants were extracted. At follow-up the patients answered a questionnaire regarding disease progression and lung involvement, which was validated by reviewing medical records and analysing radiological examinations.\n\nThe prevalence of PF was 5.6%, and the annualized incidence rate was 5.0/1000 (95%CI 3.80, 6.54). Four SNPs were associated with PF in RA; rs35705950 (MUC5B), OR = 2.5 (95%CI 1.5, 4.0), adjusted p-value = 0.00016 and q-value = 0.0021, rs111521887 (TOLLIP) OR = 1.9 (95%CI 1.3, 2.8), adjusted p-value = 0.0014 and q-value = 0.0092; rs2609255 (FAM13A) (OR = 1.7 (95%CI 1.1, 2.5), adjusted p-value = 0.013 and q-value = 0.055) and rs2736100 (TERT) OR = 1.5 (1.0, 2.2), adjusted p-value = 0.046, q-value was 0.15. Older age and rheumatoid factor-positivity were associated with increased risk, whilst methotrexate treatment was associated with a lower risk of PF.\n\nDevelopment of PF in an inception cohort of RA patients was associated with four of 12 ILD risk genes. RA-related factors except for age at diagnosis and RF-positivity were of limited importance in PF development.", "doi": "10.1093/rheumatology/keab441", "pmid": "33993221", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6276448"}], "notes": [], "created": "2021-05-21T10:58:27.692Z", "modified": "2024-01-16T13:48:39.749Z"}, {"entity": "publication", "iuid": "9c70617c2f2d4ebebfc7fd3e53a2bf25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c70617c2f2d4ebebfc7fd3e53a2bf25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c70617c2f2d4ebebfc7fd3e53a2bf25"}}, "title": "Histological and transcriptional characterization of the pancreatic acinar tissue in type 1 diabetes.", "authors": [{"family": "Granlund", "given": "Louise", "initials": "L", "orcid": "0000-0002-2888-486X", "researcher": {"href": "https://publications.scilifelab.se/researcher/56b62a5d5c924169aa6b1f755f9dce6b.json"}}, {"family": "Hedin", "given": "Anders", "initials": "A"}, {"family": "Wahlh\u00fctter", "given": "Miriam", "initials": "M"}, {"family": "Seiron", "given": "Peter", "initials": "P", "orcid": "0000-0002-1419-450X", "researcher": {"href": "https://publications.scilifelab.se/researcher/35843f2bdc714b39a6aa6db11e874171.json"}}, {"family": "Korsgren", "given": "Olle", "initials": "O"}, {"family": "Skog", "given": "Oskar", "initials": "O", "orcid": "0000-0001-9713-722X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a8a0b83f27a4a3da50c0cca253618e9.json"}}, {"family": "Lundberg", "given": "Marcus", "initials": "M", "orcid": "0000-0001-7916-2237", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c29eaaebc9945758117bc98a7b477f9.json"}}], "type": "journal article", "published": "2021-05-00", "journal": {"title": "BMJ Open Diabetes Res Care", "issn": "2052-4897", "volume": "9", "issue": "1", "issn-l": null}, "abstract": "Despite a reduced function and volume of the exocrine pancreas in type 1 diabetes, the acinar cells remain understudied in type 1 diabetes research. The hypothesis of this study is that the acinar tissue is altered in subjects with type 1 diabetes compared with subjects without diabetes.\n\nThe cell density, expression of digestive enzymes, and transcriptome of acinar tissue at varying distances from islets were analyzed using histology, immunostaining, and AmpliSeq RNA sequencing of laser capture microdissected tissue. Pancreases examined were from organ donors with or without type 1 diabetes.\n\nWe demonstrate preserved acinar nuclei density and find no support of acinar atrophy in type 1 diabetes. Staining for digestive enzymes (amylase, lipase, and trypsin) demonstrated an evenly distributed expression in the exocrine parenchyma; although occasional amylase-negative regions appeared in tissue that had been formalin-fixed and paraffin-embedded, this phenomenon was not evident in frozen tissue. Gene set enrichment analysis of whole transcriptome data identified transcriptional alterations in type 1 diabetes that were present in the acinar tissue independent of the distance from islets. Among these, the two most enriched gene sets were Myc Targets V2 and Estrogen Response Early.\n\nTaken together, these new data emphasize the involvement of the entire pancreas in type 1 diabetes pathology. The alteration of the gene sets Myc Targets V2 and Estrogen Response Early is a possible link to the increased incidence of pancreatic cancer in type 1 diabetes.", "doi": "10.1136/bmjdrc-2020-002076", "pmid": "34031141", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "9/1/e002076"}, {"db": "pmc", "key": "PMC8149357"}], "notes": [], "created": "2021-12-02T14:34:25.594Z", "modified": "2024-01-16T13:48:39.908Z"}, {"entity": "publication", "iuid": "4eba845e84a74f32b74ad40a52db41b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4eba845e84a74f32b74ad40a52db41b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4eba845e84a74f32b74ad40a52db41b0"}}, "title": "Complete Genome Sequence of an Antimicrobial-Producing Bacillus velezensis Sam8H1 Isolate from the Makgadikgadi Saltpans of Botswana.", "authors": [{"family": "Modikwe", "given": "Gorata", "initials": "G"}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L", "orcid": "0000-0001-9751-5745", "researcher": {"href": "https://publications.scilifelab.se/researcher/000321fd81b9457db66140246bbd9066.json"}}, {"family": "Mabutho", "given": "Gomolemo", "initials": "G"}, {"family": "Lebani", "given": "Kebaneilwe", "initials": "K"}, {"family": "Lebogang", "given": "Lesedi", "initials": "L"}, {"family": "Zhou", "given": "Nerve", "initials": "N", "orcid": "0000-0002-8822-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7ff4108934c4f7db17ad7539a116c54.json"}}], "type": "journal article", "published": "2021-04-29", "journal": {"title": "Microbiol Resour Announc", "issn": "2576-098X", "issn-l": "2576-098X", "volume": "10", "issue": "17", "pages": null}, "abstract": "The global antimicrobial drug resistance crisis requires urgency in searching for more effective broad-spectrum antimicrobial drugs. Here, we present a complete circular genome sequence and a plasmid of an antimicrobial-producing isolate, Bacillus velezensis strain Sam8H1, from the Makgadikgadi saltpans in Botswana. Bioinformatic analyses revealed 12 putative secondary metabolite biosynthetic gene clusters important for genome-guided drug discovery studies.", "doi": "10.1128/MRA.00175-21", "pmid": "33927034", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10/17/e00175-21"}, {"db": "pmc", "key": "PMC8086208"}], "notes": [], "created": "2021-04-30T06:41:45.566Z", "modified": "2024-01-16T13:48:39.950Z"}, {"entity": "publication", "iuid": "1b94fbe5b4794fb2be8ab1ea22127238", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b94fbe5b4794fb2be8ab1ea22127238.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b94fbe5b4794fb2be8ab1ea22127238"}}, "title": "Divergent airway microbiomes in lung transplant recipients with or without pulmonary infection.", "authors": [{"family": "P\u00e5hlman", "given": "Lisa I", "initials": "LI", "orcid": "0000-0001-6366-2309", "researcher": {"href": "https://publications.scilifelab.se/researcher/f58db990776f4e228707df2502d44728.json"}}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L"}, {"family": "Aspelund", "given": "Anna Stj\u00e4rne", "initials": "AS"}], "type": "comparative study", "published": "2021-04-23", "journal": {"title": "Respir. Res.", "issn": "1465-993X", "volume": "22", "issue": "1", "pages": "118", "issn-l": "1465-9921"}, "abstract": "Lung transplant (LTx) recipients are at increased risk for airway infections, but the cause of infection is often difficult to establish with traditional culture-based techniques. The objectives of the study was to compare the airway microbiome in LTx patients with and without ongoing airway infection and identify differences in their microbiome composition.\n\nLTx recipients were prospectively followed with bronchoalveolar lavage (BAL) during the first year after transplantation. The likelihood of airway infection at the time of sampling was graded based on clinical criteria and BAL cultures, and BAL fluid levels of the inflammatory markers heparin-binding protein (HBP), IL-1\u03b2 and IL-8 were determined with ELISA. The bacterial microbiome of the samples were analysed with 16S rDNA sequencing and characterized based on richness and evenness. The distance in microbiome composition between samples were determined using Bray-Curtis and weighted and unweighted UniFrac.\n\nA total of 46 samples from 22 patients were included in the study. Samples collected during infection and samples with high levels of inflammation were characterized by loss of bacterial diversity and a significantly different species composition. Burkholderia, Corynebacterium and Staphylococcus were enriched during infection and inflammation, whereas anaerobes and normal oropharyngeal flora were less abundant. The most common findings in BAL cultures, including Pseudomonas aeruginosa, were not enriched during infection.\n\nThis study gives important insights into the dynamics of the airway microbiome of LTx recipients, and suggests that lung infections are associated with a disruption in the homeostasis of the microbiome.", "doi": "10.1186/s12931-021-01724-w", "pmid": "33892717", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12931-021-01724-w"}, {"db": "pmc", "key": "PMC8063417"}], "notes": [], "created": "2021-04-26T12:21:11.416Z", "modified": "2024-01-16T13:48:40.020Z"}, {"entity": "publication", "iuid": "fd189a71a3c3441aa90c27ce29e18002", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd189a71a3c3441aa90c27ce29e18002.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd189a71a3c3441aa90c27ce29e18002"}}, "title": "DNA methylation in cord blood in association with prenatal depressive symptoms.", "authors": [{"family": "Kallak", "given": "Theodora Kunovac", "initials": "TK", "orcid": "0000-0002-2112-8674", "researcher": {"href": "https://publications.scilifelab.se/researcher/71623ccbc71e4a8e908d3006a1712de1.json"}}, {"family": "Br\u00e4nn", "given": "Emma", "initials": "E"}, {"family": "Fransson", "given": "Emma", "initials": "E"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Lager", "given": "Susanne", "initials": "S"}, {"family": "Comasco", "given": "Erika", "initials": "E"}, {"family": "Lyle", "given": "Robert", "initials": "R"}, {"family": "Skalkidou", "given": "Alkistis", "initials": "A"}], "type": "journal article", "published": "2021-04-12", "journal": {"title": "Clin Epigenetics", "issn": "1868-7083", "volume": "13", "issue": "1", "pages": "78", "issn-l": "1868-7075"}, "abstract": "Prenatal symptoms of depression (PND) and anxiety affect up to every third pregnancy. Children of mothers with mental health problems are at higher risk of developmental problems, possibly through epigenetic mechanisms together with other factors such as genetic and environmental. We investigated DNA methylation in cord blood in relation to PND, taking into consideration a history of depression, co-morbidity with anxiety and selective serotonin reuptake inhibitors (SSRI) use, and stratified by sex of the child. Mothers (N = 373) prospectively filled out web-based questionnaires regarding mood symptoms and SSRI use throughout pregnancy. Cord blood was collected at birth and DNA methylation was measured using Illumina MethylationEPIC array at 850 000 CpG sites throughout the genome. Differentially methylated regions were identified using Kruskal-Wallis test, and Benjamini-Hochberg adjusted p-values < 0.05 were considered significant.\n\nNo differential DNA methylation was associated with PND alone; however, differential DNA methylation was observed in children exposed to comorbid PND with anxiety symptoms compared with healthy controls in ABCF1 (log twofold change - 0.2), but not after stratification by sex of the child. DNA methylation in children exposed to PND without SSRI treatment and healthy controls both differed in comparison with SSRI exposed children at several sites and regions, among which hypomethylation was observed in CpGs in the promoter region of CRBN (log2 fold change - 0.57), involved in brain development, and hypermethylation in MDFIC (log2 fold change 0.45), associated with the glucocorticoid stress response.\n\nAlthough it is not possible to assess if these methylation differences are due to SSRI treatment itself or to more severe depression, our findings add on to existing knowledge that there might be different biological consequences for the child depending on whether maternal PND was treated with SSRIs or not.", "doi": "10.1186/s13148-021-01054-0", "pmid": "33845866", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13148-021-01054-0"}, {"db": "pmc", "key": "PMC8042709"}], "notes": [], "created": "2021-12-02T14:27:12.540Z", "modified": "2024-01-16T13:48:40.089Z"}, {"entity": "publication", "iuid": "b4782cdfe6284e678b37e60ddf9f30c8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4782cdfe6284e678b37e60ddf9f30c8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4782cdfe6284e678b37e60ddf9f30c8"}}, "title": "A spinal organ of proprioception for integrated motor action feedback.", "authors": [{"family": "Picton", "given": "Laurence D", "initials": "LD"}, {"family": "Bertuzzi", "given": "Maria", "initials": "M"}, {"family": "Pallucchi", "given": "Irene", "initials": "I"}, {"family": "Fontanel", "given": "Pierre", "initials": "P"}, {"family": "Dahlberg", "given": "Elin", "initials": "E"}, {"family": "Bj\u00f6rnfors", "given": "E Rebecka", "initials": "ER"}, {"family": "Iacoviello", "given": "Francesco", "initials": "F"}, {"family": "Shearing", "given": "Paul R", "initials": "PR"}, {"family": "El Manira", "given": "Abdeljabbar", "initials": "A"}], "type": "journal article", "published": "2021-04-07", "journal": {"title": "Neuron", "issn": "1097-4199", "issn-l": "0896-6273", "volume": "109", "issue": "7", "pages": "1188-1201.e7"}, "abstract": "Proprioception is essential for behavior and provides a sense of our body movements in physical space. Proprioceptor organs are thought to be only in the periphery. Whether the central nervous system can intrinsically sense its own movement remains unclear. Here we identify a segmental organ of proprioception in the adult zebrafish spinal cord, which is embedded by intraspinal mechanosensory neurons expressing Piezo2 channels. These cells are late-born, inhibitory, commissural neurons with unique molecular and physiological profiles reflecting a dual sensory and motor function. The central proprioceptive organ locally detects lateral body movements during locomotion and provides direct inhibitory feedback onto rhythm-generating interneurons responsible for the central motor program. This dynamically aligns central pattern generation with movement outcome for efficient locomotion. Our results demonstrate that a central proprioceptive organ monitors self-movement using hybrid neurons that merge sensory and motor entities into a unified network.", "doi": "10.1016/j.neuron.2021.01.018", "pmid": "33577748", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0896-6273(21)00040-4"}], "notes": [], "created": "2021-02-17T12:00:56.937Z", "modified": "2024-01-16T13:48:40.100Z"}, {"entity": "publication", "iuid": "ed616a14be7b4923afec00da266e0d5c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ed616a14be7b4923afec00da266e0d5c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ed616a14be7b4923afec00da266e0d5c"}}, "title": "Uncemented or cemented stems in first-time revision total hip replacement? An observational study of 867 patients including assessment of femoral bone defect size.", "authors": [{"family": "Tyson", "given": "Yosef", "initials": "Y"}, {"family": "Hillman", "given": "Christer", "initials": "C"}, {"family": "Majenburg", "given": "Norbert", "initials": "N"}, {"family": "Sk\u00f6ldenberg", "given": "Olof", "initials": "O"}, {"family": "Rolfson", "given": "Ola", "initials": "O"}, {"family": "K\u00e4rrholm", "given": "Johan", "initials": "J"}, {"family": "Mohaddes", "given": "Maziar", "initials": "M"}, {"family": "Hailer", "given": "Nils P", "initials": "NP"}], "type": "comparative study", "published": "2021-04-00", "journal": {"title": "Acta Orthop", "issn": "1745-3682", "issn-l": null, "volume": "92", "issue": "2", "pages": "143-150"}, "abstract": "Background and purpose - Uncemented stems are gradually replacing cemented stems in hip revision surgery. We compared the risk of re-revision between uncemented and cemented revision stems and assessed whether the different fixation methods are used in similar femoral bone defects.Patients and methods - 867 patients operated on with uncemented or cemented stems in first-time hip revision surgery due to aseptic loosening performed 2006-2016 were identified in the Swedish Hip Arthroplasty Register. Preoperative femoral bone defect size was assessed on radiographs of all patients. Cox regression models were fitted to estimate the adjusted risk of re-revision during different postoperative time periods. Re-revision of any component for any reason, and stem re-revision, as well as risk of cause-specific re-revision was estimated.Results - Most patients in both fixation groups had Paprosky class IIIA femoral bone defects prior to surgery, but there were more severe bone defects in the cemented group. The adjusted risk of re-revision of any component for any reason was higher in patients with uncemented compared with those with cemented revision stems during the first 3 years after index surgery (hazard ratio [HR] 4, 95% confidence interval [CI] 2-9). From the 4th year onward, the risk of re-revision of any component for any reason was similar (HR 0.5, CI 0.2-1.4). Uncemented revision stems conferred a higher risk of dislocation compared with cemented stems (HR 5, CI 1.2-23) during the first 3 years.Interpretation - Although not predominantly used in more complex femoral defects, uncemented revision stem fixation confers a slightly higher risk of re-revision during the first years, but this risk is attenuated after longer follow-up.", "doi": "10.1080/17453674.2020.1846956", "pmid": "33176549", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8159203"}], "notes": [], "created": "2020-12-15T14:19:27.710Z", "modified": "2021-11-10T12:45:17.189Z"}, {"entity": "publication", "iuid": "734a82c76b694a428848489e20b1f638", "links": {"self": {"href": "https://publications.scilifelab.se/publication/734a82c76b694a428848489e20b1f638.json"}, "display": {"href": "https://publications.scilifelab.se/publication/734a82c76b694a428848489e20b1f638"}}, "title": "COVIDENZA - A prospective, multicenter, randomized PHASE II clinical trial of enzalutamide treatment to decrease the morbidity in patients with Corona virus disease 2019 (COVID-19): a structured summary of a study protocol for a randomised controlled trial.", "authors": [{"family": "Wel\u00e9n", "given": "Karin", "initials": "K"}, {"family": "\u00d6verby", "given": "Anna K", "initials": "AK"}, {"family": "Ahlm", "given": "Clas", "initials": "C"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Robinsson", "given": "David", "initials": "D"}, {"family": "Henningsson", "given": "Anna Jonsson", "initials": "AJ"}, {"family": "Stranne", "given": "Johan", "initials": "J"}, {"family": "Bremell", "given": "Daniel", "initials": "D"}, {"family": "Angelin", "given": "Martin", "initials": "M"}, {"family": "Lindquist", "given": "Elisabeth", "initials": "E"}, {"family": "Buckland", "given": "Robert", "initials": "R"}, {"family": "Carlsson", "given": "Camilla Thellenberg", "initials": "CT"}, {"family": "Pauksens", "given": "Karlis", "initials": "K"}, {"family": "Bill-Axelsson", "given": "Anna", "initials": "A"}, {"family": "Akre", "given": "Olof", "initials": "O"}, {"family": "Ryden", "given": "Cecilia", "initials": "C"}, {"family": "Wagenius", "given": "Magnus", "initials": "M"}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"family": "Nilsson", "given": "Anna C", "initials": "AC"}, {"family": "Styrke", "given": "Johan", "initials": "J"}, {"family": "Repo", "given": "Johanna", "initials": "J"}, {"family": "Balkhed", "given": "\u00c5se \u00d6stholm", "initials": "\u00c5\u00d6"}, {"family": "Niward", "given": "Katarina", "initials": "K"}, {"family": "Gissl\u00e9n", "given": "Magnus", "initials": "M"}, {"family": "Josefsson", "given": "Andreas", "initials": "A"}], "type": "clinical trial protocol", "published": "2021-03-16", "journal": {"title": "Trials", "issn": "1745-6215", "volume": "22", "issue": "1", "pages": "209", "issn-l": null}, "abstract": "The main goal of the COVIDENZA trial is to evaluate if inhibition of testosterone signalling by enzalutamide can improve the outcome of patients hospitalised for COVID-19. The hypothesis is based on the observation that the majority of patients in need of intensive care are male, and the connection between androgen receptor signalling and expression of TMPRSS2, an enzyme important for SARS-CoV-2 host cell internalization.\n\nHospitalised COVID-19 patients will be randomised (2:1) to enzalutamide plus standard of care vs. standard of care designed to identify superiority.\n\nIncluded participants, men or women above 50 years of age, must be hospitalised for PCR confirmed COVID-19 symptoms and not in need of immediate mechanical ventilation. Major exclusion criteria are breast-feeding or pregnant women, hormonal treatment for prostate or breast cancer, treatment with immunosuppressive drugs, current symptomatic unstable cardiovascular disease (see Additional file 1 for further details). The trial is registered at Ume\u00e5 University Hospital, Region V\u00e4sterbotten, Sweden and 8 hospitals are approved for inclusion in Sweden.\n\nPatients randomised to the treatment arm will be treated orally with 160 mg (4x40 mg) enzalutamide (Xtandi\u00ae) daily, for five consecutive days. The study is not placebo controlled. The comparator is standard of care treatment for patients hospitalised with COVID-19.\n\nThe primary endpoints of the study are (time to) need of mechanical ventilation or discharge from hospital as assessed by a clinical 7-point ordinal scale (up to 30 days after inclusion).\n\nRandomisation was stratified by center and sex. Each strata was randomized separately with block size six with a 2:1 allocation ratio (enzalutamide + \"standard of care\": \"standard of care\"). The randomisation list, with consecutive subject numbers, was generated by an independent statistician using the PROC PLAN procedure of SAS version 9.4 software (SAS Institute, Inc, Cary, North Carolina) BLINDING (MASKING): This is an open-label trial.\n\nThe trial is designed to have three phases. The first, an exploration phase of 45 participants (30 treatment and 15 control) will focus on safety and includes a more extensive laboratory assessment as well as more frequent safety evaluation. The second prolongation phase, includes the first 100 participants followed by an interim analysis to define the power of the study. The third phase is the continuation of the study up to maximum 600 participants included in total.\n\nThe current protocol version is COVIDENZA v2.0 as of September 10, 2020. Recruitment started July 29, 2020 and is presently in safety pause after the first exploration phase. Recruitment is anticipated to be complete by 31 December 2021.\n\nEudract number 2020-002027-10 ClinicalTrials.gov Identifier: NCT04475601 , registered June 8, 2020 FULL PROTOCOL: The full protocol is attached as an additional file, accessible from the Trials website (Additional file 1). In the interest in expediting dissemination of this material, the familiar formatting has been eliminated; this Letter serves as a summary of the key elements of the full protocol.", "doi": "10.1186/s13063-021-05137-4", "pmid": "33726804", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7961321"}, {"db": "pii", "key": "10.1186/s13063-021-05137-4"}, {"db": "ClinicalTrials.gov", "key": "NCT04475601"}], "notes": [], "created": "2023-11-16T12:09:58.087Z", "modified": "2023-11-16T12:09:58.108Z"}, {"entity": "publication", "iuid": "a2f5235f4449487bac60b31981eea4ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2f5235f4449487bac60b31981eea4ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2f5235f4449487bac60b31981eea4ff"}}, "title": "OmicLoupe: facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons.", "authors": [{"family": "Willforss", "given": "Jakob", "initials": "J"}, {"family": "Siino", "given": "Valentina", "initials": "V"}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b7add45d810457eb84a72aebbc7b82c.json"}}], "type": "journal article", "published": "2021-03-04", "journal": {"title": "BMC Bioinformatics", "issn": "1471-2105", "volume": "22", "issue": "1", "pages": "107", "issn-l": "1471-2105"}, "abstract": "Visual exploration of gene product behavior across multiple omic datasets can pinpoint technical limitations in data and reveal biological trends. Still, such exploration is challenging as there is a need for visualizations that are tailored for the purpose.\n\nThe OmicLoupe software was developed to facilitate visual data exploration and provides more than 15 interactive cross-dataset visualizations for omics data. It expands visualizations to multiple datasets for quality control, statistical comparisons and overlap and correlation analyses, while allowing for rapid inspection and downloading of selected features. The usage of OmicLoupe is demonstrated in three different studies, where it allowed for detection of both technical data limitations and biological trends across different omic layers. An example is an analysis of SARS-CoV-2 infection based on two previously published studies, where OmicLoupe facilitated the identification of gene products with consistent expression changes across datasets at both the transcript and protein levels.\n\nOmicLoupe provides fast exploration of omics data with tailored visualizations for comparisons within and across data layers. The interactive visualizations are highly informative and are expected to be useful in various analyses of both newly generated and previously published data. OmicLoupe is available at quantitativeproteomics.org/omicloupe.", "doi": "10.1186/s12859-021-04043-5", "pmid": "33663372", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12859-021-04043-5"}, {"db": "pmc", "key": "PMC7931979"}], "notes": [], "created": "2021-12-02T14:03:39.274Z", "modified": "2021-12-02T14:03:39.297Z"}, {"entity": "publication", "iuid": "6c4c2ef9d9824560997fc338b5c48f8e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c4c2ef9d9824560997fc338b5c48f8e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c4c2ef9d9824560997fc338b5c48f8e"}}, "title": "Plasma metabolomics of presymptomatic PSEN1-H163Y mutation carriers: a pilot study.", "authors": [{"family": "Natarajan", "given": "Karthick", "initials": "K", "orcid": "0000-0001-5335-875X", "researcher": {"href": "https://publications.scilifelab.se/researcher/389c50cf68cc43c2bd154addeafe768a.json"}}, {"family": "Ullgren", "given": "Abbe", "initials": "A"}, {"family": "Khoshnood", "given": "Behzad", "initials": "B"}, {"family": "Johansson", "given": "Charlotte", "initials": "C"}, {"family": "Laffita-Mesa", "given": "Jos\u00e9 M", "initials": "JM"}, {"family": "Pannee", "given": "Josef", "initials": "J"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "Graff", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9949-2951", "researcher": {"href": "https://publications.scilifelab.se/researcher/3faadb7b187046b090d947f85d8c4dd1.json"}}], "type": "journal article", "published": "2021-03-00", "journal": {"title": "Ann Clin Transl Neurol", "issn": "2328-9503", "volume": "8", "issue": "3", "pages": "579-591", "issn-l": "2328-9503"}, "abstract": "PSEN1-H163Y carriers, at the presymptomatic stage, have reduced 18 FDG-PET binding in the cerebrum of the brain (Scholl et al., Neurobiol Aging 32:1388-1399, 2011). This could imply dysfunctional energy metabolism in the brain. In this study, plasma of presymptomatic PSEN1 mutation carriers was analyzed to understand associated metabolic changes.\n\nWe analyzed plasma from noncarriers (NC, n = 8) and presymptomatic PSEN1-H163Y mutation carriers (MC, n = 6) via untargeted metabolomics using gas and liquid chromatography coupled with mass spectrometry, which identified 1199 metabolites. All the metabolites were compared between MC and NC using univariate analysis, as well as correlated with the ratio of A\u03b21-42/A \u03b2 1-40 , using Spearman's correlation. Altered metabolites were subjected to Ingenuity Pathway Analysis (IPA).\n\nBased on principal component analysis the plasma metabolite profiles were divided into dataset A and dataset B. In dataset A, when comparing between presymptomatic MC and NC, the levels of 79 different metabolites were altered. Out of 79, only 14 were annotated metabolites. In dataset B, 37 metabolites were significantly altered between presymptomatic MC and NC and nine metabolites were annotated. In both datasets, annotated metabolites represent amino acids, fatty acyls, bile acids, hexoses, purine nucleosides, carboxylic acids, and glycerophosphatidylcholine species. 1-docosapentaenoyl-GPC was positively correlated, uric acid and glucose were negatively correlated with the ratio of plasma A\u03b21-42 /A\u03b21-40 (P < 0.05).\n\nThis study finds dysregulated metabolite classes, which are changed before the disease symptom onset. Also, it provides an opportunity to compare with sporadic Alzheimer's Disease. Observed findings in this study need to be validated in a larger and independent Familial Alzheimer's Disease (FAD) cohort.", "doi": "10.1002/acn3.51296", "pmid": "33476461", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7951103"}], "notes": [], "created": "2021-12-02T14:00:47.923Z", "modified": "2025-10-17T13:03:16.336Z"}, {"entity": "publication", "iuid": "48b0fb0b1902402caae10d57d86fc5ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48b0fb0b1902402caae10d57d86fc5ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48b0fb0b1902402caae10d57d86fc5ef"}}, "title": "Association between breast cancer risk and disease aggressiveness: Characterizing underlying gene expression patterns.", "authors": [{"family": "Ugalde-Morales", "given": "Emilio", "initials": "E", "orcid": "0000-0002-3201-6416", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e2e77664f574b95aeae3c5d14f31de5.json"}}, {"family": "Grassmann", "given": "Felix", "initials": "F", "orcid": "0000-0003-1390-7528", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a190980d904236914679e88737706b.json"}}, {"family": "Humphreys", "given": "Keith", "initials": "K"}, {"family": "Li", "given": "Jingmei", "initials": "J", "orcid": "0000-0001-8587-7511", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee0aa1afe3af4dcba58f07c8c19d11e0.json"}}, {"family": "Eriksson", "given": "Mikael", "initials": "M"}, {"family": "Tobin", "given": "Nicholas P", "initials": "NP"}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Vallon-Christersson", "given": "Johan", "initials": "J"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Czene", "given": "Kamila", "initials": "K"}], "type": "journal article", "published": "2021-02-15", "journal": {"title": "Int. J. Cancer", "issn": "1097-0215", "volume": "148", "issue": "4", "pages": "884-894", "issn-l": "0020-7136"}, "abstract": "The association between breast cancer risk defined by the Tyrer-Cuzick score (TC) and disease prognosis is not well established. Here, we investigated the relationship between 5-year TC and disease aggressiveness and then characterized underlying molecular processes. In a case-only study (n = 2474), we studied the association of TC with molecular subtypes and tumor characteristics. In a subset of patients (n = 672), we correlated gene expression to TC and computed a low-risk TC gene expression (TC-Gx) profile, that is, a profile expected to be negatively associated with risk, which we used to test for association with disease aggressiveness. We performed enrichment analysis to pinpoint molecular processes likely to be altered in low-risk tumors. A higher TC was found to be inversely associated with more aggressive surrogate molecular subtypes and tumor characteristics (P < .05) including Ki-67 proliferation status (P < 5 \u00d7 10-07 ). Our low-risk TC-Gx, based on the weighted sum of 37 expression values of genes strongly correlated with TC, was associated with basal-like (P < 5 \u00d7 10-13 ), HER2-enriched subtype (P < 5 \u00d7 10-07 ) and worse 10-year breast cancer-specific survival (log-rank P < 5 \u00d7 10-04 ). Associations between low-risk TC-Gx and more aggressive molecular subtypes were replicated in an independent cohort from The Cancer Genome Atlas database (n = 975). Gene expression that correlated with low TC was enriched in proliferation and oncogenic signaling pathways (FDR < 0.05). Moreover, higher proliferation was a key factor explaining the association with worse survival. Women who developed breast cancer despite having a low risk were diagnosed with more aggressive tumors and had a worse prognosis, most likely driven by increased proliferation. Our findings imply the need to establish risk factors associated with more aggressive breast cancer subtypes.", "doi": "10.1002/ijc.33270", "pmid": "32856720", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7818270"}], "notes": [], "created": "2020-09-30T10:33:48.257Z", "modified": "2021-11-10T12:26:58.196Z"}, {"entity": "publication", "iuid": "194b699fcc5843fd90923e2e5f9807c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/194b699fcc5843fd90923e2e5f9807c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/194b699fcc5843fd90923e2e5f9807c6"}}, "title": "Plasma proteome profiling of cardiotoxicity in patients with diffuse large B-cell lymphoma.", "authors": [{"family": "M\u00f6rth", "given": "Charlott", "initials": "C", "orcid": "0000-0002-2308-6666", "researcher": {"href": "https://publications.scilifelab.se/researcher/48e46bde9b644d8092e5b8986a441cfb.json"}}, {"family": "Sabaa", "given": "Amal Abu", "initials": "AA"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Christersson", "given": "Christina", "initials": "C"}, {"family": "Hashemi", "given": "Jamileh", "initials": "J"}, {"family": "Hashemi", "given": "Nashmil", "initials": "N"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M"}, {"family": "Molin", "given": "Daniel", "initials": "D"}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M"}, {"family": "Eriksson", "given": "Anna", "initials": "A"}, {"family": "Enblad", "given": "Gunilla", "initials": "G"}], "type": "journal article", "published": "2021-02-03", "journal": {"title": "Cardiooncology", "issn": "2057-3804", "volume": "7", "issue": "1", "pages": "6", "issn-l": null}, "abstract": "Cardiovascular toxicity is a notorious complication of doxorubicin (DXR) therapy for diffuse large B-cell lymphoma (DLBCL). Although surveillance of well-known biological markers for cardiovascular disease (CVD) as NTproBNP and Troponins may be helpful, there are no established markers to monitor for evolving CVD during treatment. New possibilities have arisen with the emergence of newer techniques allowing for analysis of plasma proteins that can be associated with cardiovascular disease. Proximity Extension Assay is one of them.\n\nWe aimed to illustrate the incidence of CVD in DLBCL patients treated with DXR and to establish whether there are plasma proteins associated with pre-existing or emerging CVD.\n\nIn 95 patients, 182 different proteins from OLINK panels, NTproBNP, Troponin I and CRP were assessed prior to, during and after treatment. For comparison, samples from controls were analyzed.\n\nIn the DLBCL cohort, 33.3% had pre-treatment CVD compared to 5.0% in the controls and 23.2% developed new CVD. Of the 32.6% who died during follow up, CVD was the cause in 4 patients. Spondin-1 (SPON-1) correlated to pre-treatment CVD (1.22 fold change, 95% CI 1.10-1.35, p = 0.00025, q = 0.045). Interleukin-1 receptor type 1 (IL-1RT1) was associated to emerging CVD (1.24 fold change, 95% CI 1.10-1.39, p = 0.00044, q = 0.082).\n\nWe observed a higher prevalence of CVD in DLBCL patients compared to controls prior to DXR therapy. Two proteins, SPON-1 and IL-1RT1, were related to pre-existing and emerging CVD in DXR treated patients. If confirmed in larger cohorts, IL-1RT1 may emerge as a reliable biomarker for unfolding CVD in DLBCL.", "doi": "10.1186/s40959-021-00092-0", "pmid": "33536059", "labels": {"Affinity Proteomics Uppsala": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7856776"}, {"db": "pii", "key": "10.1186/s40959-021-00092-0"}], "notes": [], "created": "2021-12-10T09:27:30.132Z", "modified": "2023-11-16T12:18:01.694Z"}, {"entity": "publication", "iuid": "f8af730012fe4506a599cc6e74572cca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8af730012fe4506a599cc6e74572cca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8af730012fe4506a599cc6e74572cca"}}, "title": "Genetic Risk Score for Serum 25-Hydroxyvitamin D Concentration Helps to Guide Personalized Vitamin D Supplementation in Healthy Finnish Adults.", "authors": [{"family": "Sallinen", "given": "Riitta J", "initials": "RJ", "orcid": "0000-0003-4252-0197", "researcher": {"href": "https://publications.scilifelab.se/researcher/123751d7703747db86d6d10d1a304fb8.json"}}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Ruotsalainen", "given": "Sanni", "initials": "S"}, {"family": "Mills", "given": "Robert D", "initials": "RD"}, {"family": "Miettinen", "given": "Timo A", "initials": "TA"}, {"family": "J\u00e4\u00e4skel\u00e4inen", "given": "Tuija E", "initials": "TE"}, {"family": "Lundqvist", "given": "Annamari", "initials": "A"}, {"family": "Kyll\u00f6nen", "given": "Eero", "initials": "E"}, {"family": "Kr\u00f6ger", "given": "Heikki", "initials": "H"}, {"family": "Karppinen", "given": "Jaro I", "initials": "JI"}, {"family": "Lamberg-Allardt", "given": "Christel", "initials": "C", "orcid": "0000-0001-7326-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/23f5db6a8f0f46c3812c6fdae7c7ee92.json"}}, {"family": "Viljakainen", "given": "Heli", "initials": "H"}, {"family": "Kaunisto", "given": "Mari A", "initials": "MA"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}], "type": "journal article", "published": "2021-02-01", "journal": {"title": "J. Nutr.", "issn": "1541-6100", "volume": "151", "issue": "2", "pages": "281-292", "issn-l": "0022-3166"}, "abstract": "Genetic factors modify serum 25-hydroxyvitamin D [25(OH)D] concentration and can affect the optimal intake of vitamin D.\n\nWe aimed to personalize vitamin D supplementation by applying knowledge of genetic factors affecting serum 25(OH)D concentration.\n\nWe performed a genome-wide association study of serum 25(OH)D concentration in the Finnish Health 2011 cohort (n = 3339) using linear regression and applied the results to develop a population-matched genetic risk score (GRS) for serum 25(OH)D. This GRS was used to tailor vitamin D supplementation for 96 participants of a longitudinal Digital Health Revolution (DHR) Study. The GRS, serum 25(OH)D concentrations, and personalized supplementation and dietary advice were electronically returned to participants. Serum 25(OH)D concentrations were assessed using immunoassays and vitamin D intake using FFQs. In data analyses, cross-sectional and repeated-measures statistical tests and models were applied as described in detail elsewhere.\n\nGC vitamin D-binding protein and cytochrome P450 family 2 subfamily R polypeptide 1 genes showed genome-wide significant associations with serum 25(OH)D concentration. One single nucleotide polymorphism from each locus (rs4588 and rs10741657) was used to develop the GRS. After returning data to the DHR Study participants, daily vitamin D supplement users increased from 32.6% to 60.2% (P = 6.5 \u00d7 10-6) and serum 25(OH)D concentration from 64.4 \u00b1 20.9 nmol/L to 68.5 \u00b1 19.2 nmol/L (P = 0.006) between August and November. Notably, the difference in serum 25(OH)D concentrations between participants with no risk alleles and those with 3 or 4 risk alleles decreased from 20.7 nmol/L to 8.0 nmol/L (P = 0.0063).\n\nWe developed and applied a population-matched GRS to identify individuals genetically predisposed to low serum 25(OH)D concentration. We show how the electronic return of individual genetic risk, serum 25(OH)D concentrations, and factors affecting vitamin D status can be used to tailor vitamin D supplementation. This model could be applied to other populations and countries.", "doi": "10.1093/jn/nxaa391", "pmid": "33382404", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6056509"}], "notes": [], "created": "2021-01-11T12:54:02.544Z", "modified": "2021-11-10T12:43:56.032Z"}, {"entity": "publication", "iuid": "9575d837ecc248a289d22b708e900ad2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9575d837ecc248a289d22b708e900ad2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9575d837ecc248a289d22b708e900ad2"}}, "title": "Hypoxia inducible factor-2\u03b1 importance for migration, proliferation, and self-renewal of trunk neural crest cells.", "authors": [{"family": "Niklasson", "given": "Camilla U", "initials": "CU"}, {"family": "Fredlund", "given": "Elina", "initials": "E"}, {"family": "Monni", "given": "Emanuela", "initials": "E"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Kokaia", "given": "Zaal", "initials": "Z"}, {"family": "Hammarlund", "given": "Emma U", "initials": "EU"}, {"family": "Bronner", "given": "Marianne E", "initials": "ME"}, {"family": "Mohlin", "given": "Sofie", "initials": "S", "orcid": "0000-0002-2458-3963", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e095a99e2c84d52b13973c9d46d128a.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Dev. Dyn.", "issn": "1097-0177", "volume": "250", "issue": "2", "pages": "191-236", "issn-l": "1058-8388"}, "abstract": "The neural crest is a transient embryonic stem cell population. Hypoxia inducible factor (HIF)-2\u03b1 is associated with neural crest stem cell appearance and aggressiveness in tumors. However, little is known about its role in normal neural crest development.\n\nHere, we show that HIF-2\u03b1 is expressed in trunk neural crest cells of human, murine, and avian embryos. Knockdown as well as overexpression of HIF-2\u03b1 in vivo causes developmental delays, induces proliferation, and self-renewal capacity of neural crest cells while decreasing the proportion of neural crest cells that migrate ventrally to sympathoadrenal sites. Reflecting the in vivo phenotype, transcriptome changes after loss of HIF-2\u03b1 reveal enrichment of genes associated with cancer, invasion, epithelial-to-mesenchymal transition, and growth arrest.\n\nTaken together, these results suggest that expression levels of HIF-2\u03b1 must be strictly controlled during normal trunk neural crest development and that dysregulated levels affects several important features connected to stemness, migration, and development.", "doi": "10.1002/dvdy.253", "pmid": "32940375", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Clinical Genomics Lund": "Service", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7891386"}], "notes": [], "created": "2020-11-30T08:12:02.742Z", "modified": "2021-12-02T14:08:45.947Z"}, {"entity": "publication", "iuid": "630691e8978c4592989bc0837994eb1d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/630691e8978c4592989bc0837994eb1d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/630691e8978c4592989bc0837994eb1d"}}, "title": "Genome-wide single nucleotide polymorphism markers reveal population structure and dispersal direction of an expanding nuisance algal bloom species.", "authors": [{"family": "Rengefors", "given": "Karin", "initials": "K", "orcid": "0000-0001-6297-9734", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c7353dd11fa445f9ff338db5ce8dadd.json"}}, {"family": "Gollnisch", "given": "Raphael", "initials": "R", "orcid": "0000-0001-6177-8877", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f78f6e8cacf4eba9104fbfd2ab26f66.json"}}, {"family": "Sassenhagen", "given": "Ingrid", "initials": "I"}, {"family": "H\u00e4rnstr\u00f6m Aloisi", "given": "Karolina", "initials": "K"}, {"family": "Svensson", "given": "Marie", "initials": "M"}, {"family": "Lebret", "given": "Karen", "initials": "K"}, {"family": "\u010certnerov\u00e1", "given": "Dora", "initials": "D"}, {"family": "Cresko", "given": "William A", "initials": "WA", "orcid": "0000-0002-3496-8074", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d5d9405a53046be86d108b7bd0a0850.json"}}, {"family": "Bassham", "given": "Susan", "initials": "S"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D", "orcid": "0000-0003-4713-0032", "researcher": {"href": "https://publications.scilifelab.se/researcher/d634886b77ad4331916bebc0a3b8b0e3.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "30", "issue": "4", "pages": "912-925"}, "abstract": "Species invasion and range expansion are currently under scrutiny due to increasing anthropogenic impact on the natural environment. This is also true for harmful algal blooms, which have been reported to have increased in frequency. However, this research is challenging due to the ephemeral nature, small size and mostly low concentrations of microalgae in the environment. One such species is the nuisance microalga Gonyostomum semen (Raphidophyceae), which has increased in occurrence in northern Europe in recent decades. The question of whether the species has expanded its habitat range or if it was already present in the lakes but was too rare to be detected remains unanswered. The aim of the present study was to determine the genetic structure and dispersal pathways of G. semen using RAD (restriction-site-associated DNA) tag sequencing. For G. semen, which has a huge genome (32 Gbp), we faced particular challenges, but were nevertheless able to recover over 1000 single nucleotide polymorphisms at high coverage. Our data revealed a distinct population genetic structure, demonstrating a divide of western and eastern populations that probably represent different lineages. Despite significant genetic differentiation among lakes, we found only limited isolation-by-distance. While we had expected a pattern of recent expansion northwards, the data demonstrated gene flow from the northeast/east towards the southwest/west. This genetic signature suggests that the observed gene flow may be due to dispersal by autumn migratory birds, which act as dispersal vectors of resistant resting propagules that form at the end of the G. semen blooms.", "doi": "10.1111/mec.15787", "pmid": "33386639", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "RefSeq", "key": "PRJNA659541"}], "notes": [], "created": "2021-01-12T12:32:53.386Z", "modified": "2024-01-16T13:48:40.840Z"}, {"entity": "publication", "iuid": "ef732b8cd0214be1887c4a57bb492c04", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef732b8cd0214be1887c4a57bb492c04.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef732b8cd0214be1887c4a57bb492c04"}}, "title": "Epigenome-wide cross-tissue correlation of human bone and blood DNA methylation - can blood be used as a surrogate for bone?", "authors": [{"family": "Ebrahimi", "given": "Parvaneh", "initials": "P"}, {"family": "Luthman", "given": "Holger", "initials": "H"}, {"family": "McGuigan", "given": "Fiona E", "initials": "FE", "orcid": "0000-0002-8033-9981", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cf48c3c6f71416799fca5100de388f5.json"}}, {"family": "Akesson", "given": "Kristina E", "initials": "KE"}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Epigenetics", "issn": "1559-2308", "volume": "16", "issue": "1", "pages": "92-105", "issn-l": "1559-2294"}, "abstract": "Difficulty in obtaining bone tissue is an obstacle to studying epigenetics to understand gene-environment interactions, and their role in disease pathogenesis. Blood is an obvious alternative and in this proof of principle study, our aim was to systematically investigate whether blood is a viable surrogate for bone. We measured epigenome-wide DNA methylation at 850 K CpG sites in matched trabecular bone and peripheral blood collected from the same patients at the same time-point (n = 12 women; 66-85y), to investigate the between-tissue correspondence. What constituted a CpG site with corresponding methylation in both tissues was stringently defined. Only sites highly correlated (r2 > 0.74; FDR q-value <0.05) and at least 80% similarity in methylation level (\u0394\u03b2 <0.2) between paired samples were retained. In total, 28,549 CpG sites were similarly methylated in bone and blood. Between 33% and 49% of loci associated with bone phenotypes through GWAS were represented among these sites, and major pathways relevant to bone regulation were enriched. The results from this study indicate that blood can mirror the bone methylome and capture sites related to bone regulation. This study shows that in principal, peripheral blood is a feasible surrogate for bone tissue in DNA methylation investigations. As the first step, this will provide a platform for future studies in bone epigenetics, and possibly for larger-scale epidemiological studies.", "doi": "10.1080/15592294.2020.1788325", "pmid": "32692944", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7889104"}, {"db": "figshare", "key": "10.6084/m9.figshare.12851657.v1"}], "notes": [], "created": "2020-08-04T14:50:03.380Z", "modified": "2021-11-10T12:49:08.153Z"}, {"entity": "publication", "iuid": "95f1d478c59c4366bc3dbf6010d97d4d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/95f1d478c59c4366bc3dbf6010d97d4d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/95f1d478c59c4366bc3dbf6010d97d4d"}}, "title": "A biomimetic engineered bone platform for advanced testing of prosthetic implants.", "authors": [{"family": "Sladkova-Faure", "given": "Martina", "initials": "M"}, {"family": "Pujari-Palmer", "given": "Michael", "initials": "M"}, {"family": "\u00d6hman-M\u00e4gi", "given": "Caroline", "initials": "C"}, {"family": "L\u00f3pez", "given": "Alejandro", "initials": "A"}, {"family": "Wang", "given": "Hanbin", "initials": "H"}, {"family": "Engqvist", "given": "H\u00e5kan", "initials": "H"}, {"family": "de Peppo", "given": "Giuseppe Maria", "initials": "GM"}], "type": "journal article", "published": "2020-12-17", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "22154", "issn-l": "2045-2322"}, "abstract": "Existing methods for testing prosthetic implants suffer from critical limitations, creating an urgent need for new strategies that facilitate research and development of implants with enhanced osseointegration potential. Herein, we describe a novel, biomimetic, human bone platform for advanced testing of implants in vitro, and demonstrate the scientific validity and predictive value of this approach using an assortment of complementary evaluation methods. We anchored titanium (Ti) and stainless steel (SS) implants into biomimetic scaffolds, seeded with human induced mesenchymal stem cells, to recapitulate the osseointegration process in vitro. We show distinct patterns of gene expression, matrix deposition, and mineralization in response to the two materials, with Ti implants ultimately resulting in stronger integration strength, as seen in other preclinical and clinical studies. Interestingly, RNAseq analysis reveals that the TGF-beta and the FGF2 pathways are overexpressed in response to Ti implants, while the Wnt, BMP, and IGF pathways are overexpressed in response to SS implants. High-resolution imaging shows significantly increased tissue mineralization and calcium deposition at the tissue-implant interface in response to Ti implants, contributing to a twofold increase in pullout strength compared to SS implants. Our technology creates unprecedented research opportunities towards the design of implants and biomaterials that can be personalized, and exhibit enhanced osseointegration potential, with reduced need for animal testing.", "doi": "10.1038/s41598-020-78416-w", "pmid": "33335113", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7747643"}, {"db": "pii", "key": "10.1038/s41598-020-78416-w"}], "notes": [], "created": "2022-11-25T08:01:42.131Z", "modified": "2022-11-25T08:01:42.135Z"}, {"entity": "publication", "iuid": "c04a689a952745a7b20584f2293eece0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c04a689a952745a7b20584f2293eece0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c04a689a952745a7b20584f2293eece0"}}, "title": "Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils.", "authors": [{"family": "Nascimento Lemos", "given": "Leandro", "initials": "L", "orcid": "0000-0002-0898-568X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d27ac7aa5124a0e891272bb955adde4.json"}}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L", "orcid": "0000-0001-9751-5745", "researcher": {"href": "https://publications.scilifelab.se/researcher/000321fd81b9457db66140246bbd9066.json"}}, {"family": "William Mendes", "given": "Lucas", "initials": "L", "orcid": "0000-0003-0980-7006", "researcher": {"href": "https://publications.scilifelab.se/researcher/205efe9eca574e0fad7434a25b3bc028.json"}}, {"family": "Monteiro Venturini", "given": "Andressa", "initials": "A"}, {"family": "Satler Pylro", "given": "Victor", "initials": "V", "orcid": "0000-0003-2154-9150", "researcher": {"href": "https://publications.scilifelab.se/researcher/384c2ceb3ffb4e39a44a221f9830df60.json"}}, {"family": "Tsai", "given": "Siu Mui", "initials": "SM", "orcid": "0000-0002-3733-6312", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a40fb3d3e4d4b15b5a34c3d797ace3a.json"}}], "type": "journal article", "published": "2020-12-00", "journal": {"volume": "12", "issn": "1758-2229", "issue": "6", "title": "Environ Microbiol Rep", "pages": "651-655", "issn-l": "1758-2229"}, "abstract": "Soil microbiome is one of the most heterogeneous biological systems. State-of-the-art molecular approaches such as those based on single-amplified genomes (SAGs) and metagenome assembled-genomes (MAGs) are now improving our capacity for disentailing soil microbial-mediated processes. Here, we analysed publicly available datasets of soil microbial genomes and MAG's reconstructed from the Amazon's tropical soil (primary forest and pasture) and active layer of permafrost, aiming to evaluate their genome size. Our results suggest that the Candidate Phyla Radiation (CPR)/Patescibacteria phyla have genomes with an average size fourfold smaller than the mean identified in the RefSoil database, which lacks any representative of this phylum. Also, by analysing the potential metabolism of 888 soil microbial genomes, we show that CPR/Patescibacteria representatives share similar functional profiles, but different from other microbial phyla and are frequently neglected in the soil microbial surveys. Finally, we argue that the use of MAGs may be a better choice over SAGs to expand the soil microbial databases, like RefSoil.", "doi": "10.1111/1758-2229.12880", "pmid": "32815317", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2020-09-10T13:39:31.755Z", "modified": "2024-01-16T13:48:41.226Z"}, {"entity": "publication", "iuid": "7aff62d808ef404a8b5a402908f43327", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7aff62d808ef404a8b5a402908f43327.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7aff62d808ef404a8b5a402908f43327"}}, "title": "Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells.", "authors": [{"family": "Appelberg", "given": "Sofia", "initials": "S"}, {"family": "Gupta", "given": "Soham", "initials": "S"}, {"family": "Svensson Akusj\u00e4rvi", "given": "Sara", "initials": "S"}, {"family": "Ambikan", "given": "Anoop T", "initials": "AT"}, {"family": "Mikaeloff", "given": "Flora", "initials": "F"}, {"family": "Saccon", "given": "Elisa", "initials": "E"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1"}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Sperk", "given": "Maike", "initials": "M"}, {"family": "St\u00e5hlberg", "given": "Marie", "initials": "M"}, {"family": "Krishnan", "given": "Shuba", "initials": "S"}, {"family": "Singh", "given": "Kamal", "initials": "K"}, {"family": "Penninger", "given": "Josef M", "initials": "JM"}, {"family": "Mirazimi", "given": "Ali", "initials": "A"}, {"family": "Neogi", "given": "Ujjwal", "initials": "U", "orcid": "0000-0002-0844-3338", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f8094017c2a4d0a94d72813cab526f7.json"}}], "type": "journal article", "published": "2020-12-00", "journal": {"title": "Emerg Microbes Infect", "issn": "2222-1751", "volume": "9", "issue": "1", "pages": "1748-1760", "issn-l": "2222-1751"}, "abstract": "How severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections engage cellular host pathways and innate immunity in infected cells remains largely elusive. We performed an integrative proteo-transcriptomics analysis in SARS-CoV-2 infected Huh7 cells to map the cellular response to the invading virus over time. We identified four pathways, ErbB, HIF-1, mTOR and TNF signaling, among others that were markedly modulated during the course of the SARS-CoV-2 infection in vitro. Western blot validation of the downstream effector molecules of these pathways revealed a dose-dependent activation of Akt, mTOR, S6K1 and 4E-BP1 at 24 hours post infection (hpi). However, we found a significant inhibition of HIF-1\u03b1 through 24hpi and 48hpi of the infection, suggesting a crosstalk between the SARS-CoV-2 and the Akt/mTOR/HIF-1 signaling pathways. Inhibition of the mTOR signaling pathway using Akt inhibitor MK-2206 showed a significant reduction in virus production. Further investigations are required to better understand the molecular sequelae in order to guide potential therapy in the management of severe coronavirus disease 2019 (COVID-19) patients.", "doi": "10.1080/22221751.2020.1799723", "pmid": "32691695", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7473213"}], "notes": [], "created": "2020-09-24T09:28:47.205Z", "modified": "2024-01-16T13:48:41.261Z"}, {"entity": "publication", "iuid": "fead16a7ade749c8a101ff49f4a772b3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fead16a7ade749c8a101ff49f4a772b3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fead16a7ade749c8a101ff49f4a772b3"}}, "title": "New Insights into the Microbial Profiles of Infected Root Canals in Traumatized Teeth.", "authors": [{"family": "Manoharan", "given": "Lokeshwaran", "initials": "L", "orcid": "0000-0001-9751-5745", "researcher": {"href": "https://publications.scilifelab.se/researcher/000321fd81b9457db66140246bbd9066.json"}}, {"family": "Brundin", "given": "Malin", "initials": "M"}, {"family": "Rakhimova", "given": "Olena", "initials": "O"}, {"family": "Ch\u00e1vez de Paz", "given": "Luis", "initials": "L"}, {"family": "Romani Vestman", "given": "Nelly", "initials": "N", "orcid": "0000-0002-5674-8179", "researcher": {"href": "https://publications.scilifelab.se/researcher/3273e2c1a9cc4af699a0c61d2b52077a.json"}}], "type": "journal article", "published": "2020-11-28", "journal": {"title": "J Clin Med", "issn": "2077-0383", "volume": "9", "issue": "12", "pages": "3877", "issn-l": "2077-0383"}, "abstract": "Traumatic dental injuries in young individuals are often exposed to the invasion of oral microorganisms that leads to pulp necrosis. Infective necrosis in permanent teeth not-fully-developed causes aberrant root formation. Regeneration endodontic treatments (RETs) have shown promising results by promoting continued root development by stem cells. Critical to the success of RET is the thorough disinfection of the pulpal space. To establish effective antimicrobial protocols for root canal disinfection, the invading microorganisms need to be identified. In the present study, we use a combination of culture-based and high-throughput molecular sequencing techniques to investigate the microbial profiles from traumatized teeth (30 cases) and controls, i.e., teeth with pulp infections not caused by trauma (32 cases). Overall, a high microbial diversity in traumatized necrotic teeth was observed. Eubacterium yurii subsps. yurii and margaretiae, as well as key 'bridging oral species' F. nucleatum sp., Polymorphum and Corynebacterium matruchotti, were highly associated with traumatized teeth. The microbial compositions of traumatized teeth differed considerably from those of infected teeth not caused by trauma. Age and tooth position also influence microbial compositions. In conclusion, we show that the root canal microflora of traumatized teeth is highly diverse, and it differs from root canal infections not caused by trauma.", "doi": "10.3390/jcm9123877", "pmid": "33260621", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "jcm9123877"}, {"db": "pmc", "key": "PMC7760719"}], "notes": [], "created": "2020-11-30T10:28:42.776Z", "modified": "2024-01-16T13:48:41.302Z"}, {"entity": "publication", "iuid": "d505916802d745ffaee823c537c2cad6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d505916802d745ffaee823c537c2cad6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d505916802d745ffaee823c537c2cad6"}}, "title": "The Human Adenovirus Type 2 Transcriptome: An Amazing Complexity of Alternatively Spliced mRNAs.", "authors": [{"family": "Westergren Jakobsson", "given": "Amanda", "initials": "A"}, {"family": "Segerman", "given": "Bo", "initials": "B"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Lind", "given": "Sara Bergstr\u00f6m", "initials": "SB"}, {"family": "Zhao", "given": "Hongxing", "initials": "H"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Pettersson", "given": "Ulf", "initials": "U"}, {"family": "Akusj\u00e4rvi", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-2961-5060", "researcher": {"href": "https://publications.scilifelab.se/researcher/e61349b53aba497288dd44f3e643fdf8.json"}}], "type": "journal article", "published": "2020-11-25", "journal": {"title": "J. Virol.", "issn": "1098-5514", "issn-l": "0022-538X"}, "abstract": "We have used the Nanopore long-read sequencing platform to demonstrate how amazingly complex the human adenovirus type 2 (Ad2) transcriptome is with a flexible splicing machinery producing a range of novel mRNAs both from the early and late transcription units. In total we report more than 900 alternatively spliced mRNAs produced from the Ad2 transcriptome whereof more than 850 are novel mRNAs. A surprising finding was that more than 50% of all E1A transcripts extended upstream of the previously defined transcriptional start site. The novel start sites mapped close to the inverted terminal repeat (ITR) and within the E1A enhancer region. We speculate that novel promoters or enhancer driven transcription, so-called eRNA transcription, is responsible for producing these novel mRNAs. Their existence was verified by a peptide in the Ad2 proteome that was unique for the E1A ITR mRNA. Although we show a high complexity of alternative splicing from most early and late regions, the E3 region was by far the most complex when expressed at late times of infection. More than 400 alternatively spliced mRNAs were observed in this region alone. These mRNAs included extended L4 mRNAs containing E3 and L5 sequences and readthrough mRNAs combining E3 and L5 sequences. Our findings demonstrate that the virus has a remarkable capacity to produce novel exon combinations, which will offer the virus an evolutionary advantage to change the gene expression repertoire and protein production in an evolving environment.IMPORTANCE Work in the adenovirus system led to the groundbreaking discovery of RNA splicing and alternative RNA splicing in 1977. These mechanisms are essential in mammalian evolution by increasing the coding capacity of a genome. Here, we have used a long-read sequencing technology to characterize the complexity of human adenovirus pre-mRNA splicing in detail. It is mindboggling that the viral genome, which only houses around 36,000 bp, not being much larger than a single cellular gene, generates more than 900 alternatively spliced mRNAs. Recently, adenoviruses have been used as the backbone in several promising SARS-CoV-2 vaccines. Further improvement of adenovirus-based vaccines demands that the virus can be tamed into an innocent carrier of foreign genes. This requires a full understanding of the components that govern adenovirus replication and gene expression.", "doi": "10.1128/JVI.01869-20", "pmid": "33239457", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "JVI.01869-20"}, {"db": "pmc", "key": "PMC7851563"}], "notes": [], "created": "2021-12-02T14:21:44.993Z", "modified": "2021-12-02T14:21:45.035Z"}, {"entity": "publication", "iuid": "a2b1311ee277443ca4d6f14652b535cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2b1311ee277443ca4d6f14652b535cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2b1311ee277443ca4d6f14652b535cb"}}, "title": "Naming the untouchable - environmental sequences and niche partitioning as taxonomical evidence in fungi.", "authors": [{"family": "Kalsoom Khan", "given": "Faheema", "initials": "F"}, {"family": "Kluting", "given": "Kerri", "initials": "K"}, {"family": "T\u00e5ngrot", "given": "Jeanette", "initials": "J"}, {"family": "Urbina", "given": "Hector", "initials": "H"}, {"family": "Ammunet", "given": "Tea", "initials": "T"}, {"family": "Eshghi Sahraei", "given": "Shadi", "initials": "S"}, {"family": "Ryd\u00e9n", "given": "Martin", "initials": "M"}, {"family": "Ryberg", "given": "Martin", "initials": "M"}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}}], "type": "journal article", "published": "2020-11-03", "journal": {"title": "IMA Fungus", "issn": "2210-6340", "volume": "11", "issue": "1", "pages": "23", "issn-l": null}, "abstract": "Due to their submerged and cryptic lifestyle, the vast majority of fungal species are difficult to observe and describe morphologically, and many remain known to science only from sequences detected in environmental samples. The lack of practices to delimit and name most fungal species is a staggering limitation to communication and interpretation of ecology and evolution in kingdom Fungi. Here, we use environmental sequence data as taxonomical evidence and combine phylogenetic and ecological data to generate and test species hypotheses in the class Archaeorhizomycetes (Taphrinomycotina, Ascomycota). Based on environmental amplicon sequencing from a well-studied Swedish pine forest podzol soil, we generate 68 distinct species hypotheses of Archaeorhizomycetes, of which two correspond to the only described species in the class. Nine of the species hypotheses represent 78% of the sequenced Archaeorhizomycetes community, and are supported by long read data that form the backbone for delimiting species hypothesis based on phylogenetic branch lengths.Soil fungal communities are shaped by environmental filtering and competitive exclusion so that closely related species are less likely to co-occur in a niche if adaptive traits are evolutionarily conserved. In soil profiles, distinct vertical horizons represent a testable niche dimension, and we found significantly differential distribution across samples for a well-supported pair of sister species hypotheses. Based on the combination of phylogenetic and ecological evidence, we identify two novel species for which we provide molecular diagnostics and propose names. While environmental sequences cannot be automatically translated to species, they can be used to generate phylogenetically distinct species hypotheses that can be further tested using sequences as ecological evidence. We conclude that in the case of abundantly and frequently observed species, environmental sequences can support species recognition in the absences of physical specimens, while rare taxa remain uncaptured at our sampling and sequencing intensity.", "doi": "10.1186/s43008-020-00045-9", "pmid": "33292867", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s43008-020-00045-9"}, {"db": "pmc", "key": "PMC7607712"}], "notes": [], "created": "2020-11-11T15:11:33.579Z", "modified": "2024-01-16T13:48:41.430Z"}, {"entity": "publication", "iuid": "f3ea7ecc69e24f00b6d9979e061dd885", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3ea7ecc69e24f00b6d9979e061dd885.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3ea7ecc69e24f00b6d9979e061dd885"}}, "title": "Human G-MDSCs are neutrophils at distinct maturation stages promoting tumor growth in breast cancer", "authors": [{"family": "Mehmeti-Ajradini", "given": "Meliha", "initials": "M"}, {"family": "Bergenfelz", "given": "Caroline", "initials": "C"}, {"family": "Larsson", "given": "Anna Maria", "initials": "AM"}, {"family": "Carlsson", "given": "Robert", "initials": "R"}, {"family": "Riesbeck", "given": "Kristian", "initials": "K", "orcid": "0000-0001-6274-6965", "researcher": {"href": "https://publications.scilifelab.se/researcher/d757ccad30b043748c8fe48a7308210c.json"}}, {"family": "Ahl", "given": "Jonas", "initials": "J"}, {"family": "Janols", "given": "Helena", "initials": "H"}, {"family": "Wullt", "given": "Marlene", "initials": "M"}, {"family": "Bredberg", "given": "Anders", "initials": "A"}, {"family": "K\u00e4llberg", "given": "Eva", "initials": "E"}, {"family": "Bj\u00f6rk Gunnarsdottir", "given": "Frida", "initials": "F"}, {"family": "Rydberg Millrud", "given": "Camilla", "initials": "C"}, {"family": "Ryd\u00e9n", "given": "Lisa", "initials": "L", "orcid": "0000-0001-7515-3130", "researcher": {"href": "https://publications.scilifelab.se/researcher/424bace557344431a47ffe5cdccbeb56.json"}}, {"family": "Paul", "given": "Gesine", "initials": "G"}, {"family": "Loman", "given": "Niklas", "initials": "N"}, {"family": "Adolfsson", "given": "J\u00f6rgen", "initials": "J"}, {"family": "Carneiro", "given": "Ana", "initials": "A", "orcid": "0000-0002-1818-7008", "researcher": {"href": "https://publications.scilifelab.se/researcher/12ef95bff08743398bf3a374195e043e.json"}}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Killander", "given": "Fredrika", "initials": "F"}, {"family": "Bexell", "given": "Daniel", "initials": "D"}, {"family": "Leandersson", "given": "Karin", "initials": "K", "orcid": "0000-0001-8254-3137", "researcher": {"href": "https://publications.scilifelab.se/researcher/4736923f382845c2990efb251340bfb4.json"}}], "type": "journal-article", "published": "2020-11-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "issn-l": "2575-1077", "volume": "3", "issue": "11", "pages": "e202000893"}, "abstract": "Myeloid-derived suppressor cells (MDSCs) are known to contribute to immune evasion in cancer. However, the function of the human granulocytic (G)-MDSC subset during tumor progression is largely unknown, and there are no established markers for their identification in human tumor specimens. Using gene expression profiling, mass cytometry, and tumor microarrays, we here demonstrate that human G-MDSCs occur as neutrophils at distinct maturation stages, with a disease-specific profile. G-MDSCs derived from patients with metastatic breast cancer and malignant melanoma display a unique immature neutrophil profile, that is more similar to healthy donor neutrophils than to G-MDSCs from sepsis patients. Finally, we show that primary G-MDSCs from metastatic breast cancer patients co-transplanted with breast cancer cells, promote tumor growth, and affect vessel formation, leading to myeloid immune cell exclusion. Our findings reveal a role for human G-MDSC in tumor progression and have clinical implications also for targeted immunotherapy.", "doi": "10.26508/lsa.202000893", "pmid": "32958605", "labels": {"Cellular Immunomonitoring": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7536824"}, {"db": "pii", "key": "3/11/e202000893"}], "notes": [], "created": "2020-09-24T15:35:44.836Z", "modified": "2024-11-15T09:54:18.581Z"}, {"entity": "publication", "iuid": "81637524a179454eacfeca141c6eac13", "links": {"self": {"href": "https://publications.scilifelab.se/publication/81637524a179454eacfeca141c6eac13.json"}, "display": {"href": "https://publications.scilifelab.se/publication/81637524a179454eacfeca141c6eac13"}}, "title": "Epigenetic alterations in skin homing CD4+CLA+ T cells of atopic dermatitis patients.", "authors": [{"family": "Acevedo", "given": "Nathalie", "initials": "N"}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Katayama", "given": "Shintaro", "initials": "S"}, {"family": "Bruhn", "given": "S\u00f6ren", "initials": "S"}, {"family": "Andersson", "given": "Anna", "initials": "A"}, {"family": "Wikberg", "given": "Gustav", "initials": "G"}, {"family": "Lundeberg", "given": "Lena", "initials": "L"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Greco", "given": "Dario", "initials": "D"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "S\u00f6derh\u00e4ll", "given": "Cilla", "initials": "C"}, {"family": "Scheynius", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2020-10-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "18020", "issn-l": "2045-2322"}, "abstract": "T cells expressing the cutaneous lymphocyte antigen (CLA) mediate pathogenic inflammation in atopic dermatitis (AD). The molecular alterations contributing to their dysregulation remain unclear. With the aim to elucidate putative altered pathways in AD we profiled DNA methylation levels and miRNA expression in sorted T cell populations (CD4+, CD4+CD45RA+ na\u00efve, CD4+CLA+, and CD8+) from adult AD patients and healthy controls (HC). Skin homing CD4+CLA+ T cells from AD patients showed significant differences in DNA methylation in 40 genes compared to HC (p < 0.05). Reduced DNA methylation levels in the upstream region of the interleukin-13 gene (IL13) in CD4+CLA+ T cells from AD patients correlated with increased IL13 mRNA expression in these cells. Sixteen miRNAs showed differential expression in CD4+CLA+ T cells from AD patients targeting genes in 202 biological processes (p < 0.05). An integrated network analysis of miRNAs and CpG sites identified two communities of strongly interconnected regulatory elements with strong antagonistic behaviours that recapitulated the differences between AD patients and HC. Functional analysis of the genes linked to these communities revealed their association with key cytokine signaling pathways, MAP kinase signaling and protein ubiquitination. Our findings support that epigenetic mechanisms play a role in the pathogenesis of AD by affecting inflammatory signaling molecules in skin homing CD4+CLA+ T cells and uncover putative molecules participating in AD pathways.", "doi": "10.1038/s41598-020-74798-z", "pmid": "33093567", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-74798-z"}, {"db": "pmc", "key": "PMC7582180"}], "notes": [], "created": "2020-10-26T09:04:32.192Z", "modified": "2024-01-16T13:48:41.543Z"}, {"entity": "publication", "iuid": "35f57851b81546e785433040d1f08581", "links": {"self": {"href": "https://publications.scilifelab.se/publication/35f57851b81546e785433040d1f08581.json"}, "display": {"href": "https://publications.scilifelab.se/publication/35f57851b81546e785433040d1f08581"}}, "title": "Reconstruction of the birth of a male sex chromosome present in Atlantic herring.", "authors": [{"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Chen", "given": "Junfeng", "initials": "J"}, {"family": "Herpin", "given": "Amaury", "initials": "A"}, {"family": "Pettersson", "given": "Mats E", "initials": "ME"}, {"family": "Han", "given": "Fan", "initials": "F"}, {"family": "Feng", "given": "Chungang", "initials": "C"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "P\u00e9ron", "given": "Sandrine", "initials": "S"}, {"family": "Cocco", "given": "Arianna", "initials": "A"}, {"family": "Larsson", "given": "M\u00e5rten", "initials": "M"}, {"family": "Tr\u00f6tschel", "given": "Christian", "initials": "C"}, {"family": "Poetsch", "given": "Ansgar", "initials": "A", "orcid": "0000-0002-7540-3475", "researcher": {"href": "https://publications.scilifelab.se/researcher/24924a964a1e4e9abd93d50ca404a680.json"}}, {"family": "Korsching", "given": "Kai", "initials": "K"}, {"family": "B\u00f6nigk", "given": "Wolfgang", "initials": "W"}, {"family": "K\u00f6rschen", "given": "Heinz G", "initials": "HG"}, {"family": "Berg", "given": "Florian", "initials": "F", "orcid": "0000-0003-1543-8112", "researcher": {"href": "https://publications.scilifelab.se/researcher/902b6c39c4f5463ea25888c17732fc3e.json"}}, {"family": "Folkvord", "given": "Arild", "initials": "A", "orcid": "0000-0002-4763-0590", "researcher": {"href": "https://publications.scilifelab.se/researcher/18e48870c7654bf0898cb9ff2a064b99.json"}}, {"family": "Kaupp", "given": "U Benjamin", "initials": "UB", "orcid": "0000-0002-0696-6397", "researcher": {"href": "https://publications.scilifelab.se/researcher/e94d12b7c4624985b0f6f7c8b798c969.json"}}, {"family": "Schartl", "given": "Manfred", "initials": "M", "orcid": "0000-0001-9882-5948", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f97783b5013409ebc1a6bd2df5ca92c.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2020-09-29", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "117", "issue": "39", "pages": "24359-24368", "issn-l": "0027-8424"}, "abstract": "The mechanisms underlying sex determination are astonishingly plastic. Particularly the triggers for the molecular machinery, which recalls either the male or female developmental program, are highly variable and have evolved independently and repeatedly. Fish show a huge variety of sex determination systems, including both genetic and environmental triggers. The advent of sex chromosomes is assumed to stabilize genetic sex determination. However, because sex chromosomes are notoriously cluttered with repetitive DNA and pseudogenes, the study of their evolution is hampered. Here we reconstruct the birth of a Y chromosome present in the Atlantic herring. The region is tiny (230 kb) and contains only three intact genes. The candidate male-determining gene BMPR1BBY encodes a truncated form of a BMP1B receptor, which originated by gene duplication and translocation and underwent rapid protein evolution. BMPR1BBY phosphorylates SMADs in the absence of ligand and thus has the potential to induce testis formation. The Y region also contains two genes encoding subunits of the sperm-specific Ca2+ channel CatSper required for male fertility. The herring Y chromosome conforms with a characteristic feature of many sex chromosomes, namely, suppressed recombination between a sex-determining factor and genes that are beneficial for the given sex. However, the herring Y differs from other sex chromosomes in that suppression of recombination is restricted to an \u223c500-kb region harboring the male-specific and sex-associated regions. As a consequence, any degeneration on the herring Y chromosome is restricted to those genes located in the small region affected by suppressed recombination.", "doi": "10.1073/pnas.2009925117", "pmid": "32938798", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "2009925117"}, {"db": "pmc", "key": "PMC7533707"}], "notes": [], "created": "2020-09-24T13:52:16.130Z", "modified": "2024-01-16T13:48:41.694Z"}, {"entity": "publication", "iuid": "f0dc43b7323e459ca55148bf15d20642", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0dc43b7323e459ca55148bf15d20642.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0dc43b7323e459ca55148bf15d20642"}}, "title": "Genome sequence of segmented filamentous bacteria present in the human intestine.", "authors": [{"family": "Jonsson", "given": "Hans", "initials": "H"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications.scilifelab.se/researcher/5dfdcf0109a942228d35d8dbfdede585.json"}}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Lundin", "given": "Eva", "initials": "E"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2020-09-04", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "3", "issue": "1", "pages": "485", "issn-l": "2399-3642"}, "abstract": "Segmented filamentous bacteria (SFB) are unique immune modulatory bacteria colonizing the small intestine of a variety of animals in a host-specific manner. SFB exhibit filamentous growth and attach to the host's intestinal epithelium, offering a physical route of interaction. SFB affect functions of the host immune system, among them IgA production and T-cell maturation. Until now, no human-specific SFB genome has been reported. Here, we report the metagenomic reconstruction of an SFB genome from a human ileostomy sample. Phylogenomic analysis clusters the genome with SFB genomes from mouse, rat and turkey, but the genome is genetically distinct, displaying 65-71% average amino acid identity to the others. By screening human faecal metagenomic datasets, we identified individuals carrying sequences identical to the new SFB genome. We thus conclude that a unique SFB variant exists in humans and foresee a renewed interest in the elucidation of SFB functionality in this environment.", "doi": "10.1038/s42003-020-01214-7", "pmid": "32887924", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-020-01214-7"}, {"db": "pmc", "key": "PMC7474095"}], "notes": [], "created": "2020-11-16T08:52:13.095Z", "modified": "2024-01-16T13:48:41.758Z"}, {"entity": "publication", "iuid": "2a387a31c3c54f2f9d3abce4e7efdfe2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a387a31c3c54f2f9d3abce4e7efdfe2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a387a31c3c54f2f9d3abce4e7efdfe2"}}, "title": "A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells.", "authors": [{"family": "Dias", "given": "Jos\u00e9 M", "initials": "JM", "orcid": "0000-0002-1402-0323", "researcher": {"href": "https://publications.scilifelab.se/researcher/82499805c5c24c46b8c2ec6427345c89.json"}}, {"family": "Alekseenko", "given": "Zhanna", "initials": "Z", "orcid": "0000-0002-6560-9699", "researcher": {"href": "https://publications.scilifelab.se/researcher/d78aae6139714fa3ae8221f3fb380b5a.json"}}, {"family": "Jeggari", "given": "Ashwini", "initials": "A", "orcid": "0000-0002-7155-9050", "researcher": {"href": "https://publications.scilifelab.se/researcher/083131be9eab46df9c789fb018316dff.json"}}, {"family": "Boareto", "given": "Marcelo", "initials": "M", "orcid": "0000-0002-9915-6376", "researcher": {"href": "https://publications.scilifelab.se/researcher/992734ee2f564e51b65c3d24770cc337.json"}}, {"family": "Vollmer", "given": "Jannik", "initials": "J", "orcid": "0000-0001-8341-7730", "researcher": {"href": "https://publications.scilifelab.se/researcher/793924a7af814c28a4ad66ff2fabf136.json"}}, {"family": "Kozhevnikova", "given": "Mariya", "initials": "M", "orcid": "0000-0001-9177-6303", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7a4bfdfbcc54403b818b31b24934151.json"}}, {"family": "Wang", "given": "Hui", "initials": "H", "orcid": "0000-0002-5444-1579", "researcher": {"href": "https://publications.scilifelab.se/researcher/38fc15d279b34209a72be7bd71a9338c.json"}}, {"family": "Matise", "given": "Michael P", "initials": "MP", "orcid": "0000-0003-2998-9927", "researcher": {"href": "https://publications.scilifelab.se/researcher/f861ea74deb9478fa475c5036333dfd9.json"}}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications.scilifelab.se/researcher/54b6c0ff12c148dd803f7f72c8af0d14.json"}}, {"family": "Iber", "given": "Dagmar", "initials": "D", "orcid": "0000-0001-8051-1035", "researcher": {"href": "https://publications.scilifelab.se/researcher/26137676787f477fb374d629819d898b.json"}}, {"family": "Ericson", "given": "Johan", "initials": "J", "orcid": "0000-0002-8019-7127", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a093b1609b74f74a8a8546f02946782.json"}}], "type": "journal article", "published": "2020-09-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "volume": "6", "issue": "38", "pages": null}, "abstract": "How time is measured by neural stem cells during temporal neurogenesis has remained unresolved. By combining experiments and computational modeling, we define a Shh/Gli-driven three-node timer underlying the sequential generation of motor neurons (MNs) and serotonergic neurons in the brainstem. The timer is founded on temporal decline of Gli-activator and Gli-repressor activities established through down-regulation of Gli transcription. The circuitry conforms an incoherent feed-forward loop, whereby Gli proteins not only promote expression of Phox2b and thereby MN-fate but also account for a delayed activation of a self-promoting transforming growth factor-\u03b2 (Tgf\u03b2) node triggering a fate switch by repressing Phox2b. Hysteresis and spatial averaging by diffusion of Tgf\u03b2 counteract noise and increase temporal accuracy at the population level, providing a functional rationale for the intrinsically programmed activation of extrinsic switch signals in temporal patterning. Our study defines how time is reliably encoded during the sequential specification of neurons.", "doi": "10.1126/sciadv.aba8196", "pmid": "32938678", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6/38/eaba8196"}, {"db": "pmc", "key": "PMC7494341"}], "notes": [], "created": "2020-12-07T16:28:52.509Z", "modified": "2024-01-16T13:48:41.848Z"}, {"entity": "publication", "iuid": "d90eae148c4e4df49076698b912705f4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d90eae148c4e4df49076698b912705f4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d90eae148c4e4df49076698b912705f4"}}, "title": "High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure.", "authors": [{"family": "Singh", "given": "Abhijeet", "initials": "A"}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}, {"family": "M\u00fcller", "given": "Bettina", "initials": "B"}], "type": "journal article", "published": "2020-08-27", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "11", "issue": null, "pages": "2066", "issn-l": "1664-302X"}, "abstract": "The formyltetrahydrofolate synthetase (FTHFS) gene is a molecular marker of choice to study the diversity of acetogenic communities. However, current analyses are limited due to lack of a high-throughput sequencing approach for FTHFS gene amplicons and a dedicated bioinformatics pipeline for data analysis, including taxonomic annotation and visualization of the sequence data. In the present study, we combined the barcode approach for multiplexed sequencing with unsupervised data analysis to visualize acetogenic community structure. We used samples from a biogas digester to develop proof-of-principle for our combined approach. We successfully generated high-throughput sequence data for the partial FTHFS gene and performed unsupervised data analysis using the novel bioinformatics pipeline \"AcetoScan\" presented in this study, which resulted in taxonomically annotated OTUs, phylogenetic tree, abundance plots and diversity indices. The results demonstrated that high-throughput sequencing can be used to sequence the FTHFS amplicons from a pool of samples, while the analysis pipeline AcetoScan can be reliably used to process the raw sequence data and visualize acetogenic community structure. The method and analysis pipeline described in this paper can assist in the identification and quantification of known or potentially new acetogens. The AcetoScan pipeline is freely available at https://github.com/abhijeetsingh1704/AcetoScan.", "doi": "10.3389/fmicb.2020.02066", "pmid": "32983047", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7481360"}], "notes": [], "created": "2020-09-10T10:20:24.309Z", "modified": "2024-01-16T13:48:41.857Z"}, {"entity": "publication", "iuid": "1c72116bf22e498797792df3c564ce88", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c72116bf22e498797792df3c564ce88.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c72116bf22e498797792df3c564ce88"}}, "title": "Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi.", "authors": [{"family": "Floudas", "given": "Dimitrios", "initials": "D", "orcid": "0000-0002-6119-2590", "researcher": {"href": "https://publications.scilifelab.se/researcher/d083c79383704b0f813c53f862e31ca2.json"}}, {"family": "Bentzer", "given": "Johan", "initials": "J"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Johansson", "given": "Tomas", "initials": "T"}, {"family": "Persson", "given": "Per", "initials": "P", "orcid": "0000-0001-9172-3068", "researcher": {"href": "https://publications.scilifelab.se/researcher/edffc6f9df60444a9480380c68e7d202.json"}}, {"family": "Tunlid", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2020-08-00", "journal": {"volume": "14", "issn": "1751-7370", "issue": "8", "title": "ISME J", "pages": "2046-2059", "issn-l": "1751-7362"}, "abstract": "Litter decomposing Agaricales play key role in terrestrial carbon cycling, but little is known about their decomposition mechanisms. We assembled datasets of 42 gene families involved in plant-cell-wall decomposition from seven newly sequenced litter decomposers and 35 other Agaricomycotina members, mostly white-rot and brown-rot species. Using sequence similarity and phylogenetics, we split the families into phylogroups and compared their gene composition across nutritional strategies. Subsequently, we used Raman spectroscopy to examine the ability of litter decomposers, white-rot fungi, and brown-rot fungi to decompose crystalline cellulose. Both litter decomposers and white-rot fungi share the enzymatic cellulose decomposition, whereas brown-rot fungi possess a distinct mechanism that disrupts cellulose crystallinity. However, litter decomposers and white-rot fungi differ with respect to hemicellulose and lignin degradation phylogroups, suggesting adaptation of the former group to the litter environment. Litter decomposers show high phylogroup diversity, which is indicative of high functional versatility within the group, whereas a set of white-rot species shows adaptation to bulk-wood decomposition. In both groups, we detected species that have unique characteristics associated with hitherto unknown adaptations to diverse wood and litter substrates. Our results suggest that the terms white-rot fungi and litter decomposers mask a much larger functional diversity.", "doi": "10.1038/s41396-020-0667-6", "pmid": "32382073", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41396-020-0667-6"}, {"db": "pmc", "key": "PMC7368018"}, {"db": "Dryad", "key": "10.5061/dryad.pk0p2ngk1"}], "notes": [], "created": "2020-05-15T08:57:38.045Z", "modified": "2021-12-10T10:02:12.162Z"}, {"entity": "publication", "iuid": "02aba4f1fdd44b4d9243ecec013e23e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02aba4f1fdd44b4d9243ecec013e23e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02aba4f1fdd44b4d9243ecec013e23e8"}}, "title": "Association between proteomics and obstructive sleep apnea phenotypes in a community-based cohort of women.", "authors": [{"family": "Ljunggren", "given": "Mirjam", "initials": "M", "orcid": "0000-0002-8486-6746", "researcher": {"href": "https://publications.scilifelab.se/researcher/de5ea7d89bed4fe2b28e9c2b6cf9e72a.json"}}, {"family": "Theorell-Hagl\u00f6w", "given": "Jenny", "initials": "J"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Sahlin", "given": "Carin", "initials": "C"}, {"family": "Franklin", "given": "Karl A", "initials": "KA"}, {"family": "Malinovschi", "given": "Andrei", "initials": "A"}, {"family": "Janson", "given": "Christer", "initials": "C"}, {"family": "Lindberg", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "J Sleep Res", "issn": "1365-2869", "volume": "29", "issue": "4", "pages": "e13041", "issn-l": null}, "abstract": "Proteomic-based technologies offer new opportunities to identify proteins that might reflect the cardiometabolic stress caused by different aspects of sleep-disordered breathing. We aimed to investigate whether severe obstructive sleep apnea and severe obstructive sleep apnea during rapid eye movement sleep are associated with changed levels of inflammatory and cardiac disease-related proteins in a population-based cohort of women. In the community-based \"Sleep and Health in Women\" (SHE) cohort study, 400 women underwent polysomnography, anthropometric measurements and blood sampling. Two proteomic assays (Olink Proseek\u00ae Inflammation panel and Olink Proseek\u00ae Cardiovascular II panel), each measuring 92 proteins, were analysed in a subsample of 253 women. p-Values were adjusted for multiple testing, with false discovery rate set at 10%. In unadjusted models, 57 proteins were associated with apnea-hypopnea index, 56 proteins with oxygen desaturation index and 64 proteins with rapid eye movement-apnea-hypopnea index. After adjustment for age, body mass index and plate, there were no significant associations between apnea-hypopnea index or oxygen desaturation index and any of the proteins. Severe obstructive sleep apnea during rapid eye movement sleep (rapid eye movement-apnea-hypopnea index \u2265 30) was associated with decreased levels of two anti-inflammatory proteins; Sirt2 (q-value .016) and LAP-TGF-\u03b21 (q-value .016). There was also a negative association between rapid eye movement-apnea-hypopnea index of \u2265 30 and Axin1 (q-value .095), a protein thought to facilitate TGF-\u03b2-signalling. We conclude that severe obstructive sleep apnea during rapid eye movement sleep is associated with low levels of Sirt2, LAP-TGF-\u03b21 and Axin1, anti-inflammatory proteins involved in metabolic regulation and in the atherosclerotic process. For obstructive sleep apnea based on a whole night, the associations with cardiac and inflammatory proteins are weaker, and explained to a large extent by age and body mass index.", "doi": "10.1111/jsr.13041", "pmid": "32267595", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2020-12-15T14:17:59.859Z", "modified": "2024-01-16T13:48:42.068Z"}, {"entity": "publication", "iuid": "87e07ded7de44a53ae4395ae27dfc8d4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87e07ded7de44a53ae4395ae27dfc8d4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87e07ded7de44a53ae4395ae27dfc8d4"}}, "title": "Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach", "authors": [{"family": "von der Heyde", "given": "Benedikt", "initials": "B", "orcid": "0000-0002-9889-4027", "researcher": {"href": "https://publications.scilifelab.se/researcher/803c0e0639174a50b59ae597802e824f.json"}}, {"family": "Emmanouilidou", "given": "Anastasia", "initials": "A"}, {"family": "Mazzaferro", "given": "Eugenia", "initials": "E"}, {"family": "Vicenzi", "given": "Silvia", "initials": "S"}, {"family": "H\u00f6ijer", "given": "Ida", "initials": "I"}, {"family": "Klingstr\u00f6m", "given": "Tiffany", "initials": "T"}, {"family": "Jumaa", "given": "Sitaf", "initials": "S"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Snieder", "given": "Harold", "initials": "H", "orcid": "0000-0003-1949-2298", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9276827839a4f3cb50dcaa2ad4708a5.json"}}, {"family": "de Geus", "given": "Eco", "initials": "E", "orcid": "0000-0001-6022-2666", "researcher": {"href": "https://publications.scilifelab.se/researcher/9abb01a905f347df8214d469d6c5ac45.json"}}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E", "orcid": "0000-0003-2256-6972", "researcher": {"href": "https://publications.scilifelab.se/researcher/689bc741ea6547d18de7080c84d0193e.json"}}, {"family": "Allalou", "given": "Amin", "initials": "A"}, {"family": "Brooke", "given": "Hannah L", "initials": "HL"}, {"family": "den Hoed", "given": "Marcel", "initials": "M", "orcid": "0000-0001-8081-428X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d712cc087d344b15ab9a7971640acebe.json"}}], "type": "journal-article", "published": "2020-07-16", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "11831"}, "abstract": "A meta-analysis of genome-wide association studies (GWAS) identified eight loci that are associated with heart rate variability (HRV), but candidate genes in these loci remain uncharacterized. We developed an image- and CRISPR/Cas9-based pipeline to systematically characterize candidate genes for HRV in live zebrafish embryos. Nine zebrafish orthologues of six human candidate genes were targeted simultaneously in eggs from fish that transgenically express GFP on smooth muscle cells (Tg[acta2:GFP]), to visualize the beating heart. An automated analysis of repeated 30 s recordings of beating atria in 381 live, intact zebrafish embryos at 2 and 5 days post-fertilization highlighted genes that influence HRV (hcn4 and si:dkey-65j6.2 [KIAA1755]); heart rate (rgs6 and hcn4); and the risk of sinoatrial pauses and arrests (hcn4). Exposure to 10 or 25 \u00b5M ivabradine-an open channel blocker of HCNs-for 24 h resulted in a dose-dependent higher HRV and lower heart rate at 5 days post-fertilization. Hence, our screen confirmed the role of established genes for heart rate and rhythm (RGS6 and HCN4); showed that ivabradine reduces heart rate and increases HRV in zebrafish embryos, as it does in humans; and highlighted a novel gene that plays a role in HRV (KIAA1755).", "doi": "10.1038/s41598-020-68567-1", "pmid": "32678143", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "BioImage Informatics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Genome Engineering Zebrafish": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7367351"}, {"db": "pii", "key": "10.1038/s41598-020-68567-1"}], "notes": [], "created": "2020-08-19T09:27:04.550Z", "modified": "2024-01-16T13:48:42.137Z"}, {"entity": "publication", "iuid": "f261ffa0cc8d46698138b03d99cdd77a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f261ffa0cc8d46698138b03d99cdd77a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f261ffa0cc8d46698138b03d99cdd77a"}}, "title": "AML displays increased CTCF occupancy associated with aberrant gene expression and transcription factor binding.", "authors": [{"family": "Mujahed", "given": "Huthayfa", "initials": "H"}, {"family": "Miliara", "given": "Sophia", "initials": "S"}, {"family": "Neddermeyer", "given": "Anne", "initials": "A"}, {"family": "Bengtz\u00e9n", "given": "Sofia", "initials": "S"}, {"family": "Nilsson", "given": "Christer", "initials": "C"}, {"family": "Deneberg", "given": "Stefan", "initials": "S"}, {"family": "Cordeddu", "given": "Lina", "initials": "L"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}], "type": "journal article", "published": "2020-07-16", "journal": {"title": "Blood", "issn": "1528-0020", "volume": "136", "issue": "3", "pages": "339-352", "issn-l": "0006-4971"}, "abstract": "CCTC-binding factor (CTCF) is a key regulator of gene expression through organization of the chromatin structure. Still, it is unclear how CTCF binding is perturbed in leukemia or in cancer in general. We studied CTCF binding by chromatin immunoprecipitation sequencing in cells from patients with acute myeloid leukemia (AML) and in normal bone marrow (NBM) in the context of gene expression, DNA methylation, and azacitidine exposure. CTCF binding was increased in AML compared with NBM. Aberrant CTCF binding was enriched for motifs for key myeloid transcription factors such as CEBPA, PU.1, and RUNX1. AML with TET2 mutations was characterized by a particularly strong gain of CTCF binding, highly enriched for gain in promoter regions, while AML in general was enriched for changes at enhancers. There was a strong anticorrelation between CTCF binding and DNA methylation. Gain of CTCF occupancy was associated with increased gene expression; however, the genomic location (promoter vs distal regions) and enrichment of motifs (for repressing vs activating cofactors) were decisive for the gene expression pattern. Knockdown of CTCF in K562 cells caused loss of CTCF binding and transcriptional repression of genes with changed CTCF binding in AML, as well as loss of RUNX1 binding at RUNX1/CTCF-binding sites. In addition, CTCF knockdown caused increased differentiation. Azacitidine exposure caused major changes in CTCF occupancy in AML patient cells, partly by restoring a CTCF-binding pattern similar to NBM. We conclude that AML displays an aberrant increase in CTCF occupancy that targets key genes for AML development and impacts gene expression.", "doi": "10.1182/blood.2019002326", "pmid": "32232485", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0006-4971(20)61884-5"}], "notes": [], "created": "2021-12-02T14:26:23.756Z", "modified": "2024-01-16T13:48:42.145Z"}, {"entity": "publication", "iuid": "5d10760287d3464a96f10a51a55e9a7c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d10760287d3464a96f10a51a55e9a7c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d10760287d3464a96f10a51a55e9a7c"}}, "title": "Spatio-molecular domains identified in the mouse subthalamic nucleus and neighboring glutamatergic and GABAergic brain structures.", "authors": [{"family": "Wall\u00e9n-Mackenzie", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-8713-070X", "researcher": {"href": "https://publications.scilifelab.se/researcher/eeda951c090846008ee77d1aa28e5fe1.json"}}, {"family": "Dumas", "given": "Sylvie", "initials": "S", "orcid": "0000-0002-4415-9924", "researcher": {"href": "https://publications.scilifelab.se/researcher/0393bec924d24ecfaa75cd77062b7231.json"}}, {"family": "Papathanou", "given": "Maria", "initials": "M", "orcid": "0000-0002-0845-9831", "researcher": {"href": "https://publications.scilifelab.se/researcher/281c8a847ca64d50988627c9d92f5b8a.json"}}, {"family": "Martis Thiele", "given": "Mihaela M", "initials": "MM"}, {"family": "Vlcek", "given": "Bianca", "initials": "B", "orcid": "0000-0001-5442-2303", "researcher": {"href": "https://publications.scilifelab.se/researcher/7afc70325f904d95b16a5e0fc9179e4b.json"}}, {"family": "K\u00f6nig", "given": "Niclas", "initials": "N", "orcid": "0000-0003-0899-046X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7def2d96c45b462fa50a6579ad1dad97.json"}}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}], "type": "journal article", "published": "2020-07-03", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "3", "issue": "1", "pages": "338"}, "abstract": "The subthalamic nucleus (STN) is crucial for normal motor, limbic and associative function. STN dysregulation is correlated with several brain disorders, including Parkinson's disease and obsessive compulsive disorder (OCD), for which high-frequency stimulation of the STN is increasing as therapy. However, clinical progress is hampered by poor knowledge of the anatomical-functional organization of the STN. Today, experimental mouse genetics provides outstanding capacity for functional decoding, provided selective promoters are available. Here, we implemented single-nuclei RNA sequencing (snRNASeq) of the mouse STN followed through with histological analysis of 16 candidate genes of interest. Our results demonstrate that the mouse STN is composed of at least four spatio-molecularly defined domains, each distinguished by defined sets of promoter activities. Further, molecular profiles dissociate the STN from the adjoining para-STN (PSTN) and neighboring structures of the hypothalamus, mammillary nuclei and zona incerta. Enhanced knowledge of STN\u00b4s internal organization should prove useful towards genetics-based functional decoding of this clinically relevant brain structure.", "doi": "10.1038/s42003-020-1028-8", "pmid": "32620779", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-020-1028-8"}, {"db": "pmc", "key": "PMC7334224"}], "notes": [], "created": "2020-08-10T12:44:57.714Z", "modified": "2024-01-16T13:48:42.209Z"}, {"entity": "publication", "iuid": "a5a1963fd516402bbc91e16b77379601", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a5a1963fd516402bbc91e16b77379601.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a5a1963fd516402bbc91e16b77379601"}}, "title": "A framework to assess the quality and impact of bioinformatics training across ELIXIR.", "authors": [{"family": "Gurwitz", "given": "Kim T", "initials": "KT", "orcid": "0000-0003-1992-5073", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a5bf8910c22409fa3c8121755388d0f.json"}}, {"family": "Singh Gaur", "given": "Prakash", "initials": "P", "orcid": "0000-0003-3272-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1090dcab7e4216960cf7798523179f.json"}}, {"family": "Bellis", "given": "Louisa J", "initials": "LJ", "orcid": "0000-0001-9581-870X", "researcher": {"href": "https://publications.scilifelab.se/researcher/865db60afe8b400aaf33d1c9c8648634.json"}}, {"family": "Larcombe", "given": "Lee", "initials": "L", "orcid": "0000-0003-3150-6445", "researcher": {"href": "https://publications.scilifelab.se/researcher/79426101140d4588bb672e154e5590e2.json"}}, {"family": "Alloza", "given": "Eva", "initials": "E", "orcid": "0000-0001-8385-9336", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3c0c2cdf63e4276a9d843565613e40a.json"}}, {"family": "Balint", "given": "Balint Laszlo", "initials": "BL"}, {"family": "Botzki", "given": "Alexander", "initials": "A", "orcid": "0000-0001-6691-4233", "researcher": {"href": "https://publications.scilifelab.se/researcher/79448fc432054ea6af1a0c559b28567d.json"}}, {"family": "Dimec", "given": "Jure", "initials": "J", "orcid": "0000-0002-9525-9028", "researcher": {"href": "https://publications.scilifelab.se/researcher/aec05bd8a2734f6aa26fb489fce9c630.json"}}, {"family": "Dominguez Del Angel", "given": "Victoria", "initials": "V", "orcid": "0000-0002-5514-6651", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a708fa6e9a44453b97cfc2089e06bec.json"}}, {"family": "Fernandes", "given": "Pedro L", "initials": "PL", "orcid": "0000-0003-2124-0241", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3ca6e16ecb5403f8e344f1df671fa4a.json"}}, {"family": "Korpelainen", "given": "Eija", "initials": "E"}, {"family": "Krause", "given": "Roland", "initials": "R", "orcid": "0000-0001-9938-7126", "researcher": {"href": "https://publications.scilifelab.se/researcher/86196693e4fd402ab0493246d07d5ccb.json"}}, {"family": "Kuzak", "given": "Mateusz", "initials": "M", "orcid": "0000-0003-0087-6021", "researcher": {"href": "https://publications.scilifelab.se/researcher/821ca0fb14794a349ac838ab4a7abc1c.json"}}, {"family": "Le Pera", "given": "Loredana", "initials": "L", "orcid": "0000-0002-0076-9878", "researcher": {"href": "https://publications.scilifelab.se/researcher/0371f0fbbbbe4c0d8491e17d8aa8424a.json"}}, {"family": "Lesko\u0161ek", "given": "Brane", "initials": "B", "orcid": "0000-0001-5202-2349", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d638a63af2043d2b7f8495efbd6b078.json"}}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Marek", "given": "Diana", "initials": "D", "orcid": "0000-0002-9812-6351", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1717147a0594eb6868f3f58a4b849e5.json"}}, {"family": "Martinez", "given": "Paula A", "initials": "PA", "orcid": "0000-0002-8990-1985", "researcher": {"href": "https://publications.scilifelab.se/researcher/25c618ae300f484bb3f589fd55eea782.json"}}, {"family": "Muyldermans", "given": "Tuur", "initials": "T", "orcid": "0000-0002-3926-7293", "researcher": {"href": "https://publications.scilifelab.se/researcher/be84fdc9e5d5439484f038bd28e0b97a.json"}}, {"family": "Nyg\u00e5rd", "given": "St\u00e5le", "initials": "S"}, {"family": "Palagi", "given": "Patricia M", "initials": "PM", "orcid": "0000-0001-9062-6303", "researcher": {"href": "https://publications.scilifelab.se/researcher/855d6f5c9a994ae49495522dfaf36281.json"}}, {"family": "Peterson", "given": "Hedi", "initials": "H", "orcid": "0000-0001-9951-5116", "researcher": {"href": "https://publications.scilifelab.se/researcher/be512162189d47059f1bd0755d6c16f8.json"}}, {"family": "Psomopoulos", "given": "Fotis", "initials": "F", "orcid": "0000-0002-0222-4273", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4fd426018ab421c99e9044b31066cf9.json"}}, {"family": "Spiwok", "given": "Vojtech", "initials": "V", "orcid": "0000-0001-8108-2033", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e89722bc45a4656906c79ba958cbc03.json"}}, {"family": "van Gelder", "given": "Celia W G", "initials": "CWG", "orcid": "0000-0002-0223-2329", "researcher": {"href": "https://publications.scilifelab.se/researcher/2533ac3cd3274486b5609ac643dc436b.json"}}, {"family": "Via", "given": "Allegra", "initials": "A"}, {"family": "Vidak", "given": "Marko", "initials": "M", "orcid": "0000-0001-7901-3936", "researcher": {"href": "https://publications.scilifelab.se/researcher/be1d0da74ff64f4a8ec7393577f9ba81.json"}}, {"family": "Wibberg", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1331-4311", "researcher": {"href": "https://publications.scilifelab.se/researcher/771c66b20cb448e481140f476c6244ca.json"}}, {"family": "Morgan", "given": "Sarah L", "initials": "SL", "orcid": "0000-0001-9528-8323", "researcher": {"href": "https://publications.scilifelab.se/researcher/062588ade1a843ae846c4e2b96904849.json"}}, {"family": "Rustici", "given": "Gabriella", "initials": "G", "orcid": "0000-0003-3085-1271", "researcher": {"href": "https://publications.scilifelab.se/researcher/82710a270ab04a09af1550709db32b1c.json"}}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "PLoS Comput. Biol.", "issn": "1553-7358", "volume": "16", "issue": "7", "pages": "e1007976", "issn-l": "1553-734X"}, "abstract": "ELIXIR is a pan-European intergovernmental organisation for life science that aims to coordinate bioinformatics resources in a single infrastructure across Europe; bioinformatics training is central to its strategy, which aims to develop a training community that spans all ELIXIR member states. In an evidence-based approach for strengthening bioinformatics training programmes across Europe, the ELIXIR Training Platform, led by the ELIXIR EXCELERATE Quality and Impact Assessment Subtask in collaboration with the ELIXIR Training Coordinators Group, has implemented an assessment strategy to measure quality and impact of its entire training portfolio. Here, we present ELIXIR's framework for assessing training quality and impact, which includes the following: specifying assessment aims, determining what data to collect in order to address these aims, and our strategy for centralised data collection to allow for ELIXIR-wide analyses. In addition, we present an overview of the ELIXIR training data collected over the past 4 years. We highlight the importance of a coordinated and consistent data collection approach and the relevance of defining specific metrics and answer scales for consortium-wide analyses as well as for comparison of data across iterations of the same course.", "doi": "10.1371/journal.pcbi.1007976", "pmid": "32702016", "labels": {"Bioinformatics Support and Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "PCOMPBIOL-D-19-01778"}, {"db": "pmc", "key": "PMC7377377"}], "notes": [], "created": "2020-12-15T09:16:34.028Z", "modified": "2021-11-10T12:49:57.221Z"}, {"entity": "publication", "iuid": "c1da6115eb61449fbd3f03367a285fc9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1da6115eb61449fbd3f03367a285fc9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1da6115eb61449fbd3f03367a285fc9"}}, "title": "Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion.", "authors": [{"family": "Almeida", "given": "Pedro", "initials": "P", "orcid": "0000-0001-6790-8687", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb2e2881fe7449659d89e9beb407e0a4.json"}}, {"family": "Proux-Wera", "given": "Estelle", "initials": "E"}, {"family": "Churcher", "given": "Allison", "initials": "A"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Pucholt", "given": "Pascal", "initials": "P"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Martin", "given": "Tom", "initials": "T"}, {"family": "R\u00f6nnberg-W\u00e4stljung", "given": "Ann-Christin", "initials": "AC"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Berlin", "given": "Sofia", "initials": "S"}, {"family": "Mank", "given": "Judith E", "initials": "JE"}], "type": "journal article", "published": "2020-06-30", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "issn-l": "1741-7007", "volume": "18", "issue": "1", "pages": "78"}, "abstract": "Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear.\n\nHere, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes.\n\nOur data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.", "doi": "10.1186/s12915-020-00808-1", "pmid": "32605573", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12915-020-00808-1"}, {"db": "pmc", "key": "PMC7329446"}], "notes": [], "created": "2020-07-03T05:25:52.141Z", "modified": "2021-11-10T12:50:00.669Z"}, {"entity": "publication", "iuid": "943e2024538744c492d89c63c743f034", "links": {"self": {"href": "https://publications.scilifelab.se/publication/943e2024538744c492d89c63c743f034.json"}, "display": {"href": "https://publications.scilifelab.se/publication/943e2024538744c492d89c63c743f034"}}, "title": "Single cell transcriptomics identifies stem cell-derived graft composition in a model of Parkinson's disease.", "authors": [{"family": "Tiklov\u00e1", "given": "Katar\u00edna", "initials": "K"}, {"family": "Nolbrant", "given": "Sara", "initials": "S", "orcid": "0000-0003-2184-1741", "researcher": {"href": "https://publications.scilifelab.se/researcher/91ab50f5e5874992a0703470230a8462.json"}}, {"family": "Fiorenzano", "given": "Alessandro", "initials": "A"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}, {"family": "Sharma", "given": "Yogita", "initials": "Y"}, {"family": "Heuer", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0300-7606", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc2bac2f0e63487792fd5525ee1c2b1e.json"}}, {"family": "Gillberg", "given": "Linda", "initials": "L"}, {"family": "Hoban", "given": "Deirdre B", "initials": "DB"}, {"family": "Cardoso", "given": "Tiago", "initials": "T", "orcid": "0000-0003-2686-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/08d76d0b77f14d39a6c097386e158174.json"}}, {"family": "Adler", "given": "Andrew F", "initials": "AF"}, {"family": "Birtele", "given": "Marcella", "initials": "M"}, {"family": "Lund\u00e9n-Miguel", "given": "Hilda", "initials": "H"}, {"family": "Volakakis", "given": "Nikolaos", "initials": "N"}, {"family": "Kirkeby", "given": "Agnete", "initials": "A"}, {"family": "Perlmann", "given": "Thomas", "initials": "T"}, {"family": "Parmar", "given": "Malin", "initials": "M", "orcid": "0000-0001-5002-4199", "researcher": {"href": "https://publications.scilifelab.se/researcher/c48b5aaff3bc4832a96fda4f2cf127cb.json"}}], "type": "journal article", "published": "2020-05-15", "journal": {"volume": "11", "issn": "2041-1723", "issue": "1", "pages": "2434", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Cell replacement is a long-standing and realistic goal for the treatment of Parkinson's disease (PD). Cells for transplantation can be obtained from fetal brain tissue or from stem cells. However, after transplantation, dopamine (DA) neurons are seen to be a minor component of grafts, and it has remained difficult to determine the identity of other cell types. Here, we report analysis by single-cell RNA sequencing (scRNA-seq) combined with comprehensive histological analyses to characterize intracerebral grafts from human embryonic stem cells (hESCs) and fetal tissue after functional maturation in a pre-clinical rat PD model. We show that neurons and astrocytes are major components in both fetal and stem cell-derived grafts. Additionally, we identify a cell type closely resembling a class of recently identified perivascular-like cells in stem cell-derived grafts. Thus, this study uncovers previously unknown cellular diversity in a clinically relevant cell replacement PD model.", "doi": "10.1038/s41467-020-16225-5", "pmid": "32415072", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-16225-5"}, {"db": "pmc", "key": "PMC7229159"}], "notes": [], "created": "2020-06-02T07:25:59.289Z", "modified": "2024-01-16T13:48:42.494Z"}, {"entity": "publication", "iuid": "e9a65d41693e4874b05f362bedb21539", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e9a65d41693e4874b05f362bedb21539.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e9a65d41693e4874b05f362bedb21539"}}, "title": "In-depth plasma proteomics reveals increase in circulating PD-1 during anti-PD-1 immunotherapy in patients with metastatic cutaneous melanoma.", "authors": [{"family": "Baba\u010di\u0107", "given": "Haris", "initials": "H", "orcid": "0000-0003-0813-0005", "researcher": {"href": "https://publications.scilifelab.se/researcher/45a1c5d3d2d34a9e96d112877632784c.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J"}, {"family": "Pico de Coa\u00f1a", "given": "Yago", "initials": "Y"}, {"family": "Pernemalm", "given": "Maria", "initials": "M"}, {"family": "Eriksson", "given": "Hanna", "initials": "H"}], "type": "journal article", "published": "2020-05-00", "journal": {"title": "J Immunother Cancer", "issn": "2051-1426", "volume": "8", "issue": "1", "pages": "e000204", "issn-l": null}, "abstract": "Immune checkpoint inhibitors (ICIs) have significantly improved the outcome in metastatic cutaneous melanoma (CM). However, therapy response is limited to subgroups of patients and clinically useful predictive biomarkers are lacking.\n\nTo discover treatment-related systemic changes in plasma and potential biomarkers associated with treatment outcome, we analyzed serial plasma samples from 24 patients with metastatic CM, collected before and during ICI treatment, with mass-spectrometry-based global proteomics (high-resolution isoelectric focusing liquid chromatography-mass spectrometry (HiRIEF LC-MS/MS)) and targeted proteomics with proximity extension assays (PEAs). In addition, we analyzed plasma proteomes of 24 patients with metastatic CM treated with mitogen-activated protein kinase inhibitors (MAPKis), to pinpoint changes in protein plasma levels specific to the ICI treatment. To detect plasma proteins associated with treatment response, we performed stratified analyses in anti-programmed cell death protein 1 (anti-PD-1) responders and non-responders. In addition, we analyzed the association between protein plasma levels and progression-free survival (PFS) by Cox proportional hazards models.\n\nUnbiased HiRIEF LC-MS/MS-based proteomics showed plasma levels' alterations related to anti-PD-1 treatment in 80 out of 1160 quantified proteins. Circulating PD-1 had the highest increase during anti-PD-1 treatment (log2-FC=2.03, p=0.0008) and in anti-PD-1 responders (log2-FC=2.09, p=0.005), but did not change in the MAPKis cohort. Targeted, antibody-based proteomics by PEA confirmed this observation. Anti-PD-1 responders had an increase in plasma proteins involved in T-cell response, neutrophil degranulation, inflammation, cell adhesion, and immune suppression. Furthermore, we discovered new associations between plasma proteins (eg, interleukin 6, interleukin 10, proline-rich acidic protein 1, desmocollin 3, C-C motif chemokine ligands 2, 3 and 4, vascular endothelial growth factor A) and PFS, which may serve as predictive biomarkers.\n\nWe detected an increase in circulating PD-1 during anti-PD-1 treatment, as well as diverse immune plasma proteomic signatures in anti-PD-1 responders. This study demonstrates the potential of plasma proteomics as a liquid biopsy method and in discovery of putative predictive biomarkers for anti-PD-1 treatment in metastatic CM.", "doi": "10.1136/jitc-2019-000204", "pmid": "32457125", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "jitc-2019-000204"}, {"db": "pmc", "key": "PMC7253007"}], "notes": [], "created": "2021-08-13T11:12:42.966Z", "modified": "2021-11-10T12:51:37.325Z"}, {"entity": "publication", "iuid": "9f5f8533edb94e54a14be784d8fa0566", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f5f8533edb94e54a14be784d8fa0566.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f5f8533edb94e54a14be784d8fa0566"}}, "title": "Interactive proteogenomic exploration of response to Fusarium head blight in oat varieties with different resistance.", "authors": [{"family": "Willforss", "given": "J", "initials": "J"}, {"family": "Leonova", "given": "S", "initials": "S"}, {"family": "Tillander", "given": "J", "initials": "J"}, {"family": "Andreasson", "given": "E", "initials": "E"}, {"family": "Marttila", "given": "S", "initials": "S"}, {"family": "Olsson", "given": "O", "initials": "O"}, {"family": "Chawade", "given": "A", "initials": "A"}, {"family": "Levander", "given": "F", "initials": "F"}], "type": "journal article", "published": "2020-04-30", "journal": {"title": "J Proteomics", "issn": "1876-7737", "volume": "218", "pages": "103688", "issn-l": "1874-3919"}, "abstract": "Fusarium species are cereal pathogens that cause the Fusarium Head Blight (FHB) disease. FHB can reduce yield, cause mycotoxin accumulation in the grain and reduce germination efficiency of the harvested seeds. Understanding the biochemical interactions between the host plants and the pathogen is crucial for controlling the disease and for the development of cultivars with improved tolerance to FHB. Here, we studied morphological and proteomic differences between the susceptible oat variety Belinda and the more resistant variety Argamak using variety-specific transcriptome assemblies as references. Measurements of deoxynivalenol toxin levels confirmed the partial resistance in Argamak and the susceptibility in Belinda. To jointly investigate the proteomics- and sequence data, we developed an RShiny-based interface for interactive exploration of the dataset using univariate and multivariate statistics. When applying this interface to the dataset, quantitative protein differences between Belinda and Argamak were detected, and eighteen peptides were found uniquely in Argamak during infection, among them several lipoxygenases. Such proteins can be developed as markers for Fusarium resistance breeding. In conclusion, this study provides the first proteogenomic insight on molecular Fusarium-oat interactions at both morphological and molecular levels and the data are openly available through an interactive interface for further inspection. SIGNIFICANCE: Fusarium head blight causes widespread damage to crops, and chronic and acute toxicity to human and livestock due to the accumulation of toxins during infection. In the present study, two oat varieties with differing resistance were challenged with Fusarium to understand the disease better, and studied both at morphological and molecular levels, identifying proteins which could play a role in the defense mechanism. Furthermore, a proteogenomics approach allows joint profiling of expression and sequence level differences to identify potentially functionally differing mutations. Here such analysis is made openly available through an interactive interface which allows other scientists to draw further findings from the data. This study may both serve as a basis for understanding oat disease response and developing breeding markers for Fusarium resistant oat and future proteogenomic studies using the interactive approach described.", "doi": "10.1016/j.jprot.2020.103688", "pmid": "32061841", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1874-3919(20)30056-7"}], "notes": [], "created": "2021-12-02T14:04:07.686Z", "modified": "2021-12-02T14:04:07.699Z"}, {"entity": "publication", "iuid": "65eed8901d6d42af899e7c58758820da", "links": {"self": {"href": "https://publications.scilifelab.se/publication/65eed8901d6d42af899e7c58758820da.json"}, "display": {"href": "https://publications.scilifelab.se/publication/65eed8901d6d42af899e7c58758820da"}}, "title": "The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences.", "authors": [{"family": "Drysdale", "given": "Rachel", "initials": "R", "orcid": "0000-0003-3037-0216", "researcher": {"href": "https://publications.scilifelab.se/researcher/33a39d1bd31a47fa8b97d18159cc8011.json"}}, {"family": "Cook", "given": "Charles E", "initials": "CE", "orcid": "0000-0002-4145-8048", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecc9ef8d51fc4157a3ec05a1b867b299.json"}}, {"family": "Petryszak", "given": "Robert", "initials": "R", "orcid": "0000-0001-6333-2182", "researcher": {"href": "https://publications.scilifelab.se/researcher/e28a71d259a848139d6f78b8d3d084bc.json"}}, {"family": "Baillie-Gerritsen", "given": "Vivienne", "initials": "V", "orcid": "0000-0003-3759-9494", "researcher": {"href": "https://publications.scilifelab.se/researcher/8741677b9d3345f98bcccb55f7a9113b.json"}}, {"family": "Barlow", "given": "Mary", "initials": "M", "orcid": "0000-0003-3072-6972", "researcher": {"href": "https://publications.scilifelab.se/researcher/80530fb41f3d4e918cee1d2d4bc9cb22.json"}}, {"family": "Gasteiger", "given": "Elisabeth", "initials": "E", "orcid": "0000-0003-1829-162X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1868e360a5d64ef28128abb2bb505fe0.json"}}, {"family": "Gruhl", "given": "Franziska", "initials": "F", "orcid": "0000-0002-2613-7211", "researcher": {"href": "https://publications.scilifelab.se/researcher/d962777efcff4e71a54715350e7e6b32.json"}}, {"family": "Haas", "given": "J\u00fcrgen", "initials": "J", "orcid": "0000-0002-3255-7773", "researcher": {"href": "https://publications.scilifelab.se/researcher/2df0a1f228cc4f75948d69e2071c6d53.json"}}, {"family": "Lanfear", "given": "Jerry", "initials": "J", "orcid": "0000-0002-8007-5568", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fbbf24c85954f5c9a30c462324b5879.json"}}, {"family": "Lopez", "given": "Rodrigo", "initials": "R", "orcid": "0000-0003-1256-7306", "researcher": {"href": "https://publications.scilifelab.se/researcher/812bdcf43316497fa12c464c9144bf21.json"}}, {"family": "Redaschi", "given": "Nicole", "initials": "N", "orcid": "0000-0001-8890-2268", "researcher": {"href": "https://publications.scilifelab.se/researcher/1014fb1d54b74e83ad65bab619cd472c.json"}}, {"family": "Stockinger", "given": "Heinz", "initials": "H", "orcid": "0000-0003-4666-7719", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e85405298241c09fc5c4ea2d4858c0.json"}}, {"family": "Teixeira", "given": "Daniel", "initials": "D", "orcid": "0000-0003-2110-4725", "researcher": {"href": "https://publications.scilifelab.se/researcher/2af9d42eb6894cda9078f239f062ebd6.json"}}, {"family": "Venkatesan", "given": "Aravind", "initials": "A", "orcid": "0000-0003-4019-1940", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb91f1527afa492c99fbbe75e9579a8a.json"}}, {"family": "Elixir Core Data Resource Forum", "given": "", "initials": ""}, {"family": "Blomberg", "given": "Niklas", "initials": "N", "orcid": "0000-0003-4155-5910", "researcher": {"href": "https://publications.scilifelab.se/researcher/d559b48215aa4a198d9613b0128e8eb4.json"}}, {"family": "Durinx", "given": "Christine", "initials": "C", "orcid": "0000-0003-4237-8899", "researcher": {"href": "https://publications.scilifelab.se/researcher/9691f63a3ac94222914f6e4df747c591.json"}}, {"family": "McEntyre", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1611-6935", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ccdaedf5c884aea8d4b8d99a9caf67f.json"}}], "type": "journal article", "published": "2020-04-15", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "issn-l": "1367-4803", "volume": "36", "issue": "8", "pages": "2636-2642"}, "abstract": "Supplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btz959", "pmid": "31950984", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5709034"}, {"db": "pmc", "key": "PMC7446027"}], "notes": [], "created": "2020-01-09T14:47:16.425Z", "modified": "2021-11-10T12:52:02.149Z"}, {"entity": "publication", "iuid": "db1ed54638e64638ab235cfb62758387", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db1ed54638e64638ab235cfb62758387.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db1ed54638e64638ab235cfb62758387"}}, "title": "Draft Genome Sequence of the Urinary Catheter Isolate Enterobacter ludwigii CEB04 with High Biofilm Forming Capacity.", "authors": [{"family": "Shafeeq", "given": "Sulman", "initials": "S"}, {"family": "Wang", "given": "Xiaoda", "initials": "X", "orcid": "0000-0003-0175-435X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a7de54a021a47f09821f26fb4ee2f4e.json"}}, {"family": "L\u00fcnsdorf", "given": "Heinrich", "initials": "H"}, {"family": "Brauner", "given": "Annelie", "initials": "A"}, {"family": "R\u00f6mling", "given": "Ute", "initials": "U", "orcid": "0000-0003-3812-6621", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a59ac735d61485aa43ee7a2ae3a526d.json"}}], "type": "journal article", "published": "2020-04-05", "journal": {"volume": "8", "issn": "2076-2607", "issue": "4", "title": "Microorganisms", "pages": "522", "issn-l": "2076-2607"}, "abstract": ": Enterobacter ludwigii is a fermentative Gram-negative environmental species and accidental human pathogen that belongs to the Enterobacter cloacae complex with the general characteristics of the genus Enterobacter. The clinical isolate E. ludwigii CEB04 was derived from a urinary tract catheter of an individual not suffering from catheter-associated urinary tract infection. The draft genome sequence of the high biofilm forming E. ludwigii CEB04 was determined by PacBio sequencing. The chromosome of E. ludwigii CEB04 is comprised of one contig of 4,892,375 bps containing 4596 predicted protein-coding genes and 120 noncoding RNAs. E. ludwigii CEB04 harbors several antimicrobial resistance markers and has an extended cyclic-di-GMP signaling network compared to Escherichia coli K-12.", "doi": "10.3390/microorganisms8040522", "pmid": "32260576", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7232144"}, {"db": "pii", "key": "microorganisms8040522"}], "notes": [], "created": "2020-05-04T14:34:04.659Z", "modified": "2024-01-16T13:48:42.641Z"}, {"entity": "publication", "iuid": "3be06852b34541608682142085a5994e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3be06852b34541608682142085a5994e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3be06852b34541608682142085a5994e"}}, "title": "Guidelines for curriculum and course development in higher education and training", "authors": [{"family": "Tractenberg", "given": "Rochelle E", "initials": "RE", "orcid": "0000-0002-1121-2119", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3f723902e7a4dda832e618662b86c4a.json"}}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Attwood", "given": "Teresa", "initials": "T", "orcid": "0000-0003-2409-4235", "researcher": {"href": "https://publications.scilifelab.se/researcher/25b583b3e23e42418781542fb1e1ce63.json"}}, {"family": "Via", "given": "Allegra", "initials": "A"}], "type": "posted-content", "published": "2020-04-03", "journal": {"title": "OSF", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.31235/osf.io/7qeht", "pmid": null, "labels": {"Bioinformatics Support and Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2020-12-15T09:14:26.722Z", "modified": "2025-12-18T20:06:37.352Z"}, {"entity": "publication", "iuid": "c83707e3be244e97b835f054f03476c1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c83707e3be244e97b835f054f03476c1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c83707e3be244e97b835f054f03476c1"}}, "title": "Genes and variants in hematopoiesis-related pathways are associated with gemcitabine/carboplatin-induced thrombocytopenia.", "authors": [{"family": "Bj\u00f6rn", "given": "Niclas", "initials": "N", "orcid": "0000-0001-6806-4527", "researcher": {"href": "https://publications.scilifelab.se/researcher/a39cecc1714f4331b08a47f1f1bbe7ac.json"}}, {"family": "Sigurgeirsson", "given": "Benjam\u00edn", "initials": "B"}, {"family": "Svedberg", "given": "Anna", "initials": "A"}, {"family": "Pradhananga", "given": "Sailendra", "initials": "S", "orcid": "0000-0002-0834-3169", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1917cb059924a779ac38e3023778461.json"}}, {"family": "Brand\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Koyi", "given": "Hirsh", "initials": "H", "orcid": "0000-0001-5797-7873", "researcher": {"href": "https://publications.scilifelab.se/researcher/020d1b7e7693495484dc85c4ba6f2adc.json"}}, {"family": "Lewensohn", "given": "Rolf", "initials": "R"}, {"family": "de Petris", "given": "Luigi", "initials": "L"}, {"family": "Apell\u00e1niz-Ruiz", "given": "Maria", "initials": "M"}, {"family": "Rodr\u00edguez-Antona", "given": "Cristina", "initials": "C"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Gr\u00e9en", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2020-04-00", "journal": {"volume": "20", "issn": "1473-1150", "issue": "2", "title": "Pharmacogenomics J.", "pages": "179-191", "issn-l": "1470-269X"}, "abstract": "Chemotherapy-induced myelosuppression, including thrombocytopenia, is a recurrent problem during cancer treatments that may require dose alterations or cessations that could affect the antitumor effect of the treatment. To identify genetic markers associated with treatment-induced thrombocytopenia, we whole-exome sequenced 215 non-small cell lung cancer patients homogeneously treated with gemcitabine/carboplatin. The decrease in platelets (defined as nadir/baseline) was used to assess treatment-induced thrombocytopenia. Association between germline genetic variants and thrombocytopenia was analyzed at single-nucleotide variant (SNV) (based on the optimal false discovery rate, the severity of predicted consequence, and effect), gene, and pathway levels. These analyses identified 130 SNVs/INDELs and 25 genes associated with thrombocytopenia (P-value < 0.002). Twenty-three SNVs were validated in an independent genome-wide association study (GWAS). The top associations include rs34491125 in JMJD1C (P-value = 9.07 \u00d7 10-5), the validated variants rs10491684 in DOCK8 (P-value = 1.95 \u00d7 10-4), rs6118 in SERPINA5 (P-value = 5.83 \u00d7 10-4), and rs5877 in SERPINC1 (P-value = 1.07 \u00d7 10-3), and the genes CAPZA2 (P-value = 4.03 \u00d7 10-4) and SERPINC1 (P-value = 1.55 \u00d7 10-3). The SNVs in the top-scoring pathway \"Factors involved in megakaryocyte development and platelet production\" (P-value = 3.34 \u00d7 10-4) were used to construct weighted genetic risk score (wGRS) and logistic regression models that predict thrombocytopenia. The wGRS predict which patients are at high or low toxicity risk levels, for CTCAE (odds ratio (OR) = 22.35, P-value = 1.55 \u00d7 10-8), and decrease (OR = 66.82, P-value = 5.92 \u00d7 10-9). The logistic regression models predict CTCAE grades 3-4 (receiver operator characteristics (ROC) area under the curve (AUC) = 0.79), and large decrease (ROC AUC = 0.86). We identified and validated genetic variations within hematopoiesis-related pathways that provide a solid foundation for future studies using genetic markers for predicting chemotherapy-induced thrombocytopenia and personalizing treatments.", "doi": "10.1038/s41397-019-0099-8", "pmid": "31616045", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41397-019-0099-8"}], "notes": [], "created": "2019-12-02T16:50:30.268Z", "modified": "2021-11-10T12:52:36.985Z"}, {"entity": "publication", "iuid": "64b8dd1c84934112a999fca1e18e8ac2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64b8dd1c84934112a999fca1e18e8ac2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64b8dd1c84934112a999fca1e18e8ac2"}}, "title": "Specific functions for Mediator complex subunits from different modules in the transcriptional response of Arabidopsis thaliana to abiotic stress.", "authors": [{"family": "Crawford", "given": "Tim", "initials": "T"}, {"family": "Karamat", "given": "Fazeelat", "initials": "F"}, {"family": "Lehotai", "given": "N\u00f3ra", "initials": "N"}, {"family": "Rentoft", "given": "Matilda", "initials": "M"}, {"family": "Blomberg", "given": "Jeanette", "initials": "J"}, {"family": "Strand", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Bj\u00f6rklund", "given": "Stefan", "initials": "S"}], "type": "journal article", "published": "2020-03-19", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "5073", "issn-l": "2045-2322"}, "abstract": "Adverse environmental conditions are detrimental to plant growth and development. Acclimation to abiotic stress conditions involves activation of signaling pathways which often results in changes in gene expression via networks of transcription factors (TFs). Mediator is a highly conserved co-regulator complex and an essential component of the transcriptional machinery in eukaryotes. Some Mediator subunits have been implicated in stress-responsive signaling pathways; however, much remains unknown regarding the role of plant Mediator in abiotic stress responses. Here, we use RNA-seq to analyze the transcriptional response of Arabidopsis thaliana to heat, cold and salt stress conditions. We identify a set of common abiotic stress regulons and describe the sequential and combinatorial nature of TFs involved in their transcriptional regulation. Furthermore, we identify stress-specific roles for the Mediator subunits MED9, MED16, MED18 and CDK8, and putative TFs connecting them to different stress signaling pathways. Our data also indicate different modes of action for subunits or modules of Mediator at the same gene loci, including a co-repressor function for MED16 prior to stress. These results illuminate a poorly understood but important player in the transcriptional response of plants to abiotic stress and identify target genes and mechanisms as a prelude to further biochemical characterization.", "doi": "10.1038/s41598-020-61758-w", "pmid": "32193425", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-61758-w"}, {"db": "pmc", "key": "PMC7081235"}], "notes": [], "created": "2021-07-02T06:44:54.540Z", "modified": "2021-11-10T12:52:58.039Z"}, {"entity": "publication", "iuid": "f89fbf236c224156aa48e89c92a6a48f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f89fbf236c224156aa48e89c92a6a48f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f89fbf236c224156aa48e89c92a6a48f"}}, "title": "Footprints of natural selection at the mannose-6-phosphate isomerase locus in barnacles.", "authors": [{"family": "Nunez", "given": "Joaquin C B", "initials": "JCB", "orcid": "0000-0002-3171-8918", "researcher": {"href": "https://publications.scilifelab.se/researcher/17eb1fe919d7471ebd0892307c72bea4.json"}}, {"family": "Flight", "given": "Patrick A", "initials": "PA"}, {"family": "Neil", "given": "Kimberly B", "initials": "KB"}, {"family": "Rong", "given": "Stephen", "initials": "S", "orcid": "0000-0002-6584-1391", "researcher": {"href": "https://publications.scilifelab.se/researcher/3944f25fb7a04a9b970260754505a28f.json"}}, {"family": "Eriksson", "given": "Leif A", "initials": "LA", "orcid": "0000-0001-5654-3109", "researcher": {"href": "https://publications.scilifelab.se/researcher/53b168b3ab17495783f874c427edd0c3.json"}}, {"family": "Ferranti", "given": "David A", "initials": "DA"}, {"family": "Rosenblad", "given": "Magnus Alm", "initials": "MA"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}, {"family": "Rand", "given": "David M", "initials": "DM", "orcid": "0000-0001-6817-3459", "researcher": {"href": "https://publications.scilifelab.se/researcher/668b164c47974d5d8f733551d4d2dc2f.json"}}], "type": "journal article", "published": "2020-03-10", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "117", "issue": "10", "pages": "5376-5385", "issn-l": "0027-8424"}, "abstract": "The mannose-6-phosphate isomerase (Mpi) locus in Semibalanus balanoides has been studied as a candidate gene for balancing selection for more than two decades. Previous work has shown that Mpi allozyme genotypes (fast and slow) have different frequencies across Atlantic intertidal zones due to selection on postsettlement survival (i.e., allele zonation). We present the complete gene sequence of the Mpi locus and quantify nucleotide polymorphism in S. balanoides, as well as divergence to its sister taxon Semibalanus cariosus We show that the slow allozyme contains a derived charge-altering amino acid polymorphism, and both allozyme classes correspond to two haplogroups with multiple internal haplotypes. The locus shows several footprints of balancing selection around the fast/slow site: an enrichment of positive Tajima's D for nonsynonymous mutations, an excess of polymorphism, and a spike in the levels of silent polymorphism relative to silent divergence, as well as a site frequency spectrum enriched for midfrequency mutations. We observe other departures from neutrality across the locus in both coding and noncoding regions. These include a nonsynonymous trans-species polymorphism and a recent mutation under selection within the fast haplogroup. The latter suggests ongoing allelic replacement of functionally relevant amino acid variants. Moreover, predicted models of Mpi protein structure provide insight into the functional significance of the putatively selected amino acid polymorphisms. While footprints of selection are widespread across the range of S. balanoides, our data show that intertidal zonation patterns are variable across both spatial and temporal scales. These data provide further evidence for heterogeneous selection on Mpi.", "doi": "10.1073/pnas.1918232117", "pmid": "32098846", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "1918232117"}, {"db": "pmc", "key": "PMC7071928"}, {"db": "GENBANK", "key": "MK955540"}, {"db": "GENBANK", "key": "MK955547"}, {"db": "GENBANK", "key": "MK955548"}, {"db": "GENBANK", "key": "MK955609"}, {"db": "GENBANK", "key": "MK955610"}, {"db": "GENBANK", "key": "MK955671"}, {"db": "GENBANK", "key": "MK953001"}, {"db": "GENBANK", "key": "MK953005"}], "notes": [], "created": "2020-02-27T12:43:12.731Z", "modified": "2024-01-16T13:48:42.795Z"}, {"entity": "publication", "iuid": "2327daa01a69409ebeaa040fe7f5fbd3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2327daa01a69409ebeaa040fe7f5fbd3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2327daa01a69409ebeaa040fe7f5fbd3"}}, "title": "Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants.", "authors": [{"family": "Garcia", "given": "Maxime", "initials": "M", "orcid": "0000-0003-2827-9261", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cf9b1b223f04296adcb6bd091c548de.json"}}, {"family": "Juhos", "given": "Szilveszter", "initials": "S"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Olason", "given": "Pall I", "initials": "PI"}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "DiLorenzo", "given": "Sebastian", "initials": "S"}, {"family": "Sandgren", "given": "Johanna", "initials": "J"}, {"family": "D\u00edaz De St\u00e5hl", "given": "Teresita", "initials": "T"}, {"family": "Ewels", "given": "Philip", "initials": "P", "orcid": "0000-0003-4101-2502", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d0fd82fe18b41539a761c55075f31d6.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M", "orcid": "0000-0002-1261-3790", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1dc80e61f574293a190f2f3ef464988.json"}}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}], "type": "journal article", "published": "2020-01-29", "journal": {"volume": "9", "issn": "2046-1402", "issue": null, "pages": "63", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": "Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and user-friendly workflows for WGS analyses poses a major challenge for many research groups and hampers scientific progress. Here we present Sarek, an open-source workflow to detect germline variants and somatic mutations based on sequencing data from WGS, whole-exome sequencing (WES), or gene panels. Sarek features (i) easy installation, (ii) robust portability across different computer environments, (iii) comprehensive documentation, (iv) transparent and easy-to-read code, and (v) extensive quality metrics reporting. Sarek is implemented in the Nextflow workflow language and supports both Docker and Singularity containers as well as Conda environments, making it ideal for easy deployment on any POSIX-compatible computers and cloud compute environments. Sarek follows the GATK best-practice recommendations for read alignment and pre-processing, and includes a wide range of software for the identification and annotation of germline and somatic single-nucleotide variants, insertion and deletion variants, structural variants, tumour sample purity, and variations in ploidy and copy number. Sarek offers easy, efficient, and reproducible WGS analyses, and can readily be used both as a production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups. The Sarek source code, documentation and installation instructions are freely available at https://github.com/nf-core/sarek and at https://nf-co.re/sarek/.", "doi": "10.12688/f1000research.16665.2", "pmid": "32269765", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Long-term Support WABI": "Technology development", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Clinical Genomics Stockholm": "Collaborative", "Bioinformatics Support and Infrastructure": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Technology development", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7111497"}], "notes": [], "created": "2020-04-23T08:58:58.026Z", "modified": "2024-01-16T13:48:43.022Z"}, {"entity": "publication", "iuid": "760bf7172ce74b69be827d62680c875a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/760bf7172ce74b69be827d62680c875a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/760bf7172ce74b69be827d62680c875a"}}, "title": "The round goby genome provides insights into mechanisms that may facilitate biological invasions.", "authors": [{"family": "Adrian-Kalchhauser", "given": "Irene", "initials": "I", "orcid": "0000-0002-7563-2577", "researcher": {"href": "https://publications.scilifelab.se/researcher/a81e38f709b54ce48c1381c9bf94c360.json"}}, {"family": "Blomberg", "given": "Anders", "initials": "A"}, {"family": "Larsson", "given": "Tomas", "initials": "T"}, {"family": "Musilova", "given": "Zuzana", "initials": "Z"}, {"family": "Peart", "given": "Claire R", "initials": "CR"}, {"family": "Pippel", "given": "Martin", "initials": "M"}, {"family": "Solbakken", "given": "Monica Hongroe", "initials": "MH"}, {"family": "Suurv\u00e4li", "given": "Jaanus", "initials": "J"}, {"family": "Walser", "given": "Jean-Claude", "initials": "J"}, {"family": "Wilson", "given": "Joanna Yvonne", "initials": "JY"}, {"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "Burguera", "given": "Demian", "initials": "D"}, {"family": "Gutnik", "given": "Silvia", "initials": "S"}, {"family": "Michiels", "given": "Nico", "initials": "N"}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "Pankov", "given": "Kirill", "initials": "K"}, {"family": "Schloissnig", "given": "Siegfried", "initials": "S"}, {"family": "Winkler", "given": "Sylke", "initials": "S"}], "type": "journal article", "published": "2020-01-28", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "issn-l": "1741-7007", "volume": "18", "issue": "1", "pages": "11"}, "abstract": "The invasive benthic round goby (Neogobius melanostomus) is the most successful temperate invasive fish and has spread in aquatic ecosystems on both sides of the Atlantic. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales and present promising case studies to understand factors involved the impressive ability of some species to colonize novel environments. We seize the unique opportunity presented by the round goby invasion to study genomic substrates potentially involved in colonization success.\r\n\r\nWe report a highly contiguous long-read-based genome and analyze gene families that we hypothesize to relate to the ability of these fish to deal with novel environments. The analyses provide novel insights from the large evolutionary scale to the small species-specific scale. We describe expansions in specific cytochrome P450 enzymes, a remarkably diverse innate immune system, an ancient duplication in red light vision accompanied by red skin fluorescence, evolutionary patterns of epigenetic regulators, and the presence of osmoregulatory genes that may have contributed to the round goby's capacity to invade cold and salty waters. A recurring theme across all analyzed gene families is gene expansions.\r\n\r\nThe expanded innate immune system of round goby may potentially contribute to its ability to colonize novel areas. Since other gene families also feature copy number expansions in the round goby, and since other Gobiidae also feature fascinating environmental adaptations and are excellent colonizers, further long-read genome approaches across the goby family may reveal whether gene copy number expansions are more generally related to the ability to conquer new habitats in Gobiidae or in fish.", "doi": "10.1186/s12915-019-0731-8", "pmid": "31992286", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12915-019-0731-8"}, {"db": "pmc", "key": "PMC6988351"}], "notes": [], "created": "2021-12-14T13:57:05.426Z", "modified": "2024-01-16T13:48:43.029Z"}, {"entity": "publication", "iuid": "796149f9eb4f4e3980d73a2969461850", "links": {"self": {"href": "https://publications.scilifelab.se/publication/796149f9eb4f4e3980d73a2969461850.json"}, "display": {"href": "https://publications.scilifelab.se/publication/796149f9eb4f4e3980d73a2969461850"}}, "title": "Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei.", "authors": [{"family": "Montoliu-Nerin", "given": "Merce", "initials": "M", "orcid": "0000-0002-5200-0411", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f89e94a04c6429db7e706b4d8d6626a.json"}}, {"family": "S\u00e1nchez-Garc\u00eda", "given": "Marisol", "initials": "M", "orcid": "0000-0002-0635-6281", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ccb3584fa144e178750ff2fc4666cfe.json"}}, {"family": "Bergin", "given": "Claudia", "initials": "C"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Ellis", "given": "Barbara", "initials": "B"}, {"family": "Kutschera", "given": "Verena Esther", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "Kierczak", "given": "Marcin", "initials": "M"}, {"family": "Johannesson", "given": "Hanna", "initials": "H"}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}}], "type": "journal article", "published": "2020-01-28", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "1303"}, "abstract": "The advent of novel sequencing techniques has unraveled a tremendous diversity on Earth. Genomic data allow us to understand ecology and function of organisms that we would not otherwise know existed. However, major methodological challenges remain, in particular for multicellular organisms with large genomes. Arbuscular mycorrhizal (AM) fungi are important plant symbionts with cryptic and complex multicellular life cycles, thus representing a suitable model system for method development. Here, we report a novel method for large scale, unbiased nuclear sorting, sequencing, and de novo assembling of AM fungal genomes. After comparative analyses of three assembly workflows we discuss how sequence data from single nuclei can best be used for different downstream analyses such as phylogenomics and comparative genomics of single nuclei. Based on analysis of completeness, we conclude that comprehensive de novo genome assemblies can be produced from six to seven nuclei. The method is highly applicable for a broad range of taxa, and will greatly improve our ability to study multicellular eukaryotes with complex life cycles.", "doi": "10.1038/s41598-020-58025-3", "pmid": "31992756", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Microbial Single Cell Genomics": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-58025-3"}, {"db": "pmc", "key": "PMC6987183"}], "notes": [], "created": "2020-02-03T10:35:42.153Z", "modified": "2024-01-16T13:48:43.036Z"}, {"entity": "publication", "iuid": "2fbb3c01bdfc42fcb76d81c03118c91a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2fbb3c01bdfc42fcb76d81c03118c91a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2fbb3c01bdfc42fcb76d81c03118c91a"}}, "title": "Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity.", "authors": [{"family": "Pillon", "given": "Nicolas J", "initials": "NJ", "orcid": "0000-0003-1107-9490", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b917d3e521149ec9d695c62ac2d1b85.json"}}, {"family": "Gabriel", "given": "Brendan M", "initials": "BM", "orcid": "0000-0001-6878-8779", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fa7198e43f648b5ab2da4d43f71962d.json"}}, {"family": "Dollet", "given": "Lucile", "initials": "L"}, {"family": "Smith", "given": "Jonathon A B", "initials": "JAB", "orcid": "0000-0003-2452-1655", "researcher": {"href": "https://publications.scilifelab.se/researcher/bffd42f562b3485fb50090c02aceeaef.json"}}, {"family": "Sard\u00f3n Puig", "given": "Laura", "initials": "L", "orcid": "0000-0002-0481-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/73c9841603dc43edae07c7e606776225.json"}}, {"family": "Botella", "given": "Javier", "initials": "J", "orcid": "0000-0001-9722-8519", "researcher": {"href": "https://publications.scilifelab.se/researcher/199f6b058cb342b391566273dc4faf78.json"}}, {"family": "Bishop", "given": "David J", "initials": "DJ", "orcid": "0000-0002-6956-9188", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecaa5fe4ab9649c8a90ae1fed84a222e.json"}}, {"family": "Krook", "given": "Anna", "initials": "A", "orcid": "0000-0002-0891-0258", "researcher": {"href": "https://publications.scilifelab.se/researcher/f43339bcd571486b845a3b10e241bcc4.json"}}, {"family": "Zierath", "given": "Juleen R", "initials": "JR", "orcid": "0000-0001-6891-7497", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4ef2b94ba2d44dd9b41192567a7af53.json"}}], "type": "journal article", "published": "2020-01-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "470"}, "abstract": "The molecular mechanisms underlying the response to exercise and inactivity are not fully understood. We propose an innovative approach to profile the skeletal muscle transcriptome to exercise and inactivity using 66 published datasets. Data collected from human studies of aerobic and resistance exercise, including acute and chronic exercise training, were integrated using meta-analysis methods (www.metamex.eu). Here we use gene ontology and pathway analyses to reveal selective pathways activated by inactivity, aerobic versus resistance and acute versus chronic exercise training. We identify NR4A3 as one of the most exercise- and inactivity-responsive genes, and establish a role for this nuclear receptor in mediating the metabolic responses to exercise-like stimuli in vitro. The meta-analysis (MetaMEx) also highlights the differential response to exercise in individuals with metabolic impairments. MetaMEx provides the most extensive dataset of skeletal muscle transcriptional responses to different modes of exercise and an online interface to readily interrogate the database.", "doi": "10.1038/s41467-019-13869-w", "pmid": "31980607", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-13869-w"}, {"db": "pmc", "key": "PMC6981202"}], "notes": [], "created": "2020-01-07T15:03:10.909Z", "modified": "2021-11-10T12:54:37.387Z"}, {"entity": "publication", "iuid": "798d0c199a87482abd2a408a2148a1ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/798d0c199a87482abd2a408a2148a1ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/798d0c199a87482abd2a408a2148a1ac"}}, "title": "A spontaneous mitonuclear epistasis converging on Rieske Fe-S protein exacerbates complex III deficiency in mice.", "authors": [{"family": "Purhonen", "given": "Janne", "initials": "J"}, {"family": "Grigorjev", "given": "Vladislav", "initials": "V"}, {"family": "Ekiert", "given": "Robert", "initials": "R", "orcid": "0000-0002-8879-0646", "researcher": {"href": "https://publications.scilifelab.se/researcher/18f5478e3272434f8e04014a4da545b5.json"}}, {"family": "Aho", "given": "Noora", "initials": "N"}, {"family": "Rajendran", "given": "Jayasimman", "initials": "J", "orcid": "0000-0003-3487-8260", "researcher": {"href": "https://publications.scilifelab.se/researcher/92dfb99f063c475086ad84783ab34716.json"}}, {"family": "Pietras", "given": "Rafa\u0142", "initials": "R", "orcid": "0000-0001-8424-6590", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f9c7e05c9284550ad49f0cc9237ad45.json"}}, {"family": "Truv\u00e9", "given": "Katarina", "initials": "K", "orcid": "0000-0002-2449-8283", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c36d2ff5111435aa23416cdfc359b2d.json"}}, {"family": "Wikstr\u00f6m", "given": "M\u00e5rten", "initials": "M", "orcid": "0000-0002-7527-4415", "researcher": {"href": "https://publications.scilifelab.se/researcher/66d471fc1c914756ac37da41bb759da4.json"}}, {"family": "Sharma", "given": "Vivek", "initials": "V"}, {"family": "Osyczka", "given": "Artur", "initials": "A"}, {"family": "Fellman", "given": "Vineta", "initials": "V", "orcid": "0000-0002-1355-5633", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c2179b7025441f688426ab24abd390e.json"}}, {"family": "Kallij\u00e4rvi", "given": "Jukka", "initials": "J", "orcid": "0000-0003-3773-7025", "researcher": {"href": "https://publications.scilifelab.se/researcher/c592c2565d4f42efb54b3e6016968ddf.json"}}], "type": "journal article", "published": "2020-01-16", "journal": {"volume": "11", "issn": "2041-1723", "issue": "1", "pages": "322", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "We previously observed an unexpected fivefold (35 vs. 200 days) difference in the survival of respiratory chain complex III (CIII) deficient Bcs1lp.S78G mice between two congenic backgrounds. Here, we identify a spontaneous homoplasmic mtDNA variant (m.G14904A, mt-Cybp.D254N), affecting the CIII subunit cytochrome b (MT-CYB), in the background with short survival. We utilize maternal inheritance of mtDNA to confirm this as the causative variant and show that it further decreases the low CIII activity in Bcs1lp.S78G tissues to below survival threshold by 35 days of age. Molecular dynamics simulations predict D254N to restrict the flexibility of MT-CYB ef loop, potentially affecting RISP dynamics. In Rhodobacter cytochrome bc1 complex the equivalent substitution causes a kinetics defect with longer occupancy of RISP head domain towards the quinol oxidation site. These findings represent a unique case of spontaneous mitonuclear epistasis and highlight the role of mtDNA variation as modifier of mitochondrial disease phenotypes.", "doi": "10.1038/s41467-019-14201-2", "pmid": "31949167", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-14201-2"}, {"db": "pmc", "key": "PMC6965120"}], "notes": [], "created": "2020-02-03T09:00:33.293Z", "modified": "2021-11-10T12:44:51.374Z"}, {"entity": "publication", "iuid": "72a503969cf644bfb111a0651557793a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72a503969cf644bfb111a0651557793a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72a503969cf644bfb111a0651557793a"}}, "title": "Whole genome sequencing of apparently mutation-negative MEN1 patients.", "authors": [{"family": "Backman", "given": "Samuel", "initials": "S"}, {"family": "Bajic", "given": "Duska", "initials": "D"}, {"family": "Crona", "given": "Joakim", "initials": "J"}, {"family": "Hellman", "given": "Per", "initials": "P"}, {"family": "Skogseid", "given": "Britt", "initials": "B"}, {"family": "St\u00e5lberg", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2020-01-00", "journal": {"title": "Eur. J. Endocrinol.", "issn": "1479-683X", "issn-l": "0804-4643", "volume": "182", "issue": "1", "pages": "35-45"}, "abstract": "Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant syndrome usually caused by loss-of-function mutations in the MEN1 gene. However, a minority of patients who fulfill the criteria for MEN1 are not found to harbor MEN1 mutations. Besides, some of these individuals, present with a subtly different phenotype suggestive of sporadic disease. The aim of the present study was to investigate the genetic architecture of mutation-negative MEN1.\n\nFourteen patients with a clinical diagnosis (n = 13) or suspicion (n = 1) of MEN1 who had negative genetic screening of the MEN1 gene were included.\n\nConstitutional DNA from the included patients, as well as tumor DNA from six of the patients, was subjected to whole genome sequencing. Constitutional variants were filtered against population databases and somatic variants were studied under a tumor-suppressor model.\n\nThree patients carried pathogenic variants (two splice-site variants, one missense variant) in MEN1 that had not been detected during routine clinical sequencing, one patient carried a pathogenic variant in CASR and one patient carried a gross deletion on chromosome 1q which included the CDC73 gene. Analysis of matched tumor DNA from six patients without mutations did not detect any recurrent genes fulfilling Knudson's two-hit model.\n\nThese results highlight the possibility of germline mutations being missed in routine screening, the importance of considering phenocopies in atypical or mutation-negative cases. The absence of apparent disease-causing mutations suggests that a fraction of MEN1 mutation-negative MEN1 cases may be due to the chance occurrence of several endocrine tumors in one patient.", "doi": "10.1530/EJE-19-0522", "pmid": "31658439", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "EJE-19-0522"}], "notes": [], "created": "2020-01-08T14:27:31.627Z", "modified": "2024-01-16T13:48:43.114Z"}, {"entity": "publication", "iuid": "a7bc4b57504c4cc99ed928474b6819bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a7bc4b57504c4cc99ed928474b6819bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a7bc4b57504c4cc99ed928474b6819bc"}}, "title": "Gene transfer across species boundaries in bryophytes: evidence from major life cycle stages in Homalothecium lutescens and H. sericeum.", "authors": [{"family": "Sawangproh", "given": "W", "initials": "W"}, {"family": "Heden\u00e4s", "given": "L", "initials": "L"}, {"family": "Lang", "given": "A S", "initials": "AS"}, {"family": "Hansson", "given": "B", "initials": "B"}, {"family": "Cronberg", "given": "N", "initials": "N"}], "type": "journal article", "published": "2019-12-24", "journal": {"volume": null, "issn": "1095-8290", "issue": null, "pages": null, "title": "Ann. Bot.", "issn-l": "0305-7364"}, "abstract": "The mosses Homalothecium lutescens and H. sericeum are genetically, morphologically and ecologically differentiated, mixed populations sometimes occur. In sympatric populations, intermediate character states among gametophytes and sporophytes have been observed, suggesting hybridization and introgression in such populations.\r\n\r\nWe determined genotypes using bi-allelic co-dominant single nucleotide polymorphism (SNP) markers, specific to either H. lutescens or H. sericeum, to estimate the degree of genetic mixing in 449 moss samples collected from seven sympatric and five allopatric populations on the island of \u00d6land, south Sweden. The samples represented three generations: haploid maternal gametophytes, diploid sporophytes, and haploid sporelings.\r\n\r\nAdmixture analyses of SNP genotypes identified a majority as pure H. lutescens or H. sericeum, but 76 samples were identified as mildly admixed (17%) and 17 samples (3.8%) as strongly admixed. Admixed samples were represented in all three generations in several populations. Hybridization and introgression was bidirectional.\r\n\r\nOur results demonstrate that admixed genomes are transferred between the generations, so that the populations behave as true hybrid zones. Earlier studies of sympatric bryophyte populations with admixed individuals have not been able to show that admixed alleles are transferred beyond the first generation. The presence of true hybrid zones has strong evolutionary implications because genetic material transferred across species boundaries can be directly exposed to selection in the long-lived haploid generation of the bryophyte life cycle, and contribute to local adaptation, long-time survival and speciation.", "doi": "10.1093/aob/mcz209", "pmid": "31872857", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "5686322"}], "notes": [], "created": "2020-01-07T14:39:04.363Z", "modified": "2024-01-16T13:48:43.252Z"}, {"entity": "publication", "iuid": "edac35c02fd041b1b4e22d060da8ff14", "links": {"self": {"href": "https://publications.scilifelab.se/publication/edac35c02fd041b1b4e22d060da8ff14.json"}, "display": {"href": "https://publications.scilifelab.se/publication/edac35c02fd041b1b4e22d060da8ff14"}}, "title": "Gene Expression Alterations during Development of Castration-Resistant Prostate Cancer Are Detected in Circulating Tumor Cells.", "authors": [{"family": "Josefsson", "given": "Andreas", "initials": "A"}, {"family": "Larsson", "given": "Karin", "initials": "K"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Damber", "given": "Jan-Erik", "initials": "J"}, {"family": "Wel\u00e9n", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2019-12-21", "journal": {"volume": "12", "issn": "2072-6694", "issue": "1", "pages": null, "title": "Cancers (Basel)", "issn-l": "2072-6694"}, "abstract": "Development of castration-resistant prostate cancer (CRPC) is associated with alterations in gene expression involved in steroidogenesis and androgen signaling. This study investigates whether gene expression changes related to CRPC development can be identified in circulating tumor cells (CTCs). Gene expression in paired CTC samples from 29 patients, before androgen deprivation therapy (ADT) and at CRPC relapse, was compared using a panel including 47 genes related to prostate cancer progression on a qPCR platform. Fourteen genes displayed significantly changed gene expression in CTCs at CRPC relapse compared to before start of ADT. The genes with increased expression at CRPC relapse were related to steroidogenesis, AR-signaling, and anti-apoptosis. In contrast, expression of prostate markers was downregulated at CRPC. We also show that midkine (MDK) expression in CTCs from metastatic hormone-sensitive prostate cancer (mHSPC) was associated to short cancer-specific survival (CSS). In conclusion, this study shows that gene expression patterns in CTCs reflect the development of CRPC, and that MDK expression levels in CTCs are prognostic for cancer-specific survival in mHSPC. This study emphasizes the role of CTCs in exploring mechanisms of therapy resistance, as well as a promising biomarker for prognostic and treatment-predictive purposes in advanced mHSPC.", "doi": "10.3390/cancers12010039", "pmid": "31877738", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "cancers12010039"}], "notes": [], "created": "2020-01-07T08:53:35.031Z", "modified": "2020-12-10T16:19:41.750Z"}, {"entity": "publication", "iuid": "e29ecc8466d94f73ad0bcf63ff96f578", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e29ecc8466d94f73ad0bcf63ff96f578.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e29ecc8466d94f73ad0bcf63ff96f578"}}, "title": "Protein profiling and network enrichment analysis in individuals before and after the onset of rheumatoid arthritis.", "authors": [{"family": "Brink", "given": "Mikael", "initials": "M"}, {"family": "Lundquist", "given": "Anders", "initials": "A"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Lejon", "given": "Kristina", "initials": "K"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}], "type": "journal article", "published": "2019-12-16", "journal": {"title": "Arthritis Res. Ther.", "issn": "1478-6362", "issn-l": "1478-6354", "volume": "21", "issue": "1", "pages": "288"}, "abstract": "Antibodies and upregulated cytokines and chemokines predate the onset of rheumatoid arthritis (RA) symptoms. We aimed to identify the pathways related to the early processes leading to RA development, as well as potential novel biomarkers, using multiple protein analyses.\r\n\r\nA case-control study was conducted within the Biobank of northern Sweden. The plasma samples from 118 pre-symptomatic individuals (207 samples; median predating time 4.1 years), 79 early RA patients, and 74 matched controls were analyzed. The levels of 122 unique proteins with an acknowledged relationship to autoimmunity were analyzed using 153 antibodies and a bead-based multiplex system (FlexMap3D; Luminex Corp.). The data were analyzed using multifactorial linear regression model, random forest, and network enrichment analysis (NEA) based on the 10 most significantly differentially expressed proteins for each two-by-two group comparison, using the MSigDB collection of hallmarks.\r\n\r\nThere was a high agreement between the different statistical methods to identify the most significant proteins. The adipogenesis and interferon alpha response hallmarks differentiated pre-symptomatic individuals from controls. These two hallmarks included proteins involved in innate immunity. Between pre-symptomatic individuals and RA patients, three hallmarks were identified as follows: apical junction, epithelial mesenchymal transition, and TGF-\u03b2 signaling, including proteins suggestive of cell interaction, remodulation, and fibrosis. The adipogenesis and heme metabolism hallmarks differentiated RA patients from controls.\r\n\r\nWe confirm the importance of interferon alpha signaling and lipids in the early phases of RA development. Network enrichment analysis provides a tool for a deeper understanding of molecules involved at different phases of the disease progression.", "doi": "10.1186/s13075-019-2066-9", "pmid": "31842970", "labels": {"Affinity Proteomics Stockholm": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13075-019-2066-9"}, {"db": "pmc", "key": "PMC6915963"}], "notes": [], "created": "2020-01-08T10:20:42.874Z", "modified": "2021-08-10T13:59:15.507Z"}, {"entity": "publication", "iuid": "5e8d78fd132842c38fb5e1b379715f70", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e8d78fd132842c38fb5e1b379715f70.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e8d78fd132842c38fb5e1b379715f70"}}, "title": "iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture", "authors": [{"family": "Gelali", "given": "Eleni", "initials": "E"}, {"family": "Girelli", "given": "Gabriele", "initials": "G"}, {"family": "Matsumoto", "given": "Masahiro", "initials": "M"}, {"family": "Wernersson", "given": "Erik", "initials": "E"}, {"family": "Custodio", "given": "Joaquin", "initials": "J"}, {"family": "Mota", "given": "Ana", "initials": "A"}, {"family": "Schweitzer", "given": "Maud", "initials": "M"}, {"family": "Ferenc", "given": "Katalin", "initials": "K"}, {"family": "Li", "given": "Xinge", "initials": "X"}, {"family": "Mirzazadeh", "given": "Reza", "initials": "R"}, {"family": "Agostini", "given": "Federico", "initials": "F"}, {"family": "Schell", "given": "John P", "initials": "JP"}, {"family": "Lanner", "given": "Fredrik", "initials": "F"}, {"family": "Crosetto", "given": "Nicola", "initials": "N"}, {"family": "Bienko", "given": "Magda", "initials": "M"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "DNA fluorescence in situ hybridization (DNA FISH) is a powerful method to study chromosomal organization in single cells. At present, there is a lack of free resources of DNA FISH probes and probe design tools which can be readily applied. Here, we describe iFISH, an open-source repository currently comprising 380 DNA FISH probes targeting multiple loci on the human autosomes and chromosome X, as well as a genome-wide database of optimally designed oligonucleotides and a freely accessible web interface ( http://ifish4u.org ) that can be used to design DNA FISH probes. We individually validate 153 probes and take advantage of our probe repository to quantify the extent of intermingling between multiple heterologous chromosome pairs, showing a much higher extent of intermingling in human embryonic stem cells compared to fibroblasts. In conclusion, iFISH is a versatile and expandable resource, which can greatly facilitate the use of DNA FISH in research and diagnostics.", "doi": "10.1038/s41467-019-09616-w", "pmid": "30967549", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Advanced FISH Technologies": "Technology development", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-07T15:04:55.085Z", "modified": "2020-02-12T15:15:07.277Z"}, {"entity": "publication", "iuid": "1352e2277ea64042b7223339b4060434", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1352e2277ea64042b7223339b4060434.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1352e2277ea64042b7223339b4060434"}}, "title": "Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden", "authors": [{"family": "Alaridah", "given": "Nader", "initials": "N"}, {"family": "Hallb\u00e4ck", "given": "Erika T\u00e5ng", "initials": "ET"}, {"family": "T\u00e5ngrot", "given": "Jeanette", "initials": "J"}, {"family": "Winqvist", "given": "Niclas", "initials": "N"}, {"family": "Stureg\u00e5rd", "given": "Erik", "initials": "E"}, {"family": "Flor\u00e9n-Johansson", "given": "Kerstin", "initials": "K"}, {"family": "J\u00f6nsson", "given": "Bodil", "initials": "B"}, {"family": "Tenland", "given": "Erik", "initials": "E"}, {"family": "Welinder-Olsson", "given": "Christina", "initials": "C"}, {"family": "Medstrand", "given": "Patrik", "initials": "P"}, {"family": "Kaijser", "given": "Bertil", "initials": "B"}, {"family": "Godaly", "given": "Gabriela", "initials": "G"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Epidemiological contact tracing complemented with genotyping of clinical Mycobacterium tuberculosis isolates is important for understanding disease transmission. In Sweden, tuberculosis (TB) is mostly reported in migrant and homeless where epidemiologic contact tracing could pose a problem. This study compared epidemiologic linking with genotyping in a low burden country. Mycobacterium tuberculosis isolates (n = 93) collected at Scania University Hospital in Southern Sweden were analysed with the standard genotyping method mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR) and the results were compared with whole genome sequencing (WGS). Using a maximum of twelve single nucleotide polymorphisms (SNPs) as the upper threshold of genomic relatedness noted among hosts, we identified 18 clusters with WGS comprising 52 patients with overall pairwise genetic maximum distances ranging from zero to nine SNPs. MIRU-VNTR and WGS clustered the same isolates, although the distribution differed depending on MIRU-VNTR limitations. Both genotyping techniques identified clusters where epidemiologic linking was insufficient, although WGS had higher correlation with epidemiologic data. To summarize, WGS provided better resolution of transmission than MIRU-VNTR in a setting with low TB incidence. WGS predicted epidemiologic links better which could consolidate and correct the epidemiologically linked cases, avoiding thus false clustering.", "doi": "10.1038/s41598-019-39971-z", "pmid": "30894568", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2019-04-23T15:06:38.395Z", "modified": "2020-01-21T13:56:17.604Z"}, {"entity": "publication", "iuid": "f688346e12c14ec4bf96068a3bb2d1e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f688346e12c14ec4bf96068a3bb2d1e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f688346e12c14ec4bf96068a3bb2d1e9"}}, "title": "Towards a standardized bioinformatics infrastructure for N- and O-glycomics", "authors": [{"family": "Rojas-Macias", "given": "Miguel A", "initials": "MA"}, {"family": "Mariethoz", "given": "Julien", "initials": "J"}, {"family": "Andersson", "given": "Peter", "initials": "P"}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Venkatakrishnan", "given": "Vignesh", "initials": "V"}, {"family": "Aoki", "given": "Nobuyuki P", "initials": "NP"}, {"family": "Shinmachi", "given": "Daisuke", "initials": "D"}, {"family": "Ashwood", "given": "Christopher", "initials": "C"}, {"family": "Madunic", "given": "Katarina", "initials": "K"}, {"family": "Zhang", "given": "Tao", "initials": "T"}, {"family": "Miller", "given": "Rebecca L", "initials": "RL"}, {"family": "Horlacher", "given": "Oliver", "initials": "O"}, {"family": "Struwe", "given": "Weston B", "initials": "WB"}, {"family": "Watanabe", "given": "Yu", "initials": "Y"}, {"family": "Okuda", "given": "Shujiro", "initials": "S"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Kolarich", "given": "Daniel", "initials": "D"}, {"family": "Rudd", "given": "Pauline M", "initials": "PM"}, {"family": "Wuhrer", "given": "Manfred", "initials": "M"}, {"family": "Kettner", "given": "Carsten", "initials": "C"}, {"family": "Packer", "given": "Nicolle H", "initials": "NH"}, {"family": "Aoki-Kinoshita", "given": "Kiyoko F", "initials": "KF"}, {"family": "Lisacek", "given": "Fr\u00e9d\u00e9rique", "initials": "F"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The mass spectrometry (MS)-based analysis of free polysaccharides and glycans released from proteins, lipids and proteoglycans increasingly relies on databases and software. Here, we review progress in the bioinformatics analysis of protein-released N- and O-linked glycans (N- and O-glycomics) and propose an e-infrastructure to overcome current deficits in data and experimental transparency. This workflow enables the standardized submission of MS-based glycomics information into the public repository UniCarb-DR. It implements the MIRAGE (Minimum Requirement for A Glycomics Experiment) reporting guidelines, storage of unprocessed MS data in the GlycoPOST repository and glycan structure registration using the GlyTouCan registry, thereby supporting the development and extension of a glycan structure knowledgebase.", "doi": "10.1038/s41467-019-11131-x", "pmid": "31332201", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Support and Infrastructure": "Technology development", "Glycoproteomics and MS Proteomics": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [], "notes": [], "created": "2019-09-16T11:46:23.026Z", "modified": "2024-01-16T13:46:31.254Z"}, {"entity": "publication", "iuid": "ddddcada24bb4fd693b02a2124cff7ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ddddcada24bb4fd693b02a2124cff7ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ddddcada24bb4fd693b02a2124cff7ca"}}, "title": "The genomic footprint of sexual conflict.", "authors": [{"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Martinez Barrio", "given": "Alvaro", "initials": "A"}, {"family": "Immonen", "given": "Elina", "initials": "E"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Berger", "given": "David", "initials": "D"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2019-12-00", "journal": {"volume": "3", "issn": "2397-334X", "issue": "12", "pages": "1725-1730", "title": "Nat Ecol Evol", "issn-l": "2397-334X"}, "abstract": "Genes with sex-biased expression show a number of unique properties and this has been seen as evidence for conflicting selection pressures in males and females, forming a genetic 'tug-of-war' between the sexes. However, we lack studies of taxa where an understanding of conflicting phenotypic selection in the sexes has been linked with studies of genomic signatures of sexual conflict. Here, we provide such a link. We used an insect where sexual conflict is unusually well understood, the seed beetle Callosobruchus maculatus, to test for molecular genetic signals of sexual conflict across genes with varying degrees of sex-bias in expression. We sequenced, assembled and annotated its genome and performed population resequencing of three divergent populations. Sex-biased genes showed increased levels of genetic diversity and bore a remarkably clear footprint of relaxed purifying selection. Yet, segregating genetic variation was also affected by balancing selection in weakly female-biased genes, while male-biased genes showed signs of overall purifying selection. Female-biased genes contributed disproportionally to shared polymorphism across populations, while male-biased genes, male seminal fluid protein genes and sex-linked genes did not. Genes showing genomic signatures consistent with sexual conflict generally matched life-history phenotypes known to experience sexually antagonistic selection in this species. Our results highlight metabolic and reproductive processes, confirming the key role of general life-history traits in sexual conflict.", "doi": "10.1038/s41559-019-1041-9", "pmid": "31740847", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-019-1041-9"}], "notes": [], "created": "2019-12-05T15:30:07.525Z", "modified": "2024-01-16T13:48:43.388Z"}, {"entity": "publication", "iuid": "83ee56fd4ba64120ac6e621812b34c93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/83ee56fd4ba64120ac6e621812b34c93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/83ee56fd4ba64120ac6e621812b34c93"}}, "title": "The bio.tools registry of software tools and data resources for the life sciences", "authors": [{"family": "Ison", "given": "Jon", "initials": "J", "orcid": "0000-0001-6666-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/9890e9a29aa54f37bd860605f3eb311f.json"}}, {"family": "Ienasescu", "given": "Hans", "initials": "H"}, {"family": "Chmura", "given": "Piotr", "initials": "P"}, {"family": "Rydza", "given": "Emil", "initials": "E"}, {"family": "M\u00e9nager", "given": "Herv\u00e9", "initials": "H"}, {"family": "Kala\u0161", "given": "Mat\u00fa\u0161", "initials": "M"}, {"family": "Schw\u00e4mmle", "given": "Veit", "initials": "V"}, {"family": "Gr\u00fcning", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Beard", "given": "Niall", "initials": "N"}, {"family": "Lopez", "given": "Rodrigo", "initials": "R"}, {"family": "Duvaud", "given": "Severine", "initials": "S"}, {"family": "Stockinger", "given": "Heinz", "initials": "H"}, {"family": "Persson", "given": "Bengt", "initials": "B", "orcid": "0000-0003-3165-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f116ef0ed146419cb18e742c270c4a.json"}}, {"family": "Va\u0159ekov\u00e1", "given": "Radka Svobodov\u00e1", "initials": "RS"}, {"family": "Ra\u010dek", "given": "Tom\u00e1\u0161", "initials": "T"}, {"family": "Vondr\u00e1\u0161ek", "given": "Ji\u0159\u00ed", "initials": "J"}, {"family": "Peterson", "given": "Hedi", "initials": "H"}, {"family": "Salumets", "given": "Ahto", "initials": "A"}, {"family": "Jonassen", "given": "Inge", "initials": "I"}, {"family": "Hooft", "given": "Rob", "initials": "R"}, {"family": "Nyr\u00f6nen", "given": "Tommi", "initials": "T"}, {"family": "Valencia", "given": "Alfonso", "initials": "A"}, {"family": "Capella", "given": "Salvador", "initials": "S"}, {"family": "Gelp\u00ed", "given": "Josep", "initials": "J"}, {"family": "Zambelli", "given": "Federico", "initials": "F"}, {"family": "Savakis", "given": "Babis", "initials": "B"}, {"family": "Lesko\u0161ek", "given": "Brane", "initials": "B"}, {"family": "Rapacki", "given": "Kristoffer", "initials": "K"}, {"family": "Blanchet", "given": "Christophe", "initials": "C"}, {"family": "Jimenez", "given": "Rafael", "initials": "R"}, {"family": "Oliveira", "given": "Arlindo", "initials": "A"}, {"family": "Vriend", "given": "Gert", "initials": "G"}, {"family": "Collin", "given": "Olivier", "initials": "O"}, {"family": "van Helden", "given": "Jacques", "initials": "J"}, {"family": "L\u00f8ngreen", "given": "Peter", "initials": "P"}, {"family": "Brunak", "given": "S\u00f8ren", "initials": "S"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "20", "issn": "1474-760X", "issue": "1", "pages": "164", "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( https://bio.tools ) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information.", "doi": "10.1186/s13059-019-1772-6", "pmid": "31405382", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s13059-019-1772-6"}, {"db": "pmc", "key": "PMC6691543"}], "notes": [], "created": "2019-12-17T15:48:45.940Z", "modified": "2021-07-05T12:34:46.028Z"}, {"entity": "publication", "iuid": "e56ecaac952645ad8db0b5cd142519df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e56ecaac952645ad8db0b5cd142519df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e56ecaac952645ad8db0b5cd142519df"}}, "title": "Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats.", "authors": [{"family": "Dong", "given": "Yiran", "initials": "Y"}, {"family": "Sanford", "given": "Robert A", "initials": "RA"}, {"family": "Inskeep", "given": "William P", "initials": "WP"}, {"family": "Srivastava", "given": "Vaibhav", "initials": "V"}, {"family": "Bulone", "given": "Vincent", "initials": "V"}, {"family": "Fields", "given": "Christopher J", "initials": "CJ"}, {"family": "Yau", "given": "Peter M", "initials": "PM"}, {"family": "Sivaguru", "given": "Mayandi", "initials": "M"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Fouke", "given": "Kyle W", "initials": "KW"}, {"family": "Weber", "given": "Joseph", "initials": "J"}, {"family": "Werth", "given": "Charles R", "initials": "CR"}, {"family": "Cann", "given": "Isaac K", "initials": "IK"}, {"family": "Keating", "given": "Kathleen M", "initials": "KM"}, {"family": "Khetani", "given": "Radhika S", "initials": "RS"}, {"family": "Hernandez", "given": "Alvaro G", "initials": "AG"}, {"family": "Wright", "given": "Chris", "initials": "C"}, {"family": "Band", "given": "Mark", "initials": "M"}, {"family": "Imai", "given": "Brian S", "initials": "BS"}, {"family": "Fried", "given": "Glenn A", "initials": "GA"}, {"family": "Fouke", "given": "Bruce W", "initials": "BW"}], "type": "journal article", "published": "2019-12-00", "journal": {"volume": "19", "issn": "1557-8070", "issue": "12", "pages": "1442-1458", "title": "Astrobiology", "issn-l": null}, "abstract": "The evolutionarily ancient Aquificales bacterium Sulfurihydrogenibium spp. dominates filamentous microbial mat communities in shallow, fast-flowing, and dysoxic hot-spring drainage systems around the world. In the present study, field observations of these fettuccini-like microbial mats at Mammoth Hot Springs in Yellowstone National Park are integrated with geology, geochemistry, hydrology, microscopy, and multi-omic molecular biology analyses. Strategic sampling of living filamentous mats along with the hot-spring CaCO3 (travertine) in which they are actively being entombed and fossilized has permitted the first direct linkage of Sulfurihydrogenibium spp. physiology and metabolism with the formation of distinct travertine streamer microbial biomarkers. Results indicate that, during chemoautotrophy and CO2 carbon fixation, the 87-98% Sulfurihydrogenibium-dominated mats utilize chaperons to facilitate enzyme stability and function. High-abundance transcripts and proteins for type IV pili and extracellular polymeric substances (EPSs) are consistent with their strong mucus-rich filaments tens of centimeters long that withstand hydrodynamic shear as they become encrusted by more than 5 mm of travertine per day. Their primary energy source is the oxidation of reduced sulfur (e.g., sulfide, sulfur, or thiosulfate) and the simultaneous uptake of extremely low concentrations of dissolved O2 facilitated by bd-type cytochromes. The formation of elevated travertine ridges permits the Sulfurihydrogenibium-dominated mats to create a shallow platform from which to access low levels of dissolved oxygen at the virtual exclusion of other microorganisms. These ridged travertine streamer microbial biomarkers are well preserved and create a robust fossil record of microbial physiological and metabolic activities in modern and ancient hot-spring ecosystems.", "doi": "10.1089/ast.2018.1965", "pmid": "31038352", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC6918859"}], "notes": [], "created": "2020-01-07T09:58:02.203Z", "modified": "2021-06-16T14:39:56.670Z"}, {"entity": "publication", "iuid": "33556ef6872e4dd486f166f63ea70ca1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33556ef6872e4dd486f166f63ea70ca1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33556ef6872e4dd486f166f63ea70ca1"}}, "title": "The Mastery Rubric for Bioinformatics: A tool to support design and evaluation of career-spanning education and training.", "authors": [{"family": "Tractenberg", "given": "Rochelle E", "initials": "RE"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Attwood", "given": "Teresa K", "initials": "TK"}, {"family": "Via", "given": "Allegra", "initials": "A"}], "type": "journal article", "published": "2019-11-26", "journal": {"volume": "14", "issn": "1932-6203", "issue": "11", "pages": "e0225256", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "As the life sciences have become more data intensive, the pressure to incorporate the requisite training into life-science education and training programs has increased. To facilitate curriculum development, various sets of (bio)informatics competencies have been articulated; however, these have proved difficult to implement in practice. Addressing this issue, we have created a curriculum-design and -evaluation tool to support the development of specific Knowledge, Skills and Abilities (KSAs) that reflect the scientific method and promote both bioinformatics practice and the achievement of competencies. Twelve KSAs were extracted via formal analysis, and stages along a developmental trajectory, from uninitiated student to independent practitioner, were identified. Demonstration of each KSA by a performer at each stage was initially described (Performance Level Descriptors, PLDs), evaluated, and revised at an international workshop. This work was subsequently extended and further refined to yield the Mastery Rubric for Bioinformatics (MR-Bi). The MR-Bi was validated by demonstrating alignment between the KSAs and competencies, and its consistency with principles of adult learning. The MR-Bi tool provides a formal framework to support curriculum building, training, and self-directed learning. It prioritizes the development of independence and scientific reasoning, and is structured to allow individuals (regardless of career stage, disciplinary background, or skill level) to locate themselves within the framework. The KSAs and their PLDs promote scientific problem formulation and problem solving, lending the MR-Bi durability and flexibility. With its explicit developmental trajectory, the tool can be used by developing or practicing scientists to direct their (and their team's) acquisition of new, or to deepen existing, bioinformatics KSAs. The MR-Bi is a tool that can contribute to the cultivation of a next generation of bioinformaticians who are able to design reproducible and rigorous research, and to critically analyze results from their own, and others', work.", "doi": "10.1371/journal.pone.0225256", "pmid": "31770418", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Support and Infrastructure": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pii", "key": "PONE-D-19-15839"}, {"db": "pmc", "key": "PMC6879125"}], "notes": [], "created": "2019-12-11T15:10:53.689Z", "modified": "2021-07-05T12:48:15.971Z"}, {"entity": "publication", "iuid": "cf7bf4bafff647f7ab3501fe1e844770", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf7bf4bafff647f7ab3501fe1e844770.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf7bf4bafff647f7ab3501fe1e844770"}}, "title": "TcellSubC: An Atlas of the Subcellular Proteome of Human T Cells.", "authors": [{"family": "Joshi", "given": "Rubin Narayan", "initials": "RN"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Lehmann", "given": "Robert", "initials": "R"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Tegn\u00e9r", "given": "Jesper", "initials": "J"}, {"family": "Schmidt", "given": "Angelika", "initials": "A"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M"}], "type": "journal article", "published": "2019-11-26", "journal": {"volume": "10", "issn": "1664-3224", "issue": null, "pages": "2708", "title": "Front Immunol", "issn-l": "1664-3224"}, "abstract": "We have curated an in-depth subcellular proteomic map of primary human CD4+ T cells, divided into cytosolic, nuclear and membrane fractions generated by an optimized fractionation and HiRIEF-LC-MS/MS workflow for limited amounts of primary cells. The subcellular proteome of T cells was mapped under steady state conditions, as well as upon 15 min and 1 h of T cell receptor (TCR) stimulation, respectively. We quantified the subcellular distribution of 6,572 proteins and identified a subset of 237 potentially translocating proteins, including both well-known examples and novel ones. Microscopic validation confirmed the localization of selected proteins with previously known and unknown localization, respectively. We further provide the data in an easy-to-use web platform to facilitate re-use, as the data can be relevant for basic research as well as for clinical exploitation of T cells as therapeutic targets.", "doi": "10.3389/fimmu.2019.02708", "pmid": "31849937", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Spatial Proteomics": "Collaborative", "Global Proteomics and Proteogenomics": "Technology development", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6902019"}], "notes": [], "created": "2019-12-03T08:36:31.738Z", "modified": "2021-07-08T11:26:52.822Z"}, {"entity": "publication", "iuid": "61eb5d046be64c419a684f0b51ee417c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61eb5d046be64c419a684f0b51ee417c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61eb5d046be64c419a684f0b51ee417c"}}, "title": "Identification of Novel Putative Bacterial Feruloyl Esterases From Anaerobic Ecosystems by Use of Whole-Genome Shotgun Metagenomics and Genome Binning.", "authors": [{"family": "Mogodiniyai Kasmaei", "given": "Kamyar", "initials": "K"}, {"family": "Sundh", "given": "John", "initials": "J"}], "type": "journal article", "published": "2019-11-20", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "10", "pages": "2673", "issn-l": "1664-302X"}, "abstract": "Feruloyl esterases (FAEs) can reduce the recalcitrance of lignocellulosic biomass to enzymatic hydrolysis, thereby enhancing biorefinery potentials or animal feeding values of the biomass. In addition, ferulic acid, a product of FAE activity, has applications in pharmaceutical and food/beverage industries. It is therefore of great interest to identify new FAEs to enhance understanding about this enzyme family. For this purpose, we used whole-genome shotgun metagenomics and genome binning to explore rumens of dairy cows, large intestines of horses, sediments of freshwater and forest topsoils to identify novel prokaryotic FAEs and trace the responsible microorganisms. A number of prokaryotic genomes were recovered of which, genomes of Clostridiales order and Candidatus Rhabdochlamydia genus showed FAE coding capacities. In total, five sequences were deemed as putative FAE. The BLASTP search against non-redundant protein database of NCBI indicated that these putative FAEs represented novel sequences within this enzyme family. The phylogenetic analysis showed that at least three putative sequences shared evolutionary lineage with FAEs of type A and thus could possess specific activities similar to this type of FAEs, something that is not previously found outside fungal kingdom. We nominate Candidatus Rhabdochlamydia genus as a novel FAE producing taxonomic unit.", "doi": "10.3389/fmicb.2019.02673", "pmid": "31824458", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC6879456"}], "notes": [], "created": "2022-11-24T15:08:31.364Z", "modified": "2022-11-24T15:08:31.367Z"}, {"entity": "publication", "iuid": "3441bbe4bc7b42078a3475a299853b75", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3441bbe4bc7b42078a3475a299853b75.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3441bbe4bc7b42078a3475a299853b75"}}, "title": "Lithium treatment reverses irradiation-induced changes in rodent neural progenitors and rescues cognition.", "authors": [{"family": "Zanni", "given": "Giulia", "initials": "G"}, {"family": "Goto", "given": "Shinobu", "initials": "S"}, {"family": "Fragopoulou", "given": "Adamantia F", "initials": "AF"}, {"family": "Gaudenzi", "given": "Giulia", "initials": "G"}, {"family": "Naidoo", "given": "Vinogran", "initials": "V"}, {"family": "Di Martino", "given": "Elena", "initials": "E"}, {"family": "Levy", "given": "Gabriel", "initials": "G"}, {"family": "Dominguez", "given": "Cecilia A", "initials": "CA"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Cedazo-Minguez", "given": "Angel", "initials": "A"}, {"family": "Merino-Serrais", "given": "Paula", "initials": "P"}, {"family": "Stamatakis", "given": "Antonios", "initials": "A"}, {"family": "Hermanson", "given": "Ola", "initials": "O"}, {"family": "Blomgren", "given": "Klas", "initials": "K"}], "type": "journal article", "published": "2019-11-14", "journal": {"volume": null, "issn": "1476-5578", "issue": null, "pages": null, "title": "Mol. Psychiatry", "issn-l": "1359-4184"}, "abstract": "Cranial radiotherapy in children has detrimental effects on cognition, mood, and social competence in young cancer survivors. Treatments harnessing hippocampal neurogenesis are currently of great relevance in this context. Lithium, a well-known mood stabilizer, has both neuroprotective, pro-neurogenic as well as antitumor effects, and in the current study we introduced lithium treatment 4 weeks after irradiation. Female mice received a single 4 Gy whole-brain radiation dose on postnatal day (PND) 21 and were randomized to 0.24% Li2CO 3 chow or normal chow from PND 49 to 77. Hippocampal neurogenesis was assessed on PND 77, 91, and 105. We found that lithium treatment had a pro-proliferative effect on neural progenitors, but neuronal integration occurred only after it was discontinued. Also, the treatment ameliorated deficits in spatial learning and memory retention observed in irradiated mice. Gene expression profiling and DNA methylation analysis identified two novel factors related to the observed effects, Tppp, associated with microtubule stabilization, and GAD2/65, associated with neuronal signaling. Our results show that lithium treatment reverses irradiation-induced loss of hippocampal neurogenesis and cognitive impairment even when introduced long after the injury. We propose that lithium treatment should be intermittent in order to first make neural progenitors proliferate and then, upon discontinuation, allow them to differentiate. Our findings suggest that pharmacological treatment of cognitive so-called late effects in childhood cancer survivors is possible.", "doi": "10.1038/s41380-019-0584-0", "pmid": "31723242", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41380-019-0584-0"}], "notes": [], "created": "2019-12-02T17:21:21.364Z", "modified": "2024-01-16T13:48:43.525Z"}, {"entity": "publication", "iuid": "aa89d9e0453b418f96e57796adafb08b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aa89d9e0453b418f96e57796adafb08b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aa89d9e0453b418f96e57796adafb08b"}}, "title": "Daytime melatonin levels in saliva are associated with inflammatory markers and anxiety disorders.", "authors": [{"family": "Sundberg", "given": "Isak", "initials": "I"}, {"family": "Rasmusson", "given": "Annica J", "initials": "AJ"}, {"family": "Ramklint", "given": "Mia", "initials": "M"}, {"family": "Just", "given": "David", "initials": "D"}, {"family": "Ekselius", "given": "Lisa", "initials": "L"}, {"family": "Cunningham", "given": "Janet L", "initials": "JL"}], "type": "journal article", "published": "2019-11-14", "journal": {"title": "Psychoneuroendocrinology", "issn": "0306-4530", "issn-l": null, "volume": "112", "issue": null, "pages": "104514"}, "abstract": "The bidirectional interaction between melatonin and the immune system has largely gone unexplored in a clinical context and especially in a psychiatric population. This study explored the association between melatonin during the day and inflammatory cytokines in young adult patients seeking psychiatric care.\r\n\r\nSamples and data were collected from 108 young adults (mean age 21, SD = 2) at an outpatient clinic for affective disorders. Daytime saliva melatonin levels were analyzed with enzyme-linked immunosorbent assay (ELISA) in relation to normalized serum expression levels of 72 inflammatory markers in a proximity extension assay (PEA). In a post hoc analysis the markers associated with melatonin were tested in a generalized linear model to see whether there is a relationship to anxiety disorder or depression.\r\n\r\nAfter Bonferroni correction for multiple testing, melatonin levels at 11:00 were positively correlated with CD5 (p = 4.2e-4). Melatonin levels after lunch were correlated with CCL2/MCP-1 (p = 4.2e-4), CCL3/MPI-1\u03b1 (p = 6.5e-4) and VEGF-A (p = 5.3e-6). In the generalized linear model, positive associations were found for the presence of any anxiety disorder with melatonin after lunch (p = 0.046), VEGF-A (p = 0.001) and CCL3/MPI-1\u03b1 (p = 0.001).\r\n\r\nDaytime saliva levels of melatonin were related to several inflammatory markers in young adults with psychiatric disorders. This observation likely reflects the bidirectional relationship between melatonin production and the immune system. These findings may have relevance for the understanding of psychiatric disorders and other conditions associated with low-grade inflammation.", "doi": "10.1016/j.psyneuen.2019.104514", "pmid": "31776047", "labels": {"Clinical Biomarkers": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0306-4530(19)31255-7"}], "notes": [], "created": "2019-12-06T08:10:30.672Z", "modified": "2023-04-14T13:55:54.183Z"}, {"entity": "publication", "iuid": "f59b2e091bcb45b193a18cedc4ffd706", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f59b2e091bcb45b193a18cedc4ffd706.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f59b2e091bcb45b193a18cedc4ffd706"}}, "title": "On-demand virtual research environments using microservices.", "authors": [{"family": "Capuccini", "given": "Marco", "initials": "M"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Carone", "given": "Matteo", "initials": "M"}, {"family": "Novella", "given": "Jon Ander", "initials": "JA"}, {"family": "Sadawi", "given": "Noureddin", "initials": "N"}, {"family": "Gao", "given": "Jianliang", "initials": "J"}, {"family": "Toor", "given": "Salman", "initials": "S"}, {"family": "Spjuth", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2019-11-11", "journal": {"volume": "5", "issn": "2376-5992", "issue": null, "pages": "e232", "title": "PeerJ Comput Sci", "issn-l": null}, "abstract": "The computational demands for scientific applications are continuously increasing. The emergence of cloud computing has enabled on-demand resource allocation. However, relying solely on infrastructure as a service does not achieve the degree of flexibility required by the scientific community. Here we present a microservice-oriented methodology, where scientific applications run in a distributed orchestration platform as software containers, referred to as on-demand, virtual research environments. The methodology is vendor agnostic and we provide an open source implementation that supports the major cloud providers, offering scalable management of scientific pipelines. We demonstrate applicability and scalability of our methodology in life science applications, but the methodology is general and can be applied to other scientific domains.", "doi": "10.7717/peerj-cs.232", "pmid": "33816885", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "cs-232"}, {"db": "pmc", "key": "PMC7924445"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.4204022"}], "notes": [], "created": "2019-12-12T09:36:07.847Z", "modified": "2024-01-16T13:48:43.534Z"}, {"entity": "publication", "iuid": "d9d69f752dec47f8b12abc9e37ffadb1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9d69f752dec47f8b12abc9e37ffadb1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9d69f752dec47f8b12abc9e37ffadb1"}}, "title": "Leveraging European infrastructures to access 1 million human genomes by 2022.", "authors": [{"family": "Saunders", "given": "Gary", "initials": "G"}, {"family": "Baudis", "given": "Michael", "initials": "M"}, {"family": "Becker", "given": "Regina", "initials": "R", "orcid": "0000-0002-6711-8375", "researcher": {"href": "https://publications.scilifelab.se/researcher/c14845644b2b42e3a4cad6fa2e1c5ef3.json"}}, {"family": "Beltran", "given": "Sergi", "initials": "S"}, {"family": "B\u00e9roud", "given": "Christophe", "initials": "C"}, {"family": "Birney", "given": "Ewan", "initials": "E"}, {"family": "Brooksbank", "given": "Cath", "initials": "C"}, {"family": "Brunak", "given": "S\u00f8ren", "initials": "S"}, {"family": "Van den Bulcke", "given": "Marc", "initials": "M"}, {"family": "Drysdale", "given": "Rachel", "initials": "R"}, {"family": "Capella-Gutierrez", "given": "Salvador", "initials": "S", "orcid": "0000-0002-0309-604X", "researcher": {"href": "https://publications.scilifelab.se/researcher/00b9296cc37341aaad61ee4e028b204e.json"}}, {"family": "Flicek", "given": "Paul", "initials": "P", "orcid": "0000-0002-3897-7955", "researcher": {"href": "https://publications.scilifelab.se/researcher/b36ca07bdc194e3ea616fa65a0554e00.json"}}, {"family": "Florindi", "given": "Francesco", "initials": "F"}, {"family": "Goodhand", "given": "Peter", "initials": "P"}, {"family": "Gut", "given": "Ivo", "initials": "I"}, {"family": "Heringa", "given": "Jaap", "initials": "J"}, {"family": "Holub", "given": "Petr", "initials": "P", "orcid": "0000-0002-5358-616X", "researcher": {"href": "https://publications.scilifelab.se/researcher/06225bf8600944f992b3764c1a1d2d60.json"}}, {"family": "Hooyberghs", "given": "Jef", "initials": "J"}, {"family": "Juty", "given": "Nick", "initials": "N"}, {"family": "Keane", "given": "Thomas M", "initials": "TM"}, {"family": "Korbel", "given": "Jan O", "initials": "JO"}, {"family": "Lappalainen", "given": "Ilkka", "initials": "I", "orcid": "0000-0001-5762-893X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac2adfcab1ce42669e06d8d7a9cb425f.json"}}, {"family": "Leskosek", "given": "Brane", "initials": "B"}, {"family": "Matthijs", "given": "Gert", "initials": "G"}, {"family": "Mayrhofer", "given": "Michaela Th", "initials": "MT", "orcid": "0000-0001-6932-0473", "researcher": {"href": "https://publications.scilifelab.se/researcher/7cc1782a3a6f458b990d4dd92e53bc55.json"}}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Navarro", "given": "Arcadi", "initials": "A"}, {"family": "Newhouse", "given": "Steven", "initials": "S"}, {"family": "Nyr\u00f6nen", "given": "Tommi", "initials": "T"}, {"family": "Page", "given": "Angela", "initials": "A"}, {"family": "Persson", "given": "Bengt", "initials": "B", "orcid": "0000-0003-3165-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f116ef0ed146419cb18e742c270c4a.json"}}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Parkinson", "given": "Helen", "initials": "H"}, {"family": "Rambla", "given": "Jordi", "initials": "J"}, {"family": "Salgado", "given": "David", "initials": "D"}, {"family": "Steinfelder", "given": "Erik", "initials": "E"}, {"family": "Swertz", "given": "Morris A", "initials": "MA"}, {"family": "Valencia", "given": "Alfonso", "initials": "A"}, {"family": "Varma", "given": "Susheel", "initials": "S", "orcid": "0000-0003-1687-2754", "researcher": {"href": "https://publications.scilifelab.se/researcher/08a1554bd3d3457bb4b97b4aa05ab384.json"}}, {"family": "Blomberg", "given": "Niklas", "initials": "N"}, {"family": "Scollen", "given": "Serena", "initials": "S", "orcid": "0000-0002-9311-1337", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4791e5688824613be54b9f57ce79381.json"}}], "type": "journal article", "published": "2019-11-00", "journal": {"volume": "20", "issn": "1471-0064", "issue": "11", "pages": "693-701", "title": "Nat. Rev. Genet.", "issn-l": "1471-0056"}, "abstract": "Human genomics is undergoing a step change from being a predominantly research-driven activity to one driven through health care as many countries in Europe now have nascent precision medicine programmes. To maximize the value of the genomic data generated, these data will need to be shared between institutions and across countries. In recognition of this challenge, 21 European countries recently signed a declaration to transnationally share data on at least 1 million human genomes by 2022. In this Roadmap, we identify the challenges of data sharing across borders and demonstrate that European research infrastructures are well-positioned to support the rapid implementation of widespread genomic data access.", "doi": "10.1038/s41576-019-0156-9", "pmid": "31455890", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41576-019-0156-9"}, {"db": "pmc", "key": "PMC7115898"}, {"db": "mid", "key": "EMS88057"}], "notes": [], "created": "2019-12-17T15:47:42.562Z", "modified": "2021-07-05T12:34:46.051Z"}, {"entity": "publication", "iuid": "ff423e974db94cfabfc2296c9c38de11", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff423e974db94cfabfc2296c9c38de11.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff423e974db94cfabfc2296c9c38de11"}}, "title": "The architecture of the Plasmodiophora brassicae nuclear and mitochondrial genomes.", "authors": [{"family": "Stjelja", "given": "Suzana", "initials": "S"}, {"family": "Fogelqvist", "given": "Johan", "initials": "J"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2019-10-31", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "15753", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Plasmodiophora brassicae is a soil-borne pathogen that attacks roots of cruciferous plants causing clubroot disease. The pathogen belongs to the Plasmodiophorida order in Phytomyxea. Here we used long-read SMRT technology to clarify the P. brassicae e3 genomic constituents along with comparative and phylogenetic analyses. Twenty contigs representing the nuclear genome and one mitochondrial (mt) contig were generated, together comprising 25.1 Mbp. Thirteen of the 20 nuclear contigs represented chromosomes from telomere to telomere characterized by [TTTTAGGG] sequences. Seven active gene candidates encoding synaptonemal complex-associated and meiotic-related protein homologs were identified, a finding that argues for possible genetic recombination events. The circular mt genome is large (114,663 bp), gene dense and intron rich. It shares high synteny with the mt genome of Spongospora subterranea, except in a unique 12 kb region delimited by shifts in GC content and containing tandem minisatellite- and microsatellite repeats with partially palindromic sequences. De novo annotation identified 32 protein-coding genes, 28 structural RNA genes and 19 ORFs. ORFs predicted in the repeat-rich region showed similarities to diverse organisms suggesting possible evolutionary connections. The data generated here form a refined platform for the next step involving functional analysis, all to clarify the complex biology of P. brassicae.", "doi": "10.1038/s41598-019-52274-7", "pmid": "31673019", "labels": {"National Genomics Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-52274-7"}, {"db": "pmc", "key": "PMC6823432"}], "notes": [], "created": "2019-11-24T12:29:14.530Z", "modified": "2020-01-21T13:56:17.807Z"}, {"entity": "publication", "iuid": "1d386607af314ee9b80837d571478cfa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d386607af314ee9b80837d571478cfa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d386607af314ee9b80837d571478cfa"}}, "title": "Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540.", "authors": [{"family": "Tiukova", "given": "Ievgeniia A", "initials": "IA"}, {"family": "Jiang", "given": "Huifeng", "initials": "H"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Hoeppner", "given": "Marc P", "initials": "MP"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Piskur", "given": "Jure", "initials": "J"}, {"family": "Sandgren", "given": "Mats", "initials": "M"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Gu", "given": "Zhenglong", "initials": "Z"}, {"family": "Passoth", "given": "Volkmar", "initials": "V"}], "type": "journal article", "published": "2019-10-26", "journal": {"volume": "7", "issn": "2076-2607", "issue": "11", "title": "Microorganisms", "issn-l": "2076-2607"}, "abstract": "Brettanomyces naardenensis is a spoilage yeast with potential for biotechnological applications for production of innovative beverages with low alcohol content and high attenuation degree. Here, we present the first annotated genome of B. naardenensis CBS 7540. The genome of B. naardenensis CBS 7540 was assembled into 76 contigs, totaling 11,283,072 nucleotides. In total, 5168 protein-coding sequences were annotated. The study provides functional genome annotation, phylogenetic analysis, and discusses genetic determinants behind notable stress tolerance and biotechnological potential of B. naardenensis.", "doi": "10.3390/microorganisms7110489", "pmid": "31717754", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "microorganisms7110489"}], "notes": [], "created": "2019-12-11T15:47:56.953Z", "modified": "2021-07-05T13:05:37.520Z"}, {"entity": "publication", "iuid": "55089a98c3544cc39bab177511a7809e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/55089a98c3544cc39bab177511a7809e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/55089a98c3544cc39bab177511a7809e"}}, "title": "Interoperable and scalable data analysis with microservices: applications in metabolomics.", "authors": [{"family": "Emami Khoonsari", "given": "Payam", "initials": "P"}, {"family": "Moreno", "given": "Pablo", "initials": "P"}, {"family": "Bergmann", "given": "Sven", "initials": "S"}, {"family": "Burman", "given": "Joachim", "initials": "J"}, {"family": "Capuccini", "given": "Marco", "initials": "M"}, {"family": "Carone", "given": "Matteo", "initials": "M"}, {"family": "Cascante", "given": "Marta", "initials": "M"}, {"family": "de Atauri", "given": "Pedro", "initials": "P"}, {"family": "Foguet", "given": "Carles", "initials": "C"}, {"family": "Gonzalez-Beltran", "given": "Alejandra N", "initials": "AN"}, {"family": "Hankemeier", "given": "Thomas", "initials": "T"}, {"family": "Haug", "given": "Kenneth", "initials": "K"}, {"family": "He", "given": "Sijin", "initials": "S"}, {"family": "Herman", "given": "Stephanie", "initials": "S"}, {"family": "Johnson", "given": "David", "initials": "D"}, {"family": "Kale", "given": "Namrata", "initials": "N"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Neumann", "given": "Steffen", "initials": "S"}, {"family": "Peters", "given": "Kristian", "initials": "K"}, {"family": "Pireddu", "given": "Luca", "initials": "L"}, {"family": "Rocca-Serra", "given": "Philippe", "initials": "P"}, {"family": "Roger", "given": "Pierrick", "initials": "P"}, {"family": "Rueedi", "given": "Rico", "initials": "R"}, {"family": "Ruttkies", "given": "Christoph", "initials": "C"}, {"family": "Sadawi", "given": "Noureddin", "initials": "N"}, {"family": "Salek", "given": "Reza M", "initials": "RM"}, {"family": "Sansone", "given": "Susanna-Assunta", "initials": "SA"}, {"family": "Schober", "given": "Daniel", "initials": "D"}, {"family": "Selivanov", "given": "Vitaly", "initials": "V"}, {"family": "Th\u00e9venot", "given": "Etienne A", "initials": "EA"}, {"family": "van Vliet", "given": "Michael", "initials": "M"}, {"family": "Zanetti", "given": "Gianluigi", "initials": "G"}, {"family": "Steinbeck", "given": "Christoph", "initials": "C"}, {"family": "Kultima", "given": "Kim", "initials": "K"}, {"family": "Spjuth", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2019-10-01", "journal": {"volume": "35", "issn": "1367-4811", "issue": "19", "pages": "3752-3760", "title": "Bioinformatics", "issn-l": "1367-4803"}, "abstract": "Developing a robust and performant data analysis workflow that integrates all necessary components whilst still being able to scale over multiple compute nodes is a challenging task. We introduce a generic method based on the microservice architecture, where software tools are encapsulated as Docker containers that can be connected into scientific workflows and executed using the Kubernetes container orchestrator.\n\nWe developed a Virtual Research Environment (VRE) which facilitates rapid integration of new tools and developing scalable and interoperable workflows for performing metabolomics data analysis. The environment can be launched on-demand on cloud resources and desktop computers. IT-expertise requirements on the user side are kept to a minimum, and workflows can be re-used effortlessly by any novice user. We validate our method in the field of metabolomics on two mass spectrometry, one nuclear magnetic resonance spectroscopy and one fluxomics study. We showed that the method scales dynamically with increasing availability of computational resources. We demonstrated that the method facilitates interoperability using integration of the major software suites resulting in a turn-key workflow encompassing all steps for mass-spectrometry-based metabolomics including preprocessing, statistics and identification. Microservices is a generic methodology that can serve any scientific discipline and opens up for new types of large-scale integrative science.\n\nThe PhenoMeNal consortium maintains a web portal (https://portal.phenomenal-h2020.eu) providing a GUI for launching the Virtual Research Environment. The GitHub repository https://github.com/phnmnl/ hosts the source code of all projects.\n\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btz160", "pmid": "30851093", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5372675"}, {"db": "pmc", "key": "PMC6761976"}], "notes": [], "created": "2019-12-12T09:38:14.850Z", "modified": "2024-01-16T13:48:43.729Z"}, {"entity": "publication", "iuid": "5bf650cb4a7f4b749b28c33ca56fdda5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5bf650cb4a7f4b749b28c33ca56fdda5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5bf650cb4a7f4b749b28c33ca56fdda5"}}, "title": "Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species.", "authors": [{"family": "Talla", "given": "Venkat", "initials": "V"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Kawakami", "given": "Takeshi", "initials": "T"}, {"family": "Dinc\u0103", "given": "Vlad", "initials": "V"}, {"family": "Vila", "given": "Roger", "initials": "R"}, {"family": "Friberg", "given": "Magne", "initials": "M"}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal article", "published": "2019-10-01", "journal": {"volume": "11", "issn": "1759-6653", "issue": "10", "pages": "2875-2886", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "The relative role of natural selection and genetic drift in evolution is a major topic of debate in evolutionary biology. Most knowledge spring from a small group of organisms and originate from before it was possible to generate genome-wide data on genetic variation. Hence, it is necessary to extend to a larger number of taxonomic groups, descriptive and hypothesis-based research aiming at understanding the proximate and ultimate mechanisms underlying both levels of genetic polymorphism and the efficiency of natural selection. In this study, we used data from 60 whole-genome resequenced individuals of three cryptic butterfly species (Leptidea sp.), together with novel gene annotation information and population recombination data. We characterized the overall prevalence of natural selection and investigated the effects of mutation and linked selection on regional variation in nucleotide diversity. Our analyses showed that genome-wide diversity and rate of adaptive substitutions were comparatively low, whereas nonsynonymous to synonymous polymorphism and substitution levels were comparatively high in Leptidea, suggesting small long-term effective population sizes. Still, negative selection on linked sites (background selection) has resulted in reduced nucleotide diversity in regions with relatively high gene density and low recombination rate. We also found a significant effect of mutation rate variation on levels of polymorphism. Finally, there were considerable population differences in levels of genetic diversity and pervasiveness of selection against slightly deleterious alleles, in line with expectations from differences in estimated effective population sizes.", "doi": "10.1093/gbe/evz212", "pmid": "31580421", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5580498"}, {"db": "pmc", "key": "PMC6795238"}], "notes": [], "created": "2019-12-02T17:20:06.547Z", "modified": "2024-01-16T13:48:43.736Z"}, {"entity": "publication", "iuid": "e6a1e270d26b4a0ab8775ae1c8a28632", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e6a1e270d26b4a0ab8775ae1c8a28632.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e6a1e270d26b4a0ab8775ae1c8a28632"}}, "title": "Clinical candidate and genistein analogue AXP107-11 has chemoenhancing functions in pancreatic adenocarcinoma through G protein-coupled estrogen receptor signaling.", "authors": [{"family": "Mesmar", "given": "Fahmi", "initials": "F"}, {"family": "Dai", "given": "Bingbing", "initials": "B"}, {"family": "Ibrahim", "given": "Ahmed", "initials": "A"}, {"family": "Hases", "given": "Linnea", "initials": "L"}, {"family": "Jafferali", "given": "Mohammed Hakim", "initials": "MH"}, {"family": "Jose Augustine", "given": "Jithesh", "initials": "J"}, {"family": "DiLorenzo", "given": "Sebastian", "initials": "S"}, {"family": "Kang", "given": "Ya'an", "initials": "Y"}, {"family": "Zhao", "given": "Yang", "initials": "Y"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Kim", "given": "Michael", "initials": "M"}, {"family": "Lin", "given": "Chin-Yo", "initials": "C"}, {"family": "Berkenstam", "given": "Anders", "initials": "A"}, {"family": "Fleming", "given": "Jason", "initials": "J"}, {"family": "Williams", "given": "Cecilia", "initials": "C"}], "type": "journal article", "published": "2019-09-30", "journal": {"volume": null, "issn": "2045-7634", "issue": null, "pages": null, "title": "Cancer Med", "issn-l": "2045-7634"}, "abstract": "Despite advances in cancer therapeutics, pancreatic cancer remains difficult to treat and often develops resistance to chemotherapies. We have evaluated a bioavailable genistein analogue, AXP107-11 which has completed phase Ib clinical trial, as an approach to sensitize tumor cells to chemotherapy. Using organotypic cultures of 14 patient-derived xenografts (PDX) of pancreatic ductal adenocarcinoma, we found that addition of AXP107-11 indeed sensitized 57% of cases to gemcitabine treatment. Results were validated using PDX models in vivo. Further, RNA-Seq from responsive and unresponsive tumors proposed a 41-gene treatment-predictive signature. Functional and molecular assays were performed in cell lines and demonstrated that the effect was synergistic. Transcriptome analysis indicated activation of G-protein-coupled estrogen receptor (GPER1) as the main underlying mechanism of action, which was corroborated using GPER1-selective agonists and antagonists. GPER1 expression in pancreatic tumors was indicative of survival, and our study proposes that activation of GPER1 may constitute a new avenue for pancreatic cancer therapeutics.", "doi": "10.1002/cam4.2581", "pmid": "31568691", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-12-02T17:20:33.691Z", "modified": "2024-01-16T13:48:43.797Z"}, {"entity": "publication", "iuid": "da099445320441b9b01ff5b7f8dfb049", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da099445320441b9b01ff5b7f8dfb049.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da099445320441b9b01ff5b7f8dfb049"}}, "title": "Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki- and Thorarchaeota.", "authors": [{"family": "Manoharan", "given": "Lokeshwaran", "initials": "L"}, {"family": "Kozlowski", "given": "Jessica A", "initials": "JA"}, {"family": "Murdoch", "given": "Robert W", "initials": "RW"}, {"family": "L\u00f6ffler", "given": "Frank E", "initials": "FE"}, {"family": "Sousa", "given": "Filipa L", "initials": "FL"}, {"family": "Schleper", "given": "Christa", "initials": "C"}], "type": "journal article", "published": "2019-09-10", "journal": {"volume": "10", "issn": "2150-7511", "issue": "5", "pages": null, "title": "MBio", "issn-l": null}, "abstract": "The genomes of Asgard Archaea, a novel archaeal proposed superphylum, share an enriched repertoire of eukaryotic signature genes and thus promise to provide insights into early eukaryote evolution. However, the distribution, metabolisms, cellular structures, and ecology of the members within this superphylum are not well understood. Here we provide a meta-analysis of the environmental distribution of the Asgard archaea, based on available 16S rRNA gene sequences. Metagenome sequencing of samples from a salt-crusted lagoon on the Baja California Peninsula of Mexico allowed the assembly of a new Thorarchaeota and three Lokiarchaeota genomes. Comparative analyses of all known Lokiarchaeota and Thorarchaeota genomes revealed overlapping genome content, including central carbon metabolism. Members of both groups contained putative reductive dehalogenase genes, suggesting that these organisms might be able to metabolize halogenated organic compounds. Unlike the first report on Lokiarchaeota, we identified genes encoding glycerol-1-phosphate dehydrogenase in all Loki- and Thorarchaeota genomes, suggesting that these organisms are able to synthesize bona fide archaeal lipids with their characteristic glycerol stereochemistry.IMPORTANCE Microorganisms of the superphylum Asgard Archaea are considered to be the closest living prokaryotic relatives of eukaryotes (including plants and animals) and thus promise to give insights into the early evolution of more complex life forms. However, very little is known about their biology as none of the organisms has yet been cultivated in the laboratory. Here we report on the ecological distribution of Asgard Archaea and on four newly sequenced genomes of the Lokiarchaeota and Thorarchaeota lineages that give insight into possible metabolic features that might eventually help to identify these enigmatic groups of archaea in the environment and to culture them.", "doi": "10.1128/mBio.02039-19", "pmid": "31506313", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "mBio.02039-19"}, {"db": "pmc", "key": "PMC6737245"}], "notes": [], "created": "2020-01-07T15:00:20.586Z", "modified": "2024-01-16T13:48:43.893Z"}, {"entity": "publication", "iuid": "c3ecd75f65d14557b9a425f70937c824", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3ecd75f65d14557b9a425f70937c824.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3ecd75f65d14557b9a425f70937c824"}}, "title": "Genome Sequencing of Pleurozium schreberi: The Assembled and Annotated Draft Genome of a Pleurocarpous Feather Moss.", "authors": [{"family": "Pederson", "given": "Eric R A", "initials": "ERA"}, {"family": "Warshan", "given": "Denis", "initials": "D"}, {"family": "Rasmussen", "given": "Ulla", "initials": "U"}], "type": "journal article", "published": "2019-09-04", "journal": {"volume": "9", "issn": "2160-1836", "issue": "9", "pages": "2791-2797", "title": "G3 (Bethesda)", "issn-l": "2160-1836"}, "abstract": "The pleurocarpous feather moss Pleurozium schreberi is a ubiquitous moss species which plays a fundamental role in many terrestrial ecosystems, for instance within the boreal forest, the Earth's largest terrestrial biome, this species plays a significant role in driving ecosystem nitrogen and carbon inputs and fluxes. By hosting dinitrogen (N2)-fixing cyanobacteria, the moss-cyanobacteria symbiosis constitutes the main nitrogen input into the ecosystem and by the high productivity and the low decomposability of the moss litter, Pschreberi contributes significantly to build-up soil organic matter, and therefore long-term C sequestration. Knowledge on P. schreberi genome will facilitate the development of 'omics' and system's biology approaches to gain a more complete understanding of the physiology and ecological adaptation of the moss and the mechanisms underpinning the establishment of the symbiosis. Here we present the de novo assembly and annotation of P. schreberi genome that will help investigating these questions. The sequencing was performed using the HiSeq X platform with Illumina paired-end and mate-pair libraries prepared with CTAB extracted DNA. In total, the assembled genome was approximately 318 Mb, while repetitive elements account for 28.42% of the genome and 15,992 protein-coding genes were predicted from the genome, of which 84.23% have been functionally annotated. We anticipate that the genomic data generated will constitute a significant resource to study ecological and evolutionary genomics of P. schreberi, and will be valuable for evo-devo investigations as well as our understanding of the evolution of land plants by providing the genome of a pleurocarpous moss.", "doi": "10.1534/g3.119.400279", "pmid": "31285273", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "g3.119.400279"}, {"db": "pmc", "key": "PMC6723128"}, {"db": "figshare", "key": "10.6084/m9.figshare.7775951"}], "notes": [], "created": "2019-12-02T17:20:52.764Z", "modified": "2020-01-21T13:56:17.674Z"}, {"entity": "publication", "iuid": "46cd7cf01fbc4ddf87f7503100fbaaab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46cd7cf01fbc4ddf87f7503100fbaaab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46cd7cf01fbc4ddf87f7503100fbaaab"}}, "title": "TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish.", "authors": [{"family": "Gudmundsson", "given": "Sanna", "initials": "S", "orcid": "0000-0002-2332-074X", "researcher": {"href": "https://publications.scilifelab.se/researcher/adb097c987504b2ca309e5f4e1cea5d2.json"}}, {"family": "Wilbe", "given": "Maria", "initials": "M"}, {"family": "Filipek-G\u00f3rniok", "given": "Beata", "initials": "B", "orcid": "0000-0002-6757-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/11f0b7b3e0b045f082d2aff1dd23ec0e.json"}}, {"family": "Molin", "given": "Anna-Maja", "initials": "A"}, {"family": "Ekvall", "given": "Sara", "initials": "S"}, {"family": "Johansson", "given": "Josefin", "initials": "J", "orcid": "0000-0002-5152-4096", "researcher": {"href": "https://publications.scilifelab.se/researcher/e568827124304b769a3f336d76b6954e.json"}}, {"family": "Allalou", "given": "Amin", "initials": "A"}, {"family": "Gylje", "given": "Hans", "initials": "H"}, {"family": "Kalscheuer", "given": "Vera M", "initials": "VM", "orcid": "0000-0001-6898-3259", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb8107a11ed144bc8f4c236042f9bc8c.json"}}, {"family": "Ledin", "given": "Johan", "initials": "J", "orcid": "0000-0002-7319-7735", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e482abc18c49d881d3bf0132b3fbcd.json"}}, {"family": "Anner\u00e9n", "given": "G\u00f6ran", "initials": "G"}, {"family": "Bondeson", "given": "Marie-Louise", "initials": "M"}], "type": "journal article", "published": "2019-07-24", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "9", "issue": "1", "pages": "10730"}, "abstract": "The TATA-box binding protein associated factor 1 (TAF1) protein is a key unit of the transcription factor II D complex that serves a vital function during transcription initiation. Variants of TAF1 have been associated with neurodevelopmental disorders, but TAF1's molecular functions remain elusive. In this study, we present a five-generation family affected with X-linked intellectual disability that co-segregated with a TAF1 c.3568C>T, p.(Arg1190Cys) variant. All affected males presented with intellectual disability and dysmorphic features, while heterozygous females were asymptomatic and had completely skewed X-chromosome inactivation. We investigated the role of TAF1 and its association to neurodevelopment by creating the first complete knockout model of the TAF1 orthologue in zebrafish. A crucial function of human TAF1 during embryogenesis can be inferred from the model, demonstrating that intact taf1 is essential for embryonic development. Transcriptome analysis of taf1 zebrafish knockout revealed enrichment for genes associated with neurodevelopmental processes. In conclusion, we propose that functional TAF1 is essential for embryonic development and specifically neurodevelopmental processes.", "doi": "10.1038/s41598-019-46632-8", "pmid": "31341187", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Service", "Genome Engineering Zebrafish": "Collaborative", "Bioinformatics Support and Infrastructure": "Service", "BioImage Informatics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-46632-8"}, {"db": "pmc", "key": "PMC6656882"}], "notes": [], "created": "2019-11-29T13:27:12.056Z", "modified": "2024-01-16T13:48:44.102Z"}, {"entity": "publication", "iuid": "8bf0c5c4a46d42168739d0698d72a9dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8bf0c5c4a46d42168739d0698d72a9dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8bf0c5c4a46d42168739d0698d72a9dc"}}, "title": "GUESSmyLT: Software to guess the RNA-Seq library type of paired and single end read files", "authors": [{"family": "Wik", "given": "Erik", "initials": "E"}, {"family": "Olin", "given": "Hampus", "initials": "H"}, {"family": "Haughey", "given": "Caitlin", "initials": "C"}, {"family": "Klasson", "given": "Lisa", "initials": "L"}, {"family": "Dainat", "given": "Jacques", "initials": "J", "orcid": "0000-0002-6629-0173", "researcher": {"href": "https://publications.scilifelab.se/researcher/8436881cc1814c88889b5987d7a00afb.json"}}], "type": "journal-article", "published": "2019-07-07", "journal": {"volume": "4", "issn": "2475-9066", "issue": "39", "pages": "1344", "title": "JOSS", "issn-l": "2475-9066"}, "abstract": null, "doi": "10.21105/joss.01344", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-12-05T15:34:06.955Z", "modified": "2024-01-16T13:48:44.131Z"}, {"entity": "publication", "iuid": "b47eaaf183d04aac8512a94a34b8cdcd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b47eaaf183d04aac8512a94a34b8cdcd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b47eaaf183d04aac8512a94a34b8cdcd"}}, "title": "Comment on 'AIRE-deficient patients harbor unique high-affinity disease-ameliorating autoantibodies'.", "authors": [{"family": "Landegren", "given": "Nils", "initials": "N", "orcid": "0000-0002-6163-9540", "researcher": {"href": "https://publications.scilifelab.se/researcher/13ceacb17b7448709f9bfcd593bec1e2.json"}}, {"family": "Rosen", "given": "Lindsey B", "initials": "LB", "orcid": "0000-0001-5894-3878", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ee4a40ef9343a9af897979b0e8e2dc.json"}}, {"family": "Freyhult", "given": "Eva", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "Eriksson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5473-3312", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c26578a5e548f783b9465e04fb0bfc.json"}}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Smith", "given": "Gustav", "initials": "G"}, {"family": "Ferre", "given": "Elise M N", "initials": "EMN", "orcid": "0000-0002-3285-7768", "researcher": {"href": "https://publications.scilifelab.se/researcher/41ec8466cb88424fb1d29e07c63df47c.json"}}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "Sharon", "given": "Donald", "initials": "D"}, {"family": "Snyder", "given": "Michael", "initials": "M", "orcid": "0000-0003-0784-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2594af48f3d45e68983030873c06cf5.json"}}, {"family": "Lionakis", "given": "Michail", "initials": "M"}, {"family": "Anderson", "given": "Mark", "initials": "M"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O", "orcid": "0000-0001-6091-9914", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c547dc809a14cdaa47b623cf638162b.json"}}], "type": "journal article", "published": "2019-06-27", "journal": {"volume": "8", "issn": "2050-084X", "issue": null, "title": "Elife", "issn-l": "2050-084X"}, "abstract": "The AIRE gene plays a key role in the development of central immune tolerance by promoting thymic presentation of tissue-specific molecules. Patients with AIRE-deficiency develop multiple autoimmune manifestations and display autoantibodies against the affected tissues. In 2016 it was reported that: i) the spectrum of autoantibodies in patients with AIRE-deficiency is much broader than previously appreciated; ii) neutralizing autoantibodies to type I interferons (IFNs) could provide protection against type 1 diabetes in these patients (Meyer et al., 2016). We attempted to replicate these new findings using a similar experimental approach in an independent patient cohort, and found no evidence for either conclusion.", "doi": "10.7554/eLife.43578", "pmid": "31244471", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Autoimmunity and Serology Profiling": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6597240"}, {"db": "pii", "key": "43578"}], "notes": [], "created": "2019-06-30T19:14:13.830Z", "modified": "2023-06-19T12:50:16.488Z"}, {"entity": "publication", "iuid": "fffa2a55e4ee4e7792be485b71063ffa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fffa2a55e4ee4e7792be485b71063ffa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fffa2a55e4ee4e7792be485b71063ffa"}}, "title": "Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination.", "authors": [{"family": "Dahlberg", "given": "Josef", "initials": "J", "orcid": "0000-0001-8131-6725", "researcher": {"href": "https://publications.scilifelab.se/researcher/090cf8219ee047be97d9b75b104d8b7c.json"}}, {"family": "Sun", "given": "Li", "initials": "L"}, {"family": "Persson Waller", "given": "Karin", "initials": "K"}, {"family": "\u00d6stensson", "given": "Karin", "initials": "K"}, {"family": "McGuire", "given": "Mark", "initials": "M"}, {"family": "Agen\u00e4s", "given": "Sigrid", "initials": "S"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2019-06-13", "journal": {"volume": "14", "issn": "1932-6203", "issue": "6", "pages": "e0218257", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Discoveries of bacterial communities in environments that previously have been described as sterile have in recent years radically challenged the view of these environments. In this study we aimed to use 16S rRNA sequencing to describe the composition and temporal stability of the bacterial microbiota in bovine milk from healthy udder quarters, an environment previously believed to be sterile. Sequencing of the 16S rRNA gene is a technique commonly used to describe bacterial composition and diversity in various environments. With the increased use of 16S rRNA gene sequencing, awareness of methodological pitfalls such as biases and contamination has increased although not in equal amount. Evaluation of the composition and temporal stability of the microbiota in 288 milk samples was largely hampered by background contamination, despite careful and aseptic sample processing. Sequencing of no template control samples, positive control samples, with defined levels of bacteria, and 288 milk samples with various levels of bacterial growth, revealed that the data was influenced by contaminating taxa, primarily Methylobacterium. We observed an increasing impact of contamination with decreasing microbial biomass where the contaminating taxa became dominant in samples with less than 104 bacterial cells per mL. By applying a contamination filtration on the sequence data, the amount of sequences was substantially reduced but only a minor impact on number of identified taxa and by culture known endogenous taxa was observed. This suggests that data filtration can be useful for identifying biologically relevant associations in milk microbiota data.", "doi": "10.1371/journal.pone.0218257", "pmid": "31194836", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-18-29659"}, {"db": "pmc", "key": "PMC6564671"}], "notes": [], "created": "2019-12-03T10:48:01.523Z", "modified": "2021-06-21T10:00:19.458Z"}, {"entity": "publication", "iuid": "9e94dfa9b92d448eabccf47bb68156e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e94dfa9b92d448eabccf47bb68156e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e94dfa9b92d448eabccf47bb68156e2"}}, "title": "Ultrasensitive Immunoprofiling of Plasma Extracellular Vesicles Identifies Syndecan-1 as a Potential Tool for Minimally Invasive Diagnosis of Glioma.", "authors": [{"family": "Indira Chandran", "given": "Vineesh", "initials": "V"}, {"family": "Welinder", "given": "Charlotte", "initials": "C", "orcid": "0000-0001-9626-0576", "researcher": {"href": "https://publications.scilifelab.se/researcher/924dc427398e4ba7b31eb5b4b47a89ca.json"}}, {"family": "M\u00e5nsson", "given": "Ann-Sofie", "initials": "AS"}, {"family": "Offer", "given": "Svenja", "initials": "S"}, {"family": "Freyhult", "given": "Eva", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15f303cb2044cfa81719700137e3603.json"}}, {"family": "Lund", "given": "Sigrid M", "initials": "SM"}, {"family": "Pedersen", "given": "Shona", "initials": "S", "orcid": "0000-0001-6636-0293", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c9565eb33bc4f15bdefeb1e796a728f.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Marko-Varga", "given": "Gyorgy", "initials": "G"}, {"family": "Johansson", "given": "Maria C", "initials": "MC"}, {"family": "Englund", "given": "Elisabet", "initials": "E", "orcid": "0000-0002-2708-2443", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c98fa2b2e7e4e318cd00eb1e8e3ac7a.json"}}, {"family": "Sundgren", "given": "Pia C", "initials": "PC", "orcid": "0000-0001-9237-1236", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7c755205abb4ecfabb3d5f021b7a1f6.json"}}, {"family": "Belting", "given": "Mattias", "initials": "M"}], "type": "journal article", "published": "2019-05-15", "journal": {"volume": "25", "issn": "1557-3265", "issue": "10", "title": "Clin. Cancer Res.", "pages": "3115-3127", "issn-l": "1078-0432"}, "abstract": "Liquid biopsy has great potential to improve the management of brain tumor patients at high risk of surgery-associated complications. Here, the aim was to explore plasma extracellular vesicle (plEV) immunoprofiling as a tool for noninvasive diagnosis of glioma.\n\nPlEV isolation and analysis were optimized using advanced mass spectrometry, nanoparticle tracking analysis, and electron microscopy. We then established a new procedure that combines size exclusion chromatography isolation and proximity extension assay-based ultrasensitive immunoprofiling of plEV proteins that was applied on a well-defined glioma study cohort (n = 82).\n\nAmong potential candidates, we for the first time identify syndecan-1 (SDC1) as a plEV constituent that can discriminate between high-grade glioblastoma multiforme (GBM, WHO grade IV) and low-grade glioma [LGG, WHO grade II; area under the ROC curve (AUC): 0.81; sensitivity: 71%; specificity: 91%]. These findings were independently validated by ELISA. Tumor SDC1 mRNA expression similarly discriminated between GBM and LGG in an independent glioma patient population from The Cancer Genome Atlas cohort (AUC: 0.91; sensitivity: 79%; specificity: 91%). In experimental studies with GBM cells, we show that SDC1 is efficiently sorted to secreted EVs. Importantly, we found strong support of plEVSDC1 originating from GBM tumors, as plEVSDC1 correlated with SDC1 protein expression in matched patient tumors, and plEVSDC1 was decreased postoperatively depending on the extent of surgery.\n\nOur studies support the concept of circulating plEVs as a tool for noninvasive diagnosis and monitoring of gliomas and should move this field closer to the goal of improving the management of cancer patients.", "doi": "10.1158/1078-0432.CCR-18-2946", "pmid": "30679164", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Global Proteomics and Proteogenomics": "Technology development", "Structural Proteomics": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "1078-0432.CCR-18-2946"}], "notes": [], "created": "2019-02-01T09:02:21.138Z", "modified": "2021-07-08T11:26:52.783Z"}, {"entity": "publication", "iuid": "ebb31f25c498403385dee32833ae650a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ebb31f25c498403385dee32833ae650a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ebb31f25c498403385dee32833ae650a"}}, "title": "Software engineering for scientific big data analysis.", "authors": [{"family": "Gr\u00fcning", "given": "Bj\u00f6rn A", "initials": "BA", "orcid": "0000-0002-3079-6586", "researcher": {"href": "https://publications.scilifelab.se/researcher/447295d5434d44f3998e33af808bdea3.json"}}, {"family": "Lampa", "given": "Samuel", "initials": "S", "orcid": "0000-0001-6740-9212", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4be992e2eed49c8ba1aaa0a4319ec24.json"}}, {"family": "Vaudel", "given": "Marc", "initials": "M", "orcid": "0000-0003-1179-9578", "researcher": {"href": "https://publications.scilifelab.se/researcher/920056fb632147559a0d9e3f49c6bdbd.json"}}, {"family": "Blankenberg", "given": "Daniel", "initials": "D", "orcid": "0000-0002-6833-9049", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ed1285d051048cf9a27a76e71bda3bc.json"}}], "type": "journal article", "published": "2019-05-01", "journal": {"volume": "8", "issn": "2047-217X", "issue": "5", "pages": null, "title": "Gigascience", "issn-l": "2047-217X"}, "abstract": "The increasing complexity of data and analysis methods has created an environment where scientists, who may not have formal training, are finding themselves playing the impromptu role of software engineer. While several resources are available for introducing scientists to the basics of programming, researchers have been left with little guidance on approaches needed to advance to the next level for the development of robust, large-scale data analysis tools that are amenable to integration into workflow management systems, tools, and frameworks. The integration into such workflow systems necessitates additional requirements on computational tools, such as adherence to standard conventions for robustness, data input, output, logging, and flow control. Here we provide a set of 10 guidelines to steer the creation of command-line computational tools that are usable, reliable, extensible, and in line with standards of modern coding practices.", "doi": "10.1093/gigascience/giz054", "pmid": "31121028", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5497810"}, {"db": "pmc", "key": "PMC6532757"}], "notes": [], "created": "2020-01-07T14:38:59.181Z", "modified": "2021-06-21T11:56:23.801Z"}, {"entity": "publication", "iuid": "147a11e9aff7495293bd505f345a38a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/147a11e9aff7495293bd505f345a38a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/147a11e9aff7495293bd505f345a38a1"}}, "title": "SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines.", "authors": [{"family": "Lampa", "given": "Samuel", "initials": "S", "orcid": "0000-0001-6740-9212", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4be992e2eed49c8ba1aaa0a4319ec24.json"}}, {"family": "Dahl\u00f6", "given": "Martin", "initials": "M", "orcid": "0000-0001-5447-9465", "researcher": {"href": "https://publications.scilifelab.se/researcher/32395b4dcca540a7a997b88ed20c9252.json"}}, {"family": "Alvarsson", "given": "Jonathan", "initials": "J", "orcid": "0000-0002-8682-7206", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8eb231a432647ee89b22e3e0dbbc651.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}], "type": "journal article", "published": "2019-05-01", "journal": {"volume": "8", "issn": "2047-217X", "issue": "5", "pages": null, "title": "Gigascience", "issn-l": "2047-217X"}, "abstract": "The complex nature of biological data has driven the development of specialized software tools. Scientific workflow management systems simplify the assembly of such tools into pipelines, assist with job automation, and aid reproducibility of analyses. Many contemporary workflow tools are specialized or not designed for highly complex workflows, such as with nested loops, dynamic scheduling, and parametrization, which is common in, e.g., machine learning.\n\nSciPipe is a workflow programming library implemented in the programming language Go, for managing complex and dynamic pipelines in bioinformatics, cheminformatics, and other fields. SciPipe helps in particular with workflow constructs common in machine learning, such as extensive branching, parameter sweeps, and dynamic scheduling and parametrization of downstream tasks. SciPipe builds on flow-based programming principles to support agile development of workflows based on a library of self-contained, reusable components. It supports running subsets of workflows for improved iterative development and provides a data-centric audit logging feature that saves a full audit trace for every output file of a workflow, which can be converted to other formats such as HTML, TeX, and PDF on demand. The utility of SciPipe is demonstrated with a machine learning pipeline, a genomics, and a transcriptomics pipeline.\n\nSciPipe provides a solution for agile development of complex and dynamic pipelines, especially in machine learning, through a flexible application programming interface suitable for scientists used to programming or scripting.", "doi": "10.1093/gigascience/giz044", "pmid": "31029061", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Support and Infrastructure": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pii", "key": "5480570"}, {"db": "pmc", "key": "PMC6486472"}, {"db": "figshare", "key": "10.6084/m9.figshare.3985674"}], "notes": [], "created": "2019-04-29T07:14:49.754Z", "modified": "2024-01-16T13:48:44.374Z"}, {"entity": "publication", "iuid": "b1f4d18f745842fda29e557e90de70ed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1f4d18f745842fda29e557e90de70ed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1f4d18f745842fda29e557e90de70ed"}}, "title": "Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis.", "authors": [{"family": "Tiukova", "given": "Ievgeniia A", "initials": "IA", "orcid": "0000-0002-0408-3515", "researcher": {"href": "https://publications.scilifelab.se/researcher/e007c24aef2344d582f2e3d318b3f7cd.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME"}, {"family": "Hoeppner", "given": "Marc P", "initials": "MP"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "RA"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "S\u00f6derberg", "given": "Jonas", "initials": "J"}, {"family": "Passoth", "given": "Volkmar", "initials": "V"}], "type": "journal article", "published": "2019-05-01", "journal": {"volume": "14", "issn": "1932-6203", "issue": "5", "pages": "e0215077", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Here, we present the genome of the industrial ethanol production strain Brettanomyces bruxellensis CBS 11270. The nuclear genome was found to be diploid, containing four chromosomes with sizes of ranging from 2.2 to 4.0 Mbp. A 75 Kbp mitochondrial genome was also identified. Comparing the homologous chromosomes, we detected that 0.32% of nucleotides were polymorphic, i.e. formed single nucleotide polymorphisms (SNPs), 40.6% of them were found in coding regions (i.e. 0.13% of all nucleotides formed SNPs and were in coding regions). In addition, 8,538 indels were found. The total number of protein coding genes was 4897, of them, 4,284 were annotated on chromosomes; and the mitochondrial genome contained 18 protein coding genes. Additionally, 595 genes, which were annotated, were on contigs not associated with chromosomes. A number of genes was duplicated, most of them as tandem repeats, including a six-gene cluster located on chromosome 3. There were also examples of interchromosomal gene duplications, including a duplication of a six-gene cluster, which was found on both chromosomes 1 and 4. Gene copy number analysis suggested loss of heterozygosity for 372 genes. This may reflect adaptation to relatively harsh but constant conditions of continuous fermentation. Analysis of gene topology showed that most of these losses occurred in clusters of more than one gene, the largest cluster comprising 33 genes. Comparative analysis against the wine isolate CBS 2499 revealed 88,534 SNPs and 8,133 indels. Moreover, when the scaffolds of the CBS 2499 genome assembly were aligned against the chromosomes of CBS 11270, many of them aligned completely, some have chunks aligned to different chromosomes, and some were in fact rearranged. Our findings indicate a highly dynamic genome within the species B. bruxellensis and a tendency towards reduction of gene number in long-term continuous cultivation.", "doi": "10.1371/journal.pone.0215077", "pmid": "31042716", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-18-32895"}, {"db": "pmc", "key": "PMC6493715"}], "notes": [], "created": "2019-11-24T12:41:36.969Z", "modified": "2021-07-07T15:19:08.434Z"}, {"entity": "publication", "iuid": "d75ef87849e04fe6bb610c383abae7f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d75ef87849e04fe6bb610c383abae7f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d75ef87849e04fe6bb610c383abae7f9"}}, "title": "Pervasive hybridizations in the history of wheat relatives.", "authors": [{"family": "Gl\u00e9min", "given": "Sylvain", "initials": "S"}, {"family": "Scornavacca", "given": "Celine", "initials": "C"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Burgarella", "given": "Concetta", "initials": "C"}, {"family": "Viader", "given": "V\u00e9ronique", "initials": "V"}, {"family": "Ardisson", "given": "Morgane", "initials": "M"}, {"family": "Sarah", "given": "Gautier", "initials": "G"}, {"family": "Santoni", "given": "Sylvain", "initials": "S"}, {"family": "David", "given": "Jacques", "initials": "J"}, {"family": "Ranwez", "given": "Vincent", "initials": "V"}], "type": "journal article", "published": "2019-05-00", "journal": {"volume": "5", "issn": "2375-2548", "issue": "5", "pages": "eaav9188", "title": "Sci Adv", "issn-l": "2375-2548"}, "abstract": "Cultivated wheats are derived from an intricate history of three genomes, A, B, and D, present in both diploid and polyploid species. It was recently proposed that the D genome originated from an ancient hybridization between the A and B lineages. However, this result has been questioned, and a robust phylogeny of wheat relatives is still lacking. Using transcriptome data from all diploid species and a new methodological approach, our comprehensive phylogenomic analysis revealed that more than half of the species descend from an ancient hybridization event but with a more complex scenario involving a different parent than previously thought- Aegilops mutica, an overlooked wild species-instead of the B genome. We also detected other extensive gene flow events that could explain long-standing controversies in the classification of wheat relatives.", "doi": "10.1126/sciadv.aav9188", "pmid": "31049399", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "aav9188"}, {"db": "pmc", "key": "PMC6494498"}], "notes": [], "created": "2019-12-05T15:39:13.411Z", "modified": "2020-01-21T13:53:22.787Z"}, {"entity": "publication", "iuid": "420d57a9a28043029a871feaf5d57b7f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/420d57a9a28043029a871feaf5d57b7f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/420d57a9a28043029a871feaf5d57b7f"}}, "title": "PKC\u03b6 facilitates lymphatic metastatic spread of prostate cancer cells in a mice xenograft model", "authors": [{"family": "Zang", "given": "Guangxiang", "initials": "G"}, {"family": "Mu", "given": "Yabing", "initials": "Y"}, {"family": "Gao", "given": "Linlin", "initials": "L"}, {"family": "Bergh", "given": "Anders", "initials": "A"}, {"family": "Landstr\u00f6m", "given": "Marene", "initials": "M"}], "type": "journal-article", "published": "2019-05-00", "journal": {"volume": "38", "issn": "1476-5594", "issue": "22", "pages": "4215-4231", "title": "Oncogene", "issn-l": "0950-9232"}, "abstract": "Prostate cancer disseminates primarily into the adjacent lymph nodes, which is related to a poor outcome. Atypical protein kinase C \u03b6 (PKC\u03b6) is highly expressed in aggressive prostate cancer and correlates with Gleason score, clinical stage, and poor prognosis. Here, we report the molecular mechanisms of PKC\u03b6 in lymphatic metastasis during prostate cancer progression. Using zinc-finger nuclease technology or PKC\u03b6 shRNA lentiviral particles, and orthotopic mouse xenografts, we show that PKC\u03b6-knockout or knockdown from aggressive prostate cancer (PC3 and PC3U) cells, decreasesd tumor growth and lymphatic metastasis in vivo. Intriguingly, PKC\u03b6-knockout or knockdown impaired the activation of AKT, ERK, and NF-\u03baB signaling in prostate cancer cells, thereby impairing the expression of lymphangiogenic factors and macrophage recruitment, resulting in aberrant lymphangiogenesis. Moreover, PKC\u03b6 regulated the expression of hyaluronan synthase enzymes, which is important for hyaluronan-mediated lymphatic drainage and tumor dissemination. Thus, PKC\u03b6 plays a crucial oncogenic role in the lymphatic metastasis of prostate cancer and is predicted to be a novel therapeutic target for prostate cancer.", "doi": "10.1038/s41388-019-0722-9", "pmid": "30705401", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2019-11-25T15:08:43.727Z", "modified": "2020-01-21T13:56:17.596Z"}, {"entity": "publication", "iuid": "5cb8eb65fea748b69bd38d1f1bc5e7a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5cb8eb65fea748b69bd38d1f1bc5e7a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5cb8eb65fea748b69bd38d1f1bc5e7a3"}}, "title": "Gene expression profile of extraocular muscles following resection strabismus surgery.", "authors": [{"family": "Rodr\u00edguez", "given": "Maria Angels", "initials": "MA"}, {"family": "Sandgren Hochhard", "given": "Karin", "initials": "K"}, {"family": "Vicente", "given": "Andr\u00e9", "initials": "A"}, {"family": "Liu", "given": "Jing-Xia", "initials": "JX"}, {"family": "Pedrosa Domell\u00f6f", "given": "Fatima", "initials": "F"}], "type": "journal article", "published": "2019-05-00", "journal": {"volume": "182", "issn": "1096-0007", "issue": null, "pages": "182-193", "title": "Exp. Eye Res.", "issn-l": "0014-4835"}, "abstract": "This paper aims to identify key biological processes triggered by resection surgery in the extraocular muscles (EOMs) of a rabbit model of strabismus surgery by studying changes in gene expression. Resection surgery was performed in the superior rectus of 16 rabbits and a group of non-operated rabbits served as control. Muscle samples were collected from groups of four animals 1, 2, 4 and 6 weeks after surgery and processed for RNA-sequencing and immunohistochemistry. We identified a total of 164; 136; 64 and 12 differentially expressed genes 1, 2, 4 and 6 weeks after surgery. Gene Ontology enrichment analysis revealed that differentially expressed genes were involved in biological pathways related to metabolism, response to stimulus mainly related with regulation of immune response, cell cycle and extracellular matrix. A complementary pathway analysis and network analysis performed with Ingenuity Pathway Analysis tool corroborated and completed these findings. Collagen I, fibronectin and versican, evaluated by immunofluorescence, showed that changes at the gene expression level resulted in variation at the protein level. Tenascin-C staining in resected muscles demonstrated the formation of new tendon and myotendinous junctions. These data provide new insights about the biological response of the EOMs to resection surgery and may form the basis for future strategies to improve the outcome of strabismus surgery.", "doi": "10.1016/j.exer.2019.03.022", "pmid": "30953624", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0014-4835(19)30027-2"}], "notes": [], "created": "2020-01-07T13:20:46.691Z", "modified": "2021-07-02T10:55:41.968Z"}, {"entity": "publication", "iuid": "f3999ad8c5444765b9b286d1e989c482", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3999ad8c5444765b9b286d1e989c482.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3999ad8c5444765b9b286d1e989c482"}}, "title": "The complex barnacle perfume: identification of waterborne pheromone homologues in Balanus improvisus and their differential expression during settlement", "authors": [{"family": "Abramova", "given": "Anna", "initials": "A"}, {"family": "Lind", "given": "Ulrika", "initials": "U"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}, {"family": "Rosenblad", "given": "Magnus Alm", "initials": "MA"}], "type": "journal-article", "published": "2019-04-21", "journal": {"volume": "35", "issn": "0892-7014", "issue": "4", "pages": "416-428", "title": "Biofouling", "issn-l": null}, "abstract": "A key question in barnacle biology is the nature of cues that induce gregarious settlement. One of the characterised cues is the waterborne settlement pheromone (WSP). This study aimed to identify WSP homologues in Balanus improvisus and to investigate their expression during settlement. Six WSP homologues were identified, all containing an N-terminal signal peptide, a conserved core region, and a variable C-terminus comprising several -GR- and -HDDH- motifs. The B. improvisus WSP homologues were expressed in all settlement stages but showed different expression patterns. The homologue most similar to the B. amphitrite WSP was the most abundant and was constantly expressed during settlement. In contrast, several of the other WSP homologues showed the greatest expression in the juvenile stage. The presence of several WSP homologues suggests the existence of a pheromone mix, where con-specificity might be determined by a combination of sequence characteristics and the concentration of the individual components.", "doi": "10.1080/08927014.2019.1602123", "pmid": "31142149", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-11-25T14:28:40.486Z", "modified": "2024-01-16T13:48:44.455Z"}, {"entity": "publication", "iuid": "4f784e6367354b22a9536f6d1296e833", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f784e6367354b22a9536f6d1296e833.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f784e6367354b22a9536f6d1296e833"}}, "title": "Helicase/SUMO-targeted ubiquitin ligase Uls1 interacts with the Holliday junction resolvase Yen1.", "authors": [{"family": "Bauer", "given": "Stefanie L", "initials": "SL"}, {"family": "Chen", "given": "Jiang", "initials": "J"}, {"family": "\u00c5str\u00f6m", "given": "Stefan U", "initials": "SU", "orcid": "0000-0001-7721-6908", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f6ef7643731421b9821e208bc3e53bc.json"}}], "type": "journal article", "published": "2019-03-21", "journal": {"volume": "14", "issn": "1932-6203", "issue": "3", "pages": "e0214102", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Resolution of branched DNA structures is pivotal for repair of stalled replication forks and meiotic recombination intermediates. The Yen1 nuclease cleaves both Holliday junctions and replication forks. We show that Yen1 interacts physically with Uls1, a suggested SUMO-targeted ubiquitin ligase that also contains a SWI/SNF-family ATPase-domain. Yen1 is SUMO-modified in its noncatalytic carboxyl terminus and DNA damage induces SUMOylation. SUMO-modification of Yen1 strengthens the interaction to Uls1, and mutations in SUMO interaction motifs in Uls1 weakens the interaction. However, Uls1 does not regulate the steady-state level of SUMO-modified Yen1 or chromatin-associated Yen1. In addition, SUMO-modification of Yen1 does not affect the catalytic activity in vitro. Consistent with a shared function for Uls1 and Yen1, mutations in both genes display similar phenotypes. Both uls1 and yen1 display negative genetic interactions with the alternative HJ-cleaving nuclease Mus81, manifested both in hypersensitivity to DNA damaging agents and in meiotic defects. Point mutations in ULS1 (uls1K975R and uls1C1330S, C1333S) predicted to inactivate the ATPase and ubiquitin ligase activities, respectively, are as defective as the null allele, indicating that both functions of Uls1 are essential. A micrococcal nuclease sequencing experiment showed that Uls1 had minimal effects on global nucleosome positioning/occupancy. Moreover, increased gene dosage of YEN1 partially alleviates the mus81 uls1 sensitivity to DNA damage. We suggest a preliminary model in which Uls1 acts in the same pathway as Yen1 to resolve branched DNA structures.", "doi": "10.1371/journal.pone.0214102", "pmid": "30897139", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-18-33679"}, {"db": "pmc", "key": "PMC6428284"}], "notes": [], "created": "2020-01-07T15:01:44.600Z", "modified": "2024-01-16T13:48:44.602Z"}, {"entity": "publication", "iuid": "c0e5884696a24f998e33fc5cf97d3aa8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0e5884696a24f998e33fc5cf97d3aa8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0e5884696a24f998e33fc5cf97d3aa8"}}, "title": "An ABCA4 loss-of-function mutation causes a canine form of Stargardt disease", "authors": [{"family": "M\u00e4kel\u00e4inen", "given": "Suvi", "initials": "S"}, {"family": "G\u00f2dia", "given": "Marta", "initials": "M"}, {"family": "Hellsand", "given": "Minas", "initials": "M"}, {"family": "Viluma", "given": "Agnese", "initials": "A"}, {"family": "Hahn", "given": "Daniela", "initials": "D"}, {"family": "Makdoumi", "given": "Karim", "initials": "K"}, {"family": "Zeiss", "given": "Caroline J", "initials": "CJ"}, {"family": "Mellersh", "given": "Cathryn", "initials": "C"}, {"family": "Ricketts", "given": "Sally L", "initials": "SL"}, {"family": "Narfstr\u00f6m", "given": "Kristina", "initials": "K"}, {"family": "Hallb\u00f6\u00f6k", "given": "Finn", "initials": "F"}, {"family": "Ekesten", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Bergstr\u00f6m", "given": "Tomas F", "initials": "TF"}], "type": "journal-article", "published": "2019-03-19", "journal": {"volume": "15", "issn": "1553-7404", "issue": "3", "pages": "e1007873", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Autosomal recessive retinal degenerative diseases cause visual impairment and blindness in both humans and dogs. Currently, no standard treatment is available, but pioneering gene therapy-based canine models have been instrumental for clinical trials in humans. To study a novel form of retinal degeneration in Labrador retriever dogs with clinical signs indicating cone and rod degeneration, we used whole-genome sequencing of an affected sib-pair and their unaffected parents. A frameshift insertion in the ATP binding cassette subfamily A member 4 (ABCA4) gene (c.4176insC), leading to a premature stop codon in exon 28 (p.F1393Lfs*1395), was identified. In contrast to unaffected dogs, no full-length ABCA4 protein was detected in the retina of an affected dog. The ABCA4 gene encodes a membrane transporter protein localized in the outer segments of rod and cone photoreceptors. In humans, the ABCA4 gene is associated with Stargardt disease (STGD), an autosomal recessive retinal degeneration leading to central visual impairment. A hallmark of STGD is the accumulation of lipofuscin deposits in the retinal pigment epithelium (RPE). The discovery of a canine homozygous ABCA4 loss-of-function mutation may advance the development of dog as a large animal model for human STGD.", "doi": "10.1371/journal.pgen.1007873", "pmid": "30889179", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2019-03-29T08:42:19.716Z", "modified": "2020-01-21T13:56:17.488Z"}, {"entity": "publication", "iuid": "038ed7dad7ea4781a9809dd98d11493f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/038ed7dad7ea4781a9809dd98d11493f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/038ed7dad7ea4781a9809dd98d11493f"}}, "title": "Pax6 and KDM5C co-occupy a subset of developmentally critical genes including Notch signaling regulators in neural progenitors", "authors": [{"family": "Gaudenzi", "given": "Giulia", "initials": "G", "orcid": "0000-0003-4923-6965", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba29165719cb46eba1a62c4c3e9cb232.json"}}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Walfridsson", "given": "Julian", "initials": "J"}, {"family": "Hermanson", "given": "Ola", "initials": "O", "orcid": "0000-0001-9320-7921", "researcher": {"href": "https://publications.scilifelab.se/researcher/127407b365334524be30de6c31aec5ba.json"}}], "type": "posted-content", "published": "2019-03-16", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/579219", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2020-01-07T14:44:59.328Z", "modified": "2025-12-18T20:08:24.494Z"}, {"entity": "publication", "iuid": "a5d6ff3144ff4fe7960ee2f74f763443", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a5d6ff3144ff4fe7960ee2f74f763443.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a5d6ff3144ff4fe7960ee2f74f763443"}}, "title": "The Interactome of Palmitoyl-Protein Thioesterase 1 (PPT1) Affects Neuronal Morphology and Function.", "authors": [{"family": "Sapir", "given": "Tamar", "initials": "T"}, {"family": "Segal", "given": "Michal", "initials": "M"}, {"family": "Grigoryan", "given": "Gayane", "initials": "G"}, {"family": "Hansson", "given": "Karin M", "initials": "KM"}, {"family": "James", "given": "Peter", "initials": "P"}, {"family": "Segal", "given": "Menahem", "initials": "M"}, {"family": "Reiner", "given": "Orly", "initials": "O"}], "type": "journal article", "published": "2019-03-13", "journal": {"volume": "13", "issn": "1662-5102", "issue": null, "pages": "92", "title": "Front Cell Neurosci", "issn-l": "1662-5102"}, "abstract": "Palmitoyl-protein thioesterase 1 (PPT1) is a depalmitoylation enzyme that is mutated in cases of neuronal ceroid lipofuscinosis (NCL). The hallmarks of the disease include progressive neurodegeneration and blindness, as well as seizures. In the current study, we identified 62 high-confident PPT1-binding proteins. These proteins included a self-interaction of PPT1, two V-type ATPases, calcium voltage-gated channels, cytoskeletal proteins and others. Pathway analysis suggested their involvement in seizures and neuronal morphology. We then proceeded to demonstrate that hippocampal neurons from Ppt1-/- mice exhibit structural deficits, and further investigated electrophysiology parameters in the hippocampi of mutant mice, both in brain slices and dissociated postnatal primary cultures. Our studies reveal new mechanistic features involved in the pathophysiology of this devastating neurodegenerative disease.", "doi": "10.3389/fncel.2019.00092", "pmid": "30918483", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6424868"}], "notes": [], "created": "2020-01-07T14:59:07.294Z", "modified": "2021-06-21T13:29:49.685Z"}, {"entity": "publication", "iuid": "868204592395423f990c951ba83d71d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/868204592395423f990c951ba83d71d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/868204592395423f990c951ba83d71d3"}}, "title": "Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard", "authors": [{"family": "Andrade", "given": "Pedro", "initials": "P"}, {"family": "Pinho", "given": "Catarina", "initials": "C"}, {"family": "P\u00e9rez i de Lanuza", "given": "Guillem", "initials": "G"}, {"family": "Afonso", "given": "Sandra", "initials": "S"}, {"family": "Brejcha", "given": "Jind\u0159ich", "initials": "J"}, {"family": "Rubin", "given": "Carl Johan", "initials": "CJ"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Pereira", "given": "Paulo", "initials": "P"}, {"family": "Sabatino", "given": "Stephen J", "initials": "SJ"}, {"family": "Bellati", "given": "Adriana", "initials": "A"}, {"family": "Pellitteri-Rosa", "given": "Daniele", "initials": "D"}, {"family": "Bosakova", "given": "Zuzana", "initials": "Z"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Carretero", "given": "Miguel A", "initials": "MA"}, {"family": "Feiner", "given": "Nathalie", "initials": "N"}, {"family": "Marsik", "given": "Petr", "initials": "P"}, {"family": "Paup\u00e9rio", "given": "Francisco", "initials": "F"}, {"family": "Salvi", "given": "Daniele", "initials": "D"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "While", "given": "Geoffrey M", "initials": "GM"}, {"family": "Uller", "given": "Tobias", "initials": "T"}, {"family": "Font", "given": "Enrique", "initials": "E"}, {"family": "Andersson", "given": "Leif", "initials": "L"}, {"family": "Carneiro", "given": "Miguel", "initials": "M"}], "type": "journal-article", "published": "2019-02-28", "journal": {"volume": null, "issn": "0027-8424", "issue": null, "pages": "201820320", "title": "Proc Natl Acad Sci USA", "issn-l": "0027-8424"}, "abstract": "Reptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard ( Podarcis muralis), which differ in orange and yellow pigmentation and in their ecology and behavior, are virtually undifferentiated. Genetic differences are restricted to two small regulatory regions near genes associated with pterin [sepiapterin reductase (SPR)] and carotenoid [beta-carotene oxygenase 2 (BCO2)] metabolism, demonstrating that a core gene in the housekeeping pathway of pterin biosynthesis has been coopted for bright coloration in reptiles and indicating that these loci exert pleiotropic effects on other aspects of physiology. Pigmentation differences are explained by extremely divergent alleles, and haplotype analysis revealed abundant transspecific allele sharing with other lacertids exhibiting color polymorphisms. The evolution of these conspicuous color ornaments is the result of ancient genetic variation and cross-species hybridization.", "doi": "10.1073/pnas.1820320116", "pmid": "30819892", "labels": {"National Genomics Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2019-03-08T07:59:28.818Z", "modified": "2024-01-16T13:48:44.663Z"}, {"entity": "publication", "iuid": "d8f620f34a7d4d99b2f024f02039375b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d8f620f34a7d4d99b2f024f02039375b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d8f620f34a7d4d99b2f024f02039375b"}}, "title": "Rostania revised: testing generic delimitations in Collemataceae (Peltigerales, Lecanoromycetes).", "authors": [{"family": "Ko\u0161uthov\u00e1", "given": "Alica", "initials": "A"}, {"family": "Westberg", "given": "Martin", "initials": "M"}, {"family": "T\u00e1lora", "given": "M\u00f3nica A G", "initials": "MAG"}, {"family": "Wedin", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2019-02-20", "journal": {"volume": "47", "issn": "1314-4049", "issue": "47", "pages": "17-33", "title": "MycoKeys", "issn-l": null}, "abstract": "Here, we test the current generic delimitation of Rostania (Collemataceae, Peltigerales, Ascomycota) utilizing molecular phylogeny and morphological investigations. Using DNA sequence data from the mitochondrial SSU rDNA and two nuclear protein-coding genes (MCM7 and \u03b2-tubulin) and utilizing parsimony, maximum likelihood and Bayesian phylogenetic methods, Rostania is shown to be non-monophyletic in the current sense. A new generic delimitation of Rostania is thus proposed, in which the genus is monophyletic, and three species (Rostaniacoccophylla, R.paramensis, R.quadrifida) are excluded and transferred to other genera. Rostaniaoccultata is further non-monophyletic, and a more detailed investigation of species delimitations in Rostania s. str. is needed. The new combinations Leptogiumparamense and Scytiniumquadrifidum are proposed.", "doi": "10.3897/mycokeys.47.32227", "pmid": "30820165", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6393396"}], "notes": [], "created": "2019-02-21T14:09:36.495Z", "modified": "2021-06-21T13:32:09.704Z"}, {"entity": "publication", "iuid": "8f8b8be2ec454cc494da08f27985613a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f8b8be2ec454cc494da08f27985613a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f8b8be2ec454cc494da08f27985613a"}}, "title": "Prediction of response to anti-cancer drugs becomes robust via network integration of molecular data.", "authors": [{"family": "Franco", "given": "Marcela", "initials": "M"}, {"family": "Jeggari", "given": "Ashwini", "initials": "A"}, {"family": "Peuget", "given": "Sylvain", "initials": "S"}, {"family": "B\u00f6ttger", "given": "Franziska", "initials": "F"}, {"family": "Selivanova", "given": "Galina", "initials": "G"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications.scilifelab.se/researcher/54b6c0ff12c148dd803f7f72c8af0d14.json"}}], "type": "journal article", "published": "2019-02-20", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "2379", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Despite the widening range of high-throughput platforms and exponential growth of generated data volume, the validation of biomarkers discovered from large-scale data remains a challenging field. In order to tackle cancer heterogeneity and comply with the data dimensionality, a number of network and pathway approaches were invented but rarely systematically applied to this task. We propose a new method, called NEAmarker, for finding sensitive and robust biomarkers at the pathway level. scores from network enrichment analysis transform the original space of altered genes into a lower-dimensional space of pathways. These dimensions are then correlated with phenotype variables. The method was first tested using in vitro data from three anti-cancer drug screens and then on clinical data of The Cancer Genome Atlas. It proved superior to the single-gene and alternative enrichment analyses in terms of (1) universal applicability to different data types with a possibility of cross-platform integration, (2) consistency of the discovered correlates between independent drug screens, and (3) ability to explain differential survival of treated patients. Our new screen of anti-cancer compounds validated the performance of multivariate models of drug sensitivity. The previously proposed methods of enrichment analysis could achieve comparable levels of performance in certain tests. However, only our method could discover predictors of both in vitro response and patient survival given administration of the same drug.", "doi": "10.1038/s41598-019-39019-2", "pmid": "30787419", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-39019-2"}, {"db": "pmc", "key": "PMC6382934"}], "notes": [], "created": "2020-01-07T13:26:35.148Z", "modified": "2024-01-16T13:48:44.681Z"}, {"entity": "publication", "iuid": "ef763beb1ed645cfaf970e9cf6a6afae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef763beb1ed645cfaf970e9cf6a6afae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef763beb1ed645cfaf970e9cf6a6afae"}}, "title": "Protein profiling of fine-needle aspirates reveals subtype-associated immune signatures and involvement of chemokines in breast cancer.", "authors": [{"family": "Franz\u00e9n", "given": "Bo", "initials": "B"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications.scilifelab.se/researcher/54b6c0ff12c148dd803f7f72c8af0d14.json"}}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M"}, {"family": "Hatschek", "given": "Thomas", "initials": "T"}, {"family": "Kanter", "given": "Lena", "initials": "L"}, {"family": "Ramqvist", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Kierkegaard", "given": "Jonas", "initials": "J"}, {"family": "Masucci", "given": "Giuseppe", "initials": "G"}, {"family": "Auer", "given": "Gert", "initials": "G"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "Lewensohn", "given": "Rolf", "initials": "R"}], "type": "journal article", "published": "2019-02-00", "journal": {"volume": "13", "issn": "1878-0261", "issue": "2", "pages": "376-391", "title": "Mol Oncol", "issn-l": "1574-7891"}, "abstract": "There are increasing demands for informative cancer biomarkers, accessible via minimally invasive procedures, both for initial diagnostics and for follow-up of personalized cancer therapy, including immunotherapy. Fine-needle aspiration (FNA) biopsy provides ready access to relevant tissue samples; however, the minute amounts of sample require sensitive multiplex molecular analysis to be of clinical biomarker utility. We have applied proximity extension assays (PEA) to analyze 167 proteins in FNA samples from patients with breast cancer (BC; n = 25) and benign lesions (n = 32). We demonstrate that the FNA BC samples could be divided into two main clusters, characterized by differences in expression levels of the estrogen receptor (ER) and the proliferation marker Ki67. This clustering corresponded to some extent to established BC subtypes. Our analysis also revealed several proteins whose expression levels differed between BC and benign lesions (e.g., CA9, GZMB, IL-6, VEGFA, CXCL11, PDL1, and PCD1), as well as several chemokines correlating with ER and Ki67 status (e.g., CCL4, CCL8, CCL20, CXCL8, CXCL9, and CXCL17). Finally, we also identified three signatures that could predict Ki67 status, ER status, and tumor grade, respectively, based on a small subset of proteins, which was dominated by chemokines. To our knowledge, expression profiles of CCL13 in benign lesions and BC have not previously been described but were shown herein to correlate with proliferation (P = 0.00095), suggesting a role in advanced BC. Given the broad functional range of the proteins analyzed, immune-related proteins were overrepresented among the observed alterations. Our pilot study supports the emerging role of chemokines in BC progression. Due to the minimally traumatic sampling and clinically important molecular information for therapeutic decisions, this methodology is promising for future immunoscoring and monitoring of treatment efficacy in BC.", "doi": "10.1002/1878-0261.12410", "pmid": "30451357", "labels": {"Clinical Biomarkers": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC6360506"}], "notes": [], "created": "2019-01-14T19:31:57.036Z", "modified": "2023-04-14T13:55:59.371Z"}, {"entity": "publication", "iuid": "0b748897b1af4d289817788e72a49ce6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b748897b1af4d289817788e72a49ce6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b748897b1af4d289817788e72a49ce6"}}, "title": "Plasma Profiles of Inflammatory Markers Associated With Active Tuberculosis in Antiretroviral Therapy-Naive Human Immunodeficiency Virus-Positive Individuals.", "authors": [{"family": "Olsson", "given": "Oskar", "initials": "O", "orcid": "0000-0002-5106-9222", "researcher": {"href": "https://publications.scilifelab.se/researcher/544e16146be84a898babce0889b5a0b1.json"}}, {"family": "Bj\u00f6rkman", "given": "Per", "initials": "P"}, {"family": "Jansson", "given": "Marianne", "initials": "M", "orcid": "0000-0001-6536-8146", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc2f6d7000594c2c86fb96aa0e737827.json"}}, {"family": "Balcha", "given": "Taye Tolera", "initials": "TT"}, {"family": "Mulleta", "given": "Daba", "initials": "D"}, {"family": "Yeba", "given": "Habtamu", "initials": "H"}, {"family": "Valfridsson", "given": "Christine", "initials": "C"}, {"family": "Carlsson", "given": "Fredric", "initials": "F"}, {"family": "Skogmar", "given": "Sten", "initials": "S"}], "type": "journal article", "published": "2019-02-00", "journal": {"volume": "6", "issn": "2328-8957", "issue": "2", "pages": "ofz015", "title": "Open Forum Infect Dis", "issn-l": null}, "abstract": "Diagnosis of tuberculosis (TB) in human immunodeficiency virus (HIV)-coinfected individuals is challenging. We hypothesized that combinations of inflammatory markers could facilitate identification of active TB in HIV-positive individuals.\n\nParticipants were HIV-positive, treatment-naive adults systematically investigated for TB at Ethiopian health centers. Plasma samples from 130 subjects with TB (HIV +/TB+) and 130 subjects without TB (HIV+/TB-) were tested for concentration of the following markers: CCL5, C-reactive protein (CRP), interleukin (IL)-6, IL12-p70, IL-18, IL-27, interferon-\u03b3-induced protein-10 (IP-10), procalcitonin (PCT), and soluble urokinase-type plasminogen activator receptor (suPAR). Analyzed markers were then assessed, either individually or in combination, with regard to infection status, CD4 cell count, and HIV ribonucleic acid (RNA) levels.\n\nThe HIV +/TB+ subjects had higher levels of all markers, except IL12p70, compared with HIV+/TB- subjects. The CRP showed the best performance for TB identification (median 27.9 vs 1.8 mg/L for HIV+/TB+ and HIV+/TB-, respectively; area under the curve [AUC]: 0.80). Performance was increased when CRP was combined with suPAR analysis (AUC, 0.83 [0.93 for subjects with CD4 cell count <200 cells/mm3]). Irrespective of TB status, IP-10 concentrations correlated with HIV RNA levels, and both IP-10 and IL-18 were inversely correlated to CD4 cell counts.\n\nAlthough CRP showed the best single marker discriminatory potential, combining CRP and suPAR analyses increased performance for TB identification.", "doi": "10.1093/ofid/ofz015", "pmid": "30800697", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "ofz015"}, {"db": "pmc", "key": "PMC6379652"}], "notes": [], "created": "2020-01-07T14:50:18.263Z", "modified": "2021-06-21T13:38:05.877Z"}, {"entity": "publication", "iuid": "8be07c6afe7a451a82423b08fe277d2d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8be07c6afe7a451a82423b08fe277d2d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8be07c6afe7a451a82423b08fe277d2d"}}, "title": "Transformation of mature mouse B cells into malignant plasma cells in vitro via introduction of defined genetic elements.", "authors": [{"family": "H\u00f6gstrand", "given": "Kari", "initials": "K"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Sundblad", "given": "Anne", "initials": "A"}, {"family": "Grandien", "given": "Alf", "initials": "A"}], "type": "journal article", "published": "2019-01-21", "journal": {"volume": null, "issn": "1521-4141", "issue": null, "pages": null, "title": "Eur. J. Immunol.", "issn-l": "0014-2980"}, "abstract": "An experimental system where defined alterations in gene function or gene expression levels in primary B cells would result in the development of transformed plasma cells in vitro would be useful in order to facilitate studies of the underlying molecular mechanisms of plasma cell malignancies. Here, such a system is described in which primary murine B cells rapidly become transformed into surface CD138\r\n                + , IgM-/low , CD19- IgM-secreting plasma cells as a result of expression of the transcription factors IRF4 and MYC together with simultaneous expression of BMI1, mutated p53 or silencing of p19Arf , and suppression of intrinsic apoptosis through expression of BCLXL. Analysis of gene expression patterns revealed that this combination of transforming genes resulted in expression of a number of genes previously associated with terminally differentiated B cells (plasma cells) and myeloma cells, whereas many genes associated with mature B cells and B cell lymphomas were not expressed. Upon transplantation, the transformed cells preferentially localized to the bone marrow, presenting features of a plasma cell malignancy of the IgM isotype. The present findings may also be applicable in the development of novel methods for production of monoclonal antibodies. This article is protected by copyright. All rights reserved.", "doi": "10.1002/eji.201847855", "pmid": "30664244", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-01-24T11:55:05.412Z", "modified": "2021-07-05T12:48:16.011Z"}, {"entity": "publication", "iuid": "16b41862d1d943d0a122469df5db584f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/16b41862d1d943d0a122469df5db584f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/16b41862d1d943d0a122469df5db584f"}}, "title": "The genetic diversity and evolution of diatom-diazotroph associations highlights traits favoring symbiont integration.", "authors": [{"family": "Caputo", "given": "Andrea", "initials": "A"}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA"}, {"family": "Foster", "given": "Rachel A", "initials": "RA"}], "type": "journal article", "published": "2019-01-09", "journal": {"volume": null, "issn": "1574-6968", "issue": null, "title": "FEMS Microbiol. Lett.", "issn-l": "0378-1097"}, "abstract": "Diatom diazotroph associations (DDAs) are a widespread marine planktonic symbiosis between several diatom genera and di-nitrogen-fixing bacteria. Combining single cell confocal microscopy observations and molecular genetic approaches on individual field collected cells, we determined the phylogenetic diversity, distribution, and evolution of the DDAs. Confocal analyses coupled with 3-D imaging re-evaluated the cellular location of DDA symbionts. DDA diversity was resolved by paired gene sequencing (18S rRNA and rbcL genes and 16S rRNA and nifH genes). A survey using the newly acquired sequences against public databases found sequences with high similarity (99-100%) to either host (18S rRNA) or symbiont (16S rRNA) in atypical regions for DDAs (high latitudes, anoxic basin, copepod gut). Concatenated phylogenies were congruent for the host and cyanobacteria sequences and implied co-evolution. Time-calibrated trees dated the appearance of N2 fixing planktonic symbiosis from 100-50Mya and were consistent with the symbiont cellular location: symbioses with internal partners are more ancient. An ancestral state reconstruction traced the evolution of traits in DDAs and highlight that the adaptive radiation to the marine environment was likely facilitated by the symbiosis. Our results present the evolutionary nature of DDAs and provide new genetic and phenotypic information for these biogeochemically relevant populations.", "doi": "10.1093/femsle/fny297", "pmid": "30629176", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5281432"}], "notes": [], "created": "2019-01-15T07:57:27.997Z", "modified": "2020-01-21T13:53:22.358Z"}, {"entity": "publication", "iuid": "f989e24dc1864d62a1e0808ea11f31ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f989e24dc1864d62a1e0808ea11f31ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f989e24dc1864d62a1e0808ea11f31ca"}}, "title": "Introducing ribosomal tandem repeat barcoding for fungi.", "authors": [{"family": "Wurzbacher", "given": "Christian", "initials": "C", "orcid": "0000-0001-7418-0831", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fed784d185749498b07f7458c9ccfb6.json"}}, {"family": "Larsson", "given": "Ellen", "initials": "E"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Van den Wyngaert", "given": "Silke", "initials": "S"}, {"family": "Svantesson", "given": "Sten", "initials": "S"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Kagami", "given": "Maiko", "initials": "M", "orcid": "0000-0003-3086-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6fd6b466b4143139a9709eeddf37315.json"}}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH", "orcid": "0000-0002-8052-0107", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f74b9c6c3d4e749adacffa0efb80b2.json"}}], "type": "journal article", "published": "2019-01-00", "journal": {"volume": "19", "issn": "1755-0998", "issue": "1", "pages": "118-127", "title": "Mol Ecol Resour", "issn-l": "1755-098X"}, "abstract": "Sequence comparison and analysis of the various ribosomal genetic markers are the dominant molecular methods for identification and description of fungi. However, new environmental fungal lineages known only from DNA data reveal significant gaps in our sampling of the fungal kingdom in terms of both taxonomy and marker coverage in the reference sequence databases. To facilitate the integration of reference data from all of the ribosomal markers, we present three sets of general primers that allow for amplification of the complete ribosomal operon from the ribosomal tandem repeats. The primers cover all ribosomal markers: ETS, SSU, ITS1, 5.8S, ITS2, LSU and IGS. We coupled these primers successfully with third-generation sequencing (PacBio and Nanopore sequencing) to showcase our approach on authentic fungal herbarium specimens (Basidiomycota), aquatic chytrids (Chytridiomycota) and a poorly understood lineage of early diverging fungi (Nephridiophagidae). In particular, we were able to generate high-quality reference data with Nanopore sequencing in a high-throughput manner, showing that the generation of reference data can be achieved on a regular desktop computer without the involvement of any large-scale sequencing facility. The quality of the Nanopore generated sequences was 99.85%, which is comparable with the 99.78% accuracy described for Sanger sequencing. With this work, we hope to stimulate the generation of a new comprehensive standard of ribosomal reference data with the ultimate aim to close the huge gaps in our reference datasets.", "doi": "10.1111/1755-0998.12944", "pmid": "30240145", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "ENA", "description": "https://www.ebi.ac.uk/ena/data/view/PRJEB26696", "key": "PRJEB26696"}, {"db": "GENBANK", "description": null, "key": "MH356537"}, {"db": "GENBANK", "description": null, "key": "MH356538"}, {"db": "GENBANK", "description": null, "key": "MH356539"}, {"db": "GENBANK", "description": null, "key": "MH356540"}, {"db": "GENBANK", "description": null, "key": "MH356541"}, {"db": "GENBANK", "description": null, "key": "MH356542"}, {"db": "GENBANK", "description": null, "key": "MH356543"}, {"db": "GENBANK", "description": null, "key": "MH356544"}, {"db": "GENBANK", "description": null, "key": "MH356545"}], "notes": [], "created": "2018-06-25T14:29:38.213Z", "modified": "2024-01-16T13:48:44.902Z"}, {"entity": "publication", "iuid": "a366fe5139384ade916225960fa5d8e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a366fe5139384ade916225960fa5d8e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a366fe5139384ade916225960fa5d8e1"}}, "title": "Zebrafish larvae as a model system for systematic characterization of drugs and genes in dyslipidemia and atherosclerosis", "authors": [{"family": "Bandaru", "given": "Manoj K", "initials": "MK", "orcid": "0000-0002-5664-6711", "researcher": {"href": "https://publications.scilifelab.se/researcher/024e44747cdd4f5f85c1cf61d3320b09.json"}}, {"family": "Emmanouilidou", "given": "Anastasia", "initials": "A"}, {"family": "Ranefall", "given": "Petter", "initials": "P", "orcid": "0000-0002-6699-4015", "researcher": {"href": "https://publications.scilifelab.se/researcher/4332883c0058421f8dfb85406ec03524.json"}}, {"family": "von der Heyde", "given": "Benedikt", "initials": "B", "orcid": "0000-0002-9889-4027", "researcher": {"href": "https://publications.scilifelab.se/researcher/803c0e0639174a50b59ae597802e824f.json"}}, {"family": "Mazzaferro", "given": "Eugenia", "initials": "E"}, {"family": "Klingstr\u00f6m", "given": "Tiffany", "initials": "T"}, {"family": "Masiero", "given": "Mauro", "initials": "M"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Ledin", "given": "Johan", "initials": "J", "orcid": "0000-0002-7319-7735", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e482abc18c49d881d3bf0132b3fbcd.json"}}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Brooke", "given": "Hannah L", "initials": "HL"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "den Hoed", "given": "Marcel", "initials": "M", "orcid": "0000-0001-8081-428X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d712cc087d344b15ab9a7971640acebe.json"}}], "type": "posted-content", "published": "2018-12-20", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/502674", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-08T07:55:34.310Z", "modified": "2025-12-18T20:08:39.251Z"}, {"entity": "publication", "iuid": "cec100d1ada4482681493c2ea3e13c74", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cec100d1ada4482681493c2ea3e13c74.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cec100d1ada4482681493c2ea3e13c74"}}, "title": "PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud.", "authors": [{"family": "Peters", "given": "Kristian", "initials": "K"}, {"family": "Bradbury", "given": "James", "initials": "J"}, {"family": "Bergmann", "given": "Sven", "initials": "S"}, {"family": "Capuccini", "given": "Marco", "initials": "M"}, {"family": "Cascante", "given": "Marta", "initials": "M"}, {"family": "de Atauri", "given": "Pedro", "initials": "P"}, {"family": "Ebbels", "given": "Timothy M D", "initials": "TMD"}, {"family": "Foguet", "given": "Carles", "initials": "C"}, {"family": "Glen", "given": "Robert", "initials": "R"}, {"family": "Gonzalez-Beltran", "given": "Alejandra", "initials": "A"}, {"family": "G\u00fcnther", "given": "Ulrich L", "initials": "UL"}, {"family": "Handakas", "given": "Evangelos", "initials": "E"}, {"family": "Hankemeier", "given": "Thomas", "initials": "T"}, {"family": "Haug", "given": "Kenneth", "initials": "K"}, {"family": "Herman", "given": "Stephanie", "initials": "S"}, {"family": "Holub", "given": "Petr", "initials": "P"}, {"family": "Izzo", "given": "Massimiliano", "initials": "M"}, {"family": "Jacob", "given": "Daniel", "initials": "D"}, {"family": "Johnson", "given": "David", "initials": "D"}, {"family": "Jourdan", "given": "Fabien", "initials": "F"}, {"family": "Kale", "given": "Namrata", "initials": "N"}, {"family": "Karaman", "given": "Ibrahim", "initials": "I"}, {"family": "Khalili", "given": "Bita", "initials": "B"}, {"family": "Khonsari", "given": "Payam Emami", "initials": "PE"}, {"family": "Kultima", "given": "Kim", "initials": "K"}, {"family": "Lampa", "given": "Samuel", "initials": "S"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Ludwig", "given": "Christian", "initials": "C"}, {"family": "Moreno", "given": "Pablo", "initials": "P"}, {"family": "Neumann", "given": "Steffen", "initials": "S"}, {"family": "Novella", "given": "Jon Ander", "initials": "JA"}, {"family": "O'Donovan", "given": "Claire", "initials": "C"}, {"family": "Pearce", "given": "Jake T M", "initials": "JTM"}, {"family": "Peluso", "given": "Alina", "initials": "A"}, {"family": "Piras", "given": "Marco Enrico", "initials": "ME"}, {"family": "Pireddu", "given": "Luca", "initials": "L"}, {"family": "Reed", "given": "Michelle A C", "initials": "MAC"}, {"family": "Rocca-Serra", "given": "Philippe", "initials": "P"}, {"family": "Roger", "given": "Pierrick", "initials": "P"}, {"family": "Rosato", "given": "Antonio", "initials": "A"}, {"family": "Rueedi", "given": "Rico", "initials": "R"}, {"family": "Ruttkies", "given": "Christoph", "initials": "C"}, {"family": "Sadawi", "given": "Noureddin", "initials": "N"}, {"family": "Salek", "given": "Reza M", "initials": "RM"}, {"family": "Sansone", "given": "Susanna-Assunta", "initials": "SA"}, {"family": "Selivanov", "given": "Vitaly", "initials": "V"}, {"family": "Spjuth", "given": "Ola", "initials": "O"}, {"family": "Schober", "given": "Daniel", "initials": "D"}, {"family": "Th\u00e9venot", "given": "Etienne A", "initials": "EA"}, {"family": "Tomasoni", "given": "Mattia", "initials": "M"}, {"family": "van Rijswijk", "given": "Merlijn", "initials": "M"}, {"family": "van Vliet", "given": "Michael", "initials": "M"}, {"family": "Viant", "given": "Mark R", "initials": "MR"}, {"family": "Weber", "given": "Ralf J M", "initials": "RJM"}, {"family": "Zanetti", "given": "Gianluigi", "initials": "G"}, {"family": "Steinbeck", "given": "Christoph", "initials": "C"}], "type": "journal article", "published": "2018-12-07", "journal": {"volume": null, "issn": "2047-217X", "issue": null, "title": "Gigascience", "issn-l": "2047-217X"}, "abstract": "Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism. The research field is dynamic and expanding with applications across biomedical, biotechnological and many other applied biological domains. Its computationally-intensive nature has driven requirements for open data formats, data repositories and data analysis tools. However, the rapid progress has resulted in a mosaic of independent-and sometimes incompatible-analysis methods that are difficult to connect into a useful and complete data analysis solution.\n\nPhenoMeNal (Phenome and Metabolome aNalysis) is an advanced and complete solution to set up Infrastructure-as-a-Service (IaaS) that brings workflow-oriented, interoperable metabolomics data analysis platforms into the cloud. PhenoMeNal seamlessly integrates a wide array of existing open source tools which are tested and packaged as Docker containers through the project's continuous integration process and deployed based on a kubernetes orchestration framework. It also provides a number of standardized, automated and published analysis workflows in the user interfaces Galaxy, Jupyter, Luigi and Pachyderm.\n\nPhenoMeNal constitutes a keystone solution in cloud e-infrastructures available for metabolomics. PhenoMeNal is a unique and complete solution for setting up cloud e-infrastructures through easy-to-use web interfaces that can be scaled to any custom public and private cloud environment. By harmonizing and automating software installation and configuration and through ready-to-use scientific workflow user interfaces, PhenoMeNal has succeeded in providing scientists with workflow-driven, reproducible and shareable metabolomics data analysis platforms which are interfaced through standard data formats, representative datasets, versioned, and have been tested for reproducibility and interoperability. The elastic implementation of PhenoMeNal further allows easy adaptation of the infrastructure to other application areas and 'omics research domains.", "doi": "10.1093/gigascience/giy149", "pmid": "30535405", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5232984"}], "notes": [], "created": "2019-01-14T19:40:52.962Z", "modified": "2020-01-21T13:53:22.851Z"}, {"entity": "publication", "iuid": "52812467a6ef42a3a827328042bb65c1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52812467a6ef42a3a827328042bb65c1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52812467a6ef42a3a827328042bb65c1"}}, "title": "Transcriptional and Epigenetic Changes Influencing Skeletal Muscle Metabolism in Women With Polycystic Ovary Syndrome.", "authors": [{"family": "Nilsson", "given": "Emma", "initials": "E"}, {"family": "Benrick", "given": "Anna", "initials": "A"}, {"family": "Kokosar", "given": "Milana", "initials": "M"}, {"family": "Krook", "given": "Anna", "initials": "A"}, {"family": "Lindgren", "given": "Eva", "initials": "E"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "Martis", "given": "Mihaela M", "initials": "MM"}, {"family": "H\u00f8jlund", "given": "Kurt", "initials": "K"}, {"family": "Ling", "given": "Charlotte", "initials": "C"}, {"family": "Stener-Victorin", "given": "Elisabet", "initials": "E"}], "type": "journal article", "published": "2018-12-01", "journal": {"volume": "103", "issn": "1945-7197", "issue": "12", "pages": "4465-4477", "title": "J. Clin. Endocrinol. Metab.", "issn-l": "0021-972X"}, "abstract": "Insulin resistance in skeletal muscle is a major risk factor for the development of type 2 diabetes in women with polycystic ovary syndrome (PCOS). Despite this, the mechanisms underlying insulin resistance in PCOS are largely unknown.\n\nTo investigate the genome-wide DNA methylation and gene expression patterns in skeletal muscle from women with PCOS and controls and relate them to phenotypic variations.\n\nIn a case-control study, skeletal muscle biopsies from women with PCOS (n = 17) and age-, weight-, and body mass index\u2012matched controls (n = 14) were analyzed by array-based DNA methylation and mRNA expression profiling.\n\nEighty-five unique transcripts were differentially expressed in muscle from women with PCOS vs controls, including DYRK1A, SYNPO2, SCP2, and NAMPT. Furthermore, women with PCOS had reduced expression of genes involved in immune system pathways. Two CpG sites showed differential DNA methylation after correction for multiple testing. However, an mRNA expression of \u223c30% of the differentially expressed genes correlated with DNA methylation levels of CpG sites in or near the gene. Functional follow-up studies demonstrated that KLF10 is under transcriptional control of insulin, where insulin promotes glycogen accumulation in myotubes of human muscle cells. Testosterone downregulates the expression levels of COL1A1 and MAP2K6.\n\nPCOS is associated with aberrant skeletal muscle gene expression with dysregulated pathways. Furthermore, we identified specific changes in muscle DNA methylation that may affect gene expression. This study showed that women with PCOS have epigenetic and transcriptional changes in skeletal muscle that, in part, can explain the metabolic abnormalities seen in these women.", "doi": "10.1210/jc.2018-00935", "pmid": "30113663", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5063490"}], "notes": [], "created": "2019-01-15T08:08:28.581Z", "modified": "2020-01-21T13:53:22.420Z"}, {"entity": "publication", "iuid": "fc52d1d5a1a043869becd96bf8455139", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fc52d1d5a1a043869becd96bf8455139.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fc52d1d5a1a043869becd96bf8455139"}}, "title": "Impact of forced fatty acid synthesis on metabolism and physiology of Saccharomyces cerevisiae.", "authors": [{"family": "Gossing", "given": "Michael", "initials": "M"}, {"family": "Smialowska", "given": "Agata", "initials": "A"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2018-12-01", "journal": {"volume": "18", "issn": "1567-1364", "issue": "8", "pages": null, "title": "FEMS Yeast Res.", "issn-l": "1567-1356"}, "abstract": "Nutrient sensing and signaling controls the cellular response to extracellular nutrients and intracellular metabolites. Nutrient-dependent regulation of metabolism ensures balanced energy production and expenditure. We show that disturbing energy balance by forcing fatty acid synthesis has profound impact on metabolism and physiology of the yeast cell. In addition to an expected increase in storage lipids, we observed increased \u03b2-oxidation and reduced amino acid biosynthesis, indicating increased activity of nutrient-sensitive kinase Snf1p. We also observed increased sensitivity to rapamycin as well as decreased ribosome biogenesis and translation, indicating reduced activity of nutrient-sensitive kinase target of rapamycin complex 1. Additionally, we detected increased levels of oxidative stress and lower levels of amino acids. This study provides detailed insight into cellular resource redistribution in response to forced fatty acid synthesis and enables optimized engineering of microbial lipid production.", "doi": "10.1093/femsyr/foy096", "pmid": "30169781", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5086656"}], "notes": [], "created": "2018-12-05T11:23:07.233Z", "modified": "2024-01-16T13:48:44.942Z"}, {"entity": "publication", "iuid": "ae28c25c11f74bc182125086f0dec5ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae28c25c11f74bc182125086f0dec5ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae28c25c11f74bc182125086f0dec5ca"}}, "title": "RNA-sequencing reveals long-term effects of silver nanoparticles on human lung cells", "authors": [{"family": "Gliga", "given": "Anda R", "initials": "AR"}, {"family": "Di Bucchianico", "given": "Sebastiano", "initials": "S"}, {"family": "Lindvall", "given": "Jessica", "initials": "J", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Fadeel", "given": "Bengt", "initials": "B"}, {"family": "Karlsson", "given": "Hanna L", "initials": "HL"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Despite a considerable focus on the adverse effects of silver nanoparticles (AgNPs) in recent years, studies on the potential long-term effects of AgNPs are scarce. The aim of this study was to explore the effects of AgNPs following repeated low-dose, long-term exposure of human bronchial epithelial cells. To this end, the human BEAS-2B cell line was exposed to 1\u2009\u00b5g/mL AgNPs (10\u2009nm) for 6 weeks followed by RNA-sequencing (RNA-Seq) as well as genome-wide DNA methylation analysis. The transcriptomics analysis showed that a substantial number of genes (1717) were differentially expressed following AgNP exposure whereas only marginal effects on DNA methylation were observed. Downstream analysis of the transcriptomics data identified several affected pathways including the 'fibrosis' and 'epithelial-mesenchymal transition' (EMT) pathway. Subsequently, functional validation studies were performed using AgNPs of two different sizes (10\u2009nm and 75\u2009nm). Both NPs increased collagen deposition, indicative of fibrosis, and induced EMT, as evidenced by an increased invasion index, anchorage independent cell growth, as well as cadherin switching. In conclusion, using a combination of RNA-Seq and functional assays, our study revealed that repeated low-dose, long-term exposure of human BEAS-2B cells to AgNPs is pro-fibrotic, induces EMT and cell transformation.", "doi": "10.1038/s41598-018-25085-5", "pmid": "29703973", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "ArrayExpress", "description": "RNA-Seq of BEAS-2B cells treated with low doses of Ag nanoparticles for 6 weeks", "key": "E-MTAB-6321"}, {"db": "ArrayExpress", "description": "DNA methylation profiling of BEAS-2B cells exposed to low doses of Ag nanoparticles for 6 weeks", "key": "E-MTAB-6331"}], "notes": [], "created": "2018-05-03T10:11:16.742Z", "modified": "2021-07-05T12:48:15.926Z"}, {"entity": "publication", "iuid": "6c456bc1f43a4319b5ca4ab537842052", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c456bc1f43a4319b5ca4ab537842052.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c456bc1f43a4319b5ca4ab537842052"}}, "title": "EMBLmyGFF3: a converter facilitating genome annotation submission to European Nucleotide Archive", "authors": [{"family": "Norling", "given": "Martin", "initials": "M"}, {"family": "Jareborg", "given": "Niclas", "initials": "N"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "11", "issn": "1756-0500", "issue": "1", "pages": null, "title": "BMC Res Notes", "issn-l": "1756-0500"}, "abstract": null, "doi": "10.1186/s13104-018-3686-x", "pmid": "30103816", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Support and Infrastructure": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [], "notes": [], "created": "2018-10-10T12:34:25.371Z", "modified": "2020-01-21T13:53:22.058Z"}, {"entity": "publication", "iuid": "cc30831e3cc647858c35e963f1214907", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc30831e3cc647858c35e963f1214907.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc30831e3cc647858c35e963f1214907"}}, "title": "Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere", "authors": [{"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M"}, {"family": "Simone", "given": "Domenico", "initials": "D"}, {"family": "Wu", "given": "Xiaofen", "initials": "X"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Nilsson", "given": "Emelie", "initials": "E"}, {"family": "Holmfeldt", "given": "Karin", "initials": "K"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal-article", "published": "2018-11-20", "journal": {"volume": "9", "issn": "2150-7511", "issue": "6", "pages": null, "title": "MBio", "issn-l": null}, "abstract": "The continental subsurface is suggested to contain a significant part of the earth's total biomass. However, due to the difficulty of sampling, the deep subsurface is still one of the least understood ecosystems. Therefore, microorganisms inhabiting this environment might profoundly influence the global nutrient and energy cycles. In this study, \n                in situ fixed RNA transcripts from two deep continental groundwaters from the \u00c4sp\u00f6 Hard Rock Laboratory (a Baltic Sea-influenced water with a residence time of <20\u2009years, defined as \"modern marine,\" and an \"old saline\" groundwater with a residence time of thousands of years) were subjected to metatranscriptome sequencing. Although small subunit (SSU) rRNA gene and mRNA transcripts aligned to all three domains of life, supporting activity within these community subsets, the data also suggested that the groundwaters were dominated by bacteria. Many of the SSU rRNA transcripts grouped within newly described candidate phyla or could not be mapped to known branches on the tree of life, suggesting that a large portion of the active biota in the deep biosphere remains unexplored. Despite the extremely oligotrophic conditions, mRNA transcripts revealed a diverse range of metabolic strategies that were carried out by multiple taxa in the modern marine water that is fed by organic carbon from the surface. In contrast, the carbon dioxide- and hydrogen-fed old saline water with a residence time of thousands of years predominantly showed the potential to carry out translation. This suggested these cells were active, but waiting until an energy source episodically becomes available.IMPORTANCE A newly designed sampling apparatus was used to fix RNA under in situ conditions in the deep continental biosphere and benchmarks a strategy for deep biosphere metatranscriptomic sequencing. This apparatus enabled the identification of active community members and the processes they carry out in this extremely oligotrophic environment. This work presents for the first time evidence of eukaryotic, archaeal, and bacterial activity in two deep subsurface crystalline rock groundwaters from the \u00c4sp\u00f6 Hard Rock Laboratory with different depths and geochemical characteristics. The findings highlight differences between organic carbon-fed shallow communities and carbon dioxide- and hydrogen-fed old saline waters. In addition, the data reveal a large portion of uncharacterized microorganisms, as well as the important role of candidate phyla in the deep biosphere, but also the disparity in microbial diversity when using standard microbial 16S rRNA gene amplification versus the large unknown portion of the community identified with unbiased metatranscriptomes.", "doi": "10.1128/mbio.01792-18", "pmid": "30459191", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-12-05T08:23:11.449Z", "modified": "2024-01-16T13:48:45.178Z"}, {"entity": "publication", "iuid": "b105e92bc27d4c6f92109308208147d7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b105e92bc27d4c6f92109308208147d7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b105e92bc27d4c6f92109308208147d7"}}, "title": "Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies", "authors": [{"family": "Akhter", "given": "Shirin", "initials": "S"}, {"family": "Kretzschmar", "given": "Warren W", "initials": "WW"}, {"family": "Nordal", "given": "Veronika", "initials": "V"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}, {"family": "Sundstr\u00f6m", "given": "Jens F", "initials": "JF"}], "type": "journal-article", "published": "2018-11-13", "journal": {"volume": "9", "issn": "1664-462X", "issue": null, "pages": null, "title": "Front Plant Sci", "issn-l": "1664-462X"}, "abstract": "Recent efforts to sequence the genomes and transcriptomes of several gymnosperm species have revealed an increased complexity in certain gene families in gymnosperms as compared to angiosperms. One example of this is the gymnosperm sister clade to angiosperm TM3-like MADS-box genes, which at least in the conifer lineage has expanded in number of genes. We have previously identified a member of this sub-clade, the conifer gene \n            DEFICIENS AGAMOUS LIKE 19 (DAL19), as being specifically upregulated in cone-setting shoots. Here, we show through Sanger sequencing of mRNA-derived cDNA and mapping to assembled conifer genomic sequences that DAL19 produces six mature mRNA splice variants in Picea abies. These splice variants use alternate first and last exons, while their four central exons constitute a core region present in all six transcripts. Thus, they are likely to be transcript isoforms. Quantitative Real-Time PCR revealed that two mutually exclusive first DAL19 exons are differentially expressed across meristems that will form either male or female cones, or vegetative shoots. Furthermore, mRNA in situ hybridization revealed that two mutually exclusive last DAL19 exons were expressed in a cell-specific pattern within bud meristems. Based on these findings in DAL19, we developed a sensitive approach to transcript isoform assembly from short-read sequencing of mRNA. We applied this method to 42 putative MADS-box core regions in P. abies, from which we assembled 1084 putative transcripts. We manually curated these transcripts to arrive at 933 assembled transcript isoforms of 38 putative MADS-box genes. 152 of these isoforms, which we assign to 28 putative MADS-box genes, were differentially expressed across eight female, male, and vegetative buds. We further provide evidence of the expression of 16 out of the 38 putative MADS-box genes by mapping PacBio Iso-Seq circular consensus reads derived from pooled sample sequencing to assembled transcripts. In summary, our analyses reveal the use of mutually exclusive exons of MADS-box gene isoforms during early bud development in P. abies, and we find that the large number of identified MADS-box transcripts in P. abies results not only from expansion of the gene family through gene duplication events but also from the generation of numerous splice variants.", "doi": "10.3389/fpls.2018.01625", "pmid": "30483285", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2018-12-10T06:26:27.642Z", "modified": "2020-01-21T13:56:17.461Z"}, {"entity": "publication", "iuid": "7b9a4b3254e04ef1aa2d5b21da472e47", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b9a4b3254e04ef1aa2d5b21da472e47.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b9a4b3254e04ef1aa2d5b21da472e47"}}, "title": "Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen", "authors": [{"family": "Lin", "given": "Yao Cheng", "initials": "YC"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Schiffthaler", "given": "Bastian", "initials": "B"}, {"family": "Sundstr\u00f6m", "given": "G\u00f6rel", "initials": "G"}, {"family": "Zuccolo", "given": "Andrea", "initials": "A"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "de la Torre", "given": "Amanda", "initials": "A"}, {"family": "Cossu", "given": "Rosa M", "initials": "RM"}, {"family": "Hoeppner", "given": "Marc P", "initials": "MP"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Zamani", "given": "Neda", "initials": "N"}, {"family": "Johansson", "given": "Anna", "initials": "A"}, {"family": "Mannapperuma", "given": "Chanaka", "initials": "C"}, {"family": "Robinson", "given": "Kathryn M", "initials": "KM"}, {"family": "M\u00e4hler", "given": "Niklas", "initials": "N"}, {"family": "Leitch", "given": "Ilia J", "initials": "IJ"}, {"family": "Pellicer", "given": "Jaume", "initials": "J"}, {"family": "Park", "given": "Eung Jun", "initials": "EJ"}, {"family": "Van Montagu", "given": "Marc", "initials": "M"}, {"family": "Van de Peer", "given": "Yves", "initials": "Y"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Jansson", "given": "Stefan", "initials": "S"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}], "type": "journal-article", "published": "2018-10-29", "journal": {"volume": null, "issn": "0027-8424", "issue": null, "pages": "201801437", "title": "Proc Natl Acad Sci USA", "issn-l": "0027-8424"}, "abstract": null, "doi": "10.1073/pnas.1801437115", "pmid": "30373829", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "European Nucleotide Archive", "description": "GENOME AND POPULATION SEQUENCING OF ASPEN ADVANCES POPULUS AS A MODEL SYSTEM FOR PLANT RESEARCH", "key": "PRJEB23585"}, {"db": "PlantGenie.org", "description": "ftp://plantgenie.org/Publications/Lin2018/pnas201801437/", "key": "pnas201801437"}], "notes": [], "created": "2018-10-31T12:03:08.142Z", "modified": "2024-01-16T13:48:45.277Z"}, {"entity": "publication", "iuid": "65901fc54eae4009882d7c82dd0f4ae1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/65901fc54eae4009882d7c82dd0f4ae1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/65901fc54eae4009882d7c82dd0f4ae1"}}, "title": "NormalyzerDE: Online tool for improved normalization of omics expression data and high-sensitivity differential expression analysis.", "authors": [{"family": "Willforss", "given": "Jakob", "initials": "J"}, {"family": "Chawade", "given": "Aakash", "initials": "A"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2018-10-02", "journal": {"volume": null, "issn": "1535-3907", "issue": null, "pages": null, "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Technical biases are introduced in omics datasets during data generation and interfere with the ability to study biological mechanisms. Several normalization approaches have been proposed to minimize the effects of such biases, but fluctuations in the electrospray current during LC-MS gradients causes local and sample specific bias not considered by most approaches. Here we introduce a software named NormalyzerDE that includes a generic retention time (RT)-segmented approach compatible with a wide range of global normalization approaches to reduce the effects of time-resolved bias. The software offers straightforward access to multiple normalization methods, allows for dataset evaluation and normalization quality assessment as well as subsequent or independent differential expression analysis using the empirical Bayes Limma approach. When evaluated on two spike-in datasets the RT-segmented approaches outperformed conventional approaches by detecting more peptides (8 - 36%) without loss of precision. Furthermore, differential expression analysis using the Limma approach consistently increased recall (2 - 35%) compared to ANOVA. The combination of RT-normalization and Limma was in one case able to distinguish 108% (2597 vs. 1249) more spike-in peptides compared to traditional approaches. NormalyzerDE provides widely usable tools for performing, and evaluating the outcome of, normalization and makes calculation of subsequent differential expression statistics straightforward. The program is available as a web server at http://quantitativeproteomics.org/normalyzerde.", "doi": "10.1021/acs.jproteome.8b00523", "pmid": "30277078", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Support and Infrastructure": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [], "notes": [], "created": "2019-01-15T07:52:06.446Z", "modified": "2020-01-21T13:53:22.307Z"}, {"entity": "publication", "iuid": "524aab4cca634eddbaaa020947156da9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/524aab4cca634eddbaaa020947156da9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/524aab4cca634eddbaaa020947156da9"}}, "title": "Mutation, methylation, and gene expression profiles in dup(1q)-positive pediatric B-cell precursor acute lymphoblastic leukemia.", "authors": [{"family": "Gunnarsson", "given": "Rebeqa", "initials": "R"}, {"family": "Dilorenzo", "given": "Sebastian", "initials": "S"}, {"family": "Lundin-Str\u00f6m", "given": "Kristina B", "initials": "KB"}, {"family": "Olsson", "given": "Linda", "initials": "L"}, {"family": "Biloglav", "given": "Andrea", "initials": "A"}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H", "orcid": "0000-0001-8703-1173", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a75300e8c346858ce8dd8f64ecae85.json"}}, {"family": "Rissler", "given": "Marianne", "initials": "M"}, {"family": "Wahlberg", "given": "Per", "initials": "P"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Castor", "given": "Anders", "initials": "A"}, {"family": "Behrendtz", "given": "Mikael", "initials": "M"}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}, {"family": "Paulsson", "given": "Kajsa", "initials": "K", "orcid": "0000-0001-7950-222X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2033b23811f1432c90ad860dd993e7a8.json"}}, {"family": "Isaksson", "given": "Anders", "initials": "A", "orcid": "0000-0001-6576-7825", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d38a1f99951441399c146b96e58f9ba.json"}}, {"family": "Johansson", "given": "Bertil", "initials": "B"}], "type": "journal article", "published": "2018-10-00", "journal": {"volume": "32", "issn": "1476-5551", "issue": "10", "pages": "2117-2125", "title": "Leukemia", "issn-l": "0887-6924"}, "abstract": "High-throughput sequencing was applied to investigate the mutation/methylation patterns on 1q and gene expression profiles in pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL) with/without (w/wo) dup(1q). Sequencing of the breakpoint regions and all exons on 1q in seven dup(1q)-positive cases revealed non-synonymous somatic single nucleotide variants (SNVs) in BLZF1, FMN2, KCNT2, LCE1C, NES, and PARP1. Deep sequencing of these in a validation cohort w (n = 17)/wo (n = 94) dup(1q) revealed similar SNV frequencies in the two groups (47% vs. 35%; P = 0.42). Only 0.6% of the 36,259 CpGs on 1q were differentially methylated between cases w (n = 14)/wo (n = 13) dup(1q). RNA sequencing of high hyperdiploid (HeH) and t(1;19)(q23;p13)-positive cases w (n = 14)/wo (n = 52) dup(1q) identified 252 and 424 differentially expressed genes, respectively; only seven overlapped. Of the overexpressed genes in the HeH and t(1;19) groups, 23 and 31%, respectively, mapped to 1q; 60-80% of these encode nucleic acid/protein binding factors or proteins with catalytic activity. We conclude that the pathogenetically important consequence of dup(1q) in BCP ALL is a gene-dosage effect, with the deregulated genes differing between genetic subtypes, but involving similar molecular functions, biological processes, and protein classes.", "doi": "10.1038/s41375-018-0092-2", "pmid": "29626196", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41375-018-0092-2"}, {"db": "pmc", "key": "PMC6170391"}], "notes": [], "created": "2018-10-22T10:04:01.973Z", "modified": "2024-01-16T13:48:45.412Z"}, {"entity": "publication", "iuid": "1c1ee87a79fa49479cf514aa5bbb3ec2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c1ee87a79fa49479cf514aa5bbb3ec2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c1ee87a79fa49479cf514aa5bbb3ec2"}}, "title": "Methanogens and Iron-Reducing Bacteria: the Overlooked Members of Mercury-Methylating Microbial Communities in Boreal Lakes", "authors": [{"family": "Bravo", "given": "Andrea G", "initials": "AG"}, {"family": "Peura", "given": "Sari", "initials": "S"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Ahmed", "given": "Omneya", "initials": "O"}, {"family": "Mateos-Rivera", "given": "Alejandro", "initials": "A"}, {"family": "Herrero Ortega", "given": "Sonia", "initials": "S"}, {"family": "Schaefer", "given": "Jeffra K", "initials": "JK"}, {"family": "Bouchet", "given": "Sylvain", "initials": "S"}, {"family": "Tolu", "given": "Julie", "initials": "J"}, {"family": "Bj\u00f6rn", "given": "Erik", "initials": "E"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}], "type": "journal-article", "published": "2018-09-21", "journal": {"volume": "84", "issn": "0099-2240", "issue": "23", "pages": null, "title": "Appl Environ Microbiol", "issn-l": null}, "abstract": "Methylmercury is a potent human neurotoxin which biomagnifies in aquatic food webs. Although anaerobic microorganisms containing the \n                hgcA gene potentially mediate the formation of methylmercury in natural environments, the diversity of these mercury-methylating microbial communities remains largely unexplored. Previous studies have implicated sulfate-reducing bacteria as the main mercury methylators in aquatic ecosystems. In the present study, we characterized the diversity of mercury-methylating microbial communities of boreal lake sediments using high-throughput sequencing of 16S rRNA and hgcA genes. Our results show that in the lake sediments, Methanomicrobiales and Geobacteraceae also represent abundant members of the mercury-methylating communities. In fact, incubation experiments with a mercury isotopic tracer and molybdate revealed that only between 38% and 45% of mercury methylation was attributed to sulfate reduction. These results suggest that methanogens and iron-reducing bacteria may contribute to more than half of the mercury methylation in boreal lakes.IMPORTANCE Despite the global awareness that mercury, and methylmercury in particular, is a neurotoxin to which millions of people continue to be exposed, there are sizable gaps in the understanding of the processes and organisms involved in methylmercury formation in aquatic ecosystems. In the present study, we shed light on the diversity of the microorganisms responsible for methylmercury formation in boreal lake sediments. All the microorganisms identified are associated with the processing of organic matter in aquatic systems. Moreover, our results show that the well-known mercury-methylating sulfate-reducing bacteria constituted only a minor portion of the potential mercury methylators. In contrast, methanogens and iron-reducing bacteria were important contributors to methylmercury formation, highlighting their role in mercury cycling in the environment.", "doi": "10.1128/aem.01774-18", "pmid": "30242005", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-12-10T06:30:18.313Z", "modified": "2020-01-21T13:56:17.332Z"}, {"entity": "publication", "iuid": "19f23c88f5d44289a4ff88982fe8a86d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19f23c88f5d44289a4ff88982fe8a86d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19f23c88f5d44289a4ff88982fe8a86d"}}, "title": "Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora.", "authors": [{"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Tripathy", "given": "Sucheta", "initials": "S"}, {"family": "Malar C", "given": "Mathu", "initials": "M"}, {"family": "Panda", "given": "Arijit", "initials": "A"}, {"family": "Kushwaha", "given": "Sandeep K", "initials": "SK"}, {"family": "Chawade", "given": "Aakash", "initials": "A"}, {"family": "Andreasson", "given": "Erik", "initials": "E"}, {"family": "Grenville-Briggs", "given": "Laura J", "initials": "LJ"}, {"family": "Whisson", "given": "Stephen C", "initials": "SC"}], "type": "journal article", "published": "2018-09-01", "journal": {"volume": "10", "issn": "1759-6653", "issue": "9", "pages": "2432-2442", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Species from the genus Phytophthora are well represented among organisms causing serious diseases on trees. Phytophthora plurivora has been implicated in long-term decline of woodland trees across Europe. Here we present a draft genome sequence of P. plurivora, originally isolated from diseased European beech (Fagus sylvatica) in Malm\u00f6, Sweden. When compared with other sequenced Phytophthora species, the P. plurivora genome assembly is relatively compact, spanning 41\u2009Mb. This is organized in 1,919 contigs and 1,898 scaffolds, encompassing 11,741 predicted genes, and has a repeat content of approximately 15%. Comparison of allele frequencies revealed evidence for tetraploidy in the sequenced isolate. As in other sequenced Phytophthora species, P. plurivora possesses genes for pathogenicity-associated RXLR and Crinkle and Necrosis effectors, predominantly located in gene-sparse genomic regions. Comparison of the P. plurivora RXLR effectors with orthologs in other sequenced species in the same clade (Phytophthora multivora and Phytophthora capsici) revealed that the orthologs were likely to be under neutral or purifying selection.", "doi": "10.1093/gbe/evy162", "pmid": "30060094", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5061551"}, {"db": "pmc", "key": "PMC6152947"}], "notes": [], "created": "2018-10-31T19:48:03.537Z", "modified": "2024-01-16T13:48:45.560Z"}, {"entity": "publication", "iuid": "f4879bb970374d7290430fcb284ab42c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4879bb970374d7290430fcb284ab42c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4879bb970374d7290430fcb284ab42c"}}, "title": "A fine-needle aspiration-based protein signature discriminates benign from malignant breast lesions", "authors": [{"family": "Franz\u00e9n", "given": "Bo", "initials": "B"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Hatschek", "given": "Thomas", "initials": "T"}, {"family": "Becker", "given": "Susanne", "initials": "S"}, {"family": "Wik", "given": "Lotta", "initials": "L"}, {"family": "Kierkegaard", "given": "Jonas", "initials": "J"}, {"family": "Eriksson", "given": "Annika", "initials": "A"}, {"family": "Muppani", "given": "Naveen R", "initials": "NR"}, {"family": "Auer", "given": "Gert", "initials": "G"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "Lewensohn", "given": "Rolf", "initials": "R"}], "type": "journal-article", "published": "2018-09-00", "journal": {"volume": "12", "issn": "1878-0261", "issue": "9", "pages": "1415-1428", "title": "Mol Oncol", "issn-l": "1574-7891"}, "abstract": "There are increasing demands for informative cancer biomarkers, accessible via minimally invasive procedures, both for initial diagnostics and to follow-up personalized cancer therapy. Fine-needle aspiration (FNA) biopsy provides ready access to relevant tissues; however, the minute sample amounts require sensitive multiplex molecular analysis to achieve clinical utility. We have applied proximity extension assays (PEA) and NanoString (NS) technology for analyses of proteins and of RNA, respectively, in FNA samples. Using samples from patients with breast cancer (BC, n\u00a0=\u00a025) or benign lesions (n\u00a0=\u00a033), we demonstrate that these FNA-based molecular analyses (a) can offer high sensitivity and reproducibility, (b) may provide correct diagnosis in shorter time and at a lower cost than current practice, (c) correlate with results from routine analysis (i.e., benchmarking against immunohistochemistry tests for ER, PR, HER2, and Ki67), and (d) may also help identify new markers related to immunotherapy. A specific 11-protein signature, including FGF binding protein 1, decorin, and furin, distinguished all cancer patient samples from all benign lesions in our main cohort and in smaller replication cohort. Due to the minimally traumatic sampling and rich molecular information, this combined proteomics and transcriptomic methodology is promising for diagnostics and evaluation of treatment efficacy in BC.", "doi": "10.1002/1878-0261.12350", "pmid": "30019538", "labels": {"Clinical Biomarkers": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-10-30T08:20:05.244Z", "modified": "2024-01-16T13:48:45.690Z"}, {"entity": "publication", "iuid": "8632729fa96a46f29792fa9c136defbf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8632729fa96a46f29792fa9c136defbf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8632729fa96a46f29792fa9c136defbf"}}, "title": "Life history of Parnips and the evolutionary origin of gall wasps", "authors": [{"family": "Ronquist", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3929-251X", "researcher": {"href": "https://publications.scilifelab.se/researcher/440662f277ea4756a08a7f5925b3f485.json"}}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA"}, {"family": "V\u00e5rdal", "given": "Hege", "initials": "H"}, {"family": "Nieves-Aldrey", "given": "Jos\u00e9 Luis", "initials": "JL"}], "type": "journal-article", "published": "2018-08-27", "journal": {"volume": "65", "issn": "1314-2607", "issue": null, "pages": "91-110", "title": "JHR", "issn-l": "1070-9428"}, "abstract": null, "doi": "10.3897/jhr.65.24115", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-01-16T07:52:39.649Z", "modified": "2023-06-19T13:49:29.233Z"}, {"entity": "publication", "iuid": "bf6eba36bb944d65a7a1dee876bac65a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf6eba36bb944d65a7a1dee876bac65a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf6eba36bb944d65a7a1dee876bac65a"}}, "title": "Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum.", "authors": [{"family": "Liao", "given": "Zhen", "initials": "Z"}, {"family": "Kjellin", "given": "Jonas", "initials": "J"}, {"family": "Hoeppner", "given": "Marc P", "initials": "MP"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2018-08-21", "journal": {"volume": "15", "issn": "1555-8584", "issue": "7", "pages": "937-954", "title": "RNA Biol", "issn-l": "1547-6286"}, "abstract": "Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, comparably little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals. High-throughput sequencing of small RNAs and poly(A)-selected RNAs demonstrated that the Dicer-like protein DrnB is required, and essentially specific, for global miRNA maturation in D. discoideum. Our RNA-seq data also showed that longer miRNA transcripts, generally preceded by a T-rich putative promoter motif, accumulate in a drnB knock-out strain. For two model miRNAs we defined the transcriptional start sites (TSSs) of primary (pri)-miRNAs and showed that they carry the RNA polymerase II specific m\n            7G-cap. The generation of the 3'-ends of these pri-miRNAs differs, with pri-mir-1177 reading into the downstream gene, and pri-mir-1176 displaying a distinct end. This 3\u00b4-end is processed to shorter intermediates, stabilized in DrnB-depleted cells, of which some carry a short oligo(A)-tail. Furthermore, we identified 10 new miRNAs, all DrnB dependent and developmentally regulated. Thus, the miRNA machinery in D. discoideum shares features with both plants and animals, which is in agreement with its evolutionary position and perhaps also an adaptation to its complex lifestyle: unicellular growth and multicellular development.", "doi": "10.1080/15476286.2018.1481697", "pmid": "29966484", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC6161686"}], "notes": [], "created": "2019-01-15T08:17:59.971Z", "modified": "2020-01-21T13:53:22.469Z"}, {"entity": "publication", "iuid": "f68a54ce39ff44abba37badf71d54fdf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f68a54ce39ff44abba37badf71d54fdf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f68a54ce39ff44abba37badf71d54fdf"}}, "title": "Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake", "authors": [{"family": "Peura", "given": "Sari", "initials": "S"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Aalto", "given": "Sanni L", "initials": "SL"}, {"family": "Morales", "given": "Sergio E", "initials": "SE"}, {"family": "Nyk\u00e4nen", "given": "Hannu", "initials": "H"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}], "type": "journal-article", "published": "2018-08-14", "journal": {"volume": "9", "issn": "2150-7511", "issue": "4", "pages": null, "title": "MBio", "issn-l": null}, "abstract": "Oxygen-stratified lakes are typical for the boreal zone and also a major source of greenhouse gas emissions in the region. Due to shallow light penetration, restricting the growth of phototrophic organisms, and large allochthonous organic carbon inputs from the catchment area, the lake metabolism is expected to be dominated by heterotrophic organisms. In this study, we test this assumption and show that the potential for autotrophic carbon fixation and internal carbon cycling is high throughout the water column. Further, we show that during the summer stratification carbon fixation can exceed respiration in a boreal lake even below the euphotic zone. Metagenome-assembled genomes and 16S profiling of a vertical transect of the lake revealed multiple organisms in an oxygen-depleted compartment belonging to novel or poorly characterized phyla. Many of these organisms were chemolithotrophic, potentially deriving their energy from reactions related to sulfur, iron, and nitrogen transformations. The community, as well as the functions, was stratified along the redox gradient. The autotrophic potential in the lake metagenome below the oxygenic zone was high, pointing toward a need for revising our concepts of internal carbon cycling in boreal lakes. Further, the importance of chemolithoautotrophy for the internal carbon cycling suggests that many predicted climate change-associated fluctuations in the physical properties of the lake, such as altered mixing patterns, likely have consequences for the whole-lake metabolism even beyond the impact to the phototrophic community.\n                IMPORTANCE Autotrophic organisms at the base of the food web are the only life form capable of turning inorganic carbon into the organic form, facilitating the survival of all other organisms. In certain environments, the autotrophic production is limited by environmental conditions and the food web is supported by external carbon inputs. One such environment is stratified boreal lakes, which are one of the biggest natural sources of greenhouse gas emissions in the boreal region. Thus, carbon cycling in these habitats is of utmost importance for the future climate. Here, we demonstrate a high potential for internal carbon cycling via phototrophic and novel chemolithotrophic organisms in the anoxic, poorly illuminated layers of a boreal lake. Our results significantly increase our knowledge on the microbial communities and their metabolic potential in oxygen-depleted freshwaters and help to understand and predict how climate change-induced alterations could impact the lake carbon dynamics.", "doi": "10.1128/mbio.00916-18", "pmid": "30108167", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "SRA", "description": null, "key": "SRP076290"}], "notes": [], "created": "2018-09-14T12:11:54.432Z", "modified": "2024-01-16T13:48:45.735Z"}, {"entity": "publication", "iuid": "f13c9c9517ad4598a26874bd7ff478d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f13c9c9517ad4598a26874bd7ff478d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f13c9c9517ad4598a26874bd7ff478d1"}}, "title": "Reduction in White Blood Cell, Neutrophil and Red Blood Cell counts Related to Gender, HLA and Islet Autoantibodies in Swedish TEDDY Children at Increased Risk for Type 1 Diabetes", "authors": [{"family": "Salami", "given": "Falastin", "initials": "F"}, {"family": "Lee", "given": "Hye Seung", "initials": "HS"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Larsson", "given": "Helena Elding", "initials": "HE"}, {"family": "Lernmark", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "T\u00f6rn", "given": "Carina", "initials": "C"}], "type": "journal-article", "published": "2018-08-13", "journal": {"volume": null, "issn": "1939-327X", "issue": null, "pages": "db180355", "title": "Diabetes", "issn-l": "0012-1797"}, "abstract": null, "doi": "10.2337/db18-0355", "pmid": "30104249", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-09-10T08:46:02.048Z", "modified": "2024-01-16T13:48:45.742Z"}, {"entity": "publication", "iuid": "c96afccb586a4170b645b616dc18405c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c96afccb586a4170b645b616dc18405c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c96afccb586a4170b645b616dc18405c"}}, "title": "Clonal relatedness in tumour pairs of breast cancer patients.", "authors": [{"family": "Biermann", "given": "Jana", "initials": "J"}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ"}, {"family": "Nemes", "given": "Szil\u00e1rd", "initials": "S"}, {"family": "Danielsson", "given": "Anna", "initials": "A"}, {"family": "Engqvist", "given": "Hanna", "initials": "H"}, {"family": "Werner R\u00f6nnerman", "given": "Elisabeth", "initials": "E"}, {"family": "Forssell-Aronsson", "given": "Eva", "initials": "E"}, {"family": "Kov\u00e1cs", "given": "Anik\u00f3", "initials": "A"}, {"family": "Karlsson", "given": "Per", "initials": "P"}, {"family": "Helou", "given": "Khalil", "initials": "K"}], "type": "journal article", "published": "2018-08-09", "journal": {"volume": "20", "issn": "1465-542X", "issue": "1", "pages": "96", "title": "Breast Cancer Res.", "issn-l": "1465-5411"}, "abstract": "Molecular classification of tumour clonality is currently not evaluated in multiple invasive breast carcinomas, despite evidence suggesting common clonal origins. There is no consensus about which type of data (e.g. copy number, mutation, histology) and especially which statistical method is most suitable to distinguish clonal recurrences from independent primary tumours.\r\n\r\nThirty-seven invasive breast tumour pairs were stratified according to laterality and time interval between the diagnoses of the two tumours. In a multi-omics approach, tumour clonality was analysed by integrating clinical characteristics (n\u00a0=\u200937), DNA copy number (n\u2009=\u200937), DNA methylation (n\u00a0=\u20098), gene expression microarray (n\u00a0=\u20097), RNA sequencing (n\u2009=\u20093), and SNP genotyping data (n\u2009=\u20093). Different statistical methods, e.g. the diagnostic similarity index (SI), were used to classify the tumours as clonally related recurrences or independent primary tumours.\r\n\r\nThe SI and hierarchical clustering showed similar tendencies and the highest concordance with the other methods. Concordant evidence for tumour clonality was found in 46% (17/37) of patients. Notably, no association was found between the current clinical guidelines and molecular tumour features.\r\n\r\nA more accurate classification of clonal relatedness between multiple breast tumours may help to mitigate treatment failure and relapse by integrating tumour-associated molecular features, clinical parameters, and statistical methods. Guidelines need to be defined with exact thresholds to standardise clonality testing in a routine diagnostic setting.", "doi": "10.1186/s13058-018-1022-y", "pmid": "30092821", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13058-018-1022-y"}, {"db": "GEO", "description": "Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas", "key": "GSE97293"}, {"db": "GEO", "description": "Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas [expression]", "key": "GSE97177"}], "notes": [], "created": "2018-08-16T15:30:10.983Z", "modified": "2024-01-16T13:48:45.779Z"}, {"entity": "publication", "iuid": "7f913d906ada4da797bcc7eff7343ba4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f913d906ada4da797bcc7eff7343ba4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f913d906ada4da797bcc7eff7343ba4"}}, "title": "Plasma Protein Profiling Reveal Osteoprotegerin as a Marker of Prognostic Impact for Colorectal Cancer", "authors": [{"family": "Birgisson", "given": "Helgi", "initials": "H"}, {"family": "Tsimogiannis", "given": "Kostas", "initials": "K"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}], "type": "journal-article", "published": "2018-08-00", "journal": {"volume": "11", "issn": "1936-5233", "issue": "4", "pages": "1034-1043", "title": "Transl Oncol", "issn-l": null}, "abstract": null, "doi": "10.1016/j.tranon.2018.05.012", "pmid": "29982101", "labels": {"Clinical Biomarkers": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-09-10T08:46:01.666Z", "modified": "2024-01-16T13:48:45.854Z"}, {"entity": "publication", "iuid": "598fb6275cd3459b814a52fb2c95092c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/598fb6275cd3459b814a52fb2c95092c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/598fb6275cd3459b814a52fb2c95092c"}}, "title": "Delineating closely related dinoflagellate lineages using phylotranscriptomics.", "authors": [{"family": "Annenkova", "given": "Nataliia V", "initials": "NV"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Logares", "given": "Ramiro", "initials": "R"}, {"family": "Kremp", "given": "Anke", "initials": "A"}, {"family": "Rengefors", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2018-08-00", "journal": {"volume": "54", "issn": "1529-8817", "issue": "4", "pages": "571-576", "title": "J. Phycol.", "issn-l": "0022-3646"}, "abstract": "Recently radiated dinoflagellates Apocalathium aciculiferum (collected in Lake Erken, Sweden), Apocalathium\u00a0malmogiense (Baltic Sea) and Apocalathium aff. malmogiense (Highway Lake, Antarctica) represent a lineage with an unresolved phylogeny. We determined their phylogenetic relationships using phylotranscriptomics based on 792 amino acid sequences. Our results showed that A.\u00a0aciculiferum diverged from the other two closely related lineages, consistent with their different morphologies in cell size, relative cell length and presence of spines. We hypothesized that A. aff. malmogiense and A.\u00a0malmogiense, which inhabit different hemispheres, are evolutionarily more closely related because they diverged from a marine common ancestor, adapting to a wide salinity range, while A.\u00a0aciculiferum colonized a freshwater habitat, by acquiring adaptations to this environment, in particular, salinity intolerance. We show that phylotranscriptomics can resolve the phylogeny of recently diverged protists. This has broad relevance, given that many phytoplankton species are morphologically very similar, and single genes sometimes lack the information to determine species' relationships.", "doi": "10.1111/jpy.12748", "pmid": "29676790", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-01-15T07:44:10.349Z", "modified": "2020-01-21T13:53:22.288Z"}, {"entity": "publication", "iuid": "a439b71bb4354049aea7a38ea1251988", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a439b71bb4354049aea7a38ea1251988.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a439b71bb4354049aea7a38ea1251988"}}, "title": "EviNet: a web platform for network enrichment analysis with flexible definition of gene sets.", "authors": [{"family": "Jeggari", "given": "Ashwini", "initials": "A"}, {"family": "Alekseenko", "given": "Zhanna", "initials": "Z"}, {"family": "Petrov", "given": "Iurii", "initials": "I"}, {"family": "Dias", "given": "Jos\u00e9 M", "initials": "JM"}, {"family": "Ericson", "given": "Johan", "initials": "J"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}], "type": "journal article", "published": "2018-07-02", "journal": {"volume": "46", "issn": "1362-4962", "issue": "W1", "pages": "W163-W170", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "The new web resource EviNet provides an easily run interface to network enrichment analysis for exploration of novel, experimentally defined gene sets. The major advantages of this analysis are (i) applicability to any genes found in the global network rather than only to those with pathway/ontology term annotations, (ii) ability to connect genes via different molecular mechanisms rather than within one high-throughput platform, and (iii) statistical power sufficient to detect enrichment of very small sets, down to individual genes. The users' gene sets are either defined prior to upload or derived interactively from an uploaded file by differential expression criteria. The pathways and networks used in the analysis can be chosen from the collection menu. The calculation is typically done within seconds or minutes and the stable URL is provided immediately. The results are presented in both visual (network graphs) and tabular formats using jQuery libraries. Uploaded data and analysis results are kept in separated project directories not accessible by other users. EviNet is available at https://www.evinet.org/.", "doi": "10.1093/nar/gky485", "pmid": "29893885", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5035166"}, {"db": "pmc", "key": "PMC6030852"}, {"db": "GEO", "description": "Mouse embryonic stem cells (mESCs) differentiation towards ventral hindbrain neuronal cell types [d0-d3.5]", "key": "GSE112698"}], "notes": [], "created": "2018-10-31T19:46:00.551Z", "modified": "2024-01-16T13:48:46.013Z"}, {"entity": "publication", "iuid": "3bc7fabf617f4b2f97b87a16c6b5d09c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3bc7fabf617f4b2f97b87a16c6b5d09c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3bc7fabf617f4b2f97b87a16c6b5d09c"}}, "title": "Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.", "authors": [{"family": "Garcia", "given": "Sarahi L", "initials": "SL"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Hamilton", "given": "Joshua J", "initials": "JJ"}, {"family": "Wurzbacher", "given": "Christian", "initials": "C"}, {"family": "Grossart", "given": "Hans-Peter", "initials": "H"}, {"family": "McMahon", "given": "Katherine D", "initials": "KD"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}], "type": "journal article", "published": "2018-06-27", "journal": {"volume": "3", "issn": "2379-5042", "issue": "3", "pages": null, "title": "mSphere", "issn-l": "2379-5042"}, "abstract": "Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.", "doi": "10.1128/mSphere.00202-18", "pmid": "29848762", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "3/3/e00202-18"}, {"db": "pmc", "key": "PMC5976882"}], "notes": [], "created": "2019-11-11T09:55:20.463Z", "modified": "2020-01-21T13:53:22.694Z"}, {"entity": "publication", "iuid": "2b8c29183a5c48a590784374854ca992", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b8c29183a5c48a590784374854ca992.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b8c29183a5c48a590784374854ca992"}}, "title": "Topology of membrane proteins  \u2014  predictions, limitations and variations", "authors": [{"family": "Tsirigos", "given": "Konstantinos D", "initials": "KD"}, {"family": "Govindarajan", "given": "Sudha", "initials": "S"}, {"family": "Bassot", "given": "Claudio", "initials": "C"}, {"family": "V\u00e4stermark", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Lamb", "given": "John", "initials": "J"}, {"family": "Shu", "given": "Nanjiang", "initials": "N"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal-article", "published": "2018-06-00", "journal": {"volume": "50", "issn": "0959-440X", "issue": null, "pages": "9-17", "title": "Current Opinion in Structural Biology", "issn-l": "0959-440X"}, "abstract": null, "doi": "10.1016/j.sbi.2017.10.003", "pmid": "29100082", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-10T13:10:22.947Z", "modified": "2024-01-16T13:48:46.169Z"}, {"entity": "publication", "iuid": "9845c1dd059a4e1b9256e20618d00bbe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9845c1dd059a4e1b9256e20618d00bbe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9845c1dd059a4e1b9256e20618d00bbe"}}, "title": "Testis transcriptome alterations in zebrafish  (Danio rerio)  with reduced fertility due to developmental exposure to 17\u03b1-ethinyl estradiol", "authors": [{"family": "Porseryd", "given": "T", "initials": "T"}, {"family": "Reyhanian Caspillo", "given": "N", "initials": "N"}, {"family": "Volkova", "given": "K", "initials": "K"}, {"family": "Elabbas", "given": "L", "initials": "L"}, {"family": "K\u00e4llman", "given": "T", "initials": "T"}, {"family": "Dinn\u00e9tz", "given": "P", "initials": "P"}, {"family": "Olsson", "given": "P E", "initials": "PE"}, {"family": "Porsch-H\u00e4llstr\u00f6m", "given": "I", "initials": "I"}], "type": "journal-article", "published": "2018-06-00", "journal": {"volume": "262", "issn": "0016-6480", "issue": null, "pages": "44-58", "title": "General and Comparative Endocrinology", "issn-l": "0016-6480"}, "abstract": "17\u03b1-Ethinylestradiol (EE\n                2) is a ubiquitous aquatic contaminant shown to decrease fish fertility at low concentrations, especially in fish exposed during development. The mechanisms of the decreased fertility are not fully understood. In this study, we perform transcriptome analysis by RNA sequencing of testes from zebrafish with previously reported lowered fertility due to exposure to low concentrations of EE2 during development. Fish were exposed to 1.2 and 1.6\u202fng/L (measured concentration; nominal concentrations 3 and 10\u202fng/L) of EE2 from fertilization to 80\u202fdays of age, followed by 82\u202fdays of remediation in clean water. RNA sequencing analysis revealed 249 and 16 genes to be differentially expressed after exposure to 1.2 and 1.6\u202fng/L, respectively; a larger inter-sample variation was noted in the latter. Expression of 11 genes were altered by both exposures and in the same direction. The coding sequences most affected could be categorized to the putative functions cell signalling, proteolysis, protein metabolic transport and lipid metabolic process. Several homeobox transcription factors involved in development and differentiation showed increased expression in response to EE2 and differential expression of genes related to cell death, differentiation and proliferation was observed. In addition, several genes related to steroid synthesis, testis development and function were differentially expressed. A number of genes associated with spermatogenesis in zebrafish and/or mouse were also found to be differentially expressed. Further, differences in non-coding sequences were observed, among them several differentially expressed miRNA that might contribute to testis gene regulation at post-transcriptional level. This study has generated insights of changes in gene expression that accompany fertility alterations in zebrafish males that persist after developmental exposure to environmental relevant concentrations of EE2 that persist followed by clean water to adulthood. Hopefully, this will generate hypotheses to test in search for mechanistic explanations.", "doi": "10.1016/j.ygcen.2018.03.011", "pmid": "29526718", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-06-25T14:08:54.942Z", "modified": "2020-01-21T13:56:17.387Z"}, {"entity": "publication", "iuid": "f9a8fbd98d754cffa1879583683d108c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9a8fbd98d754cffa1879583683d108c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9a8fbd98d754cffa1879583683d108c"}}, "title": "SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma.", "authors": [{"family": "Jord\u00e1n-Pla", "given": "Antonio", "initials": "A"}, {"family": "Yu", "given": "Simei", "initials": "S"}, {"family": "Waldholm", "given": "Johan", "initials": "J"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "\u00d6stlund Farrants", "given": "Ann-Kristin", "initials": "AK"}, {"family": "Visa", "given": "Neus", "initials": "N"}], "type": "journal article", "published": "2018-05-18", "journal": {"volume": "19", "issn": "1471-2164", "issue": "1", "pages": "367", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Brahma (BRM) is the only catalytic subunit of the SWI/SNF chromatin-remodeling complex of Drosophila melanogaster. The function of SWI/SNF in transcription has long been attributed to its ability to remodel nucleosomes, which requires the ATPase activity of BRM. However, recent studies have provided evidence for a non-catalytic function of BRM in the transcriptional regulation of a few specific genes.\n\nHere we have used RNA-seq and ChIP-seq to identify the BRM target genes in S2 cells, and we have used a catalytically inactive BRM mutant (K804R) that is unable to hydrolyze ATP to investigate the magnitude of the non-catalytic function of BRM in transcription regulation. We show that 49% of the BRM target genes in S2 cells are regulated through mechanisms that do not require BRM to have an ATPase activity. We also show that the catalytic and non-catalytic mechanisms of SWI/SNF regulation operate on two subsets of genes that differ in promoter architecture and are linked to different biological processes.\n\nThis study shows that the non-catalytic role of SWI/SNF in transcription regulation is far more prevalent than previously anticipated and that the genes that are regulated by SWI/SNF through ATPase-dependent and ATPase-independent mechanisms have specialized roles in different cellular and developmental processes.", "doi": "10.1186/s12864-018-4746-2", "pmid": "29776334", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-018-4746-2"}, {"db": "pmc", "key": "PMC5960078"}, {"db": "GEO", "description": "The distribution of Brahma in the genome of Drosophila melanogaster S2 cells and the roles of Brahma in transcription and pre-mRNA processin", "key": "GSE95236"}], "notes": [], "created": "2018-10-31T19:46:23.156Z", "modified": "2024-01-16T13:48:46.291Z"}, {"entity": "publication", "iuid": "6d67c0449e5843b2a82f8e00b62832e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d67c0449e5843b2a82f8e00b62832e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d67c0449e5843b2a82f8e00b62832e5"}}, "title": "Transcriptomic analysis of the harvested endothelial cells in a swine model of mechanical thrombectomy.", "authors": [{"family": "Jaff", "given": "Nasren", "initials": "N"}, {"family": "Grankvist", "given": "Rikard", "initials": "R"}, {"family": "Muhl", "given": "Lars", "initials": "L"}, {"family": "Chireh", "given": "Arvin", "initials": "A"}, {"family": "Sandell", "given": "Mikael", "initials": "M"}, {"family": "Jonsson", "given": "Stefan", "initials": "S"}, {"family": "Arnberg", "given": "Fabian", "initials": "F"}, {"family": "Eriksson", "given": "Ulf", "initials": "U"}, {"family": "Holmin", "given": "Staffan", "initials": "S"}], "type": "journal article", "published": "2018-05-14", "journal": {"volume": null, "issn": "1432-1920", "issue": null, "title": "Neuroradiology", "issn-l": "0028-3940"}, "abstract": "In mechanical thrombectomy (MT) for ischemic stroke, endothelial cells (ECs) from intracranial blood vessels adhere to the stent retriever device and can be harvested. However, understanding the molecular biology and the role of the endothelium in different pathological conditions remains insufficient. The purpose of the study was to characterize and analyze the molecular aspect of harvested ECs using cell culture and transcriptomic techniques in an MT swine model relevant to clinical ischemic stroke.\n\nIn swine, preformed thrombi were injected into the external carotid and subclavian arteries to occlude their branches. MT was performed according to clinical routine. The stent retriever device and thrombus were treated with cell dissociation buffer. The resulting cell suspension was analyzed by immunohistochemistry and was cultured. Cultured cells were analyzed using single-cell RNA sequencing (scRNA-seq) after fluorescence-activated cell sorting (FACS).\n\nA total number of 37 samples were obtained containing CD31-positive cells. Cell culture was successful in 90% of samples, and the cells expressed multiple typical EC protein markers. Eighty-nine percent of the sorted cells yielded high-quality transcriptomes, and single-cell transcriptomes from cultured cells showed that they expressed typical endothelial gene patterns. Gene expression analysis of ECs from an occluded artery did not show distinctive clustering into subtypes.\n\nECs harvested during MT can be cultured and analyzed using single-cell transcriptomic techniques. This analysis can be implemented in clinical practice to study the EC gene expression of comorbidities, such as hypertension, diabetes mellitus, and metabolic syndrome, in patients suffering from acute ischemic stroke.", "doi": "10.1007/s00234-018-2033-1", "pmid": "29761220", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00234-018-2033-1"}, {"db": "pmc", "key": "PMC5995995"}], "notes": [], "created": "2018-10-31T19:48:34.971Z", "modified": "2024-01-16T13:48:46.308Z"}, {"entity": "publication", "iuid": "1147aae594d748ba8261d71fb2525932", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1147aae594d748ba8261d71fb2525932.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1147aae594d748ba8261d71fb2525932"}}, "title": "Modulation of gene transcription and epigenetics of colon carcinoma cells by bacterial membrane vesicles.", "authors": [{"family": "Vdovikova", "given": "Svitlana", "initials": "S"}, {"family": "Gilfillan", "given": "Siv", "initials": "S"}, {"family": "Wang", "given": "Shixiong", "initials": "S"}, {"family": "Dongre", "given": "Mitesh", "initials": "M"}, {"family": "Wai", "given": "Sun Nyunt", "initials": "SN"}, {"family": "Hurtado", "given": "Antoni", "initials": "A"}], "type": "journal article", "published": "2018-05-09", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "7434", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Interactions between bacteria and colon cancer cells influence the transcription of the host cell. Yet is it undetermined whether the bacteria itself or the communication between the host and bacteria is responsible for the genomic changes in the eukaryotic cell. Now, we have investigated the genomic and epigenetic consequences of co-culturing colorectal carcinoma cells with membrane vesicles from pathogenic bacteria Vibrio cholerae and non-pathogenic commensal bacteria Escherichia coli. Our study reveals that membrane vesicles from pathogenic and commensal bacteria have a global impact on the gene expression of colon-carcinoma cells. The changes in gene expression correlate positively with both epigenetic changes and chromatin accessibility of promoters at transcription start sites of genes induced by both types of membrane vesicles. Moreover, we have demonstrated that membrane vesicles obtained only from V. cholerae induced the expression of genes associated with epithelial cell differentiation. Altogether, our study suggests that the observed genomic changes in host cells might be due to specific components of membrane vesicles and do not require communication by direct contact with the bacteria.", "doi": "10.1038/s41598-018-25308-9", "pmid": "29743643", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-25308-9"}, {"db": "pmc", "key": "PMC5943334"}], "notes": [], "created": "2019-01-15T08:25:32.974Z", "modified": "2020-01-21T13:53:22.499Z"}, {"entity": "publication", "iuid": "b0b81e150aa848f1bc76a3ffd4185fdf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0b81e150aa848f1bc76a3ffd4185fdf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0b81e150aa848f1bc76a3ffd4185fdf"}}, "title": "Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma.", "authors": [{"family": "Parris", "given": "Toshima Z", "initials": "TZ"}, {"family": "R\u00f6nnerman", "given": "Elisabeth Werner", "initials": "EW"}, {"family": "Engqvist", "given": "Hanna", "initials": "H"}, {"family": "Biermann", "given": "Jana", "initials": "J"}, {"family": "Truv\u00e9", "given": "Katarina", "initials": "K"}, {"family": "Nemes", "given": "Szil\u00e1rd", "initials": "S"}, {"family": "Forssell-Aronsson", "given": "Eva", "initials": "E"}, {"family": "Solinas", "given": "Giovanni", "initials": "G"}, {"family": "Kov\u00e1cs", "given": "Anik\u00f3", "initials": "A"}, {"family": "Karlsson", "given": "Per", "initials": "P"}, {"family": "Helou", "given": "Khalil", "initials": "K"}], "type": "journal article", "published": "2018-05-08", "journal": {"volume": "9", "issn": "1949-2553", "issue": "35", "pages": "24140-24154", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "Genomic instability contributes to the neoplastic phenotype by deregulating key cancer-related genes, which in turn can have a detrimental effect on patient outcome. DNA amplification of the 8p11-p12 genomic region has clinical and biological implications in multiple malignancies, including breast carcinoma where the amplicon has been associated with tumor progression and poor prognosis. However, oncogenes driving increased cancer-related death and recurrent genetic features associated with the 8p11-p12 amplicon remain to be identified. In this study, DNA copy number and transcriptome profiling data for 229 primary invasive breast carcinomas (corresponding to 185 patients) were evaluated in conjunction with clinicopathological features to identify putative oncogenes in 8p11-p12 amplified samples. Illumina paired-end whole transcriptome sequencing and whole-genome SNP genotyping were subsequently performed on 23 samples showing high-level regional 8p11-p12 amplification to characterize recurrent genetic variants (SNPs and indels), expressed gene fusions, gene expression profiles and allelic imbalances. We now show previously undescribed chromothripsis-like patterns spanning the 8p11-p12 genomic region and allele-specific DNA amplification events. In addition, recurrent amplification-specific genetic features were identified, including genetic variants in the HIST1H1E and UQCRHL genes and fusion transcripts containing MALAT1 non-coding RNA, which is known to be a prognostic indicator for breast cancer and stimulated by estrogen. In summary, these findings highlight novel candidate targets for improved treatment of 8p11-p12 amplified breast carcinomas.", "doi": "10.18632/oncotarget.25329", "pmid": "29844878", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "25329"}, {"db": "pmc", "key": "PMC5963621"}], "notes": [], "created": "2018-10-31T19:48:00.521Z", "modified": "2024-01-16T13:48:46.330Z"}, {"entity": "publication", "iuid": "a344bd74d02542a7bc490b8a4cbc1206", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a344bd74d02542a7bc490b8a4cbc1206.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a344bd74d02542a7bc490b8a4cbc1206"}}, "title": "O6-methylguanine\u2013induced transcriptional mutagenesis reduces p53 tumor-suppressor function", "authors": [{"family": "Ezerskyte", "given": "Monika", "initials": "M"}, {"family": "Paredes", "given": "Jo\u00e3o A", "initials": "JA"}, {"family": "Malvezzi", "given": "Stefano", "initials": "S"}, {"family": "Burns", "given": "John A", "initials": "JA"}, {"family": "Margison", "given": "Geoffrey P", "initials": "GP"}, {"family": "Olsson", "given": "Magnus", "initials": "M"}, {"family": "Scicchitano", "given": "David A", "initials": "DA"}, {"family": "Dreij", "given": "Kristian", "initials": "K"}], "type": "journal article", "published": "2018-05-01", "journal": {"volume": "115", "issn": "1091-6490", "issue": "18", "pages": "4731-4736", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Altered protein function due to mutagenesis plays an important role in disease development. This is perhaps most evident in tumorigenesis and the associated loss or gain of function of tumor-suppressor genes and oncogenes. The extent to which lesion-induced transcriptional mutagenesis (TM) influences protein function and its contribution to the development of disease is not well understood. In this study, the impact of O6-methylguanine on the transcription fidelity of p53 and the subsequent effects on the protein\u2019s function as a regulator of cell death and cell-cycle arrest were examined in human cells. Levels of TM were determined by RNA-sequencing. In cells with active DNA repair, misincorporation of uridine opposite the lesion occurred in 0.14% of the transcripts and increased to 14.7% when repair by alkylguanine\u2013DNA alkyltransferase was compromised. Expression of the dominant-negative p53 R248W mutant due to TM significantly reduced the transactivation of several established p53 target genes that mediate the tumor-suppressor function, including CDKN1A (p21) and BBC3 (PUMA). This resulted in deregulated signaling through the retinoblastoma protein and loss of G1/S cell-cycle checkpoint function. In addition, we observed impaired activation of apoptosis coupled to the reduction of the tumor-suppressor functions of p53. Taking these findings together, this work provides evidence that TM can induce phenotypic changes in mammalian cells that have important implications for the role of TM in tumorigenesis.", "doi": "10.1073/pnas.1721764115", "pmid": "29666243", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "1721764115"}], "notes": [], "created": "2018-04-20T07:29:36.693Z", "modified": "2024-01-16T13:48:46.353Z"}, {"entity": "publication", "iuid": "a0f2bd77920a4d238a730c603af1a9ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a0f2bd77920a4d238a730c603af1a9ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a0f2bd77920a4d238a730c603af1a9ef"}}, "title": "Array profiling reveals contribution of Cthrc1 to growth of the denervated rat urinary bladder.", "authors": [{"family": "Zhu", "given": "Baoyi", "initials": "B"}, {"family": "Ekman", "given": "Mari", "initials": "M"}, {"family": "Svensson", "given": "Daniel", "initials": "D"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Nilsson", "given": "Bengt-Olof", "initials": "BO"}, {"family": "Uvelius", "given": "Bengt", "initials": "B"}, {"family": "Sw\u00e4rd", "given": "Karl", "initials": "K"}], "type": "journal article", "published": "2018-05-01", "journal": {"volume": "314", "issn": "1522-1466", "issue": "5", "pages": "F893-F905", "title": "Am. J. Physiol. Renal Physiol.", "issn-l": "1522-1466"}, "abstract": "Bladder denervation and bladder outlet obstruction are urological conditions that cause bladder growth. Transcriptomic surveys in outlet obstruction have identified differentially expressed genes, but similar studies following denervation have not been done. This was addressed using a rat model in which the pelvic ganglia were cryo-ablated followed by bladder microarray analyses. At 10 days following denervation, bladder weight had increased 5.6-fold, and 2,890 mRNAs and 135 micro-RNAs (miRNAs) were differentially expressed. Comparison with array data from obstructed bladders demonstrated overlap between the conditions, and 10% of mRNAs changed significantly and in the same direction. Many mRNAs, including collagen triple helix repeat containing 1 ( Cthrc1), Prc1, Plod2, and Dkk3, and miRNAs, such as miR-212 and miR-29, resided in the shared signature. Discordantly regulated transcripts in the two models were rare, making up for <0.07% of all changes, and the gene products in this category localized to the urothelium of normal bladders. These transcripts may potentially be used to diagnose sensory denervation. Western blotting demonstrated directionally consistent changes at the protein level, with increases of, e.g., Cthrc1, Prc1, Plod2, and Dkk3. We chose Cthrc1 for further studies and found that Cthrc1 was induced in the smooth muscle cell (SMC) layer following denervation. TGF-\u03b21 stimulation and miR-30d-5p inhibition increased Cthrc1 in bladder SMCs, and knockdown and overexpression of Cthrc1 reduced and increased SMC proliferation. This work defines common and distinguishing features of bladder denervation and obstruction and suggests a role for Cthrc1 in bladder growth following denervation.", "doi": "10.1152/ajprenal.00499.2017", "pmid": "29357417", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-01-15T07:56:26.832Z", "modified": "2021-07-05T12:48:16.034Z"}, {"entity": "publication", "iuid": "55ceeadd5d334003b06f99b0bdcba393", "links": {"self": {"href": "https://publications.scilifelab.se/publication/55ceeadd5d334003b06f99b0bdcba393.json"}, "display": {"href": "https://publications.scilifelab.se/publication/55ceeadd5d334003b06f99b0bdcba393"}}, "title": "Mitochondrial Translation Efficiency Controls Cytoplasmic Protein Homeostasis", "authors": [{"family": "Suhm", "given": "Tamara", "initials": "T"}, {"family": "Kaimal", "given": "Jayasankar Mohanakrishnan", "initials": "JM"}, {"family": "Dawitz", "given": "Hannah", "initials": "H"}, {"family": "Peselj", "given": "Carlotta", "initials": "C"}, {"family": "Masser", "given": "Anna E", "initials": "AE"}, {"family": "Hanz\u00e9n", "given": "Sarah", "initials": "S"}, {"family": "Ambro\u017ei\u010d", "given": "Matev\u017e", "initials": "M"}, {"family": "Smialowska", "given": "Agata", "initials": "A"}, {"family": "Bj\u00f6rck", "given": "Markus L", "initials": "ML"}, {"family": "Brzezinski", "given": "Peter", "initials": "P"}, {"family": "Nystr\u00f6m", "given": "Thomas", "initials": "T"}, {"family": "B\u00fcttner", "given": "Sabrina", "initials": "S"}, {"family": "Andr\u00e9asson", "given": "Claes", "initials": "C"}, {"family": "Ott", "given": "Martin", "initials": "M"}], "type": "journal-article", "published": "2018-05-00", "journal": {"volume": null, "issn": "1550-4131", "issue": null, "pages": null, "title": "Cell Metabolism", "issn-l": "1550-4131"}, "abstract": null, "doi": "10.1016/j.cmet.2018.04.011", "pmid": "29754951", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-05-31T14:53:53.754Z", "modified": "2024-01-16T13:48:46.401Z"}, {"entity": "publication", "iuid": "e0e299f2920c45afa3763b218f36089f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0e299f2920c45afa3763b218f36089f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0e299f2920c45afa3763b218f36089f"}}, "title": "Expression of scavenger receptor MARCO defines a targetable tumor-associated macrophage subset in non-small cell lung cancer.", "authors": [{"family": "La Fleur", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Boura", "given": "Vanessa F", "initials": "VF"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Berglund", "given": "Anders", "initials": "A"}, {"family": "Pont\u00e9n", "given": "Victor", "initials": "V"}, {"family": "Mattsson", "given": "Johanna S M", "initials": "JSM"}, {"family": "Djureinovic", "given": "Dijana", "initials": "D"}, {"family": "Persson", "given": "Johan", "initials": "J"}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H"}, {"family": "Isaksson", "given": "Johan", "initials": "J"}, {"family": "Brand\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Koyi", "given": "Hirsh", "initials": "H"}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Karlsson", "given": "Mikael C I", "initials": "MCI"}, {"family": "Botling", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2018-04-18", "journal": {"volume": null, "issn": "1097-0215", "issue": null, "pages": null, "title": "Int. J. Cancer", "issn-l": "0020-7136"}, "abstract": "Tumor-associated macrophages (TAMs) are attractive targets for immunotherapy. Recently, studies in animal models showed that treatment with an anti-TAM antibody directed against the scavenger receptor MARCO resulted in suppression of tumor growth and metastatic dissemination. Here we investigated the expression of MARCO in relation to other macrophage markers and immune pathways in a non-small cell lung cancer (NSCLC) cohort (n\u2009=\u2009352). MARCO, CD68, CD163, MSR1 and programmed death ligand-1 (PD-L1) were analyzed by immunohistochemistry and immunofluorescence, and associations to other immune cells and regulatory pathways were studied in a subset of cases (n\u2009=\u2009199) with available RNA-seq data. We observed a large variation in macrophage density between cases and a strong correlation between CD68 and CD163, suggesting that the majority of TAMs present in NSCLC exhibit a protumor phenotype. Correlation to clinical data only showed a weak trend toward worse survival for patients with high macrophage infiltration. Interestingly, MARCO was expressed on a distinct subpopulation of TAMs, which tended to aggregate in close proximity to tumor cell nests. On the transcriptomic level, we found a positive association between MARCO gene expression and general immune response pathways including strong links to immunosuppressive TAMs, T-cell infiltration and immune checkpoint molecules. Indeed, a higher macrophage infiltration was seen in tumors expressing PD-L1, and macrophages residing within tumor cell nests co-expressed MARCO and PD-L1. Thus, MARCO is a potential new immune target for anti-TAM treatment in a subset of NSCLC patients, possibly in combination with available immune checkpoint inhibitors.", "doi": "10.1002/ijc.31545", "pmid": "29667169", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-10-31T19:47:13.069Z", "modified": "2024-01-16T13:48:46.503Z"}, {"entity": "publication", "iuid": "a2eb1c912dac479f8c9ecfd57d465144", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2eb1c912dac479f8c9ecfd57d465144.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2eb1c912dac479f8c9ecfd57d465144"}}, "title": "Evaluation of the ISL1 gene in the pathogenesis of bladder exstrophy in a Swedish cohort.", "authors": [{"family": "Arkani", "given": "Samara", "initials": "S"}, {"family": "Cao", "given": "Jia", "initials": "J"}, {"family": "Lundin", "given": "Johanna", "initials": "J"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "Barker", "given": "Gillian", "initials": "G"}, {"family": "Holmdahl", "given": "Gundela", "initials": "G"}, {"family": "Clementsson Kockum", "given": "Christina", "initials": "C"}, {"family": "Matsson", "given": "Hans", "initials": "H"}, {"family": "Nordenskj\u00f6ld", "given": "Agneta", "initials": "A"}], "type": "journal article", "published": "2018-03-29", "journal": {"volume": "5", "issn": "2054-345X", "issue": null, "pages": "18009", "title": "Hum Genome Var", "issn-l": "2054-345X"}, "abstract": "Bladder exstrophy is a congenital closure defect of the urinary bladder with a profound effect on morbidity. Although the malformation is usually sporadic, a genetic background is supported by an increased recurrence risk in relatives, higher concordance rates in monozygotic twins and several associated chromosomal aberrations. Recently, the", "doi": "10.1038/hgv.2018.9", "pmid": "29619236", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5874392"}, {"db": "ArrayExpress", "description": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5143/", "key": "E-MTAB-5143"}], "notes": [], "created": "2018-10-31T19:44:57.444Z", "modified": "2024-01-16T13:48:46.642Z"}, {"entity": "publication", "iuid": "7ee31aa5f7f14aa08202ccadeb396609", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7ee31aa5f7f14aa08202ccadeb396609.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7ee31aa5f7f14aa08202ccadeb396609"}}, "title": "Protein Expression in Tonsillar and Base of Tongue Cancer and in Relation to Human Papillomavirus (HPV) and Clinical Outcome.", "authors": [{"family": "Ramqvist", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "N\u00e4sman", "given": "Anders", "initials": "A", "orcid": "0000-0003-4602-4297", "researcher": {"href": "https://publications.scilifelab.se/researcher/368352486dc54915b6873ad1aae59ea2.json"}}, {"family": "Franz\u00e9n", "given": "Bo", "initials": "B"}, {"family": "Bersani", "given": "Cinzia", "initials": "C"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications.scilifelab.se/researcher/54b6c0ff12c148dd803f7f72c8af0d14.json"}}, {"family": "Becker", "given": "Susanne", "initials": "S"}, {"family": "Haeggblom", "given": "Linnea", "initials": "L"}, {"family": "Kolev", "given": "Aeneas", "initials": "A"}, {"family": "Dalianis", "given": "Tina", "initials": "T"}, {"family": "Munck-Wikland", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2018-03-25", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "issn-l": null, "volume": "19", "issue": "4", "pages": "978"}, "abstract": "Human papillomavirus (HPV) is a major etiological factor for tonsillar and the base of tongue cancer (TSCC/BOTSCC). HPV-positive and HPV-negative TSCC/BOTSCC present major differences in mutations, mRNA expression and clinical outcome. Earlier protein studies on TSCC/BOTSCC have mainly analyzed individual proteins. Here, the aim was to compare a larger set of cancer and immune related proteins in HPV-positive and HPV-negative TSCC/BOTSCC in relation to normal tissue, presence of HPV, and clinical outcome. Fresh frozen tissue from 42 HPV-positive and 17 HPV-negative TSCC/BOTSCC, and corresponding normal samples, were analyzed for expression of 167 proteins using two Olink multiplex immunoassays. Major differences in protein expression between TSCC/BOTSCC and normal tissue were identified, especially in chemo- and cytokines. Moreover, 34 proteins, mainly immunoregulatory proteins and chemokines, were differently expressed in HPV-positive vs HPV-negative TSCC/BOTSCC. Several proteins were potentially related to clinical outcome for HPV-positive or HPV-negative tumors. For HPV-positive tumors, these were mostly related to angiogenesis and hypoxia. Correlation with clinical outcome of one of these, VEGFA, was validated by immunohistochemistry. Differences in immune related proteins between HPV-positive and HPV-negative TSCC/BOTSCC reflect the stronger activity of the immune defense in the former. Angiogenesis related proteins might serve as potential targets for therapy in HPV-positive TSCC/BOTSCC.", "doi": "10.3390/ijms19040978", "pmid": "29587383", "labels": {"Clinical Biomarkers": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ijms19040978"}, {"db": "pmc", "key": "PMC5979357"}], "notes": [], "created": "2018-03-29T07:15:28.434Z", "modified": "2024-01-16T13:48:46.689Z"}, {"entity": "publication", "iuid": "5c73c68928714d1ca470927905211c8e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c73c68928714d1ca470927905211c8e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c73c68928714d1ca470927905211c8e"}}, "title": "Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.", "authors": [{"family": "Zhu", "given": "Yafeng", "initials": "Y"}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ", "orcid": "0000-0003-4729-4205", "researcher": {"href": "https://publications.scilifelab.se/researcher/18aebf211fa640f48a7c8d860c168e5a.json"}}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Boekel", "given": "Jorrit", "initials": "J"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications.scilifelab.se/researcher/0942e438993b494db2a3db914852c808.json"}}, {"family": "Fernandez-Woodbridge", "given": "Alejandro", "initials": "A"}, {"family": "Branca", "given": "Rui M M", "initials": "RMM"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}], "type": "journal article", "published": "2018-03-02", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "903", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Proteogenomics enable the discovery of novel peptides (from unannotated genomic protein-coding loci) and single amino acid variant peptides (derived from single-nucleotide polymorphisms and mutations). Increasing the reliability of these identifications is crucial to ensure their usefulness for genome annotation and potential application as neoantigens in cancer immunotherapy. We here present integrated proteogenomics analysis workflow (IPAW), which combines peptide discovery, curation, and validation. IPAW includes the SpectrumAI tool for automated inspection of MS/MS spectra, eliminating false identifications of single-residue substitution peptides. We employ IPAW to analyze two proteomics data sets acquired from A431 cells and five normal human tissues using extended (pH range, 3-10) high-resolution isoelectric focusing (HiRIEF) pre-fractionation and TMT-based peptide quantitation. The IPAW results provide evidence for the translation of pseudogenes, lncRNAs, short ORFs, alternative ORFs, N-terminal extensions, and intronic sequences. Moreover, our quantitative analysis indicates that protein production from certain pseudogenes and lncRNAs is tissue specific.", "doi": "10.1038/s41467-018-03311-y", "pmid": "29500430", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Global Proteomics and Proteogenomics": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-03311-y"}, {"db": "pmc", "key": "PMC5834625"}], "notes": [], "created": "2018-03-04T17:55:08.112Z", "modified": "2024-01-16T13:48:46.793Z"}, {"entity": "publication", "iuid": "822d35eda2b54d849cd9c0b5e61cf84c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/822d35eda2b54d849cd9c0b5e61cf84c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/822d35eda2b54d849cd9c0b5e61cf84c"}}, "title": "Nubbin isoform antagonism governs Drosophila intestinal immune homeostasis.", "authors": [{"family": "Lindberg", "given": "Bo G", "initials": "BG"}, {"family": "Tang", "given": "Xiongzhuo", "initials": "X"}, {"family": "Dantoft", "given": "Widad", "initials": "W"}, {"family": "Gohel", "given": "Priya", "initials": "P"}, {"family": "Seyedoleslami Esfahani", "given": "Shiva", "initials": "S"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Engstr\u00f6m", "given": "Ylva", "initials": "Y"}], "type": "journal article", "published": "2018-03-00", "journal": {"volume": "14", "issn": "1553-7374", "issue": "3", "pages": "e1006936", "title": "PLoS Pathog.", "issn-l": "1553-7366"}, "abstract": "Gut immunity is regulated by intricate and dynamic mechanisms to ensure homeostasis despite a constantly changing microbial environment. Several regulatory factors have been described to participate in feedback responses to prevent aberrant immune activity. Little is, however, known about how transcriptional programs are directly tuned to efficiently adapt host gut tissues to the current microbiome. Here we show that the POU/Oct gene nubbin (nub) encodes two transcription factor isoforms, Nub-PB and Nub-PD, which antagonistically regulate immune gene expression in Drosophila. Global transcriptional profiling of adult flies overexpressing Nub-PB in immunocompetent tissues revealed that this form is a strong transcriptional activator of a large set of immune genes. Further genetic analyses showed that Nub-PB is sufficient to drive expression both independently and in conjunction with nuclear factor kappa B (NF-\u03baB), JNK and JAK/STAT pathways. Similar overexpression of Nub-PD did, conversely, repress expression of the same targets. Strikingly, isoform co-overexpression normalized immune gene transcription, suggesting antagonistic activities. RNAi-mediated knockdown of individual nub transcripts in enterocytes confirmed antagonistic regulation by the two isoforms and that both are necessary for normal immune gene transcription in the midgut. Furthermore, enterocyte-specific Nub-PB expression levels had a strong impact on gut bacterial load as well as host lifespan. Overexpression of Nub-PB enhanced bacterial clearance of ingested Erwinia carotovora carotovora 15. Nevertheless, flies quickly succumbed to the infection, suggesting a deleterious immune response. In line with this, prolonged overexpression promoted a proinflammatory signature in the gut with induction of JNK and JAK/STAT pathways, increased apoptosis and stem cell proliferation. These findings highlight a novel regulatory mechanism of host-microbe interactions mediated by antagonistic transcription factor isoforms.", "doi": "10.1371/journal.ppat.1006936", "pmid": "29499056", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PPATHOGENS-D-17-02350"}, {"db": "pmc", "key": "PMC5851638"}], "notes": [], "created": "2019-01-15T07:55:56.735Z", "modified": "2021-07-05T12:48:16.004Z"}, {"entity": "publication", "iuid": "510dfd6804e8495085ecfb30ff4970b7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/510dfd6804e8495085ecfb30ff4970b7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/510dfd6804e8495085ecfb30ff4970b7"}}, "title": "Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases", "authors": [{"family": "Bravo", "given": "Andrea G", "initials": "AG"}, {"family": "Zopfi", "given": "Jakob", "initials": "J"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Xu", "given": "Jingying", "initials": "J"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Schaefer", "given": "Jeffra K", "initials": "JK"}, {"family": "Pot\u00e9", "given": "John", "initials": "J"}, {"family": "Cosio", "given": "Claudia", "initials": "C"}], "type": "journal-article", "published": "2018-03-00", "journal": {"volume": "12", "issn": "1751-7370", "issue": "3", "pages": "802-812", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "Microbial mercury (Hg) methylation in sediments can result in bioaccumulation of the neurotoxin methylmercury\u00a0(MMHg) in aquatic food webs. Recently, the discovery of the gene hgcA, required for Hg methylation, revealed that the diversity of Hg methylators is much broader than previously thought. However, little is known about the identity of Hg-methylating microbial organisms and the environmental factors controlling their activity and distribution in lakes. Here, we combined high-throughput sequencing of 16S rRNA and hgcA genes with the\u00a0chemical characterization of sediments impacted by a waste water treatment plant that releases significant amounts of organic matter and iron. Our results highlight that the ferruginous geochemical conditions prevailing at 1-2\u2009cm depth\u00a0are conducive to MMHg formation and that the Hg-methylating guild\u00a0is\u00a0composed of iron and sulfur-transforming bacteria, syntrophs, and methanogens. Deltaproteobacteria, notably Geobacteraceae, dominated the hgcA carrying communities, while sulfate reducers constituted only a minor component, despite being considered the main Hg methylators in many anoxic aquatic environments. Because iron is widely applied in waste water treatment, the importance of Geobacteraceae for Hg methylation and the complexity of Hg-methylating communities reported here are likely to occur worldwide in sediments impacted by waste water treatment plant discharges and in\u00a0iron-rich sediments in general.", "doi": "10.1038/s41396-017-0007-7", "pmid": "29321692", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "BioProject", "description": "Mercury methylation in the bay of Vidy", "key": "PRJEB20838"}], "notes": [], "created": "2018-09-14T12:07:23.512Z", "modified": "2024-01-16T13:48:46.847Z"}, {"entity": "publication", "iuid": "4021e997cb6a4cc2b45dd15b6222ab2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4021e997cb6a4cc2b45dd15b6222ab2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4021e997cb6a4cc2b45dd15b6222ab2a"}}, "title": "Ten steps to get started in Genome Assembly and Annotation", "authors": [{"family": "Dominguez Del Angel", "given": "Victoria", "initials": "V"}, {"family": "Hjerde", "given": "Erik", "initials": "E"}, {"family": "Sterck", "given": "Lieven", "initials": "L"}, {"family": "Capella-Gutierrez", "given": "Salvadors", "initials": "S"}, {"family": "Notredame", "given": "Cederic", "initials": "C"}, {"family": "Vinnere Pettersson", "given": "Olga", "initials": "O"}, {"family": "Amselem", "given": "Joelle", "initials": "J"}, {"family": "Bouri", "given": "Laurent", "initials": "L"}, {"family": "Bocs", "given": "Stephanie", "initials": "S"}, {"family": "Klopp", "given": "Christophe", "initials": "C"}, {"family": "Gibrat", "given": "Jean Francois", "initials": "JF"}, {"family": "Vlasova", "given": "Anna", "initials": "A"}, {"family": "Leskosek", "given": "Brane L", "initials": "BL"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Binzer-Panchal", "given": "Mahesh", "initials": "M"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}], "type": "journal-article", "published": "2018-02-05", "journal": {"volume": "7", "issn": "2046-1402", "issue": null, "pages": "148", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.13598.1", "pmid": "29568489", "labels": {"National Genomics Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Support and Infrastructure": "Technology development", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [], "notes": [], "created": "2018-02-09T10:16:05.868Z", "modified": "2024-01-16T13:48:46.950Z"}, {"entity": "publication", "iuid": "2bece02164b940219e2c7ebb877fa30e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2bece02164b940219e2c7ebb877fa30e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2bece02164b940219e2c7ebb877fa30e"}}, "title": "The discovery of the virulence gene ToxA in the wheat and barley pathogen Bipolaris sorokiniana.", "authors": [{"family": "McDonald", "given": "Megan C", "initials": "MC"}, {"family": "Ahren", "given": "Dag", "initials": "D"}, {"family": "Simpfendorfer", "given": "Steven", "initials": "S"}, {"family": "Milgate", "given": "Andrew", "initials": "A"}, {"family": "Solomon", "given": "Peter S", "initials": "PS"}], "type": "journal article", "published": "2018-02-00", "journal": {"volume": "19", "issn": "1364-3703", "issue": "2", "pages": "432-439", "title": "Mol. Plant Pathol.", "issn-l": null}, "abstract": "Bipolaris sorokiniana is the causal agent of multiple diseases on wheat and barley and is the primary constraint to cereal production throughout South Asia. Despite its significance, the molecular basis of disease is poorly understood. To address this, the genomes of three Australian isolates of B. sorokiniana were sequenced and screened for known pathogenicity genes. Sequence analysis revealed that the isolate BRIP10943 harboured the ToxA gene, which has been associated previously with disease in the wheat pathogens Parastagonospora nodorum and Pyrenophora tritici-repentis. Analysis of the regions flanking ToxA within B. sorokiniana revealed that it was embedded within a 12-kb genomic element nearly identical to the corresponding regions in P. nodorum and P. tritici-repentis. A screen of 35 Australian B. sorokiniana isolates confirmed that ToxA was present in 12 isolates. Sequencing of the ToxA genes within these isolates revealed two haplotypes, which differed by a single non-synonymous nucleotide substitution. Pathogenicity assays showed that a B. sorokiniana isolate harbouring ToxA was more virulent on wheat lines that contained the sensitivity gene when compared with a non-ToxA isolate. This work demonstrates that proteins that confer host-specific virulence can be horizontally acquired across multiple species. This acquisition can dramatically increase the virulence of pathogenic strains on susceptible cultivars, which, in an agricultural setting, can have devastating economic and social impacts.", "doi": "10.1111/mpp.12535", "pmid": "28093843", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-01-15T08:42:45.073Z", "modified": "2020-01-21T13:53:22.524Z"}, {"entity": "publication", "iuid": "c9af84ed6e2e41d4830e9f77a67c002f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9af84ed6e2e41d4830e9f77a67c002f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9af84ed6e2e41d4830e9f77a67c002f"}}, "title": "Gene expression profiling across ontogenetic stages in the wood white (Leptidea sinapis) reveals pathways linked to butterfly diapause regulation.", "authors": [{"family": "Leal", "given": "Luis", "initials": "L"}, {"family": "Talla", "given": "Venkat", "initials": "V"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "Friberg", "given": "Magne", "initials": "M"}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Dinc\u0103", "given": "Vlad", "initials": "V"}, {"family": "Vila", "given": "Roger", "initials": "R"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal article", "published": "2018-02-00", "journal": {"volume": "27", "issn": "1365-294X", "issue": "4", "pages": "935-948", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "In temperate latitudes, many insects enter diapause (dormancy) during the cold season, a period during which developmental processes come to a standstill. The wood white (Leptidea sinapis) is a butterfly species distributed across western Eurasia that shows photoperiod-induced diapause with variation in critical day-length across populations at different latitudes. We assembled transcriptomes and estimated gene expression levels at different developmental stages in experimentally induced directly developing and diapausing cohorts of a single Swedish population of L.\u00a0sinapis to investigate the regulatory mechanisms underpinning diapause initiation. Different day lengths resulted in expression changes of developmental genes and affected the rate of accumulation of signal molecules, suggesting that diapause induction might be controlled by increased activity of monoamine neurotransmitters in larvae reared under short-day light conditions. Expression differences between light treatment groups of two monoamine regulator genes (DDC and ST) were observed already in instar III larvae. Once developmental pathways were irreversibly set at instar V, a handful of genes related to dopamine production were differentially expressed leading to a significant decrease in expression of global metabolic genes and increase in expression of genes related to fatty acid synthesis and sequestration. This is in line with a time-dependent (hour-glass) model of diapause regulation where a gradual shift in the concentration of monoamine neurotransmitters and their metabolites during development of larvae under short-day conditions leads to increased storage of fat, decreased energy expenditures, and ultimately developmental stasis at the pupal stage.", "doi": "10.1111/mec.14501", "pmid": "29411442", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "BioProject", "description": "SRA experiments", "key": "PRJEB24745"}, {"db": "ArrayExpress", "description": "RNA-seq data", "key": "E\u2010MTAB\u20106454"}], "notes": [], "created": "2018-10-31T19:46:48.334Z", "modified": "2020-01-21T13:56:17.397Z"}, {"entity": "publication", "iuid": "0f64522256044b27a5fdfa915c82d881", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f64522256044b27a5fdfa915c82d881.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f64522256044b27a5fdfa915c82d881"}}, "title": "Formation of mercury methylation hotspots as a consequence of forestry operations", "authors": [{"family": "Ekl\u00f6f", "given": "Karin", "initials": "K"}, {"family": "Bishop", "given": "Kevin", "initials": "K"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Bj\u00f6rn", "given": "Erik", "initials": "E"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Skyllberg", "given": "Ulf", "initials": "U"}, {"family": "Osman", "given": "Omneya A", "initials": "OA"}, {"family": "Kronberg", "given": "Rose Marie", "initials": "RM"}, {"family": "Bravo", "given": "Andrea G", "initials": "AG"}], "type": "journal-article", "published": "2018-02-00", "journal": {"volume": "613-614", "issn": "0048-9697", "issue": null, "pages": "1069-1078", "title": "Science of The Total Environment", "issn-l": "0048-9697"}, "abstract": "Earlier studies have shown that boreal forest logging can increase the concentration and export of methylmercury (MeHg) in stream runoff. Here we test whether forestry operations create soil environments of high MeHg net formation associated with distinct microbial communities. Furthermore, we test the hypothesis that Hg methylation hotspots are more prone to form after stump harvest than stem-only harvest, because of more severe soil compaction and soil disturbance. Concentrations of MeHg, percent MeHg of total Hg (THg), and bacterial community composition were determined at 200 soil sampling positions distributed across eight catchments. Each catchment was either stem-only harvested (n=3), stem- and stump-harvested (n=2) or left undisturbed (n=3). In support of our hypothesis, higher MeHg to THg ratios was observed in one of the stump-harvested catchments. While the effects of natural variation could not be ruled out, we noted that most of the highest % MeHg was observed in water-filled cavities created by stump removal or driving damage. This catchment also featured the highest bacterial diversity and highest relative abundance of bacterial families known to include Hg methylators. We propose that water-logged and disturbed soil environments associated with stump harvest can favor methylating microorganisms, which also enhance MeHg formation.", "doi": "10.1016/j.scitotenv.2017.09.151", "pmid": "28950669", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-09-14T12:07:36.259Z", "modified": "2024-01-16T13:48:46.998Z"}, {"entity": "publication", "iuid": "0fe7cecc5d93438483d4915985cc89aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0fe7cecc5d93438483d4915985cc89aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0fe7cecc5d93438483d4915985cc89aa"}}, "title": "Bacterial secretion of D-arginine controls environmental microbial biodiversity.", "authors": [{"family": "Alvarez", "given": "Laura", "initials": "L"}, {"family": "Aliashkevich", "given": "Alena", "initials": "A"}, {"family": "de Pedro", "given": "Miguel A", "initials": "MA"}, {"family": "Cava", "given": "Felipe", "initials": "F"}], "type": "journal article", "published": "2018-02-00", "journal": {"volume": "12", "issn": "1751-7370", "issue": "2", "pages": "438-450", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "Bacteria face tough competition in polymicrobial communities. To persist in a specific niche, many species produce toxic extracellular effectors to interfere with the growth of nearby microbes. These effectors include the recently reported non-canonical D-amino acids (NCDAAs). In Vibrio cholerae, the causative agent of cholera, NCDAAs control cell wall integrity in stationary phase. Here, an analysis of the composition of the extracellular medium of V. cholerae revealed the unprecedented presence of D-Arg. Compared with other D-amino acids, D-Arg displayed higher potency and broader toxicity in terms of the number of bacterial species affected. Tolerance to D-Arg was associated with mutations in the phosphate transport and chaperone systems, whereas D-Met lethality was suppressed by mutations in cell wall determinants. These observations suggest that NCDAAs target different cellular processes. Finally, even though virtually all Vibrio species are tolerant to D-Arg, only a few can produce this D-amino acid. Indeed, we demonstrate that D-Arg may function as part of a cooperative strategy in vibrio communities to protect non-producing members from competing bacteria. Because NCDAA production is widespread in bacteria, we anticipate that D-Arg is a relevant modulator of microbial subpopulations in diverse ecosystems.", "doi": "10.1038/ismej.2017.176", "pmid": "29028003", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "ismej2017176"}, {"db": "pmc", "key": "PMC5776457"}], "notes": [], "created": "2019-01-15T08:28:36.885Z", "modified": "2020-01-21T13:53:22.518Z"}, {"entity": "publication", "iuid": "53eaaa7ffacc4f81b74119dcf025b234", "links": {"self": {"href": "https://publications.scilifelab.se/publication/53eaaa7ffacc4f81b74119dcf025b234.json"}, "display": {"href": "https://publications.scilifelab.se/publication/53eaaa7ffacc4f81b74119dcf025b234"}}, "title": "Pulmonary fibrosis in vivo displays increased p21 expression reduced by 5-HT2B receptor antagonists in vitro - a potential pathway affecting proliferation.", "authors": [{"family": "L\u00f6fdahl", "given": "Anna", "initials": "A"}, {"family": "Rydell-T\u00f6rm\u00e4nen", "given": "Kristina", "initials": "K"}, {"family": "Larsson-Callerfelt", "given": "Anna-Karin", "initials": "A"}, {"family": "Wengl\u00e9n", "given": "Christina", "initials": "C"}, {"family": "Westergren-Thorsson", "given": "Gunilla", "initials": "G"}], "type": "journal article", "published": "2018-01-31", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "1927", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Serotonin (5-hydroxytryptamine) has repeatedly been associated with the development of fibrotic disorders such as pulmonary fibrosis. By blocking the binding of 5-HT to 5-HT\r\n            2B receptors with receptor antagonists, several pro-fibrotic mechanisms can be inhibited. Bleomycin-induced pulmonary fibrosis is a model used to evaluate pathological mechanisms and pharmacological interventions. Previously we have shown attenuated fibrosis in systemic bleomycin-treated mice following treatment with two 5-HT2B receptor antagonists (EXT5 and EXT9). Our aim is to further identify cellular effects and signaling pathways associated with the anti-fibrotic effects of EXT5/9. Gene expressions in lung tissues from systemic bleomycin-treated mice were examined, revealing significant increased expression of Cdkn1\u03b1 (a gene coding for p21), particularly in distal regions of the lung. In vitro studies in human lung fibroblasts revealed increased levels of p21 (p\u2009=\u20090.0032) and pAkt (p\u2009=\u20090.12) following treatment with 5-HT (10\u2009\u00b5M). The induction of p21 and pAkt appears to be regulated by 5-HT2B receptors, with diminished protein levels following EXT9-treatment (p21 p\u2009=\u20090.0024, pAkt p\u2009=\u20090.15). Additionally, 5-HT induced fibroblast proliferation, an event significantly reduced by EXT5 (10\u2009\u00b5M) and EXT9 (10\u2009\u00b5M). In conclusion, our results suggest that 5-HT2B receptor antagonism attenuates pulmonary fibrosis in part by anti-proliferative effects, associated with inhibited pAkt/p21 signaling pathway.", "doi": "10.1038/s41598-018-20430-0", "pmid": "29386571", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-20430-0"}, {"db": "pmc", "key": "PMC5792547"}], "notes": [], "created": "2019-01-14T17:49:02.094Z", "modified": "2020-01-21T13:53:22.762Z"}, {"entity": "publication", "iuid": "db65681a7824495b8a0d65c93763a2b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db65681a7824495b8a0d65c93763a2b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db65681a7824495b8a0d65c93763a2b9"}}, "title": "A Single Bout of Electroacupuncture Remodels Epigenetic and Transcriptional Changes in Adipose Tissue in Polycystic Ovary Syndrome.", "authors": [{"family": "Kokosar", "given": "Milana", "initials": "M"}, {"family": "Benrick", "given": "Anna", "initials": "A"}, {"family": "Perfilyev", "given": "Alexander", "initials": "A"}, {"family": "Nilsson", "given": "Emma", "initials": "E"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Ling", "given": "Charlotte", "initials": "C"}, {"family": "Stener-Victorin", "given": "Elisabet", "initials": "E"}], "type": "journal article", "published": "2018-01-30", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "1878", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "A single bout of electroacupuncture results in muscle contractions and increased whole body glucose uptake in women with polycystic ovary syndrome (PCOS). Women with PCOS have transcriptional and epigenetic alterations in the adipose tissue and we hypothesized that electroacupuncture induces epigenetic and transcriptional changes to restore metabolic alterations. Twenty-one women with PCOS received a single bout of electroacupuncture, which increased the whole body glucose uptake. In subcutaneous adipose tissue biopsies, we identified treatment-induced expression changes of 2369 genes (Q\u2009<\u20090.05) and DNA methylation changes of 7055 individual genes (Q\u2009=\u20090.11). The largest increase in expression was observed for FOSB (2405%), and the largest decrease for LOC100128899 (54%). The most enriched pathways included Acute phase response signaling and LXR/RXR activation. The DNA methylation changes ranged from 1-16%, and 407 methylation sites correlated with gene expression. Among genes known to be differentially expressed in PCOS, electroacupuncture reversed the expression of 80 genes, including PPAR\u03b3 and ADIPOR2. Changes in the expression of Nr4a2 and Junb are reversed by adrenergic blockers in rats demonstrating that changes in gene expression, in part, is due to activation of the sympathetic nervous system. In conclusion, low-frequency electroacupuncture with muscle contractions remodels epigenetic and transcriptional changes that elicit metabolic improvement.", "doi": "10.1038/s41598-017-17919-5", "pmid": "29382850", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-17919-5"}, {"db": "pmc", "key": "PMC5790004"}], "notes": [], "created": "2018-12-14T13:52:37.615Z", "modified": "2020-01-21T13:53:22.064Z"}, {"entity": "publication", "iuid": "943fcace4f18487990477589f516bde1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/943fcace4f18487990477589f516bde1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/943fcace4f18487990477589f516bde1"}}, "title": "The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction.", "authors": [{"family": "Salvatore", "given": "M", "initials": "M"}, {"family": "Shu", "given": "N", "initials": "N"}, {"family": "Elofsson", "given": "A", "initials": "A"}], "type": "journal article", "published": "2018-01-00", "journal": {"volume": "27", "issn": "1469-896X", "issue": "1", "pages": "195-201", "title": "Protein Sci.", "issn-l": "0961-8368"}, "abstract": "SubCons is a recently developed method that predicts the subcellular localization of a protein. It combines predictions from four predictors using a Random Forest classifier. Here, we present the user-friendly web-interface implementation of SubCons. Starting from a protein sequence, the server rapidly predicts the subcellular localizations of an individual protein. In addition, the server accepts the submission of sets of proteins either by uploading the files or programmatically by using command line WSDL API scripts. This makes SubCons ideal for proteome wide analyses allowing the user to scan a whole proteome in few days. From the web page, it is also possible to download precalculated predictions for several eukaryotic organisms. To evaluate the performance of SubCons we present a benchmark of LocTree3 and SubCons using two recent mass-spectrometry based datasets of mouse and drosophila proteins. The server is available at http://subcons.bioinfo.se/.", "doi": "10.1002/pro.3297", "pmid": "28901589", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5734273"}], "notes": [], "created": "2017-11-10T13:09:49.314Z", "modified": "2024-01-16T13:48:47.161Z"}, {"entity": "publication", "iuid": "8f5e094a933447ccbc5cdaa743aeec5e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f5e094a933447ccbc5cdaa743aeec5e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f5e094a933447ccbc5cdaa743aeec5e"}}, "title": "MicroRNA expression profiles in non\u2011epithelial ovarian tumors.", "authors": [{"family": "Chang", "given": "Roger K", "initials": "RK"}, {"family": "Li", "given": "Xidan", "initials": "X"}, {"family": "Mu", "given": "Ninni", "initials": "N"}, {"family": "Hrydziuszko", "given": "Olga", "initials": "O"}, {"family": "Garcia-Majano", "given": "Beatriz", "initials": "B"}, {"family": "Larsson", "given": "Catharina", "initials": "C"}, {"family": "Lui", "given": "Weng-Onn", "initials": "WO"}], "type": "journal article", "published": "2018-01-00", "journal": {"volume": "52", "issn": "1791-2423", "issue": "1", "pages": "55-66", "title": "Int. J. Oncol.", "issn-l": "1791-2423"}, "abstract": "Ovarian germ cell tumors (OGCTs) and sex cord stromal tumors (SCSTs) are rare gynecologic tumors that are derived from germ and stromal cells, respectively. Unlike their epithelial counterparts, molecular pathogenesis of these tumor types is still poorly understood. Here, we characterized microRNA (miRNA) expression profiles of 9\u00a0OGCTs (2\u00a0malignant and 7\u00a0benign) and 3\u00a0SCSTs using small RNA sequencing. We observed significant miRNA expression variations among the three tumor groups. To further demonstrate the biological relevance of our findings, we selected 12\u00a0miRNAs for validation in an extended cohort of 16\u00a0OGCTs (9\u00a0benign and 7\u00a0malignant) and 7\u00a0SCSTs by reverse transcription-quantitative polymerase chain reaction. Higher expression of miR\u2011373\u20113p, miR\u2011372\u20113p and miR\u2011302c\u20113p and lower expression of miR\u2011199a\u20115p, miR\u2011214\u20115p and miR\u2011202\u20113p were reproducibly observed in malignant OGCTs as compared to benign OGCTs or SCSTs. Comparing with benign OGCTs, miR\u2011202c\u20113p and miR\u2011513c\u20115p were more abundant in SCSTs. Additionally, we examined Beclin\u00a01 (BECN1), a target of miR\u2011199a\u20115p, in the clinical samples using western blot analysis. Our results show that BECN1 expression was higher in malignant OGCTs than benign OGCTs, which is concordant with their lower miR\u2011199a\u20115p expression. This study suggests that these miRNAs may have potential value as tumor markers and implications for further understanding the molecular basis of these tumor types.", "doi": "10.3892/ijo.2017.4200", "pmid": "29138809", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5743337"}], "notes": [], "created": "2019-01-15T08:05:18.683Z", "modified": "2020-01-21T13:53:22.389Z"}, {"entity": "publication", "iuid": "a59517789b7b45b3975339f26526ebc8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a59517789b7b45b3975339f26526ebc8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a59517789b7b45b3975339f26526ebc8"}}, "title": "Phylogeny, species delimitation and revision of Pleioluma (Sapotaceae) in New Caledonia, a frequently gynodioecious genus", "authors": [{"family": "Swenson", "given": "Ulf", "initials": "U"}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA"}, {"family": "Munzinger", "given": "J\u00e9r\u00f4me", "initials": "J"}], "type": "journal-article", "published": "2018-00-00", "journal": {"volume": "31", "issn": "1030-1887", "issue": "2", "pages": "120", "title": "Aust. Systematic Bot.", "issn-l": null}, "abstract": null, "doi": "10.1071/sb17040", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-01-16T07:55:37.343Z", "modified": "2021-06-21T14:48:50.615Z"}, {"entity": "publication", "iuid": "0d4095789678406cba65e6ce25b7b0a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d4095789678406cba65e6ce25b7b0a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d4095789678406cba65e6ce25b7b0a9"}}, "title": "Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration.", "authors": [{"family": "Elewa", "given": "Ahmed", "initials": "A"}, {"family": "Wang", "given": "Heng", "initials": "H"}, {"family": "Talavera-L\u00f3pez", "given": "Carlos", "initials": "C"}, {"family": "Joven", "given": "Alberto", "initials": "A"}, {"family": "Brito", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2134-7583", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0196703e4df4518b212ed1f3322e811.json"}}, {"family": "Kumar", "given": "Anoop", "initials": "A"}, {"family": "Hameed", "given": "L Shahul", "initials": "LS"}, {"family": "Penrad-Mobayed", "given": "May", "initials": "M"}, {"family": "Yao", "given": "Zeyu", "initials": "Z"}, {"family": "Zamani", "given": "Neda", "initials": "N"}, {"family": "Abbas", "given": "Yamen", "initials": "Y"}, {"family": "Abdullayev", "given": "Ilgar", "initials": "I"}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-4624-0259", "researcher": {"href": "https://publications.scilifelab.se/researcher/d85416dce306436ab0c4cdeea22a1f59.json"}}, {"family": "Simon", "given": "Andr\u00e1s", "initials": "A"}], "type": "journal article", "published": "2017-12-22", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": "2286", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Salamanders exhibit an extraordinary ability among vertebrates to regenerate complex body parts. However, scarce genomic resources have limited our understanding of regeneration in adult salamanders. Here, we present the ~20 Gb genome and transcriptome of the Iberian ribbed newt Pleurodeles waltl, a tractable species suitable for laboratory research. We find that embryonic stem cell-specific miRNAs mir-93b and mir-427/430/302, as well as Harbinger DNA transposons carrying the Myb-like proto-oncogene have expanded dramatically in the Pleurodeles waltl genome and are co-expressed during limb regeneration. Moreover, we find that a family of salamander methyltransferases is expressed specifically in adult appendages. Using CRISPR/Cas9 technology to perturb transcription factors, we demonstrate that, unlike the axolotl, Pax3 is present and necessary for development and that contrary to mammals, muscle regeneration is normal without functional Pax7 gene. Our data provide a foundation for comparative genomic studies that generate models for the uneven distribution of regenerative capacities among vertebrates.", "doi": "10.1038/s41467-017-01964-9", "pmid": "29273779", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-017-01964-9"}, {"db": "pmc", "key": "PMC5741667"}], "notes": [], "created": "2018-01-10T09:44:17.789Z", "modified": "2021-07-07T11:44:07.846Z"}, {"entity": "publication", "iuid": "b0c456eb98294268808bdeeb2a0263c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0c456eb98294268808bdeeb2a0263c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0c456eb98294268808bdeeb2a0263c0"}}, "title": "Rho-kinase inhibitor Y-27632 and hypoxia synergistically enhance chondrocytic phenotype and modify S100 protein profiles in human chondrosarcoma cells", "authors": [{"family": "Piltti", "given": "Juha", "initials": "J"}, {"family": "Bygdell", "given": "Joakim", "initials": "J"}, {"family": "Fern\u00e1ndez-Echevarr\u00eda", "given": "Cecilia", "initials": "C"}, {"family": "Marcellino", "given": "Daniel", "initials": "D"}, {"family": "Lammi", "given": "Mikko J", "initials": "MJ"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-017-03958-5", "pmid": "28623370", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T12:54:58.518Z", "modified": "2020-01-21T13:53:21.859Z"}, {"entity": "publication", "iuid": "772771bb3bbc4cbcb15ffb55d59a1acb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/772771bb3bbc4cbcb15ffb55d59a1acb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/772771bb3bbc4cbcb15ffb55d59a1acb"}}, "title": "RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study", "authors": [{"family": "Berghoff", "given": "Bork A", "initials": "BA"}, {"family": "Karlsson", "given": "Torgny", "initials": "T"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "Wagner", "given": "E Gerhart H", "initials": "EGH"}, {"family": "Grabherr", "given": "Manfred G", "initials": "MG"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "10", "issn": "1756-0381", "issue": "1", "pages": null, "title": "BioData Mining", "issn-l": "1756-0381"}, "abstract": "Measuring how gene expression changes in the course of an experiment assesses how an organism responds on a molecular level. Sequencing of RNA molecules, and their subsequent quantification, aims to assess global gene expression changes on the RNA level (transcriptome). While advances in high-throughput RNA-sequencing (RNA-seq) technologies allow for inexpensive data generation, accurate post-processing and normalization across samples is required to eliminate any systematic noise introduced by the biochemical and/or technical processes. Existing methods thus either normalize on selected known reference genes that are invariant in expression across the experiment, assume that the majority of genes are invariant, or that the effects of up- and down-regulated genes cancel each other out during the normalization.\n\nHere, we present a novel method, \n                moose\n                         , which predicts invariant genes in silico through a dynamic programming (DP) scheme and applies a quadratic normalization based on this subset. The method allows for specifying a set of known or experimentally validated invariant genes, which guides the DP. We experimentally verified the predictions of this method in the bacterium 2\n                    Escherichia coli, and show how moose\n                         is able to (i) estimate the expression value distances between RNA-seq samples, (ii) reduce the variation of expression values across all samples, and (iii) to subsequently reveal new functional groups of genes during the late stages of DNA damage. We further applied the method to three eukaryotic data sets, on which its performance compares favourably to other methods. The software is implemented in C++ and is publicly available from http://grabherr.github.io/moose2/.2\n\nThe proposed RNA-seq normalization method, \n            moose\n                         , is a valuable alternative to existing methods, with two major advantages: (i) in silico prediction of invariant genes provides a list of potential reference genes for downstream analyses, and (ii) non-linear artefacts in RNA-seq data are handled adequately to minimize variations between replicates.2", "doi": "10.1186/s13040-017-0150-8", "pmid": "28878825", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:27:45.065Z", "modified": "2024-01-16T13:48:47.258Z"}, {"entity": "publication", "iuid": "685808b763124eb0af7fdba6c37bc156", "links": {"self": {"href": "https://publications.scilifelab.se/publication/685808b763124eb0af7fdba6c37bc156.json"}, "display": {"href": "https://publications.scilifelab.se/publication/685808b763124eb0af7fdba6c37bc156"}}, "title": "Combined genome and transcriptome sequencing to investigate the plant cell wall degrading enzyme system in the thermophilic fungus Malbranchea cinnamomea", "authors": [{"family": "H\u00fcttner", "given": "Silvia", "initials": "S"}, {"family": "Nguyen", "given": "Thanh Thuy", "initials": "TT"}, {"family": "Granchi", "given": "Zoraide", "initials": "Z"}, {"family": "Chin-A-Woeng", "given": "Thomas", "initials": "T"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Larsbrink", "given": "Johan", "initials": "J"}, {"family": "Thanh", "given": "Vu Nguyen", "initials": "VN"}, {"family": "Olsson", "given": "Lisbeth", "initials": "L"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "10", "issn": "1754-6834", "issue": "1", "pages": null, "title": "Biotechnol Biofuels", "issn-l": "1754-6834"}, "abstract": null, "doi": "10.1186/s13068-017-0956-0", "pmid": "29158777", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-12-04T09:07:43.405Z", "modified": "2020-01-21T13:53:22.634Z"}, {"entity": "publication", "iuid": "10063878eda648f79dc68fd0c818180e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10063878eda648f79dc68fd0c818180e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10063878eda648f79dc68fd0c818180e"}}, "title": "Dog ownership and the risk of cardiovascular disease and death - a nationwide cohort study.", "authors": [{"family": "Mubanga", "given": "Mwenya", "initials": "M"}, {"family": "Byberg", "given": "Liisa", "initials": "L"}, {"family": "Nowak", "given": "Christoph", "initials": "C"}, {"family": "Egenvall", "given": "Agneta", "initials": "A"}, {"family": "Magnusson", "given": "Patrik K", "initials": "PK", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ed3f066719f43b291743a8bdaf3d2a0.json"}}], "type": "journal article", "published": "2017-11-17", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "15821", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Dogs may be beneficial in reducing cardiovascular risk in their owners by providing social support and motivation for physical activity. We aimed to investigate the association of dog ownership with incident cardiovascular disease (CVD) and death in a register-based prospective nation-wide cohort (n = 3,432,153) with up to 12 years of follow-up. Self-reported health and lifestyle habits were available for 34,202 participants in the Swedish Twin Register. Time-to-event analyses with time-updated covariates were used to calculate hazard ratios (HR) with 95% confidence intervals (CI). In single- and multiple-person households, dog ownership (13.1%) was associated with lower risk of death, HR 0.67 (95% CI, 0.65-0.69) and 0.89 (0.87-0.91), respectively; and CVD death, HR 0.64 (0.59-0.70), and 0.85 (0.81-0.90), respectively. In single-person households, dog ownership was inversely associated with cardiovascular outcomes (HR composite CVD 0.92, 95% CI, 0.89-0.94). Ownership of hunting breed dogs was associated with lowest risk of CVD. Further analysis in the Twin Register could not replicate the reduced risk of CVD or death but also gave no indication of confounding by disability, comorbidities or lifestyle factors. In conclusion, dog ownership appears to be associated with lower risk of CVD in single-person households and lower mortality in the general population.", "doi": "10.1038/s41598-017-16118-6", "pmid": "29150678", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-16118-6"}, {"db": "pmc", "key": "PMC5693989"}], "notes": [], "created": "2017-11-22T08:32:46.202Z", "modified": "2021-06-21T15:00:47.391Z"}, {"entity": "publication", "iuid": "8a27a149914b497aba8916c5133fc80b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a27a149914b497aba8916c5133fc80b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a27a149914b497aba8916c5133fc80b"}}, "title": "Antibody Heavy Chain Variable Domains of Different Germline Gene Origins Diversify through Different Paths", "authors": [{"family": "Kirik", "given": "Ufuk", "initials": "U"}, {"family": "Persson", "given": "Helena", "initials": "H"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Greiff", "given": "Lennart", "initials": "L"}, {"family": "Ohlin", "given": "Mats", "initials": "M"}], "type": "journal-article", "published": "2017-11-13", "journal": {"volume": "8", "issn": "1664-3224", "issue": null, "pages": null, "title": "Front Immunol", "issn-l": "1664-3224"}, "abstract": "B cells produce antibodies, key effector molecules in health and disease. They mature their properties, including their affinity for antigen, through hypermutation events; processes that involve, e.g., base substitution, codon insertion and deletion, often in association with an isotype switch. Investigations of antibody evolution define modes whereby particular antibody responses are able to form, and such studies provide insight important for instance for development of efficient vaccines. Antibody evolution is also used \n            in vitro for the design of antibodies with improved properties. To better understand the basic concepts of antibody evolution, we analyzed the mutational paths, both in terms of amino acid substitution and insertions and deletions, taken by antibodies of the IgG isotype. The analysis focused on the evolution of the heavy chain variable domain of sets of antibodies, each with an origin in 1 of 11 different germline genes representing six human heavy chain germline gene subgroups. Investigated genes were isolated from cells of human bone marrow, a major site of antibody production, and characterized by next-generation sequencing and an in-house bioinformatics pipeline. Apart from substitutions within the complementarity determining regions, multiple framework residues including those in protein cores were targets of extensive diversification. Diversity, both in terms of substitutions, and insertions and deletions, in antibodies is focused to different positions in the sequence in a germline gene-unique manner. Altogether, our findings create a framework for understanding patterns of evolution of antibodies from defined germline genes.", "doi": "10.3389/fimmu.2017.01433", "pmid": "29180996", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Drug Discovery and Development": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-13T09:53:31.932Z", "modified": "2025-10-17T13:05:08.695Z"}, {"entity": "publication", "iuid": "ecc7551bf07d4ecf930ff13d013aeee3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ecc7551bf07d4ecf930ff13d013aeee3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ecc7551bf07d4ecf930ff13d013aeee3"}}, "title": "RNA-Seq de novo assembly and differential transcriptome analysis of the nematode Ascaridia galli in relation to in vivo exposure to flubendazole", "authors": [{"family": "Martis", "given": "Mihaela M", "initials": "MM"}, {"family": "Tarbiat", "given": "Behdad", "initials": "B"}, {"family": "Tyd\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Jansson", "given": "D\u00e9sir\u00e9e S", "initials": "DS"}, {"family": "H\u00f6glund", "given": "Johan", "initials": "J"}], "type": "journal-article", "published": "2017-11-03", "journal": {"volume": "12", "issn": "1932-6203", "issue": "11", "pages": "e0185182", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": null, "doi": "10.1371/journal.pone.0185182", "pmid": "29099835", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "BioProject", "description": "RNA-seq of the nematode Ascaridia galli exposed to flubendazole against untreated control", "key": "PRJEB20558"}], "notes": [], "created": "2017-11-06T13:08:22.384Z", "modified": "2020-01-21T13:56:17.125Z"}, {"entity": "publication", "iuid": "f892ff63669141bc8f46e7fd8d8fde48", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f892ff63669141bc8f46e7fd8d8fde48.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f892ff63669141bc8f46e7fd8d8fde48"}}, "title": "SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population.", "authors": [{"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Dahlberg", "given": "Johan", "initials": "J"}, {"family": "Olason", "given": "Pall", "initials": "P"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Karlsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-8949-2587", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df14bf33f3342408d624caa70d45b7c.json"}}, {"family": "Martin", "given": "Marcel", "initials": "M"}, {"family": "Viklund", "given": "Johan", "initials": "J"}, {"family": "K\u00e4h\u00e4ri", "given": "Andreas Kusalananda", "initials": "AK"}, {"family": "Lundin", "given": "P\u00e4r", "initials": "P"}, {"family": "Che", "given": "Huiwen", "initials": "H"}, {"family": "Thutkawkorapin", "given": "Jessada", "initials": "J"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Lampa", "given": "Samuel", "initials": "S"}, {"family": "Dahlberg", "given": "Mats", "initials": "M"}, {"family": "Hagberg", "given": "Jonas", "initials": "J", "orcid": "0000-0003-2370-6025", "researcher": {"href": "https://publications.scilifelab.se/researcher/181649773b3e451981f5ffb2da4c60b9.json"}}, {"family": "Jareborg", "given": "Niclas", "initials": "N", "orcid": "0000-0002-4520-044X", "researcher": {"href": "https://publications.scilifelab.se/researcher/09533c4bd4174ecab9ba866d22a1e585.json"}}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-1250-392X", "researcher": {"href": "https://publications.scilifelab.se/researcher/241618974ae142b38e5fe84236819f2b.json"}}, {"family": "Jonasson", "given": "Inger", "initials": "I"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Magnusson", "given": "Patrik Ke", "initials": "PK"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "25", "issn": "1476-5438", "issue": "11", "pages": "1253-1260", "title": "Eur. J. Hum. Genet.", "issn-l": "1018-4813"}, "abstract": "Here we describe the SweGen data set, a comprehensive map of genetic variation in the Swedish population. These data represent a basic resource for clinical genetics laboratories as well as for sequencing-based association studies by providing information on genetic variant frequencies in a cohort that is well matched to national patient cohorts. To select samples for this study, we first examined the genetic structure of the Swedish population using high-density SNP-array data from a nation-wide cohort of over 10 000 Swedish-born individuals included in the Swedish Twin Registry. A total of 1000 individuals, reflecting a cross-section of the population and capturing the main genetic structure, were selected for whole-genome sequencing. Analysis pipelines were developed for automated alignment, variant calling and quality control of the sequencing data. This resulted in a genome-wide collection of aggregated variant frequencies in the Swedish population that we have made available to the scientific community through the website https://swefreq.nbis.se. A total of 29.2 million single-nucleotide variants and 3.8 million indels were detected in the 1000 samples, with 9.9 million of these variants not present in current databases. Each sample contributed with an average of 7199 individual-specific variants. In addition, an average of 8645 larger structural variants (SVs) were detected per individual, and we demonstrate that the population frequencies of these SVs can be used for efficient filtering analyses. Finally, our results show that the genetic diversity within Sweden is substantial compared with the diversity among continental European populations, underscoring the relevance of establishing a local reference data set.", "doi": "10.1038/ejhg.2017.130", "pmid": "28832569", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ejhg2017130"}, {"db": "pmc", "key": "PMC5765326"}], "notes": [], "created": "2017-08-24T14:18:14.989Z", "modified": "2024-01-16T13:48:47.338Z"}, {"entity": "publication", "iuid": "b08d0d754d43447c84c8ec0f537e56ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b08d0d754d43447c84c8ec0f537e56ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b08d0d754d43447c84c8ec0f537e56ef"}}, "title": "Proteomic Analysis of Phytophthora infestans Reveals the Importance of Cell Wall Proteins in Pathogenicity", "authors": [{"family": "Resj\u00f6", "given": "Svante", "initials": "S"}, {"family": "Brus", "given": "Maja", "initials": "M"}, {"family": "Ali", "given": "Ashfaq", "initials": "A"}, {"family": "Meijer", "given": "Harold J G", "initials": "HJG"}, {"family": "Sandin", "given": "Marianne", "initials": "M"}, {"family": "Govers", "given": "Francine", "initials": "F"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Grenville-Briggs", "given": "Laura", "initials": "L"}, {"family": "Andreasson", "given": "Erik", "initials": "E"}], "type": "journal-article", "published": "2017-11-00", "journal": {"volume": "16", "issn": "1535-9476", "issue": "11", "pages": "1958-1971", "title": "Mol Cell Proteomics", "issn-l": "1535-9476"}, "abstract": null, "doi": "10.1074/mcp.m116.065656", "pmid": "28935716", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T15:36:45.771Z", "modified": "2020-01-21T13:53:21.853Z"}, {"entity": "publication", "iuid": "0ea140596e2947cbba1cff3d94b7655c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0ea140596e2947cbba1cff3d94b7655c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0ea140596e2947cbba1cff3d94b7655c"}}, "title": "Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions", "authors": [{"family": "Hubalek", "given": "Valerie", "initials": "V"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Tan", "given": "BoonFei", "initials": "B"}, {"family": "Foght", "given": "Julia", "initials": "J"}, {"family": "Wendeberg", "given": "Annelie", "initials": "A"}, {"family": "Berry", "given": "David", "initials": "D"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}], "type": "journal-article", "published": "2017-10-31", "journal": {"volume": "2", "issn": "2379-5077", "issue": "5", "pages": "e00038-17", "title": "mSystems", "issn-l": "2379-5077"}, "abstract": "Syntrophy among \n            Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methanogenic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes encode the capacity for fermentation of alkanes facilitated by energy conservation linked to H2 metabolism. Instead, the presence of inferred lifestyles based on scavenging anabolic products and intermediate fermentation products derived from detrital biomass was a common feature. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H2-producing and syntrophic alkane degrader-methanogen partnership. Compared to previous work, our report points to a higher order of complexity in microbial consortia engaged in anaerobic hydrocarbon transformation. IMPORTANCE Microbial interactions between Archaea and Bacteria mediate many important chemical transformations in the biosphere from degrading abundant polymers to synthesis of toxic compounds. Two of the most pressing issues in microbial interactions are how consortia are established and how we can modulate these microbial communities to express desirable functions. Here, we propose that public goods (i.e., metabolites of high energy demand in biosynthesis) facilitate energy conservation for life under energy-limited conditions and determine the assembly and function of the consortia. Our report suggests that an understanding of public good dynamics could result in new ways to improve microbial pollutant degradation in anaerobic systems.", "doi": "10.1128/msystems.00038-17", "pmid": "29104938", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-01-09T20:51:43.787Z", "modified": "2020-01-21T13:56:17.316Z"}, {"entity": "publication", "iuid": "8325168daff7463fa7e0e4657bd6d96a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8325168daff7463fa7e0e4657bd6d96a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8325168daff7463fa7e0e4657bd6d96a"}}, "title": "Effects of long-term low oxygen tension in human chondrosarcoma cells", "authors": [{"family": "Piltti", "given": "Juha", "initials": "J"}, {"family": "Bygdell", "given": "Joakim", "initials": "J"}, {"family": "Qu", "given": "Chengjuan", "initials": "C"}, {"family": "Lammi", "given": "Mikko J", "initials": "MJ"}], "type": "journal-article", "published": "2017-10-18", "journal": {"volume": null, "issn": "0730-2312", "issue": null, "pages": null, "title": "J. Cell. Biochem.", "issn-l": null}, "abstract": null, "doi": "10.1002/jcb.26394", "pmid": "28865129", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T12:35:57.392Z", "modified": "2020-01-21T13:53:21.710Z"}, {"entity": "publication", "iuid": "7eb6fc6150224e299c4f63c3842354ba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7eb6fc6150224e299c4f63c3842354ba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7eb6fc6150224e299c4f63c3842354ba"}}, "title": "The cagE gene sequence as a diagnostic marker to identify JP2 and non-JP2 highly leukotoxic Aggregatibacter actinomycetemcomitans serotype b strains.", "authors": [{"family": "Johansson", "given": "A", "initials": "A"}, {"family": "Claesson", "given": "R", "initials": "R"}, {"family": "H\u00f6glund \u00c5berg", "given": "C", "initials": "C"}, {"family": "Haubek", "given": "D", "initials": "D"}, {"family": "Oscarsson", "given": "J", "initials": "J"}], "type": "journal article", "published": "2017-10-00", "journal": {"volume": "52", "issn": "1600-0765", "issue": "5", "pages": "903-912", "title": "J. Periodont. Res.", "issn-l": "0022-3484"}, "abstract": "Aggregatibacter actinomycetemcomitans is involved in oral and systemic infections, and is associated with, eg aggressive forms of periodontitis and with endocarditis. The cagE gene encodes a \u224839\u00a0kDa putative exotoxin expressed by A.\u00a0actinomycetemcomitans. The level of conservation of cagE, and its possible significance in periodontal disease, has not yet been thoroughly investigated. In the present study, the role of the cagE gene as a diagnostic marker has been investigated.\n\nWe have used conventional polymerase chain reaction (PCR), quantitative PCR and whole genome sequencing data to determine the prevalence of cagE in A.\u00a0actinomycetemcomitans based on analysis of: (i) 249 isolates, collected and cultivated in a Ghanaian longitudinal cohort study; (ii) a serotype b collection of 19 strains; and (iii) the 36 A.\u00a0actinomycetemcomitans genomes available in the NCBI database.\n\nWhereas cagE was absent in the other serotypes, our data support that this gene sequence is linked to a virulent and highly leukotoxic group of serotype b strains, including both JP2 and non-JP2 genotypes of A.\u00a0actinomycetemcomitans.\n\nWe propose that cagE has the potential to be used as a PCR-based gene marker for the identification of a virulent and highly leukotoxic group of serotype b strains, including both JP2 and non-JP2 genotypes. This finding might be of importance in the risk assessment of the development of periodontal attachment loss in young individuals and hence suggested to be a relevant discovery in future development of new diagnostic tools and/or treatment strategies.", "doi": "10.1111/jre.12462", "pmid": "28397250", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "GENBANK", "key": "LT601546"}, {"db": "GENBANK", "key": "LT601547"}, {"db": "GENBANK", "key": "LT601548"}, {"db": "GENBANK", "key": "AAM68959"}, {"db": "GENBANK", "key": "AHN72937"}], "notes": [], "created": "2019-01-15T11:43:22.448Z", "modified": "2020-01-21T13:53:22.548Z"}, {"entity": "publication", "iuid": "a6910e07accd4f5495ef7e4d0c9c35cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a6910e07accd4f5495ef7e4d0c9c35cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a6910e07accd4f5495ef7e4d0c9c35cc"}}, "title": "Antibody Affinity Against 2009 A/H1N1 Influenza and Pandemrix Vaccine Nucleoproteins Differs Between Childhood Narcolepsy Patients and Controls.", "authors": [{"family": "Lind", "given": "Alexander", "initials": "A"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Ramelius", "given": "Anita", "initials": "A"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Arnheim-Dahlstr\u00f6m", "given": "Lisen", "initials": "L"}, {"family": "Lamb", "given": "Favelle", "initials": "F"}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Ambati", "given": "Aditya", "initials": "A"}, {"family": "Maeurer", "given": "Markus", "initials": "M"}, {"family": "Lima Bomfim", "given": "Izaura", "initials": "I"}, {"family": "Fink", "given": "Katharina", "initials": "K"}, {"family": "Fex", "given": "Malin", "initials": "M"}, {"family": "T\u00f6rn", "given": "Carina", "initials": "C"}, {"family": "Elding Larsson", "given": "Helena", "initials": "H"}, {"family": "Lernmark", "given": "\u00c5ke", "initials": "\u00c5"}], "type": "journal article", "published": "2017-10-00", "journal": {"volume": "30", "issn": "1557-8976", "issue": "8", "pages": "590-600", "title": "Viral Immunol.", "issn-l": "0882-8245"}, "abstract": "Increased narcolepsy incidence was observed in Sweden following the 2009 influenza vaccination with Pandemrix\u00ae. A substitution of the 2009 nucleoprotein for the 1934 variant has been implicated in narcolepsy development. The aims were to determine (a) antibody levels toward wild-type A/H1N1-2009[A/California/04/2009(H1N1)] (NP-CA2009) and Pandemrix-[A/Puerto Rico/8/1934(H1N1)] (NP-PR1934) nucleoproteins in 43 patients and 64 age-matched controls; (b) antibody affinity in reciprocal competitive assays in 11 childhood narcolepsy patients compared with 21 age-matched controls; and (c) antibody levels toward wild-type A/H1N1-2009[A/California/04/2009(H1N1)] (H1N1 NS1), not a component of the Pandemrix vaccine. In vitro transcribed and translated 35S-methionine-labeled H1N1 influenza A virus proteins were used in radiobinding reciprocal competition assays to estimate antibody levels and affinity (Kd). Childhood patients had higher NP-CA2009 (p\u2009=\u20090.0339) and NP-PR1934 (p\u2009=\u20090.0246) antibody levels compared with age-matched controls. These childhood controls had lower NP-CA2009 (p\u2009=\u20090.0221) and NP-PR1934 (p\u2009=\u20090.00619) antibodies compared with controls 13 years or older. In contrast, in patients 13 years or older, the levels of NP-PR1934 (p\u2009=\u20090.279) and NP-CA2009 (p\u2009=\u20090.0644) antibodies did not differ from the older controls. Childhood antibody affinity (Kd) against NP-CA2009 was comparable between controls (68\u2009ng/mL) and patients (74\u2009ng/mL; p\u2009=\u20090.21) with NP-CA2009 and NP-PR1934 displacement (controls: 165\u2009ng/mL; patients: 199\u2009ng/mL; p\u2009=\u20090.48). In contrast, antibody affinity against NP-PR1934 was higher in controls with either NP-PR1934 (controls: 9\u2009ng/mL; patients: 20\u2009ng/mL; p\u2009=\u20090.0031) or NP-CA2009 (controls: 14\u2009ng/mL; patients: 23\u2009ng/mL; p\u2009=\u20090.0048). A/H1N1-NS1 antibodies were detected in 0/43 of the narcolepsy patients compared with 3/64 (4.7%) controls (p\u2009=\u20090.272). Similarly, none (0/11) of the childhood patients and 1/21 (4.8%) of the childhood controls had A/H1N1-NS1 antibodies. The higher antibody affinities against NP-PR1934 in controls suggest better protection against wild-type virus. In contrast, the reduced NP-PR1934 antibody affinities among childhood narcolepsy patients suggest poor protection from the wild-type A/H1N1 virus and possibly increased risk for viral damage.", "doi": "10.1089/vim.2017.0066", "pmid": "28796576", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-12-06T13:19:22.836Z", "modified": "2020-01-21T13:53:21.900Z"}, {"entity": "publication", "iuid": "81fd04ba3bf84bc4834ed150228a7f58", "links": {"self": {"href": "https://publications.scilifelab.se/publication/81fd04ba3bf84bc4834ed150228a7f58.json"}, "display": {"href": "https://publications.scilifelab.se/publication/81fd04ba3bf84bc4834ed150228a7f58"}}, "title": "Alterations of c-di-GMP turnover proteins modulate semi-constitutive rdar biofilm formation in commensal and uropathogenic Escherichia coli.", "authors": [{"family": "Cimdins", "given": "Annika", "initials": "A"}, {"family": "Simm", "given": "Roger", "initials": "R"}, {"family": "Li", "given": "Fengyang", "initials": "F"}, {"family": "L\u00fcthje", "given": "Petra", "initials": "P"}, {"family": "Thorell", "given": "Kaisa", "initials": "K"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Brauner", "given": "Annelie", "initials": "A"}, {"family": "R\u00f6mling", "given": "Ute", "initials": "U"}], "type": "journal article", "published": "2017-10-00", "journal": {"volume": "6", "issn": "2045-8827", "issue": "5", "title": "Microbiologyopen", "issn-l": "2045-8827"}, "abstract": "Agar plate-based biofilm of enterobacteria like Escherichia coli is characterized by expression of the extracellular matrix components amyloid curli and cellulose exopolysaccharide, which can be visually enhanced upon addition of the dye Congo Red, resulting in a red, dry, and rough (rdar) colony morphology. Expression of the rdar morphotype depends on the transcriptional regulator CsgD and occurs predominantly at ambient temperature in model strains. In contrast, commensal and pathogenic isolates frequently express the csgD-dependent rdar morphotype semi-constitutively, also at human host body temperature. To unravel the molecular basis of temperature-independent rdar morphotype expression, biofilm components and c-di-GMP turnover proteins of seven commensal and uropathogenic E. coli isolates were analyzed. A diversity within the c-di-GMP signaling network was uncovered which suggests alteration of activity of the trigger phosphodiesterase YciR to contribute to (up)regulation of csgD expression and consequently semi-constitutive rdar morphotype development.", "doi": "10.1002/mbo3.508", "pmid": "28913868", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5635171"}], "notes": [], "created": "2019-01-15T08:21:16.720Z", "modified": "2020-01-21T13:53:22.475Z"}, {"entity": "publication", "iuid": "1e2ade93efce4c0f8d791467a61493cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e2ade93efce4c0f8d791467a61493cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e2ade93efce4c0f8d791467a61493cb"}}, "title": "Anti-mycobacterial activity correlates with altered DNA methylation pattern in immune cells from BCG-vaccinated subjects.", "authors": [{"family": "Verma", "given": "Deepti", "initials": "D"}, {"family": "Parasa", "given": "Venkata Ramanarao", "initials": "VR"}, {"family": "Raffetseder", "given": "Johanna", "initials": "J"}, {"family": "Martis", "given": "Mihaela", "initials": "M"}, {"family": "Mehta", "given": "Ratnesh B", "initials": "RB"}, {"family": "Netea", "given": "Mihai", "initials": "M"}, {"family": "Lerm", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2017-09-26", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "12305", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The reason for the largely variable protective effect against TB of the vaccine Bacille Calmette-Guerin (BCG) is not understood. In this study, we investigated whether epigenetic mechanisms are involved in the response of immune cells to the BCG vaccine. We isolated peripheral blood mononuclear cells (PBMCs) from BCG-vaccinated subjects and performed global DNA methylation analysis in combination with functional assays representative of innate immunity against Mycobacterium tuberculosis infection. Enhanced containment of replication was observed in monocyte-derived macrophages from a sub-group of BCG-vaccinated individuals (identified as 'responders'). A stable and robust differential DNA methylation pattern in response to BCG could be observed in PBMCs isolated from the responders but not from the non-responders. Gene ontology analysis revealed that promoters with altered DNA methylation pattern were strongly enriched among genes belonging to immune pathways in responders, however no enrichments could be observed in the non-responders. Our findings suggest that BCG-induced epigenetic reprogramming of immune cell function can enhance anti-mycobacterial immunity in macrophages. Understanding why BCG induces this response in responders but not in non-responders could provide clues to improvement of TB vaccine efficacy.", "doi": "10.1038/s41598-017-12110-2", "pmid": "28951586", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-12110-2"}, {"db": "pmc", "key": "PMC5615063"}], "notes": [], "created": "2017-10-25T15:27:48.394Z", "modified": "2024-01-16T13:48:47.507Z"}, {"entity": "publication", "iuid": "923f95c531b44fe183b15bd21bee0a6f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/923f95c531b44fe183b15bd21bee0a6f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/923f95c531b44fe183b15bd21bee0a6f"}}, "title": "Genetic risk scores and family history as predictors of schizophrenia in Nordic registers.", "authors": [{"family": "Lu", "given": "Y", "initials": "Y"}, {"family": "Pouget", "given": "J G", "initials": "JG"}, {"family": "Andreassen", "given": "O A", "initials": "OA"}, {"family": "Djurovic", "given": "S", "initials": "S"}, {"family": "Esko", "given": "T", "initials": "T"}, {"family": "Hultman", "given": "C M", "initials": "CM"}, {"family": "Metspalu", "given": "A", "initials": "A"}, {"family": "Milani", "given": "L", "initials": "L"}, {"family": "Werge", "given": "T", "initials": "T"}, {"family": "Sullivan", "given": "P F", "initials": "PF"}], "type": "journal article", "published": "2017-09-25", "journal": {"volume": null, "issn": "1469-8978", "issue": null, "pages": "1-9", "title": "Psychol Med", "issn-l": "0033-2917"}, "abstract": "Family history is a long-standing and readily obtainable risk factor for schizophrenia (SCZ). Low-cost genotyping technologies have enabled large genetic studies of SCZ, and the results suggest the utility of genetic risk scores (GRS, direct assessments of inherited common variant risk). Few studies have evaluated family history and GRS simultaneously to ask whether one can explain away the other.\n\nWe studied 5959 SCZ cases and 8717 controls from four Nordic countries. All subjects had family history data from national registers and genome-wide genotypes that were processed through the quality control procedures used by the Psychiatric Genomics Consortium. Using external training data, GRS were estimated for SCZ, bipolar disorder (BIP), major depression, autism, educational attainment, and body mass index. Multivariable modeling was used to estimate effect sizes.\n\nUsing harmonized genomic and national register data from Denmark, Estonia, Norway, and Sweden, we confirmed that family history of SCZ and GRS for SCZ and BIP were risk factors for SCZ. In a joint model, the effects of GRS for SCZ and BIP were essentially unchanged, and the effect of family history was attenuated but remained significant. The predictive capacity of a model including GRS and family history neared the minimum for clinical utility.\n\nCombining national register data with measured genetic risk factors represents an important investigative approach for psychotic disorders. Our findings suggest the potential clinical utility of combining GRS and family history for early prediction and diagnostic improvements.", "doi": "10.1017/S0033291717002665", "pmid": "28942743", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0033291717002665"}], "notes": [], "created": "2017-10-25T15:27:49.142Z", "modified": "2024-01-16T13:48:47.514Z"}, {"entity": "publication", "iuid": "e9e8da47ca5147caace04385ea2be779", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e9e8da47ca5147caace04385ea2be779.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e9e8da47ca5147caace04385ea2be779"}}, "title": "The regulation of hydroxysteroid 17\u03b2-dehydrogenase type 1 and 2 gene expression in breast cancer cell lines by estradiol, dihydrotestosterone, microRNAs, and genes related to breast cancer.", "authors": [{"family": "Hilborn", "given": "Erik", "initials": "E"}, {"family": "St\u00e5l", "given": "Olle", "initials": "O"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Jansson", "given": "Agneta", "initials": "A"}], "type": "journal article", "published": "2017-09-22", "journal": {"volume": "8", "issn": "1949-2553", "issue": "37", "pages": "62183-62194", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "To investigate the influence of estrogen, androgen, microRNAs, and genes implicated in breast cancer on the expression of HSD17B1 and HSD17B2.\n\nBreast cancer cell lines ZR-75-1, MCF7, T47D, SK-BR-3, and the immortalized epithelial cell line MCF10A were used. Cells were treated either with estradiol or dihydrotestosterone for 6, 24, 48 hours, or 7 days or treated with miRNAs or siRNAs predicted to influence HSD17B expression Results and discussion. Estradiol treatment decreased\n\nWe show that", "doi": "10.18632/oncotarget.19136", "pmid": "28977936", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "19136"}, {"db": "pmc", "key": "PMC5617496"}], "notes": [], "created": "2018-03-29T07:15:32.386Z", "modified": "2020-01-21T13:53:21.925Z"}, {"entity": "publication", "iuid": "118d534f4a2f4cc6a9430bdc114ee50b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/118d534f4a2f4cc6a9430bdc114ee50b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/118d534f4a2f4cc6a9430bdc114ee50b"}}, "title": "Copper chaperone ATOX1 regulates pluripotency factor OCT4 in preimplantation mouse embryos.", "authors": [{"family": "Celauro", "given": "Emanuele", "initials": "E"}, {"family": "Mukaj", "given": "Amisa", "initials": "A"}, {"family": "Fierro-Gonz\u00e1lez", "given": "Juan Carlos", "initials": "JC"}, {"family": "Wittung-Stafshede", "given": "Pernilla", "initials": "P", "orcid": "0000-0003-1058-1964", "researcher": {"href": "https://publications.scilifelab.se/researcher/9016aa00d62f439fb15532a1f4ba814e.json"}}], "type": "journal article", "published": "2017-09-09", "journal": {"volume": "491", "issn": "1090-2104", "issue": "1", "pages": "147-153", "title": "Biochem. Biophys. Res. Commun.", "issn-l": "0006-291X"}, "abstract": "Despite of the importance of copper (Cu) during pregnancy, the roles of Cu-binding proteins during early embryonic development are unknown. The Cu chaperone ATOX1 was recently suggested to have additional functions related to transcription and cancer. When we analyzed single-cell RNA transcript data from early mouse embryos, Atox1 transcript levels increased dramatically at the 8-cell stage and, at 16- and 32-cell embryo stages, matched those of Oct4 which expresses a transcription factor essential for pluripotency in the inner cell mass. To explore this, we probed Atox1 expression during the first week of development of mouse embryos. ATOX1 appeared ubiquitously expressed throughout the cells until compaction; in subsequent embryo stages, ATOX1 relocalized to cytoplasmic perinuclear domains in the inner cell mass. Silencing of Oct4 did not affect Atox1 expression, but silencing of Atox1 at the 2-cell stage strongly diminished Oct4 expression in 16-cell embryos.", "doi": "10.1016/j.bbrc.2017.07.064", "pmid": "28711491", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0006-291X(17)31406-7"}], "notes": [], "created": "2017-11-02T12:15:40.115Z", "modified": "2021-06-16T16:16:13.321Z"}, {"entity": "publication", "iuid": "dd70e362cb6943229c091af5a0fe1185", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd70e362cb6943229c091af5a0fe1185.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd70e362cb6943229c091af5a0fe1185"}}, "title": "Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition.", "authors": [{"family": "Amlinger", "given": "Lina", "initials": "L"}, {"family": "Hoekzema", "given": "Mirthe", "initials": "M"}, {"family": "Wagner", "given": "E Gerhart H", "initials": "EGH"}, {"family": "Koskiniemi", "given": "Sanna", "initials": "S"}, {"family": "Lundgren", "given": "Magnus", "initials": "M", "orcid": "0000-0002-1122-3352", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e56842987ca489ba79c0606d9ce6849.json"}}], "type": "journal article", "published": "2017-09-04", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "10392", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "CRISPR-Cas systems are adaptive prokaryotic immune systems protecting against horizontally transferred DNA or RNA such as viruses and other mobile genetic elements. Memory of past invaders is stored as spacers in CRISPR loci in a process called adaptation. Here we developed a novel assay where spacer integration results in fluorescence, enabling detection of memory formation in single cells and quantification of as few as 0.05% cells with expanded CRISPR arrays in a bacterial population. Using this fluorescent CRISPR Adaptation Reporter (f-CAR), we quantified adaptation of the two CRISPR arrays of the type I-E CRISPR-Cas system in Escherichia coli, and confirmed that more integration events are targeted to CRISPR-II than to CRISPR-I. The f-CAR conveniently analyzes and compares many samples, allowing new insights into adaptation. For instance, we show that in an E. coli culture the majority of acquisition events occur in late exponential phase.", "doi": "10.1038/s41598-017-10876-z", "pmid": "28871175", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-10876-z"}, {"db": "pmc", "key": "PMC5583386"}], "notes": [], "created": "2017-10-17T09:52:30.751Z", "modified": "2024-01-16T13:48:47.536Z"}, {"entity": "publication", "iuid": "f57321685c0b4169a4414640c3787e7f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f57321685c0b4169a4414640c3787e7f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f57321685c0b4169a4414640c3787e7f"}}, "title": "The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves.", "authors": [{"family": "Evkaikina", "given": "Anastasiia I", "initials": "AI"}, {"family": "Berke", "given": "Lidija", "initials": "L"}, {"family": "Romanova", "given": "Marina A", "initials": "MA"}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E"}, {"family": "Ivanova", "given": "Alexandra N", "initials": "AN"}, {"family": "Rydin", "given": "Catarina", "initials": "C"}, {"family": "Pawlowski", "given": "Katharina", "initials": "K"}, {"family": "Voitsekhovskaja", "given": "Olga V", "initials": "OV"}], "type": "journal article", "published": "2017-09-01", "journal": {"volume": "9", "issn": "1759-6653", "issue": "9", "pages": "2444-2460", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Lycopodiophyta-consisting of three orders, Lycopodiales, Isoetales and Selaginellales, with different types of shoot apical meristems (SAMs)-form the earliest branch among the extant vascular plants. They represent a sister group to all other vascular plants, from which they differ in that their leaves are microphylls-that is, leaves with a single, unbranched vein, emerging from the protostele without a leaf gap-not megaphylls. All leaves represent determinate organs originating on the flanks of indeterminate SAMs. Thus, leaf formation requires the suppression of indeterminacy, that is, of KNOX transcription factors. In seed plants, this is mediated by different groups of transcription factors including ARP and YABBY.We generated a shoot tip transcriptome of Huperzia selago (Lycopodiales) to examine the genes involved in leaf formation. Our H. selago transcriptome does not contain any ARP homolog, although transcriptomes of Selaginella spp. do. Surprisingly, we discovered a YABBY homolog, although these transcription factors were assumed to have evolved only in seed plants.The existence of a YABBY homolog in H. selago suggests that YABBY evolved already in the common ancestor of the vascular plants, and subsequently was lost in some lineages like Selaginellales, whereas ARP may have been lost in Lycopodiales. The presence of YABBY in the common ancestor of vascular plants would also support the hypothesis that this common ancestor had a simplex SAM. Furthermore, a comparison of the expression patterns of ARP in shoot tips of Selaginella kraussiana (Harrison CJ, etal. 2005. Independent recruitment of a conserved developmental mechanism during leaf evolution. Nature 434(7032):509-514.) and YABBY in shoot tips of H. selago implies that the development of microphylls, unlike megaphylls, does not seem to depend on the combined activities of ARP and YABBY. Altogether, our data show that Lycopodiophyta are a diverse group; so, in order to understand the role of Lycopodiophyta in evolution, representatives of Lycopodiales, Selaginellales, as well as of Isoetales, have to be examined.", "doi": "10.1093/gbe/evx169", "pmid": "28957460", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "4097580"}, {"db": "pmc", "key": "PMC5622374"}, {"db": "BioProject", "description": "DNA sequencing data", "key": "PRJNA281995"}], "notes": [], "created": "2017-11-03T16:20:59.430Z", "modified": "2024-01-16T13:48:47.550Z"}, {"entity": "publication", "iuid": "186d9c669252431592bb26afb3bcb39d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/186d9c669252431592bb26afb3bcb39d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/186d9c669252431592bb26afb3bcb39d"}}, "title": "A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog", "authors": [{"family": "Montero-Mendieta", "given": "Santiago", "initials": "S"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "De la Riva", "given": "Ignacio", "initials": "I"}, {"family": "Leonard", "given": "Jennifer A", "initials": "JA"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Vil\u00e0", "given": "Carles", "initials": "C"}], "type": "journal-article", "published": "2017-09-01", "journal": {"volume": "5", "issn": "2167-8359", "issue": null, "pages": "e3702", "title": "PeerJ", "issn-l": "2167-8359"}, "abstract": "Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembled \n            de-novo. We used RNA-seq to obtain the transcriptomic profile for Oreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome of O. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to build de-novo transcriptome assemblies using readily available software and is freely available at: https://github.com/biomendi/TRANSCRIPTOME-ASSEMBLY-PIPELINE/wiki.", "doi": "10.7717/peerj.3702", "pmid": "28879061", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "SRA", "description": null, "key": "SRP106442"}, {"db": "GENBANK", "description": "TSA: Oreobates cruralis, transcriptome shotgun assembly", "key": "GFNJ00000000"}, {"db": "BioProject", "description": "Oreobates cruralis isolate:MNCN/ADN:65263 Transcriptome or Gene expression", "key": "PRJNA384528"}], "notes": [], "created": "2017-10-30T09:27:45.542Z", "modified": "2024-01-16T13:48:47.564Z"}, {"entity": "publication", "iuid": "5521219aa1794ec98838a8591df79469", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5521219aa1794ec98838a8591df79469.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5521219aa1794ec98838a8591df79469"}}, "title": "Cerium oxide nanoparticles inhibit differentiation of neural stem cells.", "authors": [{"family": "Gliga", "given": "Anda R", "initials": "AR"}, {"family": "Edoff", "given": "Karin", "initials": "K"}, {"family": "Caputo", "given": "Fanny", "initials": "F"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "Blom", "given": "Hans", "initials": "H", "orcid": "0000-0002-5584-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce356a74dc84e0ea6af85397f11d869.json"}}, {"family": "Karlsson", "given": "Hanna L", "initials": "HL"}, {"family": "Ghibelli", "given": "Lina", "initials": "L"}, {"family": "Traversa", "given": "Enrico", "initials": "E"}, {"family": "Ceccatelli", "given": "Sandra", "initials": "S"}, {"family": "Fadeel", "given": "Bengt", "initials": "B"}], "type": "journal article", "published": "2017-08-24", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "9284", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Cerium oxide nanoparticles (nanoceria) display antioxidant properties and have shown cytoprotective effects both in vitro and in vivo. Here, we explored the effects of nanoceria on neural progenitor cells using the C17.2 murine cell line as a model. First, we assessed the effects of nanoceria versus samarium (Sm) doped nanoceria on cell viability in the presence of the prooxidant, DMNQ. Both particles were taken up by cells and nanoceria, but not Sm-doped nanoceria, elicited a temporary cytoprotective effect upon exposure to DMNQ. Next, we employed RNA sequencing to explore the transcriptional responses induced by nanoceria or Sm-doped nanoceria during neuronal differentiation. Detailed computational analyses showed that nanoceria altered pathways and networks relevant for neuronal development, leading us to hypothesize that nanoceria inhibits neuronal differentiation, and that nanoceria and Sm-doped nanoceria both interfere with cytoskeletal organization. We confirmed that nanoceria reduced neuron specific \u03b23-tubulin expression, a marker of neuronal differentiation, and GFAP, a neuroglial marker. Furthermore, using super-resolution microscopy approaches, we could show that both particles interfered with cytoskeletal organization and altered the structure of neural growth cones. Taken together, these results reveal that nanoceria may impact on neuronal differentiation, suggesting that nanoceria could pose a developmental neurotoxicity hazard.", "doi": "10.1038/s41598-017-09430-8", "pmid": "28839176", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Integrated Microscopy Technologies Stockholm": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-09430-8"}, {"db": "pmc", "key": "PMC5570910"}, {"db": "ArrayExpress", "description": "raw RNA-seq", "key": "E-MTAB-4398"}], "notes": [], "created": "2017-10-05T09:22:50.002Z", "modified": "2021-07-05T13:48:51.542Z"}, {"entity": "publication", "iuid": "e4ff20b402654d2cb68b4793d8c80728", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e4ff20b402654d2cb68b4793d8c80728.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e4ff20b402654d2cb68b4793d8c80728"}}, "title": "SubCons: a new ensemble method for improved human subcellular localization predictions.", "authors": [{"family": "Salvatore", "given": "M", "initials": "M"}, {"family": "Warholm", "given": "P", "initials": "P"}, {"family": "Shu", "given": "N", "initials": "N"}, {"family": "Basile", "given": "W", "initials": "W"}, {"family": "Elofsson", "given": "A", "initials": "A"}], "type": "journal article", "published": "2017-08-15", "journal": {"volume": "33", "issn": "1367-4811", "issue": "16", "pages": "2464-2470", "title": "Bioinformatics", "issn-l": "1367-4803"}, "abstract": "Knowledge of the correct protein subcellular localization is necessary for understanding the function of a protein. Unfortunately large-scale experimental studies are limited in their accuracy. Therefore, the development of prediction methods has been limited by the amount of accurate experimental data. However, recently large-scale experimental studies have provided new data that can be used to evaluate the accuracy of subcellular predictions in human cells. Using this data we examined the performance of state of the art methods and developed SubCons, an ensemble method that combines four predictors using a Random Forest classifier.\r\n\r\nSubCons outperforms earlier methods in a dataset of proteins where two independent methods confirm the subcellular localization. Given nine subcellular localizations, SubCons achieves an F1-Score of 0.79 compared to 0.70 of the second best method. Furthermore, at a FPR of 1% the true positive rate (TPR) is over 58% for SubCons compared to less than 50% for the best individual predictor.\r\n\r\nSubCons is freely available as a webserver (http://subcons.bioinfo.se) and source code from https://bitbucket.org/salvatore_marco/subcons-web-server. The golden dataset as well is available from http://subcons.bioinfo.se/pred/download.\r\n\r\narne@bioinfo.se.\r\n\r\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btx219", "pmid": "28407043", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "3603546"}], "notes": [], "created": "2017-11-10T13:08:59.009Z", "modified": "2020-01-21T13:53:21.906Z"}, {"entity": "publication", "iuid": "762da9d75b1c48ae9ed377c0491cee2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/762da9d75b1c48ae9ed377c0491cee2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/762da9d75b1c48ae9ed377c0491cee2a"}}, "title": "Targeted sequencing of tonsillar and base of tongue cancer and human papillomavirus positive unknown primary of the head and neck reveals prognostic effects of mutated FGFR3", "authors": [{"family": "Bersani", "given": "Cinzia", "initials": "C"}, {"family": "Sivars", "given": "Lars", "initials": "L"}, {"family": "Haeggblom", "given": "Linnea", "initials": "L"}, {"family": "DiLorenzo", "given": "Sebastian", "initials": "S"}, {"family": "Mints", "given": "Michael", "initials": "M"}, {"family": "\u00c4hrlund-Richter", "given": "Andreas", "initials": "A"}, {"family": "Tertipis", "given": "Nikolaos", "initials": "N"}, {"family": "Munck-Wikland", "given": "Eva", "initials": "E"}, {"family": "N\u00e4sman", "given": "Anders", "initials": "A"}, {"family": "Ramqvist", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Dalianis", "given": "Tina", "initials": "T"}], "type": "journal-article", "published": "2017-07-18", "journal": {"volume": null, "issn": "1949-2553", "issue": null, "pages": null, "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": null, "doi": "10.18632/oncotarget.15240", "pmid": "28525363", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T15:01:37.369Z", "modified": "2020-01-21T13:53:22.273Z"}, {"entity": "publication", "iuid": "a3a741c3582e433b9c7ff312acb3c831", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3a741c3582e433b9c7ff312acb3c831.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3a741c3582e433b9c7ff312acb3c831"}}, "title": "Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity.", "authors": [{"family": "Lind", "given": "Ulrika", "initials": "U"}, {"family": "J\u00e4rv\u00e5", "given": "Michael", "initials": "M"}, {"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "Pingitore", "given": "Piero", "initials": "P"}, {"family": "Karlsson", "given": "Emil", "initials": "E"}, {"family": "Wrange", "given": "Anna-Lisa", "initials": "AL"}, {"family": "Kamdal", "given": "Emelie", "initials": "E"}, {"family": "Sundell", "given": "Kristina", "initials": "K"}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C"}, {"family": "Jonsson", "given": "Per R", "initials": "PR"}, {"family": "Havenhand", "given": "Jon", "initials": "J"}, {"family": "Eriksson", "given": "Leif A", "initials": "LA"}, {"family": "Hedfalk", "given": "Kristina", "initials": "K"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2017-07-17", "journal": {"volume": "12", "issn": "1932-6203", "issue": "7", "pages": "e0181192", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Barnacles are sessile macro-invertebrates, found along rocky shores in coastal areas worldwide. The euryhaline bay barnacle Balanus improvisus (Darwin, 1854) (= Amphibalanus improvisus) can tolerate a wide range of salinities, but the molecular mechanisms underlying the osmoregulatory capacity of this truly brackish species are not well understood. Aquaporins are pore-forming integral membrane proteins that facilitate transport of water, small solutes and ions through cellular membranes, and that have been shown to be important for osmoregulation in many organisms. The knowledge of the function of aquaporins in crustaceans is, however, limited and nothing is known about them in barnacles. We here present the repertoire of aquaporins from a thecostracan crustacean, the barnacle B. improvisus, based on genome and transcriptome sequencing. Our analyses reveal that B. improvisus contains eight genes for aquaporins. Phylogenetic analysis showed that they represented members of the classical water aquaporins (Aqp1, Aqp2), the aquaglyceroporins (Glp1, Glp2), the unorthodox aquaporin (Aqp12) and the arthropod-specific big brain aquaporin (Bib). Interestingly, we also found two big brain-like proteins (BibL1 and BibL2) constituting a new group of aquaporins not yet described in arthropods. In addition, we found that the two water-specific aquaporins were expressed as C-terminal splice variants. Heterologous expression of some of the aquaporins followed by functional characterization showed that Aqp1 transported water and Glp2 water and glycerol, agreeing with the predictions of substrate specificity based on 3D modeling and phylogeny. To investigate a possible role for the B. improvisus aquaporins in osmoregulation, mRNA expression changes in adult barnacles were analysed after long-term acclimation to different salinities. The most pronounced expression difference was seen for AQP1 with a substantial (>100-fold) decrease in the mantle tissue in low salinity (3 PSU) compared to high salinity (33 PSU). Our study provides a base for future mechanistic studies on the role of aquaporins in osmoregulation.", "doi": "10.1371/journal.pone.0181192", "pmid": "28715506", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-05123"}, {"db": "pmc", "key": "PMC5513457"}, {"db": "GENBANK", "description": "sequence", "key": "KY508284"}, {"db": "GENBANK", "description": "sequence", "key": "KY508285"}, {"db": "GENBANK", "description": "sequence", "key": "KY508286"}, {"db": "GENBANK", "description": "sequence", "key": "KY508287"}, {"db": "GENBANK", "description": "sequence", "key": "KY508289"}, {"db": "GENBANK", "description": "sequence", "key": "KY508290"}, {"db": "GENBANK", "description": "sequence", "key": "KY508291"}, {"db": "GENBANK", "description": "sequence", "key": "KY508292"}, {"db": "GENBANK", "description": "sequence", "key": "KY508288"}, {"db": "GENBANK", "description": "sequence", "key": "KY508293"}, {"db": "GENBANK", "description": "sequence", "key": "KY508294"}, {"db": "GENBANK", "description": "sequence", "key": "KY508295"}, {"db": "GENBANK", "description": "sequence", "key": "KY508296"}, {"db": "GENBANK", "description": "sequence", "key": "KY508297"}, {"db": "GENBANK", "description": "sequence", "key": "KY508298"}], "notes": [], "created": "2017-10-17T09:32:54.872Z", "modified": "2024-01-16T13:48:47.750Z"}, {"entity": "publication", "iuid": "68e6f0f7bb304127afa33736575f35d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/68e6f0f7bb304127afa33736575f35d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/68e6f0f7bb304127afa33736575f35d0"}}, "title": "Identifying Bird Remains Using Ancient DNA Barcoding.", "authors": [{"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Lagerholm", "given": "Vendela K", "initials": "VK"}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA"}, {"family": "Barton", "given": "Nick", "initials": "N"}, {"family": "Bochenski", "given": "Zbigniew M", "initials": "ZM"}, {"family": "Tomek", "given": "Teresa", "initials": "T"}, {"family": "Rudling", "given": "David", "initials": "D"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Stewart", "given": "John R", "initials": "JR"}], "type": "journal article", "published": "2017-06-21", "journal": {"volume": "8", "issn": "2073-4425", "issue": "6", "pages": "169", "title": "Genes", "issn-l": "2073-4425"}, "abstract": "Bird remains that are difficult to identify taxonomically using morphological methods, are common in the palaeontological record. Other types of challenging avian material include artefacts and food items from endangered taxa, as well as remains from aircraft strikes. We here present a DNA-based method that enables taxonomic identification of bird remains, even from material where the DNA is heavily degraded. The method is based on the amplification and sequencing of two short variable parts of the 16S region in the mitochondrial genome. To demonstrate the applicability of this approach, we evaluated the method on a set of Holocene and Late Pleistocene postcranial bird bones from several palaeontological and archaeological sites in Europe with good success.", "doi": "10.3390/genes8060169", "pmid": "28635635", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "genes8060169"}, {"db": "pmc", "key": "PMC5485533"}], "notes": [], "created": "2017-11-03T13:16:04.796Z", "modified": "2021-07-07T20:31:10.826Z"}, {"entity": "publication", "iuid": "1a7366ba8d23449d91515036583cef23", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1a7366ba8d23449d91515036583cef23.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1a7366ba8d23449d91515036583cef23"}}, "title": "Protein expression in tension wood formation monitored at high tissue resolution in Populus", "authors": [{"family": "Bygdell", "given": "Joakim", "initials": "J"}, {"family": "Srivastava", "given": "Vaibhav", "initials": "V"}, {"family": "Obudulu", "given": "Ogonna", "initials": "O"}, {"family": "Srivastava", "given": "Manoj K", "initials": "MK"}, {"family": "Nilsson", "given": "Robert", "initials": "R"}, {"family": "Sundberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Trygg", "given": "Johan", "initials": "J"}, {"family": "Mellerowicz", "given": "Ewa J", "initials": "EJ"}, {"family": "Wingsle", "given": "Gunnar", "initials": "G"}], "type": "journal-article", "published": "2017-06-15", "journal": {"volume": "68", "issn": "0022-0957", "issue": "13", "pages": "3405-3417", "title": null, "issn-l": null}, "abstract": null, "doi": "10.1093/jxb/erx186", "pmid": "28633298", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T13:05:31.386Z", "modified": "2020-01-21T13:53:21.847Z"}, {"entity": "publication", "iuid": "41693810bf914d9095a1db79a7f44a49", "links": {"self": {"href": "https://publications.scilifelab.se/publication/41693810bf914d9095a1db79a7f44a49.json"}, "display": {"href": "https://publications.scilifelab.se/publication/41693810bf914d9095a1db79a7f44a49"}}, "title": "Four simple recommendations to encourage best practices in research software", "authors": [{"family": "Jim\u00e9nez", "given": "Rafael C", "initials": "RC"}, {"family": "Kuzak", "given": "Mateusz", "initials": "M"}, {"family": "Alhamdoosh", "given": "Monther", "initials": "M"}, {"family": "Barker", "given": "Michelle", "initials": "M"}, {"family": "Batut", "given": "B\u00e9r\u00e9nice", "initials": "B"}, {"family": "Borg", "given": "Mikael", "initials": "M"}, {"family": "Capella-Gutierrez", "given": "Salvador", "initials": "S"}, {"family": "Chue Hong", "given": "Neil", "initials": "N"}, {"family": "Cook", "given": "Martin", "initials": "M"}, {"family": "Corpas", "given": "Manuel", "initials": "M"}, {"family": "Flannery", "given": "Madison", "initials": "M"}, {"family": "Garcia", "given": "Leyla", "initials": "L"}, {"family": "Gelp\u00ed", "given": "Josep Ll", "initials": "JL"}, {"family": "Gladman", "given": "Simon", "initials": "S"}, {"family": "Goble", "given": "Carole", "initials": "C"}, {"family": "Gonz\u00e1lez Ferreiro", "given": "Montserrat", "initials": "M"}, {"family": "Gonzalez-Beltran", "given": "Alejandra", "initials": "A"}, {"family": "Griffin", "given": "Philippa C", "initials": "PC"}, {"family": "Gr\u00fcning", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Hagberg", "given": "Jonas", "initials": "J"}, {"family": "Holub", "given": "Petr", "initials": "P"}, {"family": "Hooft", "given": "Rob", "initials": "R"}, {"family": "Ison", "given": "Jon", "initials": "J"}, {"family": "Katz", "given": "Daniel S", "initials": "DS"}, {"family": "Lesko\u0161ek", "given": "Brane", "initials": "B"}, {"family": "L\u00f3pez G\u00f3mez", "given": "Federico", "initials": "F"}, {"family": "Oliveira", "given": "Luis J", "initials": "LJ"}, {"family": "Mellor", "given": "David", "initials": "D"}, {"family": "Mosbergen", "given": "Rowland", "initials": "R"}, {"family": "Mulder", "given": "Nicola", "initials": "N"}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y"}, {"family": "Pergl", "given": "Robert", "initials": "R"}, {"family": "Pichler", "given": "Horst", "initials": "H"}, {"family": "Pope", "given": "Bernard", "initials": "B"}, {"family": "Sanz", "given": "Ferran", "initials": "F"}, {"family": "Schneider", "given": "Maria V", "initials": "MV"}, {"family": "Stodden", "given": "Victoria", "initials": "V"}, {"family": "Suchecki", "given": "Rados\u0142aw", "initials": "R"}, {"family": "Svobodov\u00e1 Va\u0159ekov\u00e1", "given": "Radka", "initials": "R"}, {"family": "Talvik", "given": "Harry Anton", "initials": "HA"}, {"family": "Todorov", "given": "Ilian", "initials": "I"}, {"family": "Treloar", "given": "Andrew", "initials": "A"}, {"family": "Tyagi", "given": "Sonika", "initials": "S"}, {"family": "van Gompel", "given": "Maarten", "initials": "M"}, {"family": "Vaughan", "given": "Daniel", "initials": "D"}, {"family": "Via", "given": "Allegra", "initials": "A"}, {"family": "Wang", "given": "Xiaochuan", "initials": "X"}, {"family": "Watson-Haigh", "given": "Nathan S", "initials": "NS"}, {"family": "Crouch", "given": "Steve", "initials": "S"}], "type": "journal-article", "published": "2017-06-13", "journal": {"volume": "6", "issn": "2046-1402", "issue": null, "pages": "876", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.11407.1", "pmid": "28751965", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Support and Infrastructure": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-03T13:16:15.160Z", "modified": "2020-01-21T13:53:21.698Z"}, {"entity": "publication", "iuid": "fefb54b862b242c7a4164b64ca3b488b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fefb54b862b242c7a4164b64ca3b488b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fefb54b862b242c7a4164b64ca3b488b"}}, "title": "A community proposal to integrate proteomics activities in ELIXIR", "authors": [{"family": "Vizca\u00edno", "given": "Juan Antonio", "initials": "JA"}, {"family": "Walzer", "given": "Mathias", "initials": "M"}, {"family": "Jim\u00e9nez", "given": "Rafael C", "initials": "RC"}, {"family": "Bittremieux", "given": "Wout", "initials": "W"}, {"family": "Bouyssi\u00e9", "given": "David", "initials": "D"}, {"family": "Carapito", "given": "Christine", "initials": "C"}, {"family": "Corrales", "given": "Fernando", "initials": "F"}, {"family": "Ferro", "given": "Myriam", "initials": "M"}, {"family": "Heck", "given": "Albert J R", "initials": "AJR"}, {"family": "Horvatovich", "given": "Peter", "initials": "P"}, {"family": "Hubalek", "given": "Martin", "initials": "M"}, {"family": "Lane", "given": "Lydie", "initials": "L"}, {"family": "Laukens", "given": "Kris", "initials": "K"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Lisacek", "given": "Frederique", "initials": "F"}, {"family": "Novak", "given": "Petr", "initials": "P"}, {"family": "Palmblad", "given": "Magnus", "initials": "M"}, {"family": "Piovesan", "given": "Damiano", "initials": "D"}, {"family": "P\u00fchler", "given": "Alfred", "initials": "A"}, {"family": "Schw\u00e4mmle", "given": "Veit", "initials": "V"}, {"family": "Valkenborg", "given": "Dirk", "initials": "D"}, {"family": "van Rijswijk", "given": "Merlijn", "initials": "M"}, {"family": "Vondrasek", "given": "Jiri", "initials": "J"}, {"family": "Eisenacher", "given": "Martin", "initials": "M"}, {"family": "Martens", "given": "Lennart", "initials": "L"}, {"family": "Kohlbacher", "given": "Oliver", "initials": "O"}], "type": "journal-article", "published": "2017-06-13", "journal": {"volume": "6", "issn": "2046-1402", "issue": null, "pages": "875", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.11751.1", "pmid": "28713550", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Support and Infrastructure": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-03T13:16:14.669Z", "modified": "2020-01-21T13:53:21.691Z"}, {"entity": "publication", "iuid": "dc532e7f651d4cc39a2271712494c35c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc532e7f651d4cc39a2271712494c35c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc532e7f651d4cc39a2271712494c35c"}}, "title": "The transcriptome of the avian malaria parasite Plasmodium ashfordi displays host-specific gene expression.", "authors": [{"family": "Videvall", "given": "Elin", "initials": "E"}, {"family": "Cornwallis", "given": "Charlie K", "initials": "CK"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Palinauskas", "given": "Vaidas", "initials": "V"}, {"family": "Valki\u016bnas", "given": "Gediminas", "initials": "G"}, {"family": "Hellgren", "given": "Olof", "initials": "O"}], "type": "journal article", "published": "2017-06-00", "journal": {"volume": "26", "issn": "1365-294X", "issue": "11", "pages": "2939-2958", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Malaria parasites (Plasmodium spp.) include some of the world's most widespread and virulent pathogens. Our knowledge of the molecular mechanisms these parasites use to invade and exploit their hosts other than in mice and primates is, however, extremely limited. It is therefore imperative to characterize transcriptome-wide gene expression from nonmodel malaria parasites and how this varies across individual hosts. Here, we used high-throughput Illumina RNA sequencing on blood from wild-caught Eurasian siskins experimentally infected with a clonal strain of the avian malaria parasite Plasmodium ashfordi (lineage GRW2). Using a bioinformatic multistep approach to filter out host transcripts, we successfully assembled the blood-stage transcriptome of P.\u00a0ashfordi. A total of 11\u00a0954 expressed transcripts were identified, and 7860 were annotated with protein information. We quantified gene expression levels of all parasite transcripts across three hosts during two infection stages - peak and decreasing parasitemia. Interestingly, parasites from the same host displayed remarkably similar expression profiles during different infection stages, but showed large differences across hosts, indicating that P.\u00a0ashfordi may adjust its gene expression to specific host individuals. We further show that the majority of transcripts are most similar to the human parasite Plasmodium falciparum, and a large number of red blood cell invasion genes were discovered, suggesting evolutionary conserved invasion strategies between mammalian and avian Plasmodium. The transcriptome of P.\u00a0ashfordi and its host-specific gene expression advances our understanding of Plasmodium plasticity and is a valuable resource as it allows for further studies analysing gene evolution and comparisons of parasite gene expression.", "doi": "10.1111/mec.14085", "pmid": "28267239", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-01-15T07:44:42.594Z", "modified": "2020-01-21T13:53:22.294Z"}, {"entity": "publication", "iuid": "efc910bea38f4f88a004e0a8d58828eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/efc910bea38f4f88a004e0a8d58828eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/efc910bea38f4f88a004e0a8d58828eb"}}, "title": "Lower inflammatory markers in women with antenatal depression brings the M1/M2 balance into focus from a new direction", "authors": [{"family": "Edvinsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Br\u00e4nn", "given": "Emma", "initials": "E"}, {"family": "Hellgren", "given": "Charlotte", "initials": "C"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "White", "given": "Richard", "initials": "R"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "Olivier", "given": "Jocelien", "initials": "J"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Bostr\u00f6m", "given": "Adrian E", "initials": "AE"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}, {"family": "Skalkidou", "given": "Alkistis", "initials": "A"}, {"family": "Cunningham", "given": "Janet L", "initials": "JL"}, {"family": "Sundstr\u00f6m-Poromaa", "given": "Inger", "initials": "I"}], "type": "journal-article", "published": "2017-06-00", "journal": {"volume": "80", "issn": "0306-4530", "issue": null, "pages": "15-25", "title": "Psychoneuroendocrinology", "issn-l": null}, "abstract": null, "doi": "10.1016/j.psyneuen.2017.02.027", "pmid": "28292683", "labels": {"Clinical Biomarkers": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "PLA and Single Cell Proteomics": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-30T12:48:42.081Z", "modified": "2023-04-14T13:56:14.657Z"}, {"entity": "publication", "iuid": "31715c08ce5546469fc28a95c4489f27", "links": {"self": {"href": "https://publications.scilifelab.se/publication/31715c08ce5546469fc28a95c4489f27.json"}, "display": {"href": "https://publications.scilifelab.se/publication/31715c08ce5546469fc28a95c4489f27"}}, "title": "Draft genome of the oomycete pathogen Phytophthora cactorum strain LV007 isolated from European beech (Fagus sylvatica).", "authors": [{"family": "Grenville-Briggs", "given": "Laura J", "initials": "LJ"}, {"family": "Kushwaha", "given": "Sandeep K", "initials": "SK"}, {"family": "Cleary", "given": "Michelle R", "initials": "MR"}, {"family": "Witzell", "given": "Johanna", "initials": "J"}, {"family": "Savenkov", "given": "Eugene I", "initials": "EI"}, {"family": "Whisson", "given": "Stephen C", "initials": "SC"}, {"family": "Chawade", "given": "Aakash", "initials": "A"}, {"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}], "type": "journal article", "published": "2017-06-00", "journal": {"volume": "12", "issn": "2213-5960", "issue": null, "pages": "155-156", "title": "Genom Data", "issn-l": "2213-5960"}, "abstract": "Phytophthora cactorum is a broad host range phytopathogenic oomycete. P. cactorum strain LV007 was isolated from a diseased European Beech (Fagus sylvatica) in Malm\u00f6, Sweden in 2016. The draft genome of P. cactorum strain LV007 is 67.81\u00a0Mb. It contains 15,567 contigs and 21,876 predicted protein-coding genes. As reported for other phytopathogenic Phytophthora species, cytoplasmic effector proteins including RxLR and CRN families were identified. The genome sequence has been deposited at DDBJ/ENA/GenBank under the accession NBIJ00000000. The version described in this paper is version NBIJ01000000.", "doi": "10.1016/j.gdata.2017.05.010", "pmid": "28560165", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2213-5960(17)30097-1"}, {"db": "pmc", "key": "PMC5435576"}], "notes": [], "created": "2019-01-15T08:06:17.294Z", "modified": "2020-01-21T13:53:22.640Z"}, {"entity": "publication", "iuid": "1b262db9b2e649d3b068b24a164ca06f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b262db9b2e649d3b068b24a164ca06f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b262db9b2e649d3b068b24a164ca06f"}}, "title": "Draft Genome Sequence of the Mycoparasitic Oomycete Pythium oligandrum Strain CBS 530.74.", "authors": [{"family": "Kushwaha", "given": "Sandeep K", "initials": "SK"}, {"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Grenville-Briggs", "given": "Laura J", "initials": "LJ"}], "type": "journal article", "published": "2017-05-25", "journal": {"volume": "5", "issn": "2169-8287", "issue": "21", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": "The oomycete Pythium oligandrum is a mycoparasite and licenced biological control agent. Here, we report the draft genome sequence of P.\u00a0oligandrum strain CBS 530.74, which is 36.80\u00a0Mb. It contains 341 scaffolds and 11,647 predicted protein-coding genes. As reported for plant-pathogenic Pythium species, RXLR-type effector sequences are absent.", "doi": "10.1128/genomeA.00346-17", "pmid": "28546478", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5/21/e00346-17"}, {"db": "pmc", "key": "PMC5477391"}], "notes": [], "created": "2017-11-03T16:21:52.480Z", "modified": "2020-01-21T13:56:17.422Z"}, {"entity": "publication", "iuid": "0013c1ea0aa54c31903307c143eca156", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0013c1ea0aa54c31903307c143eca156.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0013c1ea0aa54c31903307c143eca156"}}, "title": "ProQ3D: improved model quality assessments using deep learning.", "authors": [{"family": "Uziela", "given": "Karolis", "initials": "K"}, {"family": "Men\u00e9ndez Hurtado", "given": "David", "initials": "D"}, {"family": "Shu", "given": "Nanjiang", "initials": "N"}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2017-05-15", "journal": {"volume": "33", "issn": "1367-4811", "issue": "10", "pages": "1578-1580", "title": "Bioinformatics", "issn-l": "1367-4803"}, "abstract": "Protein quality assessment is a long-standing problem in bioinformatics. For more than a decade we have developed state-of-art predictors by carefully selecting and optimising inputs to a machine learning method. The correlation has increased from 0.60 in ProQ to 0.81 in ProQ2 and 0.85 in ProQ3 mainly by adding a large set of carefully tuned descriptions of a protein. Here, we show that a substantial improvement can be obtained using exactly the same inputs as in ProQ2 or ProQ3 but replacing the support vector machine by a deep neural network. This improves the Pearson correlation to 0.90 (0.85 using ProQ2 input features).\r\n\r\nProQ3D is freely available both as a webserver and a stand-alone program at http://proq3.bioinfo.se/.\r\n\r\narne@bioinfo.se.\r\n\r\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btw819", "pmid": "28052925", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "btw819"}], "notes": [], "created": "2017-11-01T12:35:54.198Z", "modified": "2020-01-21T13:53:21.650Z"}, {"entity": "publication", "iuid": "6b96a366c06542319f176c1ff67cf59a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6b96a366c06542319f176c1ff67cf59a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6b96a366c06542319f176c1ff67cf59a"}}, "title": "Whole blood gene expression in adolescent chronic fatigue syndrome: an exploratory cross-sectional study suggesting altered B cell differentiation and survival.", "authors": [{"family": "Nguyen", "given": "Chinh Bkrong", "initials": "CB"}, {"family": "Als\u00f8e", "given": "Lene", "initials": "L"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Sulheim", "given": "Dag", "initials": "D"}, {"family": "Fagermoen", "given": "Even", "initials": "E"}, {"family": "Winger", "given": "Anette", "initials": "A"}, {"family": "Kaarb\u00f8", "given": "Mari", "initials": "M"}, {"family": "Nilsen", "given": "Hilde", "initials": "H"}, {"family": "Wyller", "given": "Vegard Bruun", "initials": "VB"}], "type": "journal article", "published": "2017-05-11", "journal": {"volume": "15", "issn": "1479-5876", "issue": "1", "pages": "102", "title": "J Transl Med", "issn-l": "1479-5876"}, "abstract": "Chronic fatigue syndrome (CFS) is a prevalent and disabling condition affecting adolescents. The pathophysiology is poorly understood, but immune alterations might be an important component. This study compared whole blood gene expression in adolescent CFS patients and healthy controls, and explored associations between gene expression and neuroendocrine markers, immune markers and clinical markers within the CFS group.\n\nCFS patients (12-18\u00a0years old) were recruited nation-wide to a single referral center as part of the NorCAPITAL project. A broad case definition of CFS was applied, requiring 3\u00a0months of unexplained, disabling chronic/relapsing fatigue of new onset, whereas no accompanying symptoms were necessary. Healthy controls having comparable distribution of gender and age were recruited from local schools. Whole blood samples were subjected to RNA sequencing. Immune markers were blood leukocyte counts, plasma cytokines, serum C-reactive protein and immunoglobulins. Neuroendocrine markers encompassed plasma and urine levels of catecholamines and cortisol, as well as heart rate variability indices. Clinical markers consisted of questionnaire scores for symptoms of post-exertional malaise, inflammation, fatigue, depression and trait anxiety, as well as activity recordings.\n\nA total of 29 CFS patients and 18 healthy controls were included. We identified 176 genes as differentially expressed in patients compared to controls, adjusting for age and gender factors. Gene set enrichment analyses suggested impairment of B cell differentiation and survival, as well as enhancement of innate antiviral responses and inflammation in the CFS group. A pattern of co-expression could be identified, and this pattern, as well as single gene transcripts, was significantly associated with indices of autonomic nervous activity, plasma cortisol, and blood monocyte and eosinophil counts. Also, an association with symptoms of post-exertional malaise was demonstrated.\n\nAdolescent CFS is characterized by differential gene expression pattern in whole blood suggestive of impaired B cell differentiation and survival, and enhanced innate antiviral responses and inflammation. This expression pattern is associated with neuroendocrine markers of altered HPA axis and autonomic nervous activity, and with symptoms of post-exertional malaise. Trial registration Clinical Trials NCT01040429.", "doi": "10.1186/s12967-017-1201-0", "pmid": "28494812", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12967-017-1201-0"}, {"db": "pmc", "key": "PMC5426002"}, {"db": "ClinicalTrials.gov", "key": "NCT01040429"}, {"db": "ClinicalTrials.gov", "key": "NCT01040429"}], "notes": [], "created": "2019-01-15T07:56:54.940Z", "modified": "2021-07-05T12:48:15.991Z"}, {"entity": "publication", "iuid": "788bcedf458c46bca3f4b731190d6c65", "links": {"self": {"href": "https://publications.scilifelab.se/publication/788bcedf458c46bca3f4b731190d6c65.json"}, "display": {"href": "https://publications.scilifelab.se/publication/788bcedf458c46bca3f4b731190d6c65"}}, "title": "Spatially resolved transcriptome profiling in model plant species.", "authors": [{"family": "Giacomello", "given": "Stefania", "initials": "S", "orcid": "0000-0003-0738-1574", "researcher": {"href": "https://publications.scilifelab.se/researcher/8499e792cc394c42b4240ef5fb3fd06c.json"}}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "Terebieniec", "given": "Barbara K", "initials": "BK"}, {"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fc02717a5784908b583ef5bbf09a910.json"}}, {"family": "Navarro", "given": "Jos\u00e9 Fernandez", "initials": "JF"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications.scilifelab.se/researcher/54b6c0ff12c148dd803f7f72c8af0d14.json"}}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "McKee", "given": "Lauren S", "initials": "LS"}, {"family": "Mannapperuma", "given": "Chanaka", "initials": "C"}, {"family": "Bulone", "given": "Vincent", "initials": "V"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Sundstr\u00f6m", "given": "Jens F", "initials": "JF"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2017-05-08", "journal": {"volume": "3", "issn": "2055-0278", "issue": null, "pages": "17061", "title": "NPLANTS", "issn-l": "2055-0278"}, "abstract": "Understanding complex biological systems requires functional characterization of specialized tissue domains. However, existing strategies for generating and analysing high-throughput spatial expression profiles were developed for a limited range of organisms, primarily mammals. Here we present the first available approach to generate and study high-resolution, spatially resolved functional profiles in a broad range of model plant systems. Our process includes high-throughput spatial transcriptome profiling followed by spatial gene and pathway analyses. We first demonstrate the feasibility of the technique by generating spatial transcriptome profiles from model angiosperms and gymnosperms microsections. In Arabidopsis thaliana we use the spatial data to identify differences in expression levels of 141 genes and 189 pathways in eight inflorescence tissue domains. Our combined approach of spatial transcriptomics and functional profiling offers a powerful new strategy that can be applied to a broad range of plant species, and is an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology.", "doi": "10.1038/nplants.2017.61", "pmid": "28481330", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "nplants201761"}], "notes": [], "created": "2017-08-23T14:09:59.506Z", "modified": "2024-01-16T13:48:47.983Z"}, {"entity": "publication", "iuid": "3932c9f238004aaa8daf5320158c70ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3932c9f238004aaa8daf5320158c70ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3932c9f238004aaa8daf5320158c70ff"}}, "title": "Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women.", "authors": [{"family": "Engstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Wojdacz", "given": "Tomasz K", "initials": "TK"}, {"family": "Marabita", "given": "Francesco", "initials": "F"}, {"family": "Ewels", "given": "Philip", "initials": "P"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Prezza", "given": "Nicola", "initials": "N"}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Vahter", "given": "Marie", "initials": "M"}, {"family": "Broberg", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "91", "issn": "1432-0738", "issue": "5", "pages": "2067-2078", "title": "Arch. Toxicol.", "issn-l": "0340-5761"}, "abstract": "Arsenic, a carcinogen with immunotoxic effects, is a common contaminant of drinking water and certain food worldwide. We hypothesized that chronic arsenic exposure alters gene expression, potentially by altering DNA methylation of genes encoding central components of the immune system. We therefore analyzed the transcriptomes (by RNA sequencing) and methylomes (by target-enrichment next-generation sequencing) of primary CD4-positive T cells from matched groups of four women each in the Argentinean Andes, with fivefold differences in urinary arsenic concentrations (median concentrations of urinary arsenic in the lower- and high-arsenic groups: 65 and 276 \u03bcg/l, respectively). Arsenic exposure was associated with genome-wide alterations of gene expression; principal component analysis indicated that the exposure explained 53% of the variance in gene expression among the top variable genes and 19% of 28,351 genes were differentially expressed (false discovery rate <0.05) between the exposure groups. Key genes regulating the immune system, such as tumor necrosis factor alpha and interferon gamma, as well as genes related to the NF-kappa-beta complex, were significantly downregulated in the high-arsenic group. Arsenic exposure was associated with genome-wide DNA methylation; the high-arsenic group had 3% points higher genome-wide full methylation (>80% methylation) than the lower-arsenic group. Differentially methylated regions that were hyper-methylated in the high-arsenic group showed enrichment for immune-related gene ontologies that constitute the basic functions of CD4-positive T cells, such as isotype switching and lymphocyte activation and differentiation. In conclusion, chronic arsenic exposure from drinking water was related to changes in the transcriptome and methylome of CD4-positive T cells, both genome wide and in specific genes, supporting the hypothesis that arsenic causes immunotoxicity by interfering with gene expression and regulation.", "doi": "10.1007/s00204-016-1879-4", "pmid": "27838757", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s00204-016-1879-4"}, {"db": "pmc", "key": "PMC5399044"}], "notes": [], "created": "2017-05-03T12:59:46.128Z", "modified": "2024-01-16T13:48:48.019Z"}, {"entity": "publication", "iuid": "c66fd4d2712b4701a01b8f862deca4fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c66fd4d2712b4701a01b8f862deca4fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c66fd4d2712b4701a01b8f862deca4fb"}}, "title": "Three-dimensional functional human neuronal networks in uncompressed low-density electrospun fiber scaffolds.", "authors": [{"family": "Jakobsson", "given": "Albin", "initials": "A"}, {"family": "Ottosson", "given": "Maximilian", "initials": "M"}, {"family": "Zalis", "given": "Marina Castro", "initials": "MC"}, {"family": "O'Carroll", "given": "David", "initials": "D"}, {"family": "Johansson", "given": "Ulrica Englund", "initials": "UE"}, {"family": "Johansson", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2017-05-00", "journal": {"title": "Nanomedicine", "issn": "1748-6963", "volume": "13", "issue": "4", "pages": "1563-1573", "issn-l": "1743-5889"}, "abstract": "We demonstrate an artificial three-dimensional (3D) electrical active human neuronal network system, by the growth of brain neural progenitors in highly porous low density electrospun poly-\u03b5-caprolactone (PCL) fiber scaffolds. In neuroscience research cell-based assays are important experimental instruments for studying neuronal function in health and disease. Traditional cell culture at 2D-surfaces induces abnormal cell-cell contacts and network formation. Hence, there is a tremendous need to explore in vivo-resembling 3D neural cell culture approaches. We present an improved electrospinning method for fabrication of scaffolds that promote neuronal differentiation into highly 3D integrated networks, formation of inhibitory and excitatory synapses and extensive neurite growth. Notably, in 3D scaffolds in vivo-resembling intermixed neuronal and glial cell network were formed, whereas in parallel 2D cultures a neuronal cell layer grew separated from an underlying glial cell layer. Hence, the use of the 3D cell assay presented will most likely provide more physiological relevant results.", "doi": "10.1016/j.nano.2016.12.023", "pmid": "28064005", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S1549-9634(17)30002-3"}], "notes": [], "created": "2021-12-02T14:12:42.899Z", "modified": "2021-12-02T14:12:42.916Z"}, {"entity": "publication", "iuid": "dffab84ac9294147adf1ae2039ff814d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dffab84ac9294147adf1ae2039ff814d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dffab84ac9294147adf1ae2039ff814d"}}, "title": "Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes.", "authors": [{"family": "Rineau", "given": "F", "initials": "F"}, {"family": "Lmalem", "given": "H", "initials": "H"}, {"family": "Ahren", "given": "D", "initials": "D"}, {"family": "Shah", "given": "F", "initials": "F"}, {"family": "Johansson", "given": "T", "initials": "T"}, {"family": "Coninx", "given": "L", "initials": "L"}, {"family": "Ruytinx", "given": "J", "initials": "J"}, {"family": "Nguyen", "given": "H", "initials": "H"}, {"family": "Grigoriev", "given": "I", "initials": "I"}, {"family": "Kuo", "given": "A", "initials": "A"}, {"family": "Kohler", "given": "A", "initials": "A"}, {"family": "Morin", "given": "E", "initials": "E"}, {"family": "Vangronsveld", "given": "J", "initials": "J"}, {"family": "Martin", "given": "F", "initials": "F"}, {"family": "Colpaert", "given": "J V", "initials": "JV"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "27", "issn": "1432-1890", "issue": "4", "pages": "383-396", "title": "Mycorrhiza", "issn-l": "0940-6360"}, "abstract": "Hydrophobins are small secreted proteins that are present as several gene copies in most fungal genomes. Their properties are now well understood: they are amphiphilic and assemble at hydrophilic/hydrophobic interfaces. However, their physiological functions remain largely unexplored, especially within mycorrhizal fungi. In this study, we identified hydrophobin genes and analysed their distribution in eight mycorrhizal genomes. We then measured their expression levels in three different biological conditions (mycorrhizal tissue vs. free-living mycelium, organic vs. mineral growth medium and aerial vs. submerged growth). Results confirmed that the size of the hydrophobin repertoire increased in the terminal orders of the fungal evolutionary tree. Reconciliation analysis predicted that in 41% of the cases, hydrophobins evolved from duplication events. Whatever the treatment and the fungal species, the pattern of expression of hydrophobins followed a reciprocal function, with one gene much more expressed than others from the same repertoire. These most-expressed hydrophobin genes were also among the most expressed of the whole genome, which suggests that they play a role as structural proteins. The fine-tuning of the expression of hydrophobin genes in each condition appeared complex because it differed considerably between species, in a way that could not be explained by simple ecological traits. Hydrophobin gene regulation in mycorrhizal tissue as compared with free-living mycelium, however, was significantly associated with a calculated high exposure of hydrophilic residues.", "doi": "10.1007/s00572-016-0758-4", "pmid": "28066872", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s00572-016-0758-4"}], "notes": [], "created": "2019-01-15T08:43:01.539Z", "modified": "2020-01-21T13:53:22.530Z"}, {"entity": "publication", "iuid": "9546e6c6d2a04b82b56377bedc0d7cb6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9546e6c6d2a04b82b56377bedc0d7cb6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9546e6c6d2a04b82b56377bedc0d7cb6"}}, "title": "Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast", "authors": [{"family": "Lahtvee", "given": "Petri Jaan", "initials": "PJ", "orcid": "0000-0002-3327-3190", "researcher": {"href": "https://publications.scilifelab.se/researcher/8043cd36bb0e4cf3bc8a526dd45fa311.json"}}, {"family": "S\u00e1nchez", "given": "Benjam\u00edn J", "initials": "BJ"}, {"family": "Smialowska", "given": "Agata", "initials": "A"}, {"family": "Kasvandik", "given": "Sergo", "initials": "S"}, {"family": "Elsemman", "given": "Ibrahim E", "initials": "IE"}, {"family": "Gatto", "given": "Francesco", "initials": "F"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal-article", "published": "2017-05-00", "journal": {"volume": "4", "issn": "2405-4712", "issue": "5", "pages": "495-504.e5", "title": "Cell Syst", "issn-l": null}, "abstract": "Protein synthesis is the most energy-consuming process in a proliferating cell, and understanding what controls protein abundances represents a key question in biology and biotechnology. We quantified absolute abundances of 5,354 mRNAs and 2,198 proteins in Saccharomyces cerevisiae under ten environmental conditions and protein turnover for 1,384 proteins under a reference condition. The overall correlation between mRNA and protein abundances across all conditions was low (0.46), but for differentially expressed proteins (n = 202), the median mRNA-protein correlation was 0.88. We used these data to model translation efficiencies and found that they vary more than 400-fold between genes. Non-linear regression analysis detected that mRNA abundance and translation elongation were the dominant factors controlling protein synthesis, explaining 61% and 15% of its variance. Metabolic flux balance analysis further showed that only mitochondrial fluxes were positively associated with changes at the transcript level. The present dataset represents a crucial expansion to the current resources for future studies on yeast physiology.", "doi": "10.1016/j.cels.2017.03.003", "pmid": "28365149", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2405-4712(17)30088-1"}], "notes": [], "created": "2017-11-02T12:15:40.774Z", "modified": "2023-06-19T11:48:00.857Z"}, {"entity": "publication", "iuid": "52531998261243be9fc159120f4e6afd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52531998261243be9fc159120f4e6afd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52531998261243be9fc159120f4e6afd"}}, "title": "Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease.", "authors": [{"family": "Tobiasson", "given": "Magnus", "initials": "M"}, {"family": "Abdulkadir", "given": "Hani", "initials": "H"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "Katayama", "given": "Shintaro", "initials": "S"}, {"family": "Marabita", "given": "Francesco", "initials": "F"}, {"family": "De Paepe", "given": "Ayla", "initials": "A"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "Krjutskov", "given": "Kaarel", "initials": "K"}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E"}, {"family": "Gr\u00f6vdal", "given": "Michael", "initials": "M"}, {"family": "Jansson", "given": "Monika", "initials": "M"}, {"family": "Ben Azenkoud", "given": "Asmaa", "initials": "A"}, {"family": "Corddedu", "given": "Lina", "initials": "L"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E"}, {"family": "Ungerstedt", "given": "Johanna", "initials": "J"}], "type": "journal article", "published": "2017-04-25", "journal": {"volume": "8", "issn": "1949-2553", "issue": "17", "pages": "28812-28825", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "Azacitidine (Aza) is first-line treatment for patients with high-risk myelodysplastic syndromes (MDS), although its precise mechanism of action is unknown. We performed the first study to globally evaluate the epigenetic effects of Aza on MDS bone marrow progenitor cells assessing gene expression (RNA seq), DNA methylation (Illumina 450k) and the histone modifications H3K18ac and H3K9me3 (ChIP seq). Aza induced a general increase in gene expression with 924 significantly upregulated genes but this increase showed no correlation with changes in DNA methylation or H3K18ac, and only a weak association with changes in H3K9me3. Interestingly, we observed activation of transcripts containing 15 endogenous retroviruses (ERVs) confirming previous cell line studies. DNA methylation decreased moderately in 99% of all genes, with a median \u03b2-value reduction of 0.018; the most pronounced effects seen in heterochromatin. Aza-induced hypomethylation correlated significantly with change in H3K9me3. The pattern of H3K18ac and H3K9me3 displayed large differences between patients and healthy controls without any consistent pattern induced by Aza. We conclude that the marked induction of gene expression only partly could be explained by epigenetic changes, and propose that activation of ERVs may contribute to the clinical effects of Aza in MDS.", "doi": "10.18632/oncotarget.15807", "pmid": "28427179", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "15807"}, {"db": "pmc", "key": "PMC5438694"}], "notes": [], "created": "2019-01-15T07:50:51.953Z", "modified": "2020-01-21T13:53:22.301Z"}, {"entity": "publication", "iuid": "3ab08f7ce0d64e499b1282411ce8639c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ab08f7ce0d64e499b1282411ce8639c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ab08f7ce0d64e499b1282411ce8639c"}}, "title": "Persistent Effects of Developmental Exposure to 17\u03b1-Ethinylestradiol on the Zebrafish (Danio rerio) Brain Transcriptome and Behavior", "authors": [{"family": "Porseryd", "given": "Tove", "initials": "T"}, {"family": "Volkova", "given": "Kristina", "initials": "K"}, {"family": "Reyhanian Caspillo", "given": "Nasim", "initials": "N"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "Dinnetz", "given": "Patrik", "initials": "P"}, {"family": "Porsh H\u00e4llstr\u00f6m", "given": "Inger", "initials": "I"}], "type": "journal-article", "published": "2017-04-20", "journal": {"volume": "11", "issn": "1662-5153", "issue": null, "pages": null, "title": "Front. Behav. Neurosci.", "issn-l": "1662-5153"}, "abstract": "The synthetic estrogen 17\u03b1-ethinylestradiol (EE\n            2) is an endocrine disrupting compound of concern due to its persistence and widespread presence in the aquatic environment. Effects of developmental exposure to low concentrations of EE2 in fish on reproduction and behavior not only persisted to adulthood, but have also been observed to be transmitted to several generations of unexposed progeny. To investigate the possible biological mechanisms of the persistent anxiogenic phenotype, we exposed zebrafish embryos for 80 days post fertilization to 0, 3, and 10 ng/L EE2 (measured concentrations 2.14 and 7.34 ng/L). After discontinued exposure, the animals were allowed to recover for 120 days in clean water. Adult males and females were later tested for changes in stress response and shoal cohesion, and whole-brain gene expression was analyzed with RNA sequencing. The results show increased anxiety in the novel tank and scototaxis tests, and increased shoal cohesion in fish exposed during development to EE2. RNA sequencing revealed 34 coding genes differentially expressed in male brains and 62 in female brains as a result of EE2 exposure. Several differences were observed between males and females in differential gene expression, with only one gene, sv2b, coding for a synaptic vesicle protein, that was affected by EE2 in both sexes. Functional analyses showed that in female brains, EE2 had significant effects on pathways connected to the circadian rhythm, cytoskeleton and motor proteins and synaptic proteins. A large number of non-coding sequences including 19 novel miRNAs were also differentially expressed in the female brain. The largest treatment effect in male brains was observed in pathways related to cholesterol biosynthesis and synaptic proteins. Circadian rhythm and cholesterol biosynthesis, previously implicated in anxiety behavior, might represent possible candidate pathways connecting the transcriptome changes to the alterations to behavior. Further the observed alteration in expression of genes involved in synaptogenesis and synaptic function may be important for the developmental modulations resulting in an anxiety phenotype. This study represents an initial survey of the fish brain transcriptome by RNA sequencing after long-term recovery from developmental exposure to an estrogenic compound.", "doi": "10.3389/fnbeh.2017.00069", "pmid": "28473760", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-17T09:35:55.751Z", "modified": "2020-01-21T13:56:17.414Z"}, {"entity": "publication", "iuid": "65cb7e1c59e54b4bb89c0517bccfa04f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/65cb7e1c59e54b4bb89c0517bccfa04f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/65cb7e1c59e54b4bb89c0517bccfa04f"}}, "title": "Complete Genome Sequences of the Xylose-Fermenting Candida intermedia Strains CBS 141442 and PYCC 4715", "authors": [{"family": "Moreno", "given": "Antonio D", "initials": "AD"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Olsson", "given": "Lisbeth", "initials": "L"}, {"family": "Geijer", "given": "Cecilia", "initials": "C"}], "type": "journal-article", "published": "2017-04-06", "journal": {"volume": "5", "issn": "2169-8287", "issue": "14", "pages": "e00138-17", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": null, "doi": "10.1128/genomea.00138-17", "pmid": "28385851", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-17T09:33:33.171Z", "modified": "2024-01-16T13:48:48.116Z"}, {"entity": "publication", "iuid": "280aae409a56481ab2cf2f46ae4d91fc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/280aae409a56481ab2cf2f46ae4d91fc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/280aae409a56481ab2cf2f46ae4d91fc"}}, "title": "Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species.", "authors": [{"family": "Nielsen", "given": "Jens Christian", "initials": "JC", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Grijseels", "given": "Sietske", "initials": "S"}, {"family": "Prigent", "given": "Sylvain", "initials": "S"}, {"family": "Ji", "given": "Boyang", "initials": "B"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Nielsen", "given": "Kristian Fog", "initials": "KF"}, {"family": "Frisvad", "given": "Jens Christian", "initials": "JC"}, {"family": "Workman", "given": "Mhairi", "initials": "M"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}], "type": "journal article", "published": "2017-04-03", "journal": {"volume": "2", "issn": "2058-5276", "issue": null, "pages": "17044", "title": "Nat Microbiol", "issn-l": "2058-5276"}, "abstract": "Filamentous fungi produce a wide range of bioactive compounds with important pharmaceutical applications, such as antibiotic penicillins and cholesterol-lowering statins. However, less attention has been paid to fungal secondary metabolites compared to those from bacteria. In this study, we sequenced the genomes of 9 Penicillium species and, together with 15 published genomes, we investigated the secondary metabolism of Penicillium and identified an immense, unexploited potential for producing secondary metabolites by this genus. A total of 1,317 putative biosynthetic gene clusters (BGCs) were identified, and polyketide synthase and non-ribosomal peptide synthetase based BGCs were grouped into gene cluster families and mapped to known pathways. The grouping of BGCs allowed us to study the evolutionary trajectory of pathways based on 6-methylsalicylic acid (6-MSA) synthases. Finally, we cross-referenced the predicted pathways with published data on the production of secondary metabolites and experimentally validated the production of antibiotic yanuthones in Penicillia and identified a previously undescribed compound from the yanuthone pathway. This study is the first genus-wide analysis of the genomic diversity of Penicillia and highlights the potential of these species as a source of new antibiotics and other pharmaceuticals.", "doi": "10.1038/nmicrobiol.2017.44", "pmid": "28368369", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "nmicrobiol201744"}], "notes": [], "created": "2019-01-15T07:55:00.878Z", "modified": "2021-07-05T13:05:37.577Z"}, {"entity": "publication", "iuid": "f9e58a2d79d54634826b3cb1e0ee42c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9e58a2d79d54634826b3cb1e0ee42c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9e58a2d79d54634826b3cb1e0ee42c6"}}, "title": "Green listed\u2014a CRISPR screen tool", "authors": [{"family": "Panda", "given": "Sudeepta Kumar", "initials": "SK"}, {"family": "Boddul", "given": "Sanjay V", "initials": "SV"}, {"family": "Jim\u00e9nez-Andrade", "given": "Guillermina Yanek", "initials": "GY"}, {"family": "Jiang", "given": "Long", "initials": "L"}, {"family": "Kasza", "given": "Zsolt", "initials": "Z"}, {"family": "Fernandez-Ricaud", "given": "Luciano", "initials": "L"}, {"family": "Wermeling", "given": "Fredrik", "initials": "F"}], "type": "journal-article", "published": "2017-04-01", "journal": {"volume": "33", "issn": "1367-4803", "issue": "7", "pages": "1099-1100", "title": "Bioinformatics", "issn-l": null}, "abstract": null, "doi": "10.1093/bioinformatics/btw739", "pmid": "28414855", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T12:35:56.233Z", "modified": "2020-01-21T13:53:22.688Z"}, {"entity": "publication", "iuid": "169c93a475fe4ef59a84000416d5f96c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/169c93a475fe4ef59a84000416d5f96c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/169c93a475fe4ef59a84000416d5f96c"}}, "title": "Induction of Apoptosis in Intestinal Toxicity to a Histone Deacetylase Inhibitor in a Phase I Study with Pelvic Radiotherapy.", "authors": [{"family": "Kalanxhi", "given": "Erta", "initials": "E"}, {"family": "Risberg", "given": "Karianne", "initials": "K"}, {"family": "Barua", "given": "Imon S", "initials": "IS"}, {"family": "Dueland", "given": "Svein", "initials": "S"}, {"family": "Waagene", "given": "Stein", "initials": "S"}, {"family": "Andersen", "given": "Solveig Norheim", "initials": "SN"}, {"family": "Pettersen", "given": "Solveig J", "initials": "SJ"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Redalen", "given": "Kathrine R\u00f8e", "initials": "KR"}, {"family": "Flatmark", "given": "Kjersti", "initials": "K"}, {"family": "Ree", "given": "Anne Hansen", "initials": "AH"}], "type": "journal article", "published": "2017-04-00", "journal": {"volume": "49", "issn": "2005-9256", "issue": "2", "pages": "374-386", "title": "Cancer Res Treat", "issn-l": "1598-2998"}, "abstract": "When integrating molecularly targeted compounds in radiotherapy, synergistic effects of the systemic agent and radiation may extend the limits of patient tolerance, increasing the demand for understanding the pathophysiological mechanisms of treatment toxicity. In this Pelvic Radiation and Vorinostat (PRAVO) study, we investigated mechanisms of adverse effects in response to the histone deacetylase (HDAC) inhibitor vorinostat (suberoylanilide hydroxamic acid, SAHA) when administered as a potential radiosensitiser.\n\nThis phase I study for advanced gastrointestinal carcinoma was conducted in sequential patient cohorts exposed to escalating doses of vorinostat combined with standard-fractionated palliative radiotherapy to pelvic target volumes. Gene expression microarray analysis of the study patient peripheral blood mononuclear cells (PBMC) was followed by functional validation in cultured cell lines and mice treated with SAHA.\n\nPBMC transcriptional responses to vorinostat, including induction of apoptosis, were confined to the patient cohort reporting dose-limiting intestinal toxicities. At relevant SAHA concentrations, apoptotic features (annexin V staining and caspase 3/7 activation, but not poly-(ADP-ribose)-polymerase cleavage) were observed in cultured intestinal epithelial cells. Moreover, SAHA-treated mice displayed significant weight loss.\n\nThe PRAVO study design implemented a strategy to explore treatment toxicity caused by an HDAC inhibitor when combined with radiotherapy and enabled the identification of apoptosis as a potential mechanism responsible for the dose-limiting effects of vorinostat. To the best of our knowledge, this is the first report deciphering mechanisms of normal tissue adverse effects in response to an HDAC inhibitor within a combined-modality treatment regimen.", "doi": "10.4143/crt.2016.080", "pmid": "27488871", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "crt.2016.080"}], "notes": [], "created": "2017-05-03T13:00:51.305Z", "modified": "2021-07-05T12:48:15.941Z"}, {"entity": "publication", "iuid": "a096ccc00d02499da3af87b2dd611be6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a096ccc00d02499da3af87b2dd611be6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a096ccc00d02499da3af87b2dd611be6"}}, "title": "Frequent low-level mutations of protein kinase D2 in angiolipoma", "authors": [{"family": "Hofvander", "given": "Jakob", "initials": "J"}, {"family": "Arbajian", "given": "Elsa", "initials": "E"}, {"family": "Stenkula", "given": "Karin G", "initials": "KG"}, {"family": "Lindkvist-Petersson", "given": "Karin", "initials": "K"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Nilsson", "given": "Jenny", "initials": "J"}, {"family": "Magnusson", "given": "Linda", "initials": "L"}, {"family": "von Steyern", "given": "Fredrik Vult", "initials": "FV"}, {"family": "Rissler", "given": "Pehr", "initials": "P"}, {"family": "Hornick", "given": "Jason L", "initials": "JL"}, {"family": "Mertens", "given": "Fredrik", "initials": "F"}], "type": "journal-article", "published": "2017-04-00", "journal": {"volume": "241", "issn": "0022-3417", "issue": "5", "pages": "578-582", "title": "J. Pathol", "issn-l": "0022-3417"}, "abstract": null, "doi": "10.1002/path.4865", "pmid": "28139834", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T12:35:56.912Z", "modified": "2020-01-21T13:53:21.835Z"}, {"entity": "publication", "iuid": "f184b14667ce421baf3bef07a0046a67", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f184b14667ce421baf3bef07a0046a67.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f184b14667ce421baf3bef07a0046a67"}}, "title": "NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis.", "authors": [{"family": "Jeggari", "given": "Ashwini", "initials": "A"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}], "type": "journal article", "published": "2017-03-23", "journal": {"volume": "18", "issn": "1471-2105", "issue": "Suppl 5", "pages": "118", "title": "BMC Bioinformatics", "issn-l": "1471-2105"}, "abstract": "The statistical evaluation of pathway enrichment, i.e. of gene profiles' confluence to the pathway level, allows exploring molecular landscapes using functionally annotated gene sets. However, pathway scores can also be used as predictive features in machine learning. That requires, firstly, increasing statistical power and biological relevance via a network enrichment analysis (NEA) and, secondly, a fast and convenient procedure for rendering the original data into a space of pathway scores. However, previous implementations of NEA involved multiple runs of network randomization and were therefore slow.\n\nHere, we present a new R package NEArender which can transform raw 'omics' features of experimental or clinical samples into matrices describing the same samples with many fewer NEA-based pathway scores. This is done via a parametric estimation of the null binomial distribution and is thus much faster and less biased than randomization procedures. Further, we compare estimates from these two alternative procedures and demonstrate that the summarization of individual genes to pathways increases the statistical power compared to both the default differential expression analysis on individual genes and the state-of-the-art gene set enrichment analysis. The package also contains functions for preparing input, modeling null distributions, and evaluating alternative versions of the global network.\n\nBeyond the state-of-the-art exploration of molecular data through pathway enrichment, score matrices produced by NEArender can be used in larger bioinformatics pipelines as input for phenotype modeling, predicting disease outcomes etc. This approach is often more sensitive and robust than using the original data. The package NEArender is complementary to the online NEA tool EviNet ( https://www.evinet.org ) and, unlike of the latter, enables high performance of computations off-line. The R package NEArender version 1.4 is available at CRAN repository https://cran.r-project.org/web/packages/NEArender/.", "doi": "10.1186/s12859-017-1534-y", "pmid": "28361684", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12859-017-1534-y"}, {"db": "pmc", "key": "PMC5374688"}], "notes": [], "created": "2019-01-15T07:43:39.403Z", "modified": "2020-01-21T13:53:22.281Z"}, {"entity": "publication", "iuid": "9199b6ea51d04aa2b2f5f831a3d4e154", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9199b6ea51d04aa2b2f5f831a3d4e154.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9199b6ea51d04aa2b2f5f831a3d4e154"}}, "title": "Draft Genome Sequence of the Mycoparasitic Oomycete Pythium periplocum Strain CBS 532.74.", "authors": [{"family": "Kushwaha", "given": "Sandeep K", "initials": "SK"}, {"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Grenville-Briggs", "given": "Laura J", "initials": "LJ"}], "type": "journal article", "published": "2017-03-23", "journal": {"volume": "5", "issn": "2169-8287", "issue": "12", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": "The oomycete Pythium periplocum is an aggressive mycoparasite of a number of plant pathogenic fungi and oomycetes and therefore has potential as a biological control agent. Here, we report the first draft genome sequence of P. periplocum, which comprises 35.89\u00a0Mb. It contains 1,043 scaffolds and 14,399 predicted protein-coding genes.", "doi": "10.1128/genomeA.00057-17", "pmid": "28336598", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5/12/e00057-17"}, {"db": "pmc", "key": "PMC5364223"}], "notes": [], "created": "2017-11-03T16:21:53.141Z", "modified": "2020-01-21T13:56:17.350Z"}, {"entity": "publication", "iuid": "ecbaa43f8e1f4ee0accd6bafac629dce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ecbaa43f8e1f4ee0accd6bafac629dce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ecbaa43f8e1f4ee0accd6bafac629dce"}}, "title": "Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.", "authors": [{"family": "Antonelli", "given": "Alexandre", "initials": "A"}, {"family": "Hettling", "given": "Hannes", "initials": "H"}, {"family": "Condamine", "given": "Fabien L", "initials": "FL"}, {"family": "Vos", "given": "Karin", "initials": "K"}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH"}, {"family": "Sanderson", "given": "Michael J", "initials": "MJ"}, {"family": "Sauquet", "given": "Herv\u00e9", "initials": "H"}, {"family": "Scharn", "given": "Ruud", "initials": "R"}, {"family": "Silvestro", "given": "Daniele", "initials": "D"}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "Bacon", "given": "Christine D", "initials": "CD"}, {"family": "Oxelman", "given": "Bengt", "initials": "B"}, {"family": "Vos", "given": "Rutger A", "initials": "RA"}], "type": "journal article", "published": "2017-03-01", "journal": {"volume": "66", "issn": "1076-836X", "issue": "2", "pages": "152-166", "title": "Syst. Biol.", "issn-l": "1063-5157"}, "abstract": "Rapidly growing biological data-including molecular sequences and fossils-hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a \"Dated Tree of Life\" where all node ages are directly comparable. [Bayesian phylogenetics; data mining; divide-and-conquer methods; GenBank; multilocus multispecies coalescent; next-generation sequencing; palms; primates; tree calibration.].", "doi": "10.1093/sysbio/syw066", "pmid": "27616324", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "syw066"}, {"db": "pmc", "key": "PMC5410925"}, {"db": "Dryad", "key": "10.5061/dryad.sk81k"}], "notes": [], "created": "2019-01-14T19:03:30.954Z", "modified": "2021-06-21T15:55:31.210Z"}, {"entity": "publication", "iuid": "0d5fa939ffd84f5eb9884fe38f94ad39", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d5fa939ffd84f5eb9884fe38f94ad39.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d5fa939ffd84f5eb9884fe38f94ad39"}}, "title": "SpeciesGeoCoder: Fast Categorization of Species Occurrences for Analyses of Biodiversity, Biogeography, Ecology, and Evolution.", "authors": [{"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "Zizka", "given": "Alexander", "initials": "A"}, {"family": "Cali\u00f3", "given": "Maria Fernanda", "initials": "MF"}, {"family": "Scharn", "given": "Ruud", "initials": "R"}, {"family": "Silvestro", "given": "Daniele", "initials": "D"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}], "type": "journal article", "published": "2017-03-01", "journal": {"volume": "66", "issn": "1076-836X", "issue": "2", "pages": "145-151", "title": "Syst. Biol.", "issn-l": "1063-5157"}, "abstract": "Understanding the patterns and processes underlying the uneven distribution of biodiversity across space constitutes a major scientific challenge in systematic biology and biogeography, which largely relies on effectively mapping and making sense of rapidly increasing species occurrence data. There is thus an urgent need for making the process of coding species into spatial units faster, automated, transparent, and reproducible. Here we present SpeciesGeoCoder, an open-source software package written in Python and R, that allows for easy coding of species into user-defined operational units. These units may be of any size and be purely spatial (i.e., polygons) such as countries and states, conservation areas, biomes, islands, biodiversity hotspots, and areas of endemism, but may also include elevation ranges. This flexibility allows scoring species into complex categories, such as those encountered in topographically and ecologically heterogeneous landscapes. In addition, SpeciesGeoCoder can be used to facilitate sorting and cleaning of occurrence data obtained from online databases, and for testing the impact of incorrect identification of specimens on the spatial coding of species. The various outputs of SpeciesGeoCoder include quantitative biodiversity statistics, global and local distribution maps, and files that can be used directly in many phylogeny-based applications for ancestral range reconstruction, investigations of biome evolution, and other comparative methods. Our simulations indicate that even datasets containing hundreds of millions of records can be analyzed in relatively short time using a standard computer. We exemplify the use of SpeciesGeoCoder by inferring the historical dispersal of birds across the Isthmus of Panama, showing that lowland species crossed the Isthmus about twice as frequently as montane species with a marked increase in the number of dispersals during the last 10 million years. [ancestral area reconstruction; biodiversity patterns; ecology; evolution; point in polygon; species distribution data.].", "doi": "10.1093/sysbio/syw064", "pmid": "27486181", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "syw064"}, {"db": "pmc", "key": "PMC5410971"}, {"db": "Dryad", "key": "10.5061/dryad.tm32k"}], "notes": [], "created": "2019-01-14T19:02:47.673Z", "modified": "2021-06-21T15:56:01.806Z"}, {"entity": "publication", "iuid": "82328e28bb30498ca7414a9ad5c2ecf2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/82328e28bb30498ca7414a9ad5c2ecf2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/82328e28bb30498ca7414a9ad5c2ecf2"}}, "title": "Tracing Cellular Origin of Human Exosomes Using Multiplex Proximity Extension Assays", "authors": [{"family": "Larssen", "given": "Pia", "initials": "P"}, {"family": "Wik", "given": "Lotta", "initials": "L"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P"}, {"family": "Eldh", "given": "Maria", "initials": "M"}, {"family": "L\u00f6f", "given": "Liza", "initials": "L"}, {"family": "Ronquist", "given": "K G\u00f6ran", "initials": "KG"}, {"family": "Dubois", "given": "Louise", "initials": "L"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Gallant", "given": "Caroline J", "initials": "CJ"}, {"family": "Oelrich", "given": "Johan", "initials": "J"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Ronquist", "given": "Gunnar", "initials": "G"}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "Gabrielsson", "given": "Susanne", "initials": "S"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}], "type": "journal-article", "published": "2017-03-00", "journal": {"volume": "16", "issn": "1535-9476", "issue": "3", "pages": "502-511", "title": "Mol Cell Proteomics", "issn-l": "1535-9476"}, "abstract": null, "doi": "10.1074/mcp.m116.064725", "pmid": "28111361", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T12:55:02.303Z", "modified": "2023-04-14T13:56:17.086Z"}, {"entity": "publication", "iuid": "0d12224d115c4264913af93ddf48ea97", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d12224d115c4264913af93ddf48ea97.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d12224d115c4264913af93ddf48ea97"}}, "title": "Towards a whole-genome sequence for rye (Secale cereale L.).", "authors": [{"family": "Bauer", "given": "Eva", "initials": "E"}, {"family": "Schmutzer", "given": "Thomas", "initials": "T"}, {"family": "Barilar", "given": "Ivan", "initials": "I"}, {"family": "Mascher", "given": "Martin", "initials": "M"}, {"family": "Gundlach", "given": "Heidrun", "initials": "H"}, {"family": "Martis", "given": "Mihaela M", "initials": "MM"}, {"family": "Twardziok", "given": "Sven O", "initials": "SO"}, {"family": "Hackauf", "given": "Bernd", "initials": "B"}, {"family": "Gordillo", "given": "Andres", "initials": "A"}, {"family": "Wilde", "given": "Peer", "initials": "P"}, {"family": "Schmidt", "given": "Malthe", "initials": "M"}, {"family": "Korzun", "given": "Viktor", "initials": "V"}, {"family": "Mayer", "given": "Klaus F X", "initials": "KF"}, {"family": "Schmid", "given": "Karl", "initials": "K"}, {"family": "Sch\u00f6n", "given": "Chris-Carolin", "initials": "CC"}, {"family": "Scholz", "given": "Uwe", "initials": "U"}], "type": "journal article", "published": "2017-03-00", "journal": {"volume": "89", "issn": "1365-313X", "issue": "5", "pages": "853-869", "title": "Plant J.", "issn-l": "0960-7412"}, "abstract": "We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun sequencing of the 7.9-Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8\u00a0Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27\u00a0784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S.\u00a0vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high-density Rye600k genotyping array with 600\u00a0843 markers, which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome-wide map of selection signals differentiating the divergent gene pools. This rye whole-genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.", "doi": "10.1111/tpj.13436", "pmid": "27888547", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "GENBANK", "key": "ERS455621"}, {"db": "GENBANK", "key": "ERS455631"}, {"db": "GENBANK", "key": "ERS1115868"}], "notes": [], "created": "2017-05-03T13:00:45.334Z", "modified": "2020-01-21T13:53:21.218Z"}, {"entity": "publication", "iuid": "9d31db38ff3e46ff85f710dfcf4c086c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d31db38ff3e46ff85f710dfcf4c086c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d31db38ff3e46ff85f710dfcf4c086c"}}, "title": "High GC content causes orphan proteins to be intrinsically disordered.", "authors": [{"family": "Basile", "given": "Walter", "initials": "W"}, {"family": "Sachenkova", "given": "Oxana", "initials": "O"}, {"family": "Light", "given": "Sara", "initials": "S"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2017-03-00", "journal": {"volume": "13", "issn": "1553-7358", "issue": "3", "pages": "e1005375", "title": "PLoS Comput. Biol.", "issn-l": "1553-734X"}, "abstract": "De novo creation of protein coding genes involves the formation of short ORFs from noncoding regions; some of these ORFs might then become fixed in the population. These orphan proteins need to, at the bare minimum, not cause serious harm to the organism, meaning that they should for instance not aggregate. Therefore, although the creation of short ORFs could be truly random, the fixation should be subjected to some selective pressure. The selective forces acting on orphan proteins have been elusive, and contradictory results have been reported. In Drosophila young proteins are more disordered than ancient ones, while the opposite trend is present in yeast. To the best of our knowledge no valid explanation for this difference has been proposed. To solve this riddle we studied structural properties and age of proteins in 187 eukaryotic organisms. We find that, with the exception of length, there are only small differences in the properties between proteins of different ages. However, when we take the GC content into account we noted that it could explain the opposite trends observed for orphans in yeast (low GC) and Drosophila (high GC). GC content is correlated with codons coding for disorder promoting amino acids. This leads us to propose that intrinsic disorder is not a strong determining factor for fixation of orphan proteins. Instead these proteins largely resemble random proteins given a particular GC level. During evolution the properties of a protein change faster than the GC level causing the relationship between disorder and GC to gradually weaken.", "doi": "10.1371/journal.pcbi.1005375", "pmid": "28355220", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PCOMPBIOL-D-16-01242"}, {"db": "pmc", "key": "PMC5389847"}], "notes": [], "created": "2017-11-10T13:08:08.198Z", "modified": "2020-01-21T13:53:21.871Z"}, {"entity": "publication", "iuid": "3e47041311a44189b48417dec4292e33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e47041311a44189b48417dec4292e33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e47041311a44189b48417dec4292e33"}}, "title": "Antibody-encoding repertoires of bone marrow and peripheral blood\u2014a focus on IgE", "authors": [{"family": "Levin", "given": "Mattias", "initials": "M"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Palmason", "given": "Robert", "initials": "R"}, {"family": "Greiff", "given": "Lennart", "initials": "L"}, {"family": "Ohlin", "given": "Mats", "initials": "M", "orcid": "0000-0002-5105-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/fda1d1ed0b074a04a69b0c8b036dd001.json"}}], "type": "journal-article", "published": "2017-03-00", "journal": {"volume": "139", "issn": "1085-8725", "issue": "3", "pages": "1026-1030", "title": "Journal of Allergy and Clinical Immunology", "issn-l": "0091-6749"}, "abstract": null, "doi": "10.1016/j.jaci.2016.06.040", "pmid": "27521279", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0091-6749(16)30779-5"}], "notes": [], "created": "2017-05-03T12:59:52.904Z", "modified": "2024-01-16T13:48:48.371Z"}, {"entity": "publication", "iuid": "052b591e68464a66bde48f99012b379e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/052b591e68464a66bde48f99012b379e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/052b591e68464a66bde48f99012b379e"}}, "title": "Defining the human copper proteome and analysis of its expression variation in cancers.", "authors": [{"family": "Blockhuys", "given": "S", "initials": "S"}, {"family": "Celauro", "given": "E", "initials": "E"}, {"family": "Hildesj\u00f6", "given": "C", "initials": "C"}, {"family": "Feizi", "given": "A", "initials": "A"}, {"family": "St\u00e5l", "given": "O", "initials": "O"}, {"family": "Fierro-Gonz\u00e1lez", "given": "J C", "initials": "JC"}, {"family": "Wittung-Stafshede", "given": "P", "initials": "P", "orcid": "0000-0003-1058-1964", "researcher": {"href": "https://publications.scilifelab.se/researcher/9016aa00d62f439fb15532a1f4ba814e.json"}}], "type": "journal article", "published": "2017-02-22", "journal": {"volume": "9", "issn": "1756-591X", "issue": "2", "pages": "112-123", "title": "Metallomics", "issn-l": "1756-5901"}, "abstract": "Copper (Cu) is essential for living organisms, and acts as a cofactor in many metabolic enzymes. To avoid the toxicity of free Cu, organisms have specific transport systems that 'chaperone' the metal to targets. Cancer progression is associated with increased cellular Cu concentrations, whereby proliferative immortality, angiogenesis and metastasis are cancer hallmarks with defined requirements for Cu. The aim of this study is to gather all known Cu-binding proteins and reveal their putative involvement in cancers using the available database resources of RNA transcript levels. Using the database along with manual curation, we identified a total of 54 Cu-binding proteins (named the human Cu proteome). Next, we retrieved RNA expression levels in cancer versus normal tissues from the TCGA database for the human Cu proteome in 18 cancer types, and noted an intricate pattern of up- and downregulation of the genes in different cancers. Hierarchical clustering in combination with bioinformatics and functional genomics analyses allowed for the prediction of cancer-related Cu-binding proteins; these were specifically inspected for the breast cancer data. Finally, for the Cu chaperone ATOX1, which is the only Cu-binding protein proposed to have transcription factor activities, we validated its predicted over-expression in patient breast cancer tissue at the protein level. This collection of Cu-binding proteins, with RNA expression patterns in different cancers, will serve as an excellent resource for mechanistic-molecular studies of Cu-dependent processes in cancer.", "doi": "10.1039/c6mt00202a", "pmid": "27942658", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2019-01-15T08:23:52.183Z", "modified": "2021-06-16T16:16:13.314Z"}, {"entity": "publication", "iuid": "2f60cc890070451880d67bdcfb11753f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f60cc890070451880d67bdcfb11753f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f60cc890070451880d67bdcfb11753f"}}, "title": "RhoA knockout fibroblasts lose tumor-inhibitory capacity in vitro and promote tumor growth in vivo.", "authors": [{"family": "Alkasalias", "given": "Twana", "initials": "T"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Hennig", "given": "Katharina", "initials": "K"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Lebbink", "given": "Robert Jan", "initials": "RJ"}, {"family": "Fielden", "given": "Matthew", "initials": "M"}, {"family": "Turunen", "given": "S Pauliina", "initials": "SP"}, {"family": "Lehti", "given": "Kaisa", "initials": "K"}, {"family": "Kashuba", "given": "Vladimir", "initials": "V"}, {"family": "Madapura", "given": "Harsha S", "initials": "HS"}, {"family": "Bozoky", "given": "Benedek", "initials": "B"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Balland", "given": "Martial", "initials": "M"}, {"family": "Guv\u00e9n", "given": "Hayrettin", "initials": "H"}, {"family": "Klein", "given": "George", "initials": "G"}, {"family": "Gad", "given": "Annica K B", "initials": "AK"}, {"family": "Pavlova", "given": "Tatiana", "initials": "T"}], "type": "journal article", "published": "2017-02-21", "journal": {"volume": "114", "issn": "1091-6490", "issue": "8", "pages": "E1413-E1421", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Fibroblasts are a main player in the tumor-inhibitory microenvironment. Upon tumor initiation and progression, fibroblasts can lose their tumor-inhibitory capacity and promote tumor growth. The molecular mechanisms that underlie this switch have not been defined completely. Previously, we identified four proteins overexpressed in cancer-associated fibroblasts and linked to Rho GTPase signaling. Here, we show that knocking out the Ras homolog family member A (RhoA) gene in normal fibroblasts decreased their tumor-inhibitory capacity, as judged by neighbor suppression in vitro and accompanied by promotion of tumor growth in vivo. This also induced PC3 cancer cell motility and increased colony size in 2D cultures. RhoA knockout in fibroblasts induced vimentin intermediate filament reorganization, accompanied by reduced contractile force and increased stiffness of cells. There was also loss of wide F-actin stress fibers and large focal adhesions. In addition, we observed a significant loss of \u03b1-smooth muscle actin, which indicates a difference between RhoA knockout fibroblasts and classic cancer-associated fibroblasts. In 3D collagen matrix, RhoA knockout reduced fibroblast branching and meshwork formation and resulted in more compactly clustered tumor-cell colonies in coculture with PC3 cells, which might boost tumor stem-like properties. Coculturing RhoA knockout fibroblasts and PC3 cells induced expression of proinflammatory genes in both. Inflammatory mediators may induce tumor cell stemness. Network enrichment analysis of transcriptomic changes, however, revealed that the Rho signaling pathway per se was significantly triggered only after coculturing with tumor cells. Taken together, our findings in vivo and in vitro indicate that Rho signaling governs the inhibitory effects by fibroblasts on tumor-cell growth.", "doi": "10.1073/pnas.1621161114", "pmid": "28174275", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Spatial Proteomics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "1621161114"}, {"db": "pmc", "key": "PMC5338371"}], "notes": [], "created": "2017-10-30T12:42:04.006Z", "modified": "2021-07-05T16:33:38.606Z"}, {"entity": "publication", "iuid": "f35c109acf9743b79cb359d6a7b17c91", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f35c109acf9743b79cb359d6a7b17c91.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f35c109acf9743b79cb359d6a7b17c91"}}, "title": "The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish.", "authors": [{"family": "Adrian-Kalchhauser", "given": "Irene", "initials": "I"}, {"family": "Svensson", "given": "Ola", "initials": "O"}, {"family": "Kutschera", "given": "Verena E", "initials": "VE"}, {"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "Pippel", "given": "Martin", "initials": "M"}, {"family": "Winkler", "given": "Sylke", "initials": "S"}, {"family": "Schloissnig", "given": "Siegfried", "initials": "S"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}, {"family": "Burkhardt-Holm", "given": "Patricia", "initials": "P"}], "type": "journal article", "published": "2017-02-16", "journal": {"volume": "18", "issn": "1471-2164", "issue": "1", "pages": "177", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Vertebrate mitochondrial genomes are optimized for fast replication and low cost of RNA expression. Accordingly, they are devoid of introns, are transcribed as polycistrons and contain very little intergenic sequences. Usually, vertebrate mitochondrial genomes measure between 16.5 and 17 kilobases (kb).\n\nDuring genome sequencing projects for two novel vertebrate models, the invasive round goby and the sand goby, we found that the sand goby genome is exceptionally small (16.4\u00a0kb), while the mitochondrial genome of the round goby is much larger than expected for a vertebrate. It is 19\u00a0kb in size and is thus one of the largest fish and even vertebrate mitochondrial genomes known to date. The expansion is attributable to a sequence insertion downstream of the putative transcriptional start site. This insertion carries traces of repeats from the control region, but is mostly novel. To get more information about this phenomenon, we gathered all available mitochondrial genomes of Gobiidae and of nine gobioid species, performed phylogenetic analyses, analysed gene arrangements, and compared gobiid mitochondrial genome sizes, ecological information and other species characteristics with respect to the mitochondrial phylogeny. This allowed us amongst others to identify a unique arrangement of tRNAs among Ponto-Caspian gobies.\n\nOur results indicate that the round goby mitochondrial genome may contain novel features. Since mitochondrial genome organisation is tightly linked to energy metabolism, these features may be linked to its invasion success. Also, the unique tRNA arrangement among Ponto-Caspian gobies may be helpful in studying the evolution of this highly adaptive and invasive species group. Finally, we find that the phylogeny of gobiids can be further refined by the use of longer stretches of linked DNA sequence.", "doi": "10.1186/s12864-017-3550-8", "pmid": "28209125", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-017-3550-8"}, {"db": "pmc", "key": "PMC5314710"}], "notes": [], "created": "2017-11-01T12:54:58.955Z", "modified": "2024-01-16T13:48:48.415Z"}, {"entity": "publication", "iuid": "1ca13a5dbc2c44329bbbefec4d917ee0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ca13a5dbc2c44329bbbefec4d917ee0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ca13a5dbc2c44329bbbefec4d917ee0"}}, "title": "microRNAs with AAGUGC seed motif constitute an integral part of an oncogenic signaling network.", "authors": [{"family": "Zhou", "given": "Y", "initials": "Y"}, {"family": "Frings", "given": "O", "initials": "O"}, {"family": "Branca", "given": "R M", "initials": "RM"}, {"family": "Boekel", "given": "J", "initials": "J"}, {"family": "le Sage", "given": "C", "initials": "C"}, {"family": "Fredlund", "given": "E", "initials": "E"}, {"family": "Agami", "given": "R", "initials": "R"}, {"family": "Orre", "given": "L M", "initials": "LM"}], "type": "journal article", "published": "2017-02-09", "journal": {"volume": "36", "issn": "1476-5594", "issue": "6", "pages": "731-745", "title": "Oncogene", "issn-l": "0950-9232"}, "abstract": "microRNA (miRNA) dysregulation is a common feature of cancer cells, but the complex roles of miRNAs in cancer are not fully elucidated. Here, we used functional genomics to identify oncogenic miRNAs in non-small cell lung cancer and evaluate their impact on response to epidermal growth factor (EGFR)-targeting therapy. Our data demonstrate that miRNAs with an AAGUGC motif in their seed sequence increase both cancer cell proliferation and sensitivity to EGFR inhibitors. Global transcriptomics, proteomics and target prediction resulted in the identification of several tumor suppressors involved in the G1/S transition as AAGUGC-miRNA targets. The clinical implications of our findings were evaluated by analysis of AAGUGC-miRNA expression in multiple cancer types, supporting the link between this miRNA seed family, their tumor suppressor targets and cancer cell proliferation. In conclusion, we propose the AAGUGC seed motif as an oncomotif and that oncomotif-miRNAs promote cancer cell proliferation. These findings have potential therapeutic implications, especially in selecting patients for EGFR-targeting therapy.", "doi": "10.1038/onc.2016.242", "pmid": "27477696", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "onc2016242"}, {"db": "pmc", "key": "PMC5311252"}], "notes": [], "created": "2017-05-03T13:00:40.536Z", "modified": "2020-01-21T13:56:16.909Z"}, {"entity": "publication", "iuid": "c63ea0fe49dd453798aca844add7e849", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c63ea0fe49dd453798aca844add7e849.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c63ea0fe49dd453798aca844add7e849"}}, "title": "The in silico identification and characterization of a bread wheat/Triticum militinae introgression line.", "authors": [{"family": "Abrouk", "given": "Michael", "initials": "M"}, {"family": "Balc\u00e1rkov\u00e1", "given": "Barbora", "initials": "B"}, {"family": "\u0160imkov\u00e1", "given": "Hana", "initials": "H"}, {"family": "Kom\u00ednkova", "given": "Eva", "initials": "E"}, {"family": "Martis", "given": "Mihaela M", "initials": "MM"}, {"family": "Jakobson", "given": "Irena", "initials": "I"}, {"family": "Timofejeva", "given": "Ljudmilla", "initials": "L"}, {"family": "Rey", "given": "Elodie", "initials": "E"}, {"family": "Vr\u00e1na", "given": "Jan", "initials": "J"}, {"family": "Kilian", "given": "Andrzej", "initials": "A"}, {"family": "J\u00e4rve", "given": "Kadri", "initials": "K"}, {"family": "Dole\u017eel", "given": "Jaroslav", "initials": "J"}, {"family": "Val\u00e1rik", "given": "Miroslav", "initials": "M"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "15", "issn": "1467-7652", "issue": "2", "pages": "249-256", "title": "Plant Biotechnol. J.", "issn-l": "1467-7644"}, "abstract": "The capacity of the bread wheat (Triticum aestivum) genome to tolerate introgression from related genomes can be exploited for wheat improvement. A resistance to powdery mildew expressed by a derivative of the cross-bread wheat cv. T\u00e4hti\u00a0\u00d7\u00a0T.\u00a0militinae (Tm) is known to be due to the incorporation of a Tm segment into the long arm of chromosome 4A. Here, a newly developed in silico method termed rearrangement identification and characterization (RICh) has been applied to characterize the introgression. A virtual gene order, assembled using the GenomeZipper approach, was obtained for the native copy of chromosome 4A; it incorporated 570 4A DArTseq markers to produce a zipper comprising 2132 loci. A comparison between the native and introgressed forms of the 4AL chromosome arm showed that the introgressed region is located at the distal part of the arm. The Tm segment, derived from chromosome 7G, harbours 131 homoeologs of the 357 genes present on the corresponding region of Chinese Spring 4AL. The estimated number of Tm genes transferred along with the disease resistance gene was 169. Characterizing the introgression's position, gene content and internal gene order should not only facilitate gene isolation, but may also be informative with respect to chromatin structure and behaviour studies.", "doi": "10.1111/pbi.12610", "pmid": "27510270", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5259550"}], "notes": [], "created": "2017-05-03T13:00:44.730Z", "modified": "2020-01-21T13:53:21.406Z"}, {"entity": "publication", "iuid": "0b27d073b90240b18860ecc4d243d200", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b27d073b90240b18860ecc4d243d200.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b27d073b90240b18860ecc4d243d200"}}, "title": "Draft Genome Sequences of Semiconstitutive Red, Dry, and Rough Biofilm-Forming Commensal and Uropathogenic Escherichia coli Isolates.", "authors": [{"family": "Cimdins", "given": "Annika", "initials": "A"}, {"family": "L\u00fcthje", "given": "Petra", "initials": "P"}, {"family": "Li", "given": "Fengyang", "initials": "F"}, {"family": "Ahmad", "given": "Irfan", "initials": "I"}, {"family": "Brauner", "given": "Annelie", "initials": "A"}, {"family": "R\u00f6mling", "given": "Ute", "initials": "U"}], "type": "journal article", "published": "2017-01-26", "journal": {"volume": "5", "issn": "2169-8287", "issue": "4", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": "Strains of Escherichia coli exhibit diverse biofilm formation capabilities. E.\u00a0coli K-12 expresses the red, dry, and rough (rdar) morphotype below 30\u00b0C, whereas clinical isolates frequently display the rdar morphotype semiconstitutively. We sequenced the genomes of eight E.\u00a0coli strains to subsequently investigate the molecular basis of semiconstitutive rdar morphotype expression.", "doi": "10.1128/genomeA.01249-16", "pmid": "28126929", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "5/4/e01249-16"}, {"db": "pmc", "key": "PMC5270688"}], "notes": [], "created": "2017-10-17T07:55:03.116Z", "modified": "2020-01-21T13:56:17.431Z"}, {"entity": "publication", "iuid": "5cd81ab25d5347f49efbc2f7906190f7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5cd81ab25d5347f49efbc2f7906190f7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5cd81ab25d5347f49efbc2f7906190f7"}}, "title": "Early onset of inflammation during ontogeny of bipolar disorder: the NLRP2 inflammasome gene distinctly differentiates between patients and healthy controls in the transition between iPS cell and neural stem cell stages", "authors": [{"family": "Vizlin-Hodzic", "given": "D", "initials": "D"}, {"family": "Zhai", "given": "Q", "initials": "Q"}, {"family": "Illes", "given": "S", "initials": "S"}, {"family": "S\u00f6dersten", "given": "K", "initials": "K"}, {"family": "Truv\u00e9", "given": "K", "initials": "K"}, {"family": "Parris", "given": "T Z", "initials": "TZ"}, {"family": "Sobhan", "given": "P K", "initials": "PK"}, {"family": "Salmela", "given": "S", "initials": "S"}, {"family": "Kosalai", "given": "S T", "initials": "ST"}, {"family": "Kanduri", "given": "C", "initials": "C"}, {"family": "Strandberg", "given": "J", "initials": "J"}, {"family": "Seth", "given": "H", "initials": "H"}, {"family": "Bontell", "given": "T O", "initials": "TO"}, {"family": "Hanse", "given": "E", "initials": "E"}, {"family": "\u00c5gren", "given": "H", "initials": "H"}, {"family": "Funa", "given": "K", "initials": "K"}], "type": "journal-article", "published": "2017-01-24", "journal": {"volume": "7", "issn": "2158-3188", "issue": "1", "pages": "e1010", "title": "Transl Psychiatry", "issn-l": "2158-3188"}, "abstract": null, "doi": "10.1038/tp.2016.284", "pmid": "28117838", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T12:55:00.969Z", "modified": "2020-01-21T13:53:21.828Z"}, {"entity": "publication", "iuid": "e7ef68a1bed844139e2810dea9b1fd70", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e7ef68a1bed844139e2810dea9b1fd70.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e7ef68a1bed844139e2810dea9b1fd70"}}, "title": "NLK-mediated phosphorylation of HDAC1 negatively regulates Wnt signaling.", "authors": [{"family": "Masoumi", "given": "Katarzyna Chmielarska", "initials": "KC"}, {"family": "Daams", "given": "Ren\u00e9e", "initials": "R"}, {"family": "Sime", "given": "Wondossen", "initials": "W"}, {"family": "Siino", "given": "Valentina", "initials": "V"}, {"family": "Ke", "given": "Hengning", "initials": "H"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Massoumi", "given": "Ramin", "initials": "R"}], "type": "journal article", "published": "2017-01-15", "journal": {"volume": "28", "issn": "1939-4586", "issue": "2", "pages": "346-355", "title": "Mol. Biol. Cell", "issn-l": "1059-1524"}, "abstract": "The Wnt signaling pathway is essential in regulating various cellular processes. Different mechanisms of inhibition for Wnt signaling have been proposed. Besides \u03b2-catenin degradation through the proteasome, nemo-like kinase (NLK) is another molecule that is known to negatively regulate Wnt signaling. However, the mechanism by which NLK mediates the inhibition of Wnt signaling was not known. In the present study, we used primary embryonic fibroblast cells isolated from NLK-deficient mice and showed that these cells proliferate faster and have a shorter cell cycle than wild-type cells. In NLK-knockout cells, we observed sustained interaction between Lef1 and \u03b2-catenin, leading to elevated luciferase reporter of \u03b2-catenin/Lef1-mediated transcriptional activation. The mechanism for the reduced \u03b2-catenin/Lef1 promoter activation was explained by phosphorylation of HDAC1 at serine 421 via NLK. The phosphorylation of HDAC1 was achieved only in the presence of wild-type NLK because a catalytically inactive mutant of NLK was unable to phosphorylate HDAC1 and reduced the luciferase reporter of \u03b2-catenin/Lef1-mediated transcriptional activation. This result suggests that NLK and HDAC1 together negatively regulate Wnt signaling, which is vital in preventing aberrant proliferation of nontransformed primary fibroblast cells.", "doi": "10.1091/mbc.E16-07-0547", "pmid": "27903773", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "mbc.E16-07-0547"}, {"db": "pmc", "key": "PMC5231902"}], "notes": [], "created": "2019-01-15T07:52:59.999Z", "modified": "2020-01-21T13:53:22.314Z"}, {"entity": "publication", "iuid": "7f747305169e493a98de0d03fb8b658a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f747305169e493a98de0d03fb8b658a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f747305169e493a98de0d03fb8b658a"}}, "title": "Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III inStreptococcus pyogenes", "authors": [{"family": "Le\u00a0Rhun", "given": "Ana\u00efs", "initials": "A"}, {"family": "L\u00e9crivain", "given": "Anne Laure", "initials": "AL"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E"}, {"family": "Broglia", "given": "Laura", "initials": "L"}, {"family": "Della\u00a0Beffa", "given": "Cristina", "initials": "C"}, {"family": "Charpentier", "given": "Emmanuelle", "initials": "E"}], "type": "journal-article", "published": "2017-01-12", "journal": {"volume": null, "issn": "0305-1048", "issue": null, "pages": "gkw1316", "title": "Nucleic Acids Res", "issn-l": null}, "abstract": "A better understanding of transcriptional and post-transcriptional regulation of gene expression in bacteria relies on studying their transcriptome. RNA sequencing methods are used not only to assess RNA abundance but also the exact boundaries of primary and processed transcripts. Here, we developed a method, called identification of specific cleavage position (ISCP), which enables the identification of direct endoribonuclease targets in vivo by comparing the 5\u0384 and 3\u0384 ends of processed transcripts between wild type and RNase deficient strains. To demonstrate the ISCP method, we used as a model the double-stranded specific RNase III in the human pathogen Streptococcus pyogenes. We mapped 92 specific cleavage positions (SCPs) among which, 48 were previously described and 44 are new, with the characteristic 2 nucleotides 3\u0384 overhang of RNase III. Most SCPs were located in untranslated regions of RNAs. We screened for RNase III targets using transcriptomic differential expression analysis (DEA) and compared those with the RNase III targets identified using the ISCP method. Our study shows that in S. pyogenes, under standard growth conditions, RNase III has a limited impact both on antisense transcripts and on global gene expression with the expression of most of the affected genes being downregulated in an RNase III deletion mutant.", "doi": "10.1093/nar/gkw1316", "pmid": "28082390", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-04T15:14:47.764Z", "modified": "2020-01-21T13:53:22.542Z"}, {"entity": "publication", "iuid": "69d3f8ae22854c9087ae31716554c354", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69d3f8ae22854c9087ae31716554c354.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69d3f8ae22854c9087ae31716554c354"}}, "title": "Rye B chromosomes encode a functional Argonaute-like protein with in\u00a0vitro slicer activities similar to its A chromosome paralog.", "authors": [{"family": "Ma", "given": "Wei", "initials": "W"}, {"family": "Gabriel", "given": "Tobias Sebastian", "initials": "TS"}, {"family": "Martis", "given": "Mihaela Maria", "initials": "MM"}, {"family": "Gursinsky", "given": "Torsten", "initials": "T"}, {"family": "Schubert", "given": "Veit", "initials": "V"}, {"family": "Vr\u00e1na", "given": "Jan", "initials": "J"}, {"family": "Dole\u017eel", "given": "Jaroslav", "initials": "J"}, {"family": "Grundlach", "given": "Heidrun", "initials": "H"}, {"family": "Altschmied", "given": "Lothar", "initials": "L"}, {"family": "Scholz", "given": "Uwe", "initials": "U"}, {"family": "Himmelbach", "given": "Axel", "initials": "A"}, {"family": "Behrens", "given": "Sven-Erik", "initials": "SE"}, {"family": "Banaei-Moghaddam", "given": "Ali Mohammad", "initials": "AM"}, {"family": "Houben", "given": "Andreas", "initials": "A"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "213", "issn": "1469-8137", "issue": "2", "pages": "916-928", "title": "New Phytol.", "issn-l": "0028-646X"}, "abstract": "B chromosomes (Bs) are supernumerary, dispensable parts of the nuclear genome, which appear in many different species of eukaryote. So far, Bs have been considered to be genetically inert elements without any functional genes. Our comparative transcriptome analysis and the detection of active RNA polymerase II (RNAPII) in the proximity of B chromatin demonstrate that the Bs of rye (Secale cereale) contribute to the transcriptome. In total, 1954 and 1218 B-derived transcripts with an open reading frame were expressed in generative and vegetative tissues, respectively. In addition to B-derived transposable element transcripts, a high percentage of short transcripts without detectable similarity to known proteins and gene fragments from A chromosomes (As) were found, suggesting an ongoing gene erosion process. In\u00a0vitro analysis of the A- and B-encoded AGO4B protein variants demonstrated that both possess RNA slicer activity. These data demonstrate unambiguously the presence of a functional AGO4B gene on Bs and that these Bs carry both functional protein coding genes and pseudogene copies. Thus, B-encoded genes may provide an additional level of gene control and complexity in combination with their related A-located genes. Hence, physiological effects, associated with the presence of Bs, may partly be explained by the activity of B-located (pseudo)genes.", "doi": "10.1111/nph.14110", "pmid": "27468091", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:44.433Z", "modified": "2020-01-21T13:53:21.320Z"}, {"entity": "publication", "iuid": "02c9e94d276149cd93952ef5577ea324", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02c9e94d276149cd93952ef5577ea324.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02c9e94d276149cd93952ef5577ea324"}}, "title": "Expression of Transient Receptor Potential Channels in the Purified Human Pancreatic \u03b2-Cells.", "authors": [{"family": "Marabita", "given": "Francesco", "initials": "F"}, {"family": "Islam", "given": "Md Shahidul", "initials": "MS"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "46", "issn": "1536-4828", "issue": "1", "pages": "97-101", "title": "Pancreas", "issn-l": "0885-3177"}, "abstract": "Members of the transient receptor potential (TRP) channels are involved in mediating the electrical excitability and stimulus-secretion coupling in the pancreatic \u03b2-cells. The expression and the relative abundance of different TRP channels in the human \u03b2-cells are unknown. The objective of this study was to examine the expression of the TRP channels and their relative abundance in the human \u03b2-cell.\n\nRNA sequencing data obtained from human islets, fluorescence-activated cell sorting-purified human \u03b2-cell and human pancreatic acinar cells were analyzed. Gene counts and fragments per kilobase per million mapped reads were obtained.\n\nAmong the TRPC family only the TRPC1 was expressed in the human \u03b2-cell. TRPV1 channels were not expressed in the human \u03b2-cells. Among the TRPM family, TRPM4, TRPM7, TRPM2, and TRPM3 were expressed in the human \u03b2-cell. Of the remaining TRP channels, TRPP2, TRPML1, and TRPML3 were expressed in these cells.\n\nBy analyzing the RNA sequencing data, we have detected for the first time the TRP channels that are expressed in the purified human \u03b2-cells, in comparison to the other relevant pancreatic cell types. Our study provides an opportunity to focus on these TRP channels for a better understanding of the electrophysiology and stimulus-secretion coupling in these cells.", "doi": "10.1097/MPA.0000000000000685", "pmid": "27464700", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:43.824Z", "modified": "2020-01-21T13:53:21.201Z"}, {"entity": "publication", "iuid": "32c370e02d384d7e896285e4a06530ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/32c370e02d384d7e896285e4a06530ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/32c370e02d384d7e896285e4a06530ad"}}, "title": "Both maternal and offspring Elovl2 genotypes determine systemic DHA levels in perinatal mice.", "authors": [{"family": "Pauter", "given": "Anna M", "initials": "AM"}, {"family": "Trattner", "given": "Sofia", "initials": "S"}, {"family": "Gonzalez-Bengtsson", "given": "Amanda", "initials": "A"}, {"family": "Talamonti", "given": "Emanuela", "initials": "E"}, {"family": "Asadi", "given": "Abolfazl", "initials": "A"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Jacobsson", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "58", "issn": "1539-7262", "issue": "1", "pages": "111-123", "title": "J. Lipid Res.", "issn-l": "0022-2275"}, "abstract": "The molecular details relevant to dietary supplementation of the omega-3 fatty acid DHA in mothers as well as in their offspring are not clear. The PUFA elongase, elongation of very long-chain fatty acid (ELOVL)2, is a critical enzyme in the formation of DHA in mammals. In order to address the question regarding the origin of DHA during perinatal life, we have used DHA-deficient Elovl2-ablated mice as a model system to analyze the maternal impact on the DHA level in their offspring of various genotypes. Elovl2(-/-) mothers maintained on control diet had significantly lower systemic levels of DHA compared with the Elovl2(+/-) and Elovl2(+/+) mothers. Dietary DHA administration during the pregnancy and lactation periods led to increased DHA accretion in maternal tissues and serum of all genotypes. The proportion of DHA in the liver and serum of the Elovl2(-/-) offspring was significantly lower than in the Elovl2(+/+) offspring. Remarkably, the DHA level in the Elovl2(+/-) offspring nursed by DHA-free-fed Elovl2(-/-) mothers was almost as high as in +/+ pups delivered by +/+ mothers, suggesting that endogenous synthesis in the offspring can compensate for maternal DHA deficiency. Maternal DHA supplementation had a strong impact on offspring hepatic gene expression, especially of the fatty acid transporter, Mfsd2a, suggesting a dynamic interplay between DHA synthesis and DHA uptake in the control of systemic levels in the offspring.", "doi": "10.1194/jlr.M070862", "pmid": "27864326", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "jlr.M070862"}, {"db": "pmc", "key": "PMC5234714"}], "notes": [], "created": "2017-05-03T13:00:47.686Z", "modified": "2020-01-21T13:53:21.284Z"}, {"entity": "publication", "iuid": "f0189e06f40849b6aa396efe9d60aad1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0189e06f40849b6aa396efe9d60aad1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0189e06f40849b6aa396efe9d60aad1"}}, "title": "Validation and development of MTH1 inhibitors for treatment of cancer.", "authors": [{"family": "Warpman Berglund", "given": "U", "initials": "U"}, {"family": "Sanjiv", "given": "K", "initials": "K"}, {"family": "Gad", "given": "H", "initials": "H"}, {"family": "Kalder\u00e9n", "given": "C", "initials": "C"}, {"family": "Koolmeister", "given": "T", "initials": "T"}, {"family": "Pham", "given": "T", "initials": "T"}, {"family": "Gokturk", "given": "C", "initials": "C"}, {"family": "Jafari", "given": "R", "initials": "R"}, {"family": "Maddalo", "given": "G", "initials": "G"}, {"family": "Seashore-Ludlow", "given": "B", "initials": "B"}, {"family": "Chernobrovkin", "given": "A", "initials": "A"}, {"family": "Manoilov", "given": "A", "initials": "A"}, {"family": "Pateras", "given": "I S", "initials": "IS"}, {"family": "Rasti", "given": "A", "initials": "A"}, {"family": "Jemth", "given": "A-S", "initials": "AS"}, {"family": "Alml\u00f6f", "given": "I", "initials": "I"}, {"family": "Loseva", "given": "O", "initials": "O"}, {"family": "Visnes", "given": "T", "initials": "T"}, {"family": "Einarsdottir", "given": "B O", "initials": "BO"}, {"family": "Gaugaz", "given": "F Z", "initials": "FZ"}, {"family": "Saleh", "given": "A", "initials": "A"}, {"family": "Platzack", "given": "B", "initials": "B"}, {"family": "Wallner", "given": "O A", "initials": "OA"}, {"family": "Vallin", "given": "K S A", "initials": "KS"}, {"family": "Henriksson", "given": "M", "initials": "M"}, {"family": "Wakchaure", "given": "P", "initials": "P"}, {"family": "Borhade", "given": "S", "initials": "S"}, {"family": "Herr", "given": "P", "initials": "P"}, {"family": "Kallberg", "given": "Y", "initials": "Y"}, {"family": "Baranczewski", "given": "P", "initials": "P"}, {"family": "Homan", "given": "E J", "initials": "EJ"}, {"family": "Wiita", "given": "E", "initials": "E"}, {"family": "Nagpal", "given": "V", "initials": "V"}, {"family": "Meijer", "given": "T", "initials": "T"}, {"family": "Schipper", "given": "N", "initials": "N"}, {"family": "Rudd", "given": "S G", "initials": "SG"}, {"family": "Br\u00e4utigam", "given": "L", "initials": "L"}, {"family": "Lindqvist", "given": "A", "initials": "A"}, {"family": "Filppula", "given": "A", "initials": "A"}, {"family": "Lee", "given": "T-C", "initials": "TC"}, {"family": "Artursson", "given": "P", "initials": "P"}, {"family": "Nilsson", "given": "J A", "initials": "JA"}, {"family": "Gorgoulis", "given": "V G", "initials": "VG"}, {"family": "Lehti\u00f6", "given": "J", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Zubarev", "given": "R A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}, {"family": "Scobie", "given": "M", "initials": "M"}, {"family": "Helleday", "given": "T", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}], "type": "journal article", "published": "2016-12-00", "journal": {"volume": "27", "issn": "1569-8041", "issue": "12", "pages": "2275-2283", "title": "Ann. Oncol.", "issn-l": "0923-7534"}, "abstract": "Previously, we showed cancer cells rely on the MTH1 protein to prevent incorporation of otherwise deadly oxidised nucleotides into DNA and we developed MTH1 inhibitors which selectively kill cancer cells. Recently, several new and potent inhibitors of MTH1 were demonstrated to be non-toxic to cancer cells, challenging the utility of MTH1 inhibition as a target for cancer treatment.\n\nHuman cancer cell lines were exposed in vitro to MTH1 inhibitors or depleted of MTH1 by siRNA or shRNA. 8-oxodG was measured by immunostaining and modified comet assay. Thermal Proteome profiling, proteomics, cellular thermal shift assays, kinase and CEREP panel were used for target engagement, mode of action and selectivity investigations of MTH1 inhibitors. Effect of MTH1 inhibition on tumour growth was explored in BRAF V600E-mutated malignant melanoma patient derived xenograft and human colon cancer SW480 and HCT116 xenograft models.\n\nHere, we demonstrate that recently described MTH1 inhibitors, which fail to kill cancer cells, also fail to introduce the toxic oxidized nucleotides into DNA. We also describe a new MTH1 inhibitor TH1579, (Karonudib), an analogue of TH588, which is a potent, selective MTH1 inhibitor with good oral availability and demonstrates excellent pharmacokinetic and anti-cancer properties in vivo.\n\nWe demonstrate that in order to kill cancer cells MTH1 inhibitors must also introduce oxidized nucleotides into DNA. Furthermore, we describe TH1579 as a best-in-class MTH1 inhibitor, which we expect to be useful in order to further validate the MTH1 inhibitor concept.", "doi": "10.1093/annonc/mdw429", "pmid": "27827301", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Clinical Proteomics Mass spectrometry": "Collaborative", "Chemical Proteomics": "Service", "Advanced Mass Spectrometry Proteomics": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Chemical Biology Consortium Sweden": "Collaborative", "Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0923-7534(19)36552-4"}], "notes": "Laboratories for Chemical Biology at Karolinska Institutet (LCBKI)\r\nADME of Therapeutics (UDOPP)", "created": "2017-05-03T12:58:49.192Z", "modified": "2025-10-17T13:05:09.110Z"}, {"entity": "publication", "iuid": "17d3f0529e1043fb8ddc82759f401c5f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/17d3f0529e1043fb8ddc82759f401c5f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/17d3f0529e1043fb8ddc82759f401c5f"}}, "title": "Spatial subsidies in spider diets vary with shoreline structure: Complementary evidence from molecular diet analysis and stable isotopes.", "authors": [{"family": "Hamb\u00e4ck", "given": "Peter A", "initials": "PA"}, {"family": "Weingartner", "given": "Elisabeth", "initials": "E"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Wirta", "given": "Helena", "initials": "H"}, {"family": "Roslin", "given": "Tomas", "initials": "T"}], "type": "journal article", "published": "2016-12-00", "journal": {"volume": "6", "issn": "2045-7758", "issue": "23", "pages": "8431-8439", "title": "Ecol Evol", "issn-l": "2045-7758"}, "abstract": "Inflow of matter and organisms may strongly affect the local density and diversity of organisms. This effect is particularly evident on shores where organisms with aquatic larval stages enter the terrestrial food web. The identities of such trophic links are not easily estimated as spiders, a dominant group of shoreline predator, have external digestion. We compared trophic links and the prey diversity of spiders on different shore types along the Baltic Sea: on open shores and on shores with a reed belt bordering the water. A priori, we hypothesized that the physical structure of the shoreline reduces the flow between ecosystem and the subsidies across the sea-land interface. To circumvent the lack of morphologically detectable remains of spider prey, we used a combination of stable isotope and molecular gut content analyses. The two tools used for diet analysis revealed complementary information on spider diets. The stable isotope analysis indicated that spiders on open shores had a marine signal of carbon isotopes, while spiders on reedy shores had a terrestrial signal. The molecular analysis revealed a diverse array of dipteran and lepidopteran prey, where spiders on open and reedy shores shared a similar diet with a comparable proportion of chironomids, the larvae of which live in the marine system. Comparing the methods suggests that differences in isotope composition of the two spider groups occurred because of differences in the chironomid diets: as larvae, chironomids of reedy shores likely fed on terrestrial detritus and acquired a terrestrial isotope signature, while chironomids of open shores utilized an algal diet and acquired a marine isotope signature. Our results illustrate how different methods of diet reconstruction may shed light on complementary aspects of nutrient transfer. Overall, they reveal that reed belts can reduce connectivity between habitats, but also function as a source of food for predators.", "doi": "10.1002/ece3.2536", "pmid": "28031795", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "ECE32536"}, {"db": "pmc", "key": "PMC5167037"}], "notes": [], "created": "2017-05-03T13:00:36.753Z", "modified": "2021-07-07T20:31:10.709Z"}, {"entity": "publication", "iuid": "a94d98b34bdd4bdf93dfda75060b5e8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a94d98b34bdd4bdf93dfda75060b5e8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a94d98b34bdd4bdf93dfda75060b5e8a"}}, "title": "Identification of Shared and Unique Serum Lipid Profiles in Diabetes Mellitus and Myocardial Infarction.", "authors": [{"family": "Kjellqvist", "given": "Sanela", "initials": "S"}, {"family": "Klose", "given": "Christian", "initials": "C"}, {"family": "Surma", "given": "Michal A", "initials": "MA"}, {"family": "Hindy", "given": "George", "initials": "G"}, {"family": "Mollet", "given": "In\u00eas G", "initials": "IG"}, {"family": "Johansson", "given": "Anna", "initials": "A"}, {"family": "Chavaux", "given": "Patrick", "initials": "P"}, {"family": "Gottfries", "given": "Johan", "initials": "J"}, {"family": "Simons", "given": "Kai", "initials": "K"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Fernandez", "given": "C\u00e9line", "initials": "C"}], "type": "journal article", "published": "2016-11-29", "journal": {"volume": "5", "issn": "2047-9980", "issue": "12", "pages": "e004503", "title": "J Am Heart Assoc", "issn-l": "2047-9980"}, "abstract": "Diabetes mellitus (DM) and cardiovascular disease are associated with dyslipidemia, but the detailed lipid molecular pattern in both diseases remains unknown.\n\nWe used shotgun mass spectrometry to determine serum levels of 255 molecular lipids in 316 controls, 171 DM, and 99 myocardial infarction (MI) events from a cohort derived from the Malm\u00f6 Diet and Cancer study. Orthogonal projections to latent structures analyses were conducted between the lipids and clinical parameters describing DM or MI. Fatty acid desaturases (FADS) and elongation of very long chain fatty acid protein 5 (ELOVL5) activities were estimated by calculating product to precursor ratios of polyunsaturated fatty acids in complex lipids. FADS genotypes encoding these desaturases were then tested for association with lipid levels and ratios. Differences in the levels of lipids belonging to the phosphatidylcholine and triacylglyceride (TAG) classes contributed the most to separating DM from controls. TAGs also played a dominating role in discriminating MI from controls. Levels of C18:2 fatty acids in complex lipids were lower both in DM and MI versus controls (DM, P=0.004; MI, P=6.0E-06) at least due to an acceleration in the metabolic flux from C18:2 to C20:4 (eg, increased estimated ELOVL5: DM, P=0.02; MI, P=0.04, and combined elongase-desaturase activities: DM, P=3.0E-06; MI, P=2.0E-06). Minor allele carriers of FADS genotypes were associated with increased levels of C18:2 (P\u22640.007) and lower desaturase activity (P\u22640.002).\n\nWe demonstrate a possible relationship between decreased levels of C18:2 in complex lipids and DM or MI. We thereby highlight the importance of molecular lipids in the pathogenesis of both diseases.", "doi": "10.1161/JAHA.116.004503", "pmid": "27899364", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "JAHA.116.004503"}, {"db": "pmc", "key": "PMC5210412"}], "notes": [], "created": "2017-05-03T13:00:33.073Z", "modified": "2021-07-08T11:52:17.021Z"}, {"entity": "publication", "iuid": "9dcf6f5308fa4f2da723f73fd428d53a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9dcf6f5308fa4f2da723f73fd428d53a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9dcf6f5308fa4f2da723f73fd428d53a"}}, "title": "Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles.", "authors": [{"family": "Lampa", "given": "Samuel", "initials": "S"}, {"family": "Alvarsson", "given": "Jonathan", "initials": "J"}, {"family": "Spjuth", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2016-11-24", "journal": {"volume": "8", "issn": "1758-2946", "issue": null, "pages": "67", "title": "J Cheminform", "issn-l": "1758-2946"}, "abstract": "Predictive modelling in drug discovery is challenging to automate as it often contains multiple analysis steps and might involve cross-validation and parameter tuning that create complex dependencies between tasks. With large-scale data or when using computationally demanding modelling methods, e-infrastructures such as high-performance or cloud computing are required, adding to the existing challenges of fault-tolerant automation. Workflow management systems can aid in many of these challenges, but the currently available systems are lacking in the functionality needed to enable agile and flexible predictive modelling. We here present an approach inspired by elements of the flow-based programming paradigm, implemented as an extension of the Luigi system which we name SciLuigi. We also discuss the experiences from using the approach when modelling a large set of biochemical interactions using a shared computer cluster.Graphical abstract.", "doi": "10.1186/s13321-016-0179-6", "pmid": "27942268", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "179"}, {"db": "pmc", "key": "PMC5123367"}], "notes": [], "created": "2017-05-03T13:00:47.390Z", "modified": "2020-01-21T13:53:21.370Z"}, {"entity": "publication", "iuid": "e9badd25eb314fd19db593e64594aecf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e9badd25eb314fd19db593e64594aecf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e9badd25eb314fd19db593e64594aecf"}}, "title": "A microarray whole-genome gene expression dataset in a rat model of inflammatory corneal angiogenesis.", "authors": [{"family": "Mukwaya", "given": "Anthony", "initials": "A"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Xeroudaki", "given": "Maria", "initials": "M"}, {"family": "Peebo", "given": "Beatrice", "initials": "B"}, {"family": "Ali", "given": "Zaheer", "initials": "Z"}, {"family": "Lennikov", "given": "Anton", "initials": "A"}, {"family": "Jensen", "given": "Lasse Dahl Ejby", "initials": "LD"}, {"family": "Lagali", "given": "Neil", "initials": "N"}], "type": "journal article", "published": "2016-11-22", "journal": {"volume": "3", "issn": "2052-4463", "issue": null, "pages": "160103", "title": "Sci Data", "issn-l": "2052-4463"}, "abstract": "In angiogenesis with concurrent inflammation, many pathways are activated, some linked to VEGF and others largely VEGF-independent. Pathways involving inflammatory mediators, chemokines, and micro-RNAs may play important roles in maintaining a pro-angiogenic environment or mediating angiogenic regression. Here, we describe a gene expression dataset to facilitate exploration of pro-angiogenic, pro-inflammatory, and remodelling/normalization-associated genes during both an active capillary sprouting phase, and in the restoration of an avascular phenotype. The dataset was generated by microarray analysis of the whole transcriptome in a rat model of suture-induced inflammatory corneal neovascularisation. Regions of active capillary sprout growth or regression in the cornea were harvested and total RNA extracted from four biological replicates per group. High quality RNA was obtained for gene expression analysis using microarrays. Fold change of selected genes was validated by qPCR, and protein expression was evaluated by immunohistochemistry. We provide a gene expression dataset that may be re-used to investigate corneal neovascularisation, and may also have implications in other contexts of inflammation-mediated angiogenesis.", "doi": "10.1038/sdata.2016.103", "pmid": "27874850", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "sdata2016103"}, {"db": "pmc", "key": "PMC5119432"}], "notes": [], "created": "2017-05-03T13:00:41.157Z", "modified": "2021-07-05T12:48:16.053Z"}, {"entity": "publication", "iuid": "790e394caced42ffaed2df3298176125", "links": {"self": {"href": "https://publications.scilifelab.se/publication/790e394caced42ffaed2df3298176125.json"}, "display": {"href": "https://publications.scilifelab.se/publication/790e394caced42ffaed2df3298176125"}}, "title": "Deletion of FtsH11 protease has impact on chloroplast structure and function in Arabidopsis thaliana when grown under continuous light.", "authors": [{"family": "Wagner", "given": "Raik", "initials": "R"}, {"family": "von Sydow", "given": "Lotta", "initials": "L"}, {"family": "Aigner", "given": "Harald", "initials": "H"}, {"family": "Netotea", "given": "Sergiu", "initials": "S"}, {"family": "Brugi\u00e8re", "given": "Sabine", "initials": "S"}, {"family": "Sj\u00f6gren", "given": "Lars", "initials": "L"}, {"family": "Ferro", "given": "Myriam", "initials": "M"}, {"family": "Clarke", "given": "Adrian", "initials": "A"}, {"family": "Funk", "given": "Christiane", "initials": "C"}], "type": "journal article", "published": "2016-11-00", "journal": {"volume": "39", "issn": "1365-3040", "issue": "11", "pages": "2530-2544", "title": "Plant Cell Environ.", "issn-l": "0140-7791"}, "abstract": "The membrane-integrated metalloprotease FtsH11 of Arabidopsis thaliana is proposed to be dual-targeted to mitochondria and chloroplasts. A bleached phenotype was observed in ftsh11 grown at long days or continuous light, pointing to disturbances in the chloroplast. Within the chloroplast, FtsH11 was found to be located exclusively in the envelope. Two chloroplast-located proteins of unknown function (Tic22-like protein and YGGT-A) showed significantly higher abundance in envelope membranes and intact chloroplasts of ftsh11 and therefore qualify as potential substrates for the FtsH11 protease. No proteomic changes were observed in the mitochondria of 6-week-old ftsh11 compared with wild type, and FtsH11 was not immunodetected in these organelles. The abundance of plastidic proteins, especially of photosynthetic proteins, was altered even during standard growth conditions in total leaves of ftsh11. At continuous light, the amount of photosystem I decreased relative to photosystem II, accompanied by a drastic change of the chloroplast morphology and a drop of non-photochemical quenching. FtsH11 is crucial for chloroplast structure and function during growth in prolonged photoperiod.", "doi": "10.1111/pce.12808", "pmid": "27479913", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:45.028Z", "modified": "2020-01-21T13:53:21.334Z"}, {"entity": "publication", "iuid": "ef35bfff77544139a459abea6201ff56", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef35bfff77544139a459abea6201ff56.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef35bfff77544139a459abea6201ff56"}}, "title": "Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock.", "authors": [{"family": "Bagnoud", "given": "Alexandre", "initials": "A"}, {"family": "Chourey", "given": "Karuna", "initials": "K"}, {"family": "Hettich", "given": "Robert L", "initials": "RL"}, {"family": "de Bruijn", "given": "Ino", "initials": "I"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Leupin", "given": "Olivier X", "initials": "OX"}, {"family": "Schwyn", "given": "Bernhard", "initials": "B"}, {"family": "Bernier-Latmani", "given": "Rizlan", "initials": "R"}], "type": "journal article", "published": "2016-10-14", "journal": {"volume": "7", "issn": "2041-1723", "issue": null, "pages": "12770", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present.", "doi": "10.1038/ncomms12770", "pmid": "27739431", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ncomms12770"}, {"db": "pmc", "key": "PMC5067608"}], "notes": [], "created": "2017-05-03T13:00:40.242Z", "modified": "2020-01-21T13:53:21.447Z"}, {"entity": "publication", "iuid": "2413d5f4ab0b41d7b39874104dc31007", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2413d5f4ab0b41d7b39874104dc31007.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2413d5f4ab0b41d7b39874104dc31007"}}, "title": "ProQ3: Improved model quality assessments using Rosetta energy terms.", "authors": [{"family": "Uziela", "given": "Karolis", "initials": "K"}, {"family": "Shu", "given": "Nanjiang", "initials": "N"}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2016-10-04", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "33509", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Quality assessment of protein models using no other information than the structure of the model itself has been shown to be useful for structure prediction. Here, we introduce two novel methods, ProQRosFA and ProQRosCen, inspired by the state-of-art method ProQ2, but using a completely different description of a protein model. ProQ2 uses contacts and other features calculated from a model, while the new predictors are based on Rosetta energies: ProQRosFA uses the full-atom energy function that takes into account all atoms, while ProQRosCen uses the coarse-grained centroid energy function. The two new predictors also include residue conservation and terms corresponding to the agreement of a model with predicted secondary structure and surface area, as in ProQ2. We show that the performance of these predictors is on par with ProQ2 and significantly better than all other model quality assessment programs. Furthermore, we show that combining the input features from all three predictors, the resulting predictor ProQ3 performs better than any of the individual methods. ProQ3, ProQRosFA and ProQRosCen are freely available both as a webserver and stand-alone programs at http://proq3.bioinfo.se/.", "doi": "10.1038/srep33509", "pmid": "27698390", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "srep33509"}, {"db": "pmc", "key": "PMC5048106"}], "notes": [], "created": "2017-05-03T13:00:42.093Z", "modified": "2020-01-21T13:53:21.242Z"}, {"entity": "publication", "iuid": "119244bc942c4e0da3c251f66062cc10", "links": {"self": {"href": "https://publications.scilifelab.se/publication/119244bc942c4e0da3c251f66062cc10.json"}, "display": {"href": "https://publications.scilifelab.se/publication/119244bc942c4e0da3c251f66062cc10"}}, "title": "Aberrant activation of the PI3K/mTOR pathway promotes resistance to sorafenib in AML.", "authors": [{"family": "Lindblad", "given": "O", "initials": "O"}, {"family": "Cordero", "given": "E", "initials": "E"}, {"family": "Puissant", "given": "A", "initials": "A"}, {"family": "Macaulay", "given": "L", "initials": "L"}, {"family": "Ramos", "given": "A", "initials": "A"}, {"family": "Kabir", "given": "N N", "initials": "NN"}, {"family": "Sun", "given": "J", "initials": "J"}, {"family": "Vallon-Christersson", "given": "J", "initials": "J"}, {"family": "Haraldsson", "given": "K", "initials": "K"}, {"family": "Hemann", "given": "M T", "initials": "MT"}, {"family": "Borg", "given": "\u00c5", "initials": "\u00c5"}, {"family": "Levander", "given": "F", "initials": "F"}, {"family": "Stegmaier", "given": "K", "initials": "K"}, {"family": "Pietras", "given": "K", "initials": "K"}, {"family": "R\u00f6nnstrand", "given": "L", "initials": "L"}, {"family": "Kazi", "given": "J U", "initials": "JU"}], "type": "journal article", "published": "2016-09-29", "journal": {"volume": "35", "issn": "1476-5594", "issue": "39", "pages": "5119-5131", "title": "Oncogene", "issn-l": "0950-9232"}, "abstract": "Therapy directed against oncogenic FLT3 has been shown to induce response in patients with acute myeloid leukemia (AML), but these responses are almost always transient. To address the mechanism of FLT3 inhibitor resistance, we generated two resistant AML cell lines by sustained treatment with the FLT3 inhibitor sorafenib. Parental cell lines carry the FLT3-ITD (tandem duplication) mutation and are highly responsive to FLT3 inhibitors, whereas resistant cell lines display resistance to multiple FLT3 inhibitors. Sanger sequencing and protein mass-spectrometry did not identify any acquired mutations in FLT3 in the resistant cells. Moreover, sorafenib treatment effectively blocked FLT3 activation in resistant cells, whereas it was unable to block colony formation or cell survival, suggesting that the resistant cells are no longer FLT3 dependent. Gene expression analysis of sensitive and resistant cell lines, as well as of blasts from patients with sorafenib-resistant AML, suggested an enrichment of the PI3K/mTOR pathway in the resistant phenotype, which was further supported by next-generation sequencing and phospho-specific-antibody array analysis. Furthermore, a selective PI3K/mTOR inhibitor, gedatolisib, efficiently blocked proliferation, colony and tumor formation, and induced apoptosis in resistant cell lines. Gedatolisib significantly extended survival of mice in a sorafenib-resistant AML patient-derived xenograft model. Taken together, our data suggest that aberrant activation of the PI3K/mTOR pathway in FLT3-ITD-dependent AML results in resistance to drugs targeting FLT3.", "doi": "10.1038/onc.2016.41", "pmid": "26999641", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "onc201641"}], "notes": [], "created": "2017-05-03T13:00:40.848Z", "modified": "2020-01-21T13:53:21.224Z"}, {"entity": "publication", "iuid": "b39ad5762f1f469e9363beabd643bd45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b39ad5762f1f469e9363beabd643bd45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b39ad5762f1f469e9363beabd643bd45"}}, "title": "Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes.", "authors": [{"family": "Lindqvist", "given": "C M\u00e5rten", "initials": "CM"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Carlsson Alml\u00f6f", "given": "Jonas", "initials": "J"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "\u00d6vern\u00e4s", "given": "Elin", "initials": "E"}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J"}, {"family": "Frost", "given": "Britt-Marie", "initials": "BM"}, {"family": "Grand\u00e9r", "given": "Dan", "initials": "D"}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "Palle", "given": "Josefine", "initials": "J"}, {"family": "Forestier", "given": "Erik", "initials": "E"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Berglund", "given": "Eva C", "initials": "EC"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2016-09-27", "journal": {"volume": "7", "issn": "1949-2553", "issue": "39", "pages": "64071-64088", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "To characterize the mutational patterns of acute lymphoblastic leukemia (ALL) we performed deep next generation sequencing of 872 cancer genes in 172 diagnostic and 24 relapse samples from 172 pediatric ALL patients. We found an overall greater mutational burden and more driver mutations in T-cell ALL (T-ALL) patients compared to B-cell precursor ALL (BCP-ALL) patients. In addition, the majority of the mutations in T-ALL had occurred in the original leukemic clone, while most of the mutations in BCP-ALL were subclonal. BCP-ALL patients carrying any of the recurrent translocations ETV6-RUNX1, BCR-ABL or TCF3-PBX1 harbored few mutations in driver genes compared to other BCP-ALL patients. Specifically in BCP-ALL, we identified ATRX as a novel putative driver gene and uncovered an association between somatic mutations in the Notch signaling pathway at ALL diagnosis and increased risk of relapse. Furthermore, we identified EP300, ARID1A and SH2B3 as relapse-associated genes. The genes highlighted in our study were frequently involved in epigenetic regulation, associated with germline susceptibility to ALL, and present in minor subclones at diagnosis that became dominant at relapse. We observed a high degree of clonal heterogeneity and evolution between diagnosis and relapse in both BCP-ALL and T-ALL, which could have implications for the treatment efficiency.", "doi": "10.18632/oncotarget.11773", "pmid": "27590521", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "11773"}, {"db": "pmc", "key": "PMC5325426"}], "notes": [], "created": "2017-05-08T07:58:29.639Z", "modified": "2024-01-16T13:48:49.489Z"}, {"entity": "publication", "iuid": "2903a78b77f64c7ea269a373cfdb54a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2903a78b77f64c7ea269a373cfdb54a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2903a78b77f64c7ea269a373cfdb54a2"}}, "title": "Combinatorial identification of DNA methylation patterns over age in the human brain.", "authors": [{"family": "Torabi Moghadam", "given": "Behrooz", "initials": "B"}, {"family": "Dabrowski", "given": "Michal", "initials": "M"}, {"family": "Kaminska", "given": "Bozena", "initials": "B"}, {"family": "Grabherr", "given": "Manfred G", "initials": "MG"}, {"family": "Komorowski", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2016-09-23", "journal": {"volume": "17", "issn": "1471-2105", "issue": "1", "pages": "393", "title": "BMC Bioinformatics", "issn-l": "1471-2105"}, "abstract": "DNA methylation plays a key role in developmental processes, which is reflected in changing methylation patterns at specific CpG sites over the lifetime of an individual. The underlying mechanisms are complex and possibly affect multiple genes or entire pathways.\n\nWe applied a multivariate approach to identify combinations of CpG sites that undergo modifications when transitioning between developmental stages. Monte Carlo feature selection produced a list of ranked and statistically significant CpG sites, while rule-based models allowed for identifying particular methylation changes in these sites. Our rule-based classifier reports combinations of CpG sites, together with changes in their methylation status in the form of easy-to-read IF-THEN rules, which allows for identification of the genes associated with the underlying sites.\n\nWe utilized machine learning and statistical methods to discretize decision class (age) values to get a general pattern of methylation changes over the lifespan. The CpG sites present in the significant rules were annotated to genes involved in brain formation, general development, as well as genes linked to cancer and Alzheimer's disease.", "doi": "10.1186/s12859-016-1259-3", "pmid": "27663458", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12859-016-1259-3"}, {"db": "pmc", "key": "PMC5034667"}], "notes": [], "created": "2017-05-03T13:00:46.505Z", "modified": "2020-01-21T13:53:21.254Z"}, {"entity": "publication", "iuid": "55f421381d2d4faeaf23f46a98ff460f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/55f421381d2d4faeaf23f46a98ff460f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/55f421381d2d4faeaf23f46a98ff460f"}}, "title": "The distribution of \u03b1-kleisin during meiosis in the holocentromeric plant Luzula elegans.", "authors": [{"family": "Ma", "given": "Wei", "initials": "W"}, {"family": "Schubert", "given": "Veit", "initials": "V"}, {"family": "Martis", "given": "Mihaela Maria", "initials": "MM"}, {"family": "Hause", "given": "Gerd", "initials": "G"}, {"family": "Liu", "given": "Zhaojun", "initials": "Z"}, {"family": "Shen", "given": "Yi", "initials": "Y"}, {"family": "Conrad", "given": "Udo", "initials": "U"}, {"family": "Shi", "given": "Wenqing", "initials": "W"}, {"family": "Scholz", "given": "Uwe", "initials": "U"}, {"family": "Taudien", "given": "Stefan", "initials": "S"}, {"family": "Cheng", "given": "Zhukuan", "initials": "Z"}, {"family": "Houben", "given": "Andreas", "initials": "A"}], "type": "journal article", "published": "2016-09-00", "journal": {"volume": "24", "issn": "1573-6849", "issue": "3", "pages": "393-405", "title": "Chromosome Res.", "issn-l": "0967-3849"}, "abstract": "Holocentric chromosomes occur in a number of independent eukaryotic lineages, and they form holokinetic kinetochores along the entire poleward chromatid surfaces. Due to this alternative chromosome structure, Luzula elegans sister chromatids segregate already in anaphase I followed by the segregation of the homologues in anaphase II. However, not yet known is the localization and dynamics of cohesin and the structure of the synaptonemal complex (SC) during meiosis. We show here that the \u03b1-kleisin subunit of cohesin localizes at the centromeres of both mitotic and meiotic metaphase chromosomes and that it, thus, may contribute to assemble the centromere in L. elegans. This localization and the formation of a tripartite SC structure indicate that the prophase I behaviour of L. elegans is similar as in monocentric species.", "doi": "10.1007/s10577-016-9529-5", "pmid": "27294972", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s10577-016-9529-5"}], "notes": [], "created": "2017-05-03T13:00:37.339Z", "modified": "2020-01-21T13:53:21.302Z"}, {"entity": "publication", "iuid": "17050c6756994b8aac25bf604512b098", "links": {"self": {"href": "https://publications.scilifelab.se/publication/17050c6756994b8aac25bf604512b098.json"}, "display": {"href": "https://publications.scilifelab.se/publication/17050c6756994b8aac25bf604512b098"}}, "title": "Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes", "authors": [{"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Nilsson", "given": "Louise K J", "initials": "LKJ"}, {"family": "Brunius", "given": "Carl", "initials": "C"}, {"family": "Dabir\u00e9", "given": "Roch K", "initials": "RK"}, {"family": "Hopkins", "given": "Richard", "initials": "R"}, {"family": "Terenius", "given": "Olle", "initials": "O"}], "type": "journal-article", "published": "2016-09-00", "journal": {"volume": "6", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/srep22806", "pmid": "26960555", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T13:16:05.270Z", "modified": "2020-01-21T13:53:21.704Z"}, {"entity": "publication", "iuid": "ed7f5f36d4e94d1ea7f19c5e84ee0e96", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ed7f5f36d4e94d1ea7f19c5e84ee0e96.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ed7f5f36d4e94d1ea7f19c5e84ee0e96"}}, "title": "Advancing the global proteome survey platform by using an oriented single chain antibody fragment immobilization approach", "authors": [{"family": "S\u00e4ll", "given": "Anna", "initials": "A"}, {"family": "Persson", "given": "Helena", "initials": "H"}, {"family": "Ohlin", "given": "Mats", "initials": "M"}, {"family": "Borrebaeck", "given": "Carl A K", "initials": "CAK"}, {"family": "Wingren", "given": "Christer", "initials": "C"}], "type": "journal-article", "published": "2016-09-00", "journal": {"volume": "33", "issn": "1871-6784", "issue": "5", "pages": "503-513", "title": "New Biotechnology", "issn-l": "1871-6784"}, "abstract": null, "doi": "10.1016/j.nbt.2015.12.001", "pmid": "26703809", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-01T12:35:56.571Z", "modified": "2020-01-21T13:53:21.816Z"}, {"entity": "publication", "iuid": "0f0978e8393c47ffa311daa47b6c29a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f0978e8393c47ffa311daa47b6c29a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f0978e8393c47ffa311daa47b6c29a0"}}, "title": "The Adipose Transcriptional Response to Insulin Is Determined by Obesity, Not Insulin Sensitivity.", "authors": [{"family": "Ryd\u00e9n", "given": "Mikael", "initials": "M"}, {"family": "Hrydziuszko", "given": "Olga", "initials": "O"}, {"family": "Mileti", "given": "Enrichetta", "initials": "E"}, {"family": "Raman", "given": "Amitha", "initials": "A"}, {"family": "Bornholdt", "given": "Jette", "initials": "J"}, {"family": "Boyd", "given": "Mette", "initials": "M"}, {"family": "Toft", "given": "Eva", "initials": "E"}, {"family": "Qvist", "given": "Veronica", "initials": "V"}, {"family": "N\u00e4slund", "given": "Erik", "initials": "E"}, {"family": "Thorell", "given": "Anders", "initials": "A"}, {"family": "Andersson", "given": "Daniel P", "initials": "DP"}, {"family": "Dahlman", "given": "Ingrid", "initials": "I"}, {"family": "Gao", "given": "Hui", "initials": "H"}, {"family": "Sandelin", "given": "Albin", "initials": "A"}, {"family": "Daub", "given": "Carsten O", "initials": "CO"}, {"family": "Arner", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2016-08-30", "journal": {"volume": "16", "issn": "2211-1247", "issue": "9", "pages": "2317-2326", "title": "Cell Rep", "issn-l": null}, "abstract": "Metabolically healthy obese subjects display preserved insulin sensitivity and a beneficial white adipose tissue gene expression pattern. However, this observation stems from fasting studies when insulin levels are low. We investigated adipose gene expression by 5'Cap-mRNA sequencing in 17 healthy non-obese (NO), 21 insulin-sensitive severely obese (ISO), and 30 insulin-resistant severely obese (IRO) subjects, before and 2\u00a0hr into a hyperinsulinemic euglycemic clamp. ISO and IRO subjects displayed a clear but globally similar transcriptional response to\u00a0insulin, which differed from the small effects observed in NO subjects. In the obese, 231 genes were altered; 71 were enriched in ISO subjects (e.g., phosphorylation processes), and 52 were enriched in IRO subjects (e.g., cellular stimuli). Common cardio-metabolic risk factors and gender do not influence these findings. This study demonstrates that differences in the acute transcriptional response to insulin are primarily driven by obesity per se, challenging the notion of healthy obese adipose tissue, at least in severe obesity.", "doi": "10.1016/j.celrep.2016.07.070", "pmid": "27545890", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2211-1247(16)31014-2"}], "notes": [], "created": "2017-05-03T12:59:49.929Z", "modified": "2024-01-16T13:48:49.601Z"}, {"entity": "publication", "iuid": "79da525d578e49858d9311a9c79edce3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79da525d578e49858d9311a9c79edce3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79da525d578e49858d9311a9c79edce3"}}, "title": "Factors regulating capillary remodeling in a reversible model of inflammatory corneal angiogenesis.", "authors": [{"family": "Mukwaya", "given": "Anthony", "initials": "A"}, {"family": "Peebo", "given": "Beatrice", "initials": "B"}, {"family": "Xeroudaki", "given": "Maria", "initials": "M"}, {"family": "Ali", "given": "Zaheer", "initials": "Z"}, {"family": "Lennikov", "given": "Anton", "initials": "A"}, {"family": "Jensen", "given": "Lasse", "initials": "L"}, {"family": "Lagali", "given": "Neil", "initials": "N"}], "type": "journal article", "published": "2016-08-26", "journal": {"volume": "6", "issn": "2045-2322", "issue": "1", "pages": "32137", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Newly formed microcapillary networks arising in adult organisms by angiogenic and inflammatory stimuli contribute to pathologies such as corneal and retinal blindness, tumor growth, and metastasis. Therapeutic inhibition of pathologic angiogenesis has focused on targeting the VEGF pathway, while comparatively little attention has been given to remodeling of the new microcapillaries into a stabilized, functional, and persistent vascular network. Here, we used a novel reversible model of inflammatory angiogenesis in the rat cornea to investigate endogenous factors rapidly invoked to remodel, normalize and regress microcapillaries as part of the natural response to regain corneal avascularity. Rapid reversal of an inflammatory angiogenic stimulus suppressed granulocytic activity, enhanced recruitment of remodelling macrophages, induced capillary intussusception, and enriched pathways and processes involving immune cells, chemokines, morphogenesis, axonal guidance, and cell motility, adhesion, and cytoskeletal functions. Whole transcriptome gene expression analysis revealed suppression of numerous inflammatory and angiogenic factors and enhancement of endogenous inhibitors. Many of the identified genes function independently of VEGF and represent potentially new targets for molecular control of the critical process of microvascular remodeling and regression in the cornea.", "doi": "10.1038/srep32137", "pmid": "27561355", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "srep32137"}, {"db": "pmc", "key": "PMC4999823"}], "notes": [], "created": "2017-11-01T12:35:55.899Z", "modified": "2021-06-21T15:55:05.487Z"}, {"entity": "publication", "iuid": "f3b837cdbca347c89c384242401e4ac5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3b837cdbca347c89c384242401e4ac5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3b837cdbca347c89c384242401e4ac5"}}, "title": "Large-scale ligand-based predictive modelling using support vector machines.", "authors": [{"family": "Alvarsson", "given": "Jonathan", "initials": "J"}, {"family": "Lampa", "given": "Samuel", "initials": "S"}, {"family": "Schaal", "given": "Wesley", "initials": "W"}, {"family": "Andersson", "given": "Claes", "initials": "C"}, {"family": "Wikberg", "given": "Jarl E S", "initials": "JE"}, {"family": "Spjuth", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2016-08-10", "journal": {"volume": "8", "issn": "1758-2946", "issue": null, "pages": "39", "title": "J Cheminform", "issn-l": "1758-2946"}, "abstract": "The increasing size of datasets in drug discovery makes it challenging to build robust and accurate predictive models within a reasonable amount of time. In order to investigate the effect of dataset sizes on predictive performance and modelling time, ligand-based regression models were trained on open datasets of varying sizes of up to 1.2\u00a0million chemical structures. For modelling, two implementations of support vector machines (SVM) were used. Chemical structures were described by the signatures molecular descriptor. Results showed that for the larger datasets, the LIBLINEAR SVM implementation performed on par with the well-established libsvm with a radial basis function kernel, but with dramatically less time for model building even on modest computer resources. Using a non-linear kernel proved to be infeasible for large data sizes, even with substantial computational resources on a computer cluster. To deploy the resulting models, we extended the Bioclipse decision support framework to support models from LIBLINEAR and made our models of logD and solubility available from within Bioclipse.", "doi": "10.1186/s13321-016-0151-5", "pmid": "27516811", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "151"}, {"db": "pmc", "key": "PMC4980776"}], "notes": [], "created": "2017-05-03T13:00:47.093Z", "modified": "2020-01-21T13:53:21.566Z"}, {"entity": "publication", "iuid": "0300fd9b271a4510bac41c3d9f9f4d32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0300fd9b271a4510bac41c3d9f9f4d32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0300fd9b271a4510bac41c3d9f9f4d32"}}, "title": "Compounds from the marine sponge Cribrochalina vasculum offer a way to target IGF-1R mediated signaling in tumor cells", "authors": [{"family": "Zovko", "given": "Ana", "initials": "A"}, {"family": "Novak", "given": "Metka", "initials": "M"}, {"family": "H\u00e5\u00e5g", "given": "Petra", "initials": "P"}, {"family": "Kovalerchick", "given": "Dimitry", "initials": "D"}, {"family": "Holmlund", "given": "Teresa", "initials": "T"}, {"family": "F\u00e4rneg\u00e5rdh", "given": "Katarina", "initials": "K"}, {"family": "Ilan", "given": "Micha", "initials": "M"}, {"family": "Carmeli", "given": "Shmuel", "initials": "S"}, {"family": "Lewensohn", "given": "Rolf", "initials": "R"}, {"family": "Viktorsson", "given": "Kristina", "initials": "K"}], "type": "journal-article", "published": "2016-08-02", "journal": {"volume": "7", "issn": "1949-2553", "issue": "31", "pages": "50258-50276", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "In this work two acetylene alcohols, compound 1 and compound 2, which were isolated and identified from the sponge Cribrochalina vasculum, and which showed anti-tumor effects were further studied with respect to targets and action mechanisms. Gene expression analyses suggested insulin like growth factor receptor (IGF-1R) signaling to be instrumental in controlling anti-tumor efficacy of these compounds in non-small cell lung cancer (NSCLC). Indeed compounds 1 and 2 inhibited phosphorylation of IGF-1R\u03b2 as well as reduced its target signaling molecules IRS-1 and PDK1 allowing inhibition of pro-survival signaling. In silico docking indicated that compound 1 binds to the kinase domain of IGF-1R at the same binding site as the well known tyrosine kinase inhibitor AG1024. Indeed, cellular thermal shift assay (CETSA) confirmed that C. vasculum compound 1 binds to IGF-1R but not to the membrane localized tyrosine kinase receptor EGFR. Importantly, we demonstrate that compound 1 causes IGF-1R\u03b2 but not Insulin Receptor degradation specifically in tumor cells with no effects seen in normal diploid fibroblasts. Thus, these compounds hold potential as novel therapeutic agents targeting IGF-1R signaling for anti-tumor treatment.", "doi": "10.18632/oncotarget.10361", "pmid": "27384680", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-01T12:55:02.663Z", "modified": "2020-01-21T13:53:22.021Z"}, {"entity": "publication", "iuid": "b3a286d069224a51b9dc64f519db5867", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b3a286d069224a51b9dc64f519db5867.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b3a286d069224a51b9dc64f519db5867"}}, "title": "MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies.", "authors": [{"family": "Norling", "given": "Martin", "initials": "M"}, {"family": "Karlsson-Lindsj\u00f6", "given": "Oskar E", "initials": "OE"}, {"family": "Gourl\u00e9", "given": "Hadrien", "initials": "H"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}, {"family": "Hayer", "given": "Juliette", "initials": "J"}], "type": "journal article", "published": "2016-08-01", "journal": {"volume": "11", "issn": "1932-6203", "issue": "8", "pages": "e0160334", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Metagenomics, the sequence characterization of all genomes within a sample, is widely used as a virus discovery tool as well as a tool to study viral diversity of animals. Metagenomics can be considered to have three main steps; sample collection and preparation, sequencing and finally bioinformatics. Bioinformatic analysis of metagenomic datasets is in itself a complex process, involving few standardized methodologies, thereby hampering comparison of metagenomics studies between research groups. In this publication the new bioinformatics framework MetLab is presented, aimed at providing scientists with an integrated tool for experimental design and analysis of viral metagenomes. MetLab provides support in designing the metagenomics experiment by estimating the sequencing depth needed for the complete coverage of a species. This is achieved by applying a methodology to calculate the probability of coverage using an adaptation of Stevens' theorem. It also provides scientists with several pipelines aimed at simplifying the analysis of viral metagenomes, including; quality control, assembly and taxonomic binning. We also implement a tool for simulating metagenomics datasets from several sequencing platforms. The overall aim is to provide virologists with an easy to use tool for designing, simulating and analyzing viral metagenomes. The results presented here include a benchmark towards other existing software, with emphasis on detection of viruses as well as speed of applications. This is packaged, as comprehensive software, readily available for Linux and OSX users at https://github.com/norling/metlab.", "doi": "10.1371/journal.pone.0160334", "pmid": "27479078", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-16-12234"}, {"db": "pmc", "key": "PMC4968819"}], "notes": [], "created": "2017-05-03T13:00:50.126Z", "modified": "2020-01-21T13:53:21.376Z"}, {"entity": "publication", "iuid": "6a88e152041646e592f187ab8cda3826", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6a88e152041646e592f187ab8cda3826.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6a88e152041646e592f187ab8cda3826"}}, "title": "Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria.", "authors": [{"family": "Eiler", "given": "Alexander", "initials": "A"}, {"family": "Mondav", "given": "Rhiannon", "initials": "R", "orcid": "0000-0002-5574-5531", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c421592deaa4c1a80abe628c621c901.json"}}, {"family": "Sinclair", "given": "Lucas", "initials": "L"}, {"family": "Fernandez-Vidal", "given": "Leyden", "initials": "L"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Schwientek", "given": "Patrick", "initials": "P"}, {"family": "Martinez-Garcia", "given": "Manuel", "initials": "M"}, {"family": "Torrents", "given": "David", "initials": "D"}, {"family": "McMahon", "given": "Katherine D", "initials": "KD"}, {"family": "Andersson", "given": "Siv Ge", "initials": "SG"}, {"family": "Stepanauskas", "given": "Ramunas", "initials": "R", "orcid": "0000-0003-4458-3108", "researcher": {"href": "https://publications.scilifelab.se/researcher/f137bed7e7fd44a8bd556ffa4e6689a4.json"}}, {"family": "Woyke", "given": "Tanja", "initials": "T"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}], "type": "journal article", "published": "2016-08-00", "journal": {"volume": "10", "issn": "1751-7370", "issue": "8", "pages": "1902-1914", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "Most free-living planktonic cells are streamlined and in spite of their limitations in functional flexibility, their vast populations have radiated into a wide range of aquatic habitats. Here we compared the metabolic potential of subgroups in the Alphaproteobacteria lineage SAR11 adapted to marine and freshwater habitats. Our results suggest that the successful leap from marine to freshwaters in SAR11 was accompanied by a loss of several carbon degradation pathways and a rewiring of the central metabolism. Examples for these are C1 and methylated compounds degradation pathways, the Entner-Doudouroff pathway, the glyoxylate shunt and anapleuretic carbon fixation being absent from the freshwater genomes. Evolutionary reconstructions further suggest that the metabolic modules making up these important freshwater metabolic traits were already present in the gene pool of ancestral marine SAR11 populations. The loss of the glyoxylate shunt had already occurred in the common ancestor of the freshwater subgroup and its closest marine relatives, suggesting that the adaptation to freshwater was a gradual process. Furthermore, our results indicate rapid evolution of TRAP transporters in the freshwater clade involved in the uptake of low molecular weight carboxylic acids. We propose that such gradual tuning of metabolic pathways and transporters toward locally available organic substrates is linked to the formation of subgroups within the SAR11 clade and that this process was critical for the freshwater clade to find and fix an adaptive phenotype.", "doi": "10.1038/ismej.2015.260", "pmid": "26784354", "labels": {"Microbial Single Cell Genomics": "Collaborative", "Bioinformatics Support and Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "ismej2015260"}, {"db": "pmc", "key": "PMC5029164"}], "notes": [], "created": "2017-05-02T12:56:54.912Z", "modified": "2021-06-16T15:16:02.394Z"}, {"entity": "publication", "iuid": "9b7e9f8ea973458aa258683e955aaa1c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b7e9f8ea973458aa258683e955aaa1c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b7e9f8ea973458aa258683e955aaa1c"}}, "title": "Transcriptomic analysis reveals how a lack of potassium ions increases Sulfolobus acidocaldarius sensitivity to pH changes.", "authors": [{"family": "Buetti-Dinh", "given": "Antoine", "initials": "A"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Friedman", "given": "Ran", "initials": "R"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2016-08-00", "journal": {"volume": "162", "issn": "1465-2080", "issue": "8", "pages": "1422-1434", "title": "Microbiology (Reading, Engl.)", "issn-l": "1350-0872"}, "abstract": "Extremely acidophilic microorganisms (optimum growth pH of \u22643) maintain a near neutral cytoplasmic pH via several homeostatic mechanisms, including an inside positive membrane potential created by potassium ions. Transcriptomic responses to pH stress in the thermoacidophilic archaeon, Sulfolobus acidocaldarius were investigated by growing cells without added sodium and/or potassium ions at both optimal and sub-optimal pH. Culturing the cells in the absence of added sodium or potassium ions resulted in a reduced growth rate compared to full-salt conditions as well as 43 and 75 significantly different RNA transcript ratios, respectively. Differentially expressed RNA transcripts during growth in the absence of added sodium ions included genes coding for permeases, a sodium/proline transporter and electron transport proteins. In contrast, culturing without added potassium ions resulted in higher RNA transcripts for similar genes as a lack of sodium ions plus genes related to spermidine that has a general role in response to stress and a decarboxylase that potentially consumes protons. The greatest RNA transcript response occurred when S. acidocaldarius cells were grown in the absence of potassium and/or sodium at a sub-optimal pH. These adaptations included those listed above plus osmoregulated glucans and mechanosensitive channels that have previously been shown to respond to osmotic stress. In addition, data analyses revealed two co-expressed IclR family transcriptional regulator genes with a previously unknown role in the S. acidocaldarius pH stress response. Our study provides additional evidence towards the importance of potassium in acidophile growth at acidic pH.", "doi": "10.1099/mic.0.000314", "pmid": "27230583", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:44.120Z", "modified": "2020-01-21T13:53:21.364Z"}, {"entity": "publication", "iuid": "57b77b874057458eaa21f9cb61d8bfe7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/57b77b874057458eaa21f9cb61d8bfe7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/57b77b874057458eaa21f9cb61d8bfe7"}}, "title": "Serum nuclear magnetic resonance-based metabolomics and outcome in diffuse large B-cell lymphoma patients - a pilot study.", "authors": [{"family": "Stenson", "given": "Martin", "initials": "M"}, {"family": "Pedersen", "given": "Anders", "initials": "A"}, {"family": "Hasselblom", "given": "Sverker", "initials": "S"}, {"family": "Nilsson-Ehle", "given": "Herman", "initials": "H"}, {"family": "Karlsson", "given": "Bengt G\u00f6ran", "initials": "BG"}, {"family": "Pinto", "given": "Rui", "initials": "R"}, {"family": "Andersson", "given": "Per-Ola", "initials": "PO"}], "type": "journal article", "published": "2016-08-00", "journal": {"volume": "57", "issn": "1029-2403", "issue": "8", "pages": "1814-1822", "title": "Leuk. Lymphoma", "issn-l": "1026-8022"}, "abstract": "The prognosis for diffuse large B-cell lymphoma (DLBCL) patients with early relapse or refractory disease is dismal. To determine if clinical outcome correlated to diverse serum metabolomic profiles, we used (1)H nuclear magnetic resonance (NMR) spectroscopy and compared two groups of DLBCL patients treated with immunochemotherapy: i) refractory/early relapse (REF/REL; n=27) and ii) long-term progression-free (CURED; n\u2009=\u200960). A supervised multivariate analysis showed a separation between the groups. Among discriminating metabolites higher in the REF/REL group were the amino acids lysine and arginine, the degradation product cadaverine and a compound in oxidative stress (2-hydroxybutyrate). In contrast, the amino acids aspartate, valine and ornithine, and a metabolite in the glutathione cycle, pyroglutamate, were higher in CURED patients. Together, our data indicate that NMR-based serum metabolomics can identify a signature for DLBCL patients with high-risk of failing immunochemotherapy, prompting for larger validating studies which could lead to more individualized treatment of this disease.", "doi": "10.3109/10428194.2016.1140164", "pmid": "26887805", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:51.012Z", "modified": "2025-10-17T13:04:00.417Z"}, {"entity": "publication", "iuid": "403a4e5cca764ae6b1c60d58671d00c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/403a4e5cca764ae6b1c60d58671d00c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/403a4e5cca764ae6b1c60d58671d00c3"}}, "title": "Short Chain Fatty Acids (SCFA) Reprogram Gene Expression in Human Malignant Epithelial and Lymphoid Cells.", "authors": [{"family": "Astakhova", "given": "Lidiia", "initials": "L"}, {"family": "Ngara", "given": "Mtakai", "initials": "M"}, {"family": "Babich", "given": "Olga", "initials": "O"}, {"family": "Prosekov", "given": "Aleksandr", "initials": "A"}, {"family": "Asyakina", "given": "Lyudmila", "initials": "L"}, {"family": "Dyshlyuk", "given": "Lyubov", "initials": "L"}, {"family": "Midtvedt", "given": "Tore", "initials": "T"}, {"family": "Zhou", "given": "Xiaoying", "initials": "X"}, {"family": "Ernberg", "given": "Ingemar", "initials": "I"}, {"family": "Matskova", "given": "Liudmila", "initials": "L"}], "type": "journal article", "published": "2016-07-21", "journal": {"volume": "11", "issn": "1932-6203", "issue": "7", "pages": "e0154102", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The effect of short chain fatty acids (SCFAs) on gene expression in human, malignant cell lines was investigated, with a focus on signaling pathways. The commensal microbial flora produce high levels of SCFAs with established physiologic effects in humans. The most abundant SCFA metabolite in the human microflora is n-butyric acid. It is well known to activate endogenous latent Epstein-Barr virus (EBV), that was used as a reference read out system and extended to EBV+ epithelial cancer cell lines. N-butyric acid and its salt induced inflammatory and apoptotic responses in tumor cells of epithelial and lymphoid origin. Epithelial cell migration was inhibited. The n-butyric gene activation was reduced by knock-down of the cell membrane transporters MCT-1 and -4 by siRNA. N-butyric acid show biologically significant effects on several important cellular functions, also with relevance for tumor cell phenotype.", "doi": "10.1371/journal.pone.0154102", "pmid": "27441625", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-15-52288"}, {"db": "pmc", "key": "PMC4956219"}], "notes": [], "created": "2017-05-03T13:00:49.238Z", "modified": "2020-01-21T13:53:21.290Z"}, {"entity": "publication", "iuid": "cfdd15c7d1904ce192df0182dbe98a14", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cfdd15c7d1904ce192df0182dbe98a14.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cfdd15c7d1904ce192df0182dbe98a14"}}, "title": "DNA Content in Extracellular Vesicles Isolated from Porcine Coronary Venous Blood Directly after Myocardial Ischemic Preconditioning.", "authors": [{"family": "Svennerholm", "given": "Kristina", "initials": "K"}, {"family": "Rodsand", "given": "Pouria", "initials": "P"}, {"family": "Hellman", "given": "Urban", "initials": "U"}, {"family": "Waldenstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Lundholm", "given": "Marie", "initials": "M"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Biber", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Ronquist", "given": "Gunnar", "initials": "G"}, {"family": "Haney", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2016-07-19", "journal": {"volume": "11", "issn": "1932-6203", "issue": "7", "pages": "e0159105", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Extracellular vesicles (EV) are nano-sized membranous structures released from most cells. They have the capacity to carry bioactive molecules and gene expression signals between cells, thus mediating intercellular communication. It is believed that EV confer protection after ischemic preconditioning (IPC). We hypothesize that myocardial ischemic preconditioning will lead to rapid alteration of EV DNA content in EV collected from coronary venous effluent.\n\nIn a porcine myocardial ischemic preconditioning model, EV were isolated from coronary venous blood before and after IPC by differential centrifugation steps culminating in preparative ultracentrifugation combined with density gradient ultracentrifugation. The EV preparation was validated, the DNA was extracted and further characterized by DNA sequencing followed by bioinformatics analysis.\n\nPorcine genomic DNA fragments representing each chromosome, including mitochondrial DNA sequences, were detected in EV isolated before and after IPC. There was no difference detected in the number of sequenced gene fragments (reads) or in the genomic coverage of the sequenced DNA fragments in EV isolated before and after IPC. Gene ontology analysis showed an enrichment of genes coding for ion channels, enzymes and proteins for basal metabolism and vesicle biogenesis and specific cardiac proteins.\n\nThis study demonstrates that porcine EV isolated from coronary venous blood plasma contain fragments of DNA from the entire genome, including the mitochondria. In this model we did not find specific qualitative or quantitative changes of the DNA content in EV collected immediately after an in vivo myocardial IPC provocation. This does not rule out the possibility that EV DNA content changes in response to myocardial IPC which could occur in a later time frame.", "doi": "10.1371/journal.pone.0159105", "pmid": "27434143", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-16-15607"}, {"db": "pmc", "key": "PMC4951030"}], "notes": [], "created": "2017-05-03T13:00:25.481Z", "modified": "2024-01-16T13:48:49.783Z"}, {"entity": "publication", "iuid": "c09d047816424105b1a983d7235229eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c09d047816424105b1a983d7235229eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c09d047816424105b1a983d7235229eb"}}, "title": "Peroxisome Proliferator-activated Receptor \u03b3 Coactivator-1 \u03b1 Isoforms Selectively Regulate Multiple Splicing Events on Target Genes.", "authors": [{"family": "Mart\u00ednez-Redondo", "given": "Vicente", "initials": "V"}, {"family": "Jannig", "given": "Paulo R", "initials": "PR"}, {"family": "Correia", "given": "Jorge C", "initials": "JC"}, {"family": "Ferreira", "given": "Duarte M S", "initials": "DM"}, {"family": "Cervenka", "given": "Igor", "initials": "I"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Sinha", "given": "Indranil", "initials": "I"}, {"family": "Izadi", "given": "Manizheh", "initials": "M"}, {"family": "Pettersson-Klein", "given": "Amanda T", "initials": "AT"}, {"family": "Agudelo", "given": "Leandro Z", "initials": "LZ"}, {"family": "Gimenez-Cassina", "given": "Alfredo", "initials": "A"}, {"family": "Brum", "given": "Patricia C", "initials": "PC"}, {"family": "Dahlman-Wright", "given": "Karin", "initials": "K"}, {"family": "Ruas", "given": "Jorge L", "initials": "JL"}], "type": "journal article", "published": "2016-07-15", "journal": {"volume": "291", "issn": "1083-351X", "issue": "29", "pages": "15169-15184", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Endurance and resistance exercise training induces specific and profound changes in the skeletal muscle transcriptome. Peroxisome proliferator-activated receptor \u03b3 coactivator-1 \u03b1 (PGC-1\u03b1) coactivators are not only among the genes differentially induced by distinct training methods, but they also participate in the ensuing signaling cascades that allow skeletal muscle to adapt to each type of exercise. Although endurance training preferentially induces PGC-1\u03b11 expression, resistance exercise activates the expression of PGC-1\u03b12, -\u03b13, and -\u03b14. These three alternative PGC-1\u03b1 isoforms lack the arginine/serine-rich (RS) and RNA recognition motifs characteristic of PGC-1\u03b11. Discrete functions for PGC-1\u03b11 and -\u03b14 have been described, but the biological role of PGC-1\u03b12 and -\u03b13 remains elusive. Here we show that different PGC-1\u03b1 variants can affect target gene splicing through diverse mechanisms, including alternative promoter usage. By analyzing the exon structure of the target transcripts for each PGC-1\u03b1 isoform, we were able to identify a large number of previously unknown PGC-1\u03b12 and -\u03b13 target genes and pathways in skeletal muscle. In particular, PGC-1\u03b12 seems to mediate a decrease in the levels of cholesterol synthesis genes. Our results suggest that the conservation of the N-terminal activation and repression domains (and not the RS/RNA recognition motif) is what determines the gene programs and splicing options modulated by each PGC-1\u03b1 isoform. By using skeletal muscle-specific transgenic mice for PGC-1\u03b11 and -\u03b14, we could validate, in vivo, splicing events observed in in vitro studies. These results show that alternative PGC-1\u03b1 variants can affect target gene expression both quantitatively and qualitatively and identify novel biological pathways under the control of this system of coactivators.", "doi": "10.1074/jbc.M115.705822", "pmid": "27231350", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "M115.705822"}, {"db": "pmc", "key": "PMC4946932"}], "notes": [], "created": "2017-05-08T07:58:40.937Z", "modified": "2021-07-05T12:48:16.046Z"}, {"entity": "publication", "iuid": "8d483764e68e49618ce4bf3ff3eb1ca1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d483764e68e49618ce4bf3ff3eb1ca1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d483764e68e49618ce4bf3ff3eb1ca1"}}, "title": "Dinosaur: A Refined Open-Source Peptide MS Feature Detector.", "authors": [{"family": "Teleman", "given": "Johan", "initials": "J"}, {"family": "Chawade", "given": "Aakash", "initials": "A"}, {"family": "Sandin", "given": "Marianne", "initials": "M"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2016-07-01", "journal": {"volume": "15", "issn": "1535-3907", "issue": "7", "pages": "2143-2151", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "In bottom-up mass spectrometry (MS)-based proteomics, peptide isotopic and chromatographic traces (features) are frequently used for label-free quantification in data-dependent acquisition MS but can also be used for the improved identification of chimeric spectra or sample complexity characterization. Feature detection is difficult because of the high complexity of MS proteomics data from biological samples, which frequently causes features to intermingle. In addition, existing feature detection algorithms commonly suffer from compatibility issues, long computation times, or poor performance on high-resolution data. Because of these limitations, we developed a new tool, Dinosaur, with increased speed and versatility. Dinosaur has the functionality to sample algorithm computations through quality-control plots, which we call a plot trail. From the evaluation of this plot trail, we introduce several algorithmic improvements to further improve the robustness and performance of Dinosaur, with the detection of features for 98% of MS/MS identifications in a benchmark data set, and no other algorithm tested in this study passed 96% feature detection. We finally used Dinosaur to reimplement a published workflow for peptide identification in chimeric spectra, increasing chimeric identification from 26% to 32% over the standard workflow. Dinosaur is operating-system-independent and is freely available as open source on https://github.com/fickludd/dinosaur .", "doi": "10.1021/acs.jproteome.6b00016", "pmid": "27224449", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC4933939"}], "notes": [], "created": "2017-05-03T13:00:39.109Z", "modified": "2020-01-21T13:53:21.346Z"}, {"entity": "publication", "iuid": "97d259ee9d6047f5bbafe84bc41b97bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/97d259ee9d6047f5bbafe84bc41b97bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/97d259ee9d6047f5bbafe84bc41b97bc"}}, "title": "PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics.", "authors": [{"family": "Fernandez-Ricaud", "given": "Luciano", "initials": "L"}, {"family": "Kourtchenko", "given": "Olga", "initials": "O"}, {"family": "Zackrisson", "given": "Martin", "initials": "M"}, {"family": "Warringer", "given": "Jonas", "initials": "J"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2016-06-23", "journal": {"volume": "17", "issn": "1471-2105", "issue": null, "pages": "249", "title": "BMC Bioinformatics", "issn-l": "1471-2105"}, "abstract": "Phenomics is a field in functional genomics that records variation in organismal phenotypes in the genetic, epigenetic or environmental context at a massive scale. For microbes, the key phenotype is the growth in population size because it contains information that is directly linked to fitness. Due to technical innovations and extensive automation our capacity to record complex and dynamic microbial growth data is rapidly outpacing our capacity to dissect and visualize this data and extract the fitness components it contains, hampering progress in all fields of microbiology.\n\nTo automate visualization, analysis and exploration of complex and highly resolved microbial growth data as well as standardized extraction of the fitness components it contains, we developed the software PRECOG (PREsentation and Characterization Of Growth-data). PRECOG allows the user to quality control, interact with and evaluate microbial growth data with ease, speed and accuracy, also in cases of non-standard growth dynamics. Quality indices filter high- from low-quality growth experiments, reducing false positives. The pre-processing filters in PRECOG are computationally inexpensive and yet functionally comparable to more complex neural network procedures. We provide examples where data calibration, project design and feature extraction methodologies have a clear impact on the estimated growth traits, emphasising the need for proper standardization in data analysis.\n\nPRECOG is a tool that streamlines growth data pre-processing, phenotypic trait extraction, visualization, distribution and the creation of vast and informative phenomics databases.", "doi": "10.1186/s12859-016-1134-2", "pmid": "27334112", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Support and Infrastructure": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1186/s12859-016-1134-2"}, {"db": "pmc", "key": "PMC4917999"}], "notes": [], "created": "2017-05-03T13:00:46.214Z", "modified": "2020-01-21T13:53:21.357Z"}, {"entity": "publication", "iuid": "79b25de8804c4969841cf047609ff26d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79b25de8804c4969841cf047609ff26d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79b25de8804c4969841cf047609ff26d"}}, "title": "Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.", "authors": [{"family": "D\u00edez", "given": "Beatriz", "initials": "B"}, {"family": "Nylander", "given": "Johan A A", "initials": "JA"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}, {"family": "Dupont", "given": "Christopher L", "initials": "CL"}, {"family": "Allen", "given": "Andrew E", "initials": "AE"}, {"family": "Yooseph", "given": "Shibu", "initials": "S"}, {"family": "Rusch", "given": "Douglas B", "initials": "DB"}, {"family": "Bergman", "given": "Birgitta", "initials": "B"}], "type": "journal article", "published": "2016-05-19", "journal": {"volume": "11", "issn": "1932-6203", "issue": "5", "pages": "e0155757", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context. Shotgun sequencing of size fractionated microbial communities from 0.1 \u03bcm to 20 \u03bcm and subsequent phylogenetic analysis indicated that cyanobacteria account for up to 15% of annotated reads, with the genera Prochlorococcus and Synechococcus comprising 90% of the cyanobacterial reads, even in the largest size fraction (3.0-20 mm). Phylogenetic analyses of cyanobacterial light-harvesting genes (chl-binding pcb/isiA, allophycocyanin (apcAB), phycocyanin (cpcAB) and phycoerythin (cpeAB)) mostly identified picocyanobacteria clades comprised of overlapping sequences obtained from Indian Ocean, Atlantic and/or Pacific Oceans samples. Habitat reconstructions coupled with phylogenetic analysis of the Indian Ocean samples suggested that large Synechococcus-like ancestors in coastal waters expanded their ecological niche towards open oligotrophic waters in the Indian Ocean through lineage diversification and associated streamlining of genomes (e.g. loss of phycobilisomes and acquisition of Chl b); resulting in contemporary small celled Prochlorococcus. Comparative metagenomic analysis with picocyanobacteria populations in other oceans suggests that this evolutionary scenario may be globally important.", "doi": "10.1371/journal.pone.0155757", "pmid": "27196065", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-15-30061"}, {"db": "pmc", "key": "PMC4890579"}, {"db": "ENA", "description": "sequences", "key": "PRJEB8968"}], "notes": [], "created": "2017-05-03T13:00:49.533Z", "modified": "2020-01-21T13:56:17.073Z"}, {"entity": "publication", "iuid": "e418bc5f3b0e4895be1006cb94cbf3c8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e418bc5f3b0e4895be1006cb94cbf3c8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e418bc5f3b0e4895be1006cb94cbf3c8"}}, "title": "Inclusion of dyad-repeat pattern improves topology prediction of transmembrane \u03b2-barrel proteins.", "authors": [{"family": "Hayat", "given": "Sikander", "initials": "S"}, {"family": "Peters", "given": "Christoph", "initials": "C"}, {"family": "Shu", "given": "Nanjiang", "initials": "N"}, {"family": "Tsirigos", "given": "Konstantinos D", "initials": "KD"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2016-05-15", "journal": {"volume": "32", "issn": "1367-4811", "issue": "10", "pages": "1571-1573", "title": "Bioinformatics", "issn-l": "1367-4803"}, "abstract": ": Accurate topology prediction of transmembrane \u03b2-barrels is still an open question. Here, we present BOCTOPUS2, an improved topology prediction method for transmembrane \u03b2-barrels that can also identify the barrel domain, predict the topology and identify the orientation of residues in transmembrane \u03b2-strands. The major novelty of BOCTOPUS2 is the use of the dyad-repeat pattern of lipid and pore facing residues observed in transmembrane \u03b2-barrels. In a cross-validation test on a benchmark set of 42 proteins, BOCTOPUS2 predicts the correct topology in 69% of the proteins, an improvement of more than 10% over the best earlier method (BOCTOPUS) and in addition, it produces significantly fewer erroneous predictions on non-transmembrane \u03b2-barrel proteins.\n\nBOCTOPUS2 webserver along with full dataset and source code is available at http://boctopus.bioinfo.se/\n\n: arne@bioinfo.se\n\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btw025", "pmid": "26794316", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "btw025"}], "notes": [], "created": "2017-05-03T13:00:43.232Z", "modified": "2020-01-21T13:53:21.430Z"}, {"entity": "publication", "iuid": "ddc25aa6267a42e6a9830d34cead5abb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ddc25aa6267a42e6a9830d34cead5abb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ddc25aa6267a42e6a9830d34cead5abb"}}, "title": "Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)", "authors": [{"family": "Nilsson", "given": "R Henrik", "initials": "RH"}, {"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "Mart\u00edn", "given": "Mar\u00eda P", "initials": "MP"}, {"family": "Tedersoo", "given": "Leho", "initials": "L"}, {"family": "Ryberg", "given": "Martin K", "initials": "MK"}, {"family": "Larsson", "given": "Ellen", "initials": "E"}, {"family": "Wurzbacher", "given": "Christian", "initials": "C"}, {"family": "Abarenkov", "given": "Kessy", "initials": "K"}], "type": "journal-article", "published": "2016-05-13", "journal": {"volume": "13", "issn": "1314-4049", "issue": null, "pages": "21-33", "title": "MycoKeys", "issn-l": null}, "abstract": null, "doi": "10.3897/mycokeys.13.8579", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-08T07:58:45.067Z", "modified": "2021-06-21T15:57:42.263Z"}, {"entity": "publication", "iuid": "1bbb53c9a0e54de0a25640f9b9319b91", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1bbb53c9a0e54de0a25640f9b9319b91.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1bbb53c9a0e54de0a25640f9b9319b91"}}, "title": "The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing.", "authors": [{"family": "Martinez Barrio", "given": "Alvaro", "initials": "A"}, {"family": "Lamichhaney", "given": "Sangeet", "initials": "S"}, {"family": "Fan", "given": "Guangyi", "initials": "G"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Pettersson", "given": "Mats", "initials": "M"}, {"family": "Zhang", "given": "He", "initials": "H"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "H\u00f6ppner", "given": "Marc", "initials": "M"}, {"family": "Jern", "given": "Patric", "initials": "P"}, {"family": "Martin", "given": "Marcel", "initials": "M"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Liu", "given": "Xin", "initials": "X"}, {"family": "Chen", "given": "Wenbin", "initials": "W"}, {"family": "Liang", "given": "Xinming", "initials": "X"}, {"family": "Shi", "given": "Chengcheng", "initials": "C"}, {"family": "Fu", "given": "Yuanyuan", "initials": "Y"}, {"family": "Ma", "given": "Kailong", "initials": "K"}, {"family": "Zhan", "given": "Xiao", "initials": "X"}, {"family": "Feng", "given": "Chungang", "initials": "C"}, {"family": "Gustafson", "given": "Ulla", "initials": "U"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "S\u00e4llman Alm\u00e9n", "given": "Markus", "initials": "M"}, {"family": "Blass", "given": "Martina", "initials": "M"}, {"family": "Casini", "given": "Michele", "initials": "M"}, {"family": "Folkvord", "given": "Arild", "initials": "A"}, {"family": "Laikre", "given": "Linda", "initials": "L"}, {"family": "Ryman", "given": "Nils", "initials": "N"}, {"family": "Ming-Yuen Lee", "given": "Simon", "initials": "S"}, {"family": "Xu", "given": "Xun", "initials": "X"}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal article", "published": "2016-05-03", "journal": {"volume": "5", "issn": "2050-084X", "issue": null, "title": "Elife", "issn-l": "2050-084X"}, "abstract": "Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of reproduction. We identify almost 500 independent loci associated with a recent niche expansion from marine (Atlantic Ocean) to brackish waters (Baltic Sea), and more than 100 independent loci showing genetic differentiation between spring- and autumn-spawning populations irrespective of geographic origin. Our results show that both coding and non-coding changes contribute to adaptation. Haplotype blocks, often spanning multiple genes and maintained by selection, are associated with genetic differentiation.", "doi": "10.7554/eLife.12081", "pmid": "27138043", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC4854517"}, {"db": "NCBI Assembly", "description": "Genome assembly", "key": "GCA_000966335.1"}, {"db": "Dryad", "description": "Gene annotation and genetic variants", "key": "10.5061/dryad.5r774"}, {"db": "SRA", "description": "Population sequencing reads, set 1", "key": "SRP017094"}, {"db": "SRA", "description": "Population sequencing reads, set 2", "key": "SRP017095"}, {"db": "SRA", "description": "Population sequencing reads, set 3", "key": "SRP056617"}], "notes": [], "created": "2017-05-03T13:00:32.482Z", "modified": "2024-01-16T13:48:50.106Z"}, {"entity": "publication", "iuid": "0997fff6de91435e9c43a1b1be58382d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0997fff6de91435e9c43a1b1be58382d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0997fff6de91435e9c43a1b1be58382d"}}, "title": "Regulating retrotransposon activity through the use of alternative transcription start sites.", "authors": [{"family": "Persson", "given": "Jenna", "initials": "J"}, {"family": "Steglich", "given": "Babett", "initials": "B"}, {"family": "Smialowska", "given": "Agata", "initials": "A"}, {"family": "Boyd", "given": "Mette", "initials": "M"}, {"family": "Bornholdt", "given": "Jette", "initials": "J"}, {"family": "Andersson", "given": "Robin", "initials": "R"}, {"family": "Schurra", "given": "Catherine", "initials": "C"}, {"family": "Arcangioli", "given": "Benoit", "initials": "B"}, {"family": "Sandelin", "given": "Albin", "initials": "A"}, {"family": "Nielsen", "given": "Olaf", "initials": "O"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}], "type": "journal article", "published": "2016-05-00", "journal": {"volume": "17", "issn": "1469-3178", "issue": "5", "pages": "753-768", "title": "EMBO Rep.", "issn-l": "1469-221X"}, "abstract": "Retrotransposons, the ancestors of retroviruses, have the potential for gene disruption and genomic takeover if not kept in check. Paradoxically, although host cells repress these elements by multiple mechanisms, they are transcribed and are even activated under stress conditions. Here, we describe a new mechanism of retrotransposon regulation through transcription start site (TSS) selection by altered nucleosome occupancy. We show that Fun30 chromatin remodelers cooperate to maintain a high level of nucleosome occupancy at retrotransposon-flanking long terminal repeat (LTR) elements. This enforces the use of a downstream TSS and the production of a truncated RNA incapable of reverse transcription and retrotransposition. However, in stressed cells, nucleosome occupancy at LTR elements is reduced, and the TSS shifts to allow for productive transcription. We propose that controlled retrotransposon transcription from a nonproductive TSS allows for rapid stress-induced activation, while preventing uncontrolled transposon activity in the genome.", "doi": "10.15252/embr.201541866", "pmid": "26902262", "labels": {"Bioinformatics and Expression Analysis (BEA)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "embr.201541866"}, {"db": "pmc", "key": "PMC5341516"}], "notes": [], "created": "2017-05-03T13:00:50.428Z", "modified": "2020-01-21T13:53:21.212Z"}, {"entity": "publication", "iuid": "762bbefed17d40b092e210bfa9f9bc8e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/762bbefed17d40b092e210bfa9f9bc8e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/762bbefed17d40b092e210bfa9f9bc8e"}}, "title": "The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions.", "authors": [{"family": "Engel", "given": "Philipp", "initials": "P"}, {"family": "Kwong", "given": "Waldan K", "initials": "WK"}, {"family": "McFrederick", "given": "Quinn", "initials": "Q"}, {"family": "Anderson", "given": "Kirk E", "initials": "KE"}, {"family": "Barribeau", "given": "Seth Michael", "initials": "SM"}, {"family": "Chandler", "given": "James Angus", "initials": "JA"}, {"family": "Cornman", "given": "R Scott", "initials": "RS"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "de Miranda", "given": "Joachim R", "initials": "JR"}, {"family": "Doublet", "given": "Vincent", "initials": "V"}, {"family": "Emery", "given": "Olivier", "initials": "O"}, {"family": "Evans", "given": "Jay D", "initials": "JD"}, {"family": "Farinelli", "given": "Laurent", "initials": "L"}, {"family": "Flenniken", "given": "Michelle L", "initials": "ML"}, {"family": "Granberg", "given": "Fredrik", "initials": "F"}, {"family": "Grasis", "given": "Juris A", "initials": "JA"}, {"family": "Gauthier", "given": "Laurent", "initials": "L"}, {"family": "Hayer", "given": "Juliette", "initials": "J"}, {"family": "Koch", "given": "Hauke", "initials": "H"}, {"family": "Kocher", "given": "Sarah", "initials": "S"}, {"family": "Martinson", "given": "Vincent G", "initials": "VG"}, {"family": "Moran", "given": "Nancy", "initials": "N"}, {"family": "Munoz-Torres", "given": "Monica", "initials": "M"}, {"family": "Newton", "given": "Irene", "initials": "I"}, {"family": "Paxton", "given": "Robert J", "initials": "RJ"}, {"family": "Powell", "given": "Eli", "initials": "E"}, {"family": "Sadd", "given": "Ben M", "initials": "BM"}, {"family": "Schmid-Hempel", "given": "Paul", "initials": "P"}, {"family": "Schmid-Hempel", "given": "Regula", "initials": "R"}, {"family": "Song", "given": "Se Jin", "initials": "SJ"}, {"family": "Schwarz", "given": "Ryan S", "initials": "RS"}, {"family": "vanEngelsdorp", "given": "Dennis", "initials": "D"}, {"family": "Dainat", "given": "Benjamin", "initials": "B"}], "type": "journal article", "published": "2016-04-26", "journal": {"volume": "7", "issn": "2150-7511", "issue": "2", "pages": "e02164-e02115", "title": "MBio", "issn-l": null}, "abstract": "As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the microbiome. The bee microbiome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee microbiome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health.", "doi": "10.1128/mBio.02164-15", "pmid": "27118586", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "mBio.02164-15"}, {"db": "pmc", "key": "PMC4850275"}], "notes": [], "created": "2017-05-03T13:00:45.629Z", "modified": "2020-01-21T13:53:21.327Z"}, {"entity": "publication", "iuid": "2b58050fe2b240c8b52b4467173d95e4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b58050fe2b240c8b52b4467173d95e4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b58050fe2b240c8b52b4467173d95e4"}}, "title": "EPH/ephrin profile and EPHB2 expression predicts patient survival in breast cancer.", "authors": [{"family": "Husa", "given": "Anna-Maria", "initials": "AM"}, {"family": "Magi\u0107", "given": "\u017deljana", "initials": "\u017d"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Fornander", "given": "Tommy", "initials": "T"}, {"family": "P\u00e9rez-Tenorio", "given": "Gizeh", "initials": "G"}], "type": "journal article", "published": "2016-04-19", "journal": {"volume": "7", "issn": "1949-2553", "issue": "16", "pages": "21362-21380", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "The EPH and ephrins function as both receptor and ligands and the output on their complex signaling is currently investigated in cancer. Previous work shows that some EPH family members have clinical value in breast cancer, suggesting that this family could be a source of novel clinical targets. Here we quantified the mRNA expression levels of EPH receptors and their ligands, ephrins, in 65 node positive breast cancer samples by RT-PCR with TaqMan\u00ae Micro Fluidics Cards Microarray. Upon hierarchical clustering of the mRNA expression levels, we identified a subgroup of patients with high expression, and poor clinical outcome. EPHA2, EPHA4, EFNB1, EFNB2, EPHB2 and EPHB6 were significantly correlated with the cluster groups and particularly EPHB2 was an independent prognostic factor in multivariate analysis and in four public databases. The EPHB2 protein expression was also analyzed by immunohistochemistry in paraffin embedded material (cohort 2). EPHB2 was detected in the membrane and cytoplasmic cell compartments and there was an inverse correlation between membranous and cytoplasmic EPHB2. Membranous EPHB2 predicted longer breast cancer survival in both univariate and multivariate analysis while cytoplasmic EPHB2 indicated shorter breast cancer survival in univariate analysis. Concluding: the EPH/EFN cluster analysis revealed that high EPH/EFN mRNA expression is an independent prognostic factor for poor survival. Especially EPHB2 predicted poor breast cancer survival in several materials and EPHB2 protein expression has also prognostic value depending on cell localization.", "doi": "10.18632/oncotarget.7246", "pmid": "26870995", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "7246"}, {"db": "pmc", "key": "PMC5008291"}], "notes": [], "created": "2017-05-03T13:00:50.721Z", "modified": "2020-01-21T13:53:21.278Z"}, {"entity": "publication", "iuid": "ef032226393a47a7831a6fa1a7ef225f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef032226393a47a7831a6fa1a7ef225f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef032226393a47a7831a6fa1a7ef225f"}}, "title": "Improved topology prediction using the terminal hydrophobic helices rule.", "authors": [{"family": "Peters", "given": "Christoph", "initials": "C"}, {"family": "Tsirigos", "given": "Konstantinos D", "initials": "KD"}, {"family": "Shu", "given": "Nanjiang", "initials": "N"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2016-04-15", "journal": {"volume": "32", "issn": "1367-4811", "issue": "8", "pages": "1158-1162", "title": "Bioinformatics", "issn-l": "1367-4803"}, "abstract": "The translocon recognizes sufficiently hydrophobic regions of a protein and inserts them into the membrane. Computational methods try to determine what hydrophobic regions are recognized by the translocon. Although these predictions are quite accurate, many methods still fail to distinguish marginally hydrophobic transmembrane (TM) helices and equally hydrophobic regions in soluble protein domains. In vivo, this problem is most likely avoided by targeting of the TM-proteins, so that non-TM proteins never see the translocon. Proteins are targeted to the translocon by an N-terminal signal peptide. The targeting is also aided by the fact that the N-terminal helix is more hydrophobic than other TM-helices. In addition, we also recently found that the C-terminal helix is more hydrophobic than central helices. This information has not been used in earlier topology predictors.\n\nHere, we use the fact that the N- and C-terminal helices are more hydrophobic to develop a new version of the first-principle-based topology predictor, SCAMPI. The new predictor has two main advantages; first, it can be used to efficiently separate membrane and non-membrane proteins directly without the use of an extra prefilter, and second it shows improved performance for predicting the topology of membrane proteins that contain large non-membrane domains.\n\nThe predictor, a web server and all datasets are available at http://scampi.bioinfo.se/\n\narne@bioinfo.se\n\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btv709", "pmid": "26644416", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "btv709"}], "notes": [], "created": "2017-05-02T12:58:17.637Z", "modified": "2020-01-21T13:53:21.441Z"}, {"entity": "publication", "iuid": "29043aa893ee4780af9812c166522a99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29043aa893ee4780af9812c166522a99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29043aa893ee4780af9812c166522a99"}}, "title": "Identification and Characterization of IgdE, a Novel IgG-degrading Protease of Streptococcus suis with Unique Specificity for Porcine IgG.", "authors": [{"family": "Spoerry", "given": "Christian", "initials": "C"}, {"family": "Seele", "given": "Jana", "initials": "J"}, {"family": "Valentin-Weigand", "given": "Peter", "initials": "P"}, {"family": "Baums", "given": "Christoph G", "initials": "CG"}, {"family": "von Pawel-Rammingen", "given": "Ulrich", "initials": "U"}], "type": "journal article", "published": "2016-04-08", "journal": {"volume": "291", "issn": "1083-351X", "issue": "15", "pages": "7915-7925", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Streptococcus suisis a major endemic pathogen of pigs causing meningitis, arthritis, and other diseases. ZoonoticS. suisinfections are emerging in humans causing similar pathologies as well as severe conditions such as toxic shock-like syndrome. Recently, we discovered an IdeS family protease ofS. suisthat exclusively cleaves porcine IgM and represents the first virulence factor described, linkingS. suisto pigs as their natural host. Here we report the identification and characterization of a novel, unrelated protease ofS. suisthat exclusively targets porcine IgG. This enzyme, designated IgdE forimmunoglobulinG-degradingenzyme ofS. suis, is a cysteine protease distinct from previous characterized streptococcal immunoglobulin degrading proteases of the IdeS family and mediates efficient cleavage of the hinge region of porcine IgG with a high degree of specificity. The findings that allS. suisstrains investigated possess the IgG proteolytic activity and that piglet serum samples contain specific antibodies against IgdE strongly indicate that the protease is expressedin vivoduring infection and represents a novel and putative important bacterial virulence/colonization determinant, and a thus potential therapeutic target.", "doi": "10.1074/jbc.M115.711440", "pmid": "26861873", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "M115.711440"}, {"db": "pmc", "key": "PMC4824999"}], "notes": [], "created": "2017-05-03T13:00:42.410Z", "modified": "2020-01-21T13:53:21.265Z"}, {"entity": "publication", "iuid": "4fd1515f4ad64f6792ce578cadcba6d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4fd1515f4ad64f6792ce578cadcba6d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4fd1515f4ad64f6792ce578cadcba6d2"}}, "title": "Whole-body fat oxidation increases more by prior exercise than overnight fasting in elite endurance athletes.", "authors": [{"family": "Andersson Hall", "given": "Ulrika", "initials": "U"}, {"family": "Edin", "given": "Fredrik", "initials": "F"}, {"family": "Pedersen", "given": "Anders", "initials": "A"}, {"family": "Madsen", "given": "Klavs", "initials": "K"}], "type": "journal article", "published": "2016-04-00", "journal": {"volume": "41", "issn": "1715-5320", "issue": "4", "pages": "430-437", "title": "Appl Physiol Nutr Metab", "issn-l": "1715-5312"}, "abstract": "The purpose of this study was to compare whole-body fat oxidation kinetics after prior exercise with overnight fasting in elite endurance athletes. Thirteen highly trained athletes (9 men and 4 women; maximal oxygen uptake: 66 \u00b1 1 mL\u00b7min(-1)\u00b7kg(-1)) performed 3 identical submaximal incremental tests on a cycle ergometer using a cross-over design. A control test (CON) was performed 3 h after a standardized breakfast, a fasting test (FAST) 12 h after a standardized evening meal, and a postexercise test (EXER) after standardized breakfast, endurance exercise, and 2 h fasting recovery. The test consisted of 3 min each at 30%, 40%, 50%, 60%, 70%, and 80% of maximal oxygen uptake and fat oxidation rates were measured through indirect calorimetry. During CON, maximal fat oxidation rate was 0.51 \u00b1 0.04 g\u00b7min(-1) compared with 0.69 \u00b1 0.04 g\u00b7min(-1) in FAST (P < 0.01), and 0.89 \u00b1 0.05 g\u00b7min(-1) in EXER (P < 0.01). Across all intensities, EXER was significantly higher than FAST and FAST was higher than CON (P < 0.01). Blood insulin levels were lower and free fatty acid and cortisol levels were higher at the start of EXER compared with CON and FAST (P < 0.05). Plasma nuclear magnetic resonance-metabolomics showed similar changes in both EXER and FAST, including increased levels of fatty acids and succinate. In conclusion, prior exercise significantly increases whole-body fat oxidation during submaximal exercise compared with overnight fasting. Already high rates of maximal fat oxidation in elite endurance athletes were increased by approximately 75% after prior exercise and fasting recovery.", "doi": "10.1139/apnm-2015-0452", "pmid": "26988766", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service", "Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:45.921Z", "modified": "2025-10-17T13:04:00.566Z"}, {"entity": "publication", "iuid": "9c7992409f3d425cb633929d763c1cc2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c7992409f3d425cb633929d763c1cc2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c7992409f3d425cb633929d763c1cc2"}}, "title": "RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans.", "authors": [{"family": "Christel", "given": "Stephan", "initials": "S"}, {"family": "Fridlund", "given": "Jimmy", "initials": "J"}, {"family": "Buetti-Dinh", "given": "Antoine", "initials": "A"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Watkin", "given": "Elizabeth L", "initials": "EL"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2016-04-00", "journal": {"volume": "363", "issn": "1574-6968", "issue": "7", "title": "FEMS Microbiol. Lett.", "issn-l": "0378-1097"}, "abstract": "Acidithiobacillus ferrivorans is an acidophile implicated in low-temperature biomining for the recovery of metals from sulfide minerals. Acidithiobacillus ferrivorans obtains its energy from the oxidation of inorganic sulfur compounds, and genes encoding several alternative pathways have been identified. Next-generation sequencing of At. ferrivorans RNA transcripts identified the genes coding for metabolic and electron transport proteins for energy conservation from tetrathionate as electron donor. RNA transcripts suggested that tetrathionate was hydrolyzed by the tetH1 gene product to form thiosulfate, elemental sulfur and sulfate. Despite two of the genes being truncated, RNA transcripts for the SoxXYZAB complex had higher levels than for thiosulfate quinone oxidoreductase (doxDAgenes). However, a lack of heme-binding sites in soxX suggested that DoxDA was responsible for thiosulfate metabolism. Higher RNA transcript counts also suggested that elemental sulfur was metabolized by heterodisulfide reductase (hdrgenes) rather than sulfur oxygenase reductase (sor). The sulfite produced as a product of heterodisulfide reductase was suggested to be oxidized by a pathway involving the sat gene product or abiotically react with elemental sulfur to form thiosulfate. Finally, several electron transport complexes were involved in energy conservation. This study has elucidated the previously unknown At. ferrivorans tetrathionate metabolic pathway that is important in biomining.", "doi": "10.1093/femsle/fnw057", "pmid": "26956550", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "fnw057"}], "notes": [], "created": "2017-05-03T13:00:06.848Z", "modified": "2024-01-16T13:48:50.282Z"}, {"entity": "publication", "iuid": "37aec34c32ae4409972c0b6085bf7614", "links": {"self": {"href": "https://publications.scilifelab.se/publication/37aec34c32ae4409972c0b6085bf7614.json"}, "display": {"href": "https://publications.scilifelab.se/publication/37aec34c32ae4409972c0b6085bf7614"}}, "title": "Global genome splicing analysis reveals an increased number of alternatively spliced genes with aging.", "authors": [{"family": "Rodr\u00edguez", "given": "Sof\u00eda A", "initials": "SA"}, {"family": "Grochov\u00e1", "given": "Diana", "initials": "D"}, {"family": "McKenna", "given": "Tom\u00e1s", "initials": "T"}, {"family": "Borate", "given": "Bhavesh", "initials": "B"}, {"family": "Trivedi", "given": "Niraj S", "initials": "NS"}, {"family": "Erdos", "given": "Michael R", "initials": "MR"}, {"family": "Eriksson", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2016-04-00", "journal": {"volume": "15", "issn": "1474-9726", "issue": "2", "pages": "267-278", "title": "Aging Cell", "issn-l": "1474-9718"}, "abstract": "Alternative splicing (AS) is a key regulatory mechanism for the development of different tissues; however, not much is known about changes to alternative splicing during aging. Splicing events may become more frequent and widespread genome-wide as tissues age and the splicing machinery stringency decreases. Using skin, skeletal muscle, bone, thymus, and white adipose tissue from wild-type C57BL6/J male mice (4 and 18 months old), we examined the effect of age on splicing by AS analysis of the differential exon usage of the genome. The results identified a considerable number of AS genes in skeletal muscle, thymus, bone, and white adipose tissue between the different age groups (ranging from 27 to 246 AS genes corresponding to 0.3-3.2% of the total number of genes analyzed). For skin, skeletal muscle, and bone, we included a later age group (28 months old) that showed that the number of alternatively spliced genes increased with age in all three tissues (P < 0.01). Analysis of alternatively spliced genes across all tissues by gene ontology and pathway analysis identified 158 genes involved in RNA processing. Additional analysis of AS in a mouse model for the premature aging disease Hutchinson-Gilford progeria syndrome was performed. The results show that expression of the mutant protein, progerin, is associated with an impaired developmental splicing. As progerin accumulates, the number of genes with AS increases compared to in wild-type skin. Our results indicate the existence of a mechanism for increased AS during aging in several tissues, emphasizing that AS has a more important role in the aging process than previously known.", "doi": "10.1111/acel.12433", "pmid": "26685868", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pmc", "key": "PMC4783335"}], "notes": [], "created": "2017-05-02T12:58:25.017Z", "modified": "2024-01-16T13:48:50.295Z"}, {"entity": "publication", "iuid": "81a49441bd744cc2a2236bfae261bc67", "links": {"self": {"href": "https://publications.scilifelab.se/publication/81a49441bd744cc2a2236bfae261bc67.json"}, "display": {"href": "https://publications.scilifelab.se/publication/81a49441bd744cc2a2236bfae261bc67"}}, "title": "VEGFR2 pY949 signalling regulates adherens junction integrity and metastatic spread.", "authors": [{"family": "Li", "given": "Xiujuan", "initials": "X"}, {"family": "Padhan", "given": "Narendra", "initials": "N"}, {"family": "Sj\u00f6str\u00f6m", "given": "Elisabet O", "initials": "EO"}, {"family": "Roche", "given": "Francis P", "initials": "FP"}, {"family": "Testini", "given": "Chiara", "initials": "C"}, {"family": "Honkura", "given": "Naoki", "initials": "N"}, {"family": "S\u00e1inz-Jaspeado", "given": "Miguel", "initials": "M"}, {"family": "Gordon", "given": "Emma", "initials": "E"}, {"family": "Bentley", "given": "Katie", "initials": "K"}, {"family": "Philippides", "given": "Andrew", "initials": "A"}, {"family": "Tolmachev", "given": "Vladimir", "initials": "V"}, {"family": "Dejana", "given": "Elisabetta", "initials": "E"}, {"family": "Stan", "given": "Radu V", "initials": "RV"}, {"family": "Vestweber", "given": "Dietmar", "initials": "D"}, {"family": "Ballmer-Hofer", "given": "Kurt", "initials": "K"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}, {"family": "Pietras", "given": "Kristian", "initials": "K"}, {"family": "Jansson", "given": "Leif", "initials": "L"}, {"family": "Claesson-Welsh", "given": "Lena", "initials": "L"}], "type": "journal article", "published": "2016-03-23", "journal": {"volume": "7", "issn": "2041-1723", "issue": null, "pages": "11017", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The specific role of VEGFA-induced permeability and vascular leakage in physiology and pathology has remained unclear. Here we show that VEGFA-induced vascular leakage depends on signalling initiated via the VEGFR2 phosphosite Y949, regulating dynamic c-Src and VE-cadherin phosphorylation. Abolished Y949 signalling in the mouse mutant Vegfr2(Y949F/Y949F) leads to VEGFA-resistant endothelial adherens junctions and a block in molecular extravasation. Vessels in Vegfr2(Y949F/Y949F) mice remain sensitive to inflammatory cytokines, and vascular morphology, blood pressure and flow parameters are normal. Tumour-bearing Vegfr2(Y949F/Y949F) mice display reduced vascular leakage and oedema, improved response to chemotherapy and, importantly, reduced metastatic spread. The inflammatory infiltration in the tumour micro-environment is unaffected. Blocking VEGFA-induced disassembly of endothelial junctions, thereby suppressing tumour oedema and metastatic spread, may be preferable to full vascular suppression in the treatment of certain cancer forms.", "doi": "10.1038/ncomms11017", "pmid": "27005951", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms11017"}, {"db": "pmc", "key": "PMC4814575"}], "notes": [], "created": "2017-05-03T12:59:57.333Z", "modified": "2024-01-16T13:48:50.333Z"}, {"entity": "publication", "iuid": "da070d8735fd4f078a75e7d156c3a6bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da070d8735fd4f078a75e7d156c3a6bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da070d8735fd4f078a75e7d156c3a6bb"}}, "title": "Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante's Cave, Northern Sweden.", "authors": [{"family": "Zepeda Mendoza", "given": "Marie Lisandra", "initials": "ML"}, {"family": "Lundberg", "given": "Johannes", "initials": "J"}, {"family": "Ivarsson", "given": "Magnus", "initials": "M"}, {"family": "Campos", "given": "Paula", "initials": "P"}, {"family": "Nylander", "given": "Johan A A", "initials": "JA"}, {"family": "Sallstedt", "given": "Therese", "initials": "T"}, {"family": "Dalen", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2016-03-17", "journal": {"volume": "11", "issn": "1932-6203", "issue": "3", "pages": "e0151577", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Speleothems are secondary mineral deposits normally formed by water supersaturated with calcium carbonate percolating into underground caves, and are often associated with low-nutrient and mostly non-phototrophic conditions. Tjuv-Ante's cave is a shallow-depth cave formed by the action of waves, with granite and dolerite as major components, and opal-A and calcite as part of the speleothems, making it a rare kind of cave. We generated two DNA shotgun sequencing metagenomic datasets from the interior of a speleothem from Tjuv-Ante's cave representing areas of old and relatively recent speleothem formation. We used these datasets to perform i) an evaluation of the use of these speleothems as past biodiversity archives, ii) functional and taxonomic profiling of the speleothem's different formation periods, and iii) taxonomic comparison of the metagenomic results to previous microscopic analyses from a nearby speleothem of the same cave. Our analyses confirm the abundance of Actinobacteria and fungi as previously reported by microscopic analyses on this cave, however we also discovered a larger biodiversity. Interestingly, we identified photosynthetic genes, as well as genes related to iron and sulphur metabolism, suggesting the presence of chemoautotrophs. Furthermore, we identified taxa and functions related to biomineralization. However, we could not confidently establish the use of this type of speleothems as biological paleoarchives due to the potential leaching from the outside of the cave and the DNA damage that we propose has been caused by the fungal chemical etching.", "doi": "10.1371/journal.pone.0151577", "pmid": "26985997", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-15-42576"}, {"db": "pmc", "key": "PMC4795671"}], "notes": [], "created": "2017-05-03T13:00:48.935Z", "modified": "2021-07-07T20:31:10.929Z"}, {"entity": "publication", "iuid": "b7701c9dee484c0fad71e9f69706cc27", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7701c9dee484c0fad71e9f69706cc27.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7701c9dee484c0fad71e9f69706cc27"}}, "title": "In Situ Staining and Laser Capture Microdissection of Lymph Node Residing SIV Gag-Specific CD8+ T cells--A Tool to Interrogate a Functional Immune Response Ex Vivo.", "authors": [{"family": "Tjernlund", "given": "Annelie", "initials": "A"}, {"family": "Burgener", "given": "Adam", "initials": "A"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Peng", "given": "Tao", "initials": "T"}, {"family": "Zhu", "given": "Jia", "initials": "J"}, {"family": "\u00d6hrmalm", "given": "Lars", "initials": "L"}, {"family": "Picker", "given": "Louis J", "initials": "LJ"}, {"family": "Broliden", "given": "Kristina", "initials": "K"}, {"family": "McElrath", "given": "M Juliana", "initials": "MJ"}, {"family": "Corey", "given": "Lawrence", "initials": "L"}], "type": "journal article", "published": "2016-03-17", "journal": {"volume": "11", "issn": "1932-6203", "issue": "3", "pages": "e0149907", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "While a plethora of data describes the essential role of systemic CD8+ T cells in the control of SIV replication little is known about the local in situ CD8+ T cell immune responses against SIV at the intact tissue level, due to technical limitations. In situ staining, using GagCM9 Qdot 655 multimers, were here combined with laser capture microdissection to detect and collect SIV Gag CM9 specific CD8+ T cells in lymph node tissue from SIV infected rhesus macaques. CD8+ T cells from SIV infected and uninfected rhesus macaques were also collected and compared to the SIV GagCM9 specific CD8+ T cells. Illumina bead array and transcriptional analyses were used to assess the transcriptional profiles and the three different CD8+ T cell populations displayed unique transcriptional patterns. This pilot study demonstrates that rapid and specific immunostaining combined with laser capture microdissection in concert with transcriptional profiling may be used to elucidate phenotypic differences between CD8+ T cells in SIV infection. Such technologies may be useful to determine differences in functional activities of HIV/SIV specific T cells.", "doi": "10.1371/journal.pone.0149907", "pmid": "26986062", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-15-46881"}, {"db": "pmc", "key": "PMC4795610"}], "notes": [], "created": "2017-05-03T13:00:48.630Z", "modified": "2021-07-05T12:48:16.040Z"}, {"entity": "publication", "iuid": "61db8ba720fb47f987a590d2723035c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61db8ba720fb47f987a590d2723035c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61db8ba720fb47f987a590d2723035c5"}}, "title": "The FAIR Guiding Principles for scientific data management and stewardship.", "authors": [{"family": "Wilkinson", "given": "Mark D", "initials": "MD"}, {"family": "Dumontier", "given": "Michel", "initials": "M"}, {"family": "Aalbersberg", "given": "I Jsbrand Jan", "initials": "IJ"}, {"family": "Appleton", "given": "Gabrielle", "initials": "G"}, {"family": "Axton", "given": "Myles", "initials": "M"}, {"family": "Baak", "given": "Arie", "initials": "A"}, {"family": "Blomberg", "given": "Niklas", "initials": "N"}, {"family": "Boiten", "given": "Jan-Willem", "initials": "JW"}, {"family": "da Silva Santos", "given": "Luiz Bonino", "initials": "LB"}, {"family": "Bourne", "given": "Philip E", "initials": "PE"}, {"family": "Bouwman", "given": "Jildau", "initials": "J"}, {"family": "Brookes", "given": "Anthony J", "initials": "AJ"}, {"family": "Clark", "given": "Tim", "initials": "T"}, {"family": "Crosas", "given": "Merc\u00e8", "initials": "M"}, {"family": "Dillo", "given": "Ingrid", "initials": "I"}, {"family": "Dumon", "given": "Olivier", "initials": "O"}, {"family": "Edmunds", "given": "Scott", "initials": "S"}, {"family": "Evelo", "given": "Chris T", "initials": "CT"}, {"family": "Finkers", "given": "Richard", "initials": "R"}, {"family": "Gonzalez-Beltran", "given": "Alejandra", "initials": "A"}, {"family": "Gray", "given": "Alasdair J G", "initials": "AJ"}, {"family": "Groth", "given": "Paul", "initials": "P"}, {"family": "Goble", "given": "Carole", "initials": "C"}, {"family": "Grethe", "given": "Jeffrey S", "initials": "JS"}, {"family": "Heringa", "given": "Jaap", "initials": "J"}, {"family": "'t Hoen", "given": "Peter A C", "initials": "PA"}, {"family": "Hooft", "given": "Rob", "initials": "R"}, {"family": "Kuhn", "given": "Tobias", "initials": "T"}, {"family": "Kok", "given": "Ruben", "initials": "R"}, {"family": "Kok", "given": "Joost", "initials": "J"}, {"family": "Lusher", "given": "Scott J", "initials": "SJ"}, {"family": "Martone", "given": "Maryann E", "initials": "ME"}, {"family": "Mons", "given": "Albert", "initials": "A"}, {"family": "Packer", "given": "Abel L", "initials": "AL"}, {"family": "Persson", "given": "Bengt", "initials": "B", "orcid": "0000-0003-3165-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f116ef0ed146419cb18e742c270c4a.json"}}, {"family": "Rocca-Serra", "given": "Philippe", "initials": "P"}, {"family": "Roos", "given": "Marco", "initials": "M"}, {"family": "van Schaik", "given": "Rene", "initials": "R"}, {"family": "Sansone", "given": "Susanna-Assunta", "initials": "SA"}, {"family": "Schultes", "given": "Erik", "initials": "E"}, {"family": "Sengstag", "given": "Thierry", "initials": "T"}, {"family": "Slater", "given": "Ted", "initials": "T"}, {"family": "Strawn", "given": "George", "initials": "G"}, {"family": "Swertz", "given": "Morris A", "initials": "MA"}, {"family": "Thompson", "given": "Mark", "initials": "M"}, {"family": "van der Lei", "given": "Johan", "initials": "J"}, {"family": "van Mulligen", "given": "Erik", "initials": "E"}, {"family": "Velterop", "given": "Jan", "initials": "J"}, {"family": "Waagmeester", "given": "Andra", "initials": "A"}, {"family": "Wittenburg", "given": "Peter", "initials": "P"}, {"family": "Wolstencroft", "given": "Katherine", "initials": "K"}, {"family": "Zhao", "given": "Jun", "initials": "J"}, {"family": "Mons", "given": "Barend", "initials": "B"}], "type": "journal article", "published": "2016-03-15", "journal": {"volume": "3", "issn": "2052-4463", "issue": null, "pages": "160018", "title": "Sci Data", "issn-l": "2052-4463"}, "abstract": "There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.", "doi": "10.1038/sdata.2016.18", "pmid": "26978244", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "sdata201618"}, {"db": "pmc", "key": "PMC4792175"}], "notes": [], "created": "2017-05-03T13:00:41.473Z", "modified": "2021-07-05T12:34:46.011Z"}, {"entity": "publication", "iuid": "d3f3b77df7bb441495c74fa77e664015", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d3f3b77df7bb441495c74fa77e664015.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d3f3b77df7bb441495c74fa77e664015"}}, "title": "Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.", "authors": [{"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}], "type": "journal article", "published": "2016-03-00", "journal": {"volume": "202", "issn": "1943-2631", "issue": "3", "pages": "1185-1200", "title": "Genetics", "issn-l": "0016-6731"}, "abstract": "A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.", "doi": "10.1534/genetics.115.183152", "pmid": "26721855", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "genetics.115.183152"}, {"db": "pmc", "key": "PMC4788117"}], "notes": [], "created": "2017-05-02T12:58:54.740Z", "modified": "2024-01-16T13:48:50.392Z"}, {"entity": "publication", "iuid": "3b5eb129e2be4e0b84d7d43b08724d8d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b5eb129e2be4e0b84d7d43b08724d8d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b5eb129e2be4e0b84d7d43b08724d8d"}}, "title": "Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors.", "authors": [{"family": "Shah", "given": "Firoz", "initials": "F"}, {"family": "Nicol\u00e1s", "given": "C\u00e9sar", "initials": "C"}, {"family": "Bentzer", "given": "Johan", "initials": "J"}, {"family": "Ellstr\u00f6m", "given": "Magnus", "initials": "M"}, {"family": "Smits", "given": "Mark", "initials": "M"}, {"family": "Rineau", "given": "Francois", "initials": "F"}, {"family": "Canb\u00e4ck", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Floudas", "given": "Dimitrios", "initials": "D"}, {"family": "Carleer", "given": "Robert", "initials": "R"}, {"family": "Lackner", "given": "Gerald", "initials": "G"}, {"family": "Braesel", "given": "Jana", "initials": "J"}, {"family": "Hoffmeister", "given": "Dirk", "initials": "D"}, {"family": "Henrissat", "given": "Bernard", "initials": "B"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Johansson", "given": "Tomas", "initials": "T"}, {"family": "Hibbett", "given": "David S", "initials": "DS"}, {"family": "Martin", "given": "Francis", "initials": "F"}, {"family": "Persson", "given": "Per", "initials": "P"}, {"family": "Tunlid", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2016-03-00", "journal": {"volume": "209", "issn": "1469-8137", "issue": "4", "pages": "1705-1719", "title": "New Phytol.", "issn-l": "0028-646X"}, "abstract": "Ectomycorrhizal fungi are thought to have a key role in mobilizing organic nitrogen that is trapped in soil organic matter (SOM). However, the extent to which ectomycorrhizal fungi decompose SOM and the mechanism by which they do so remain unclear, considering that they have lost many genes encoding lignocellulose-degrading enzymes that are present in their saprotrophic ancestors. Spectroscopic analyses and transcriptome profiling were used to examine the mechanisms by which five species of ectomycorrhizal fungi, representing at least four origins of symbiosis, decompose SOM extracted from forest soils. In the presence of glucose and when acquiring nitrogen, all species converted the organic matter in the SOM extract using oxidative mechanisms. The transcriptome expressed during oxidative decomposition has diverged over evolutionary time. Each species expressed a different set of transcripts encoding proteins associated with oxidation of lignocellulose by saprotrophic fungi. The decomposition 'toolbox' has diverged through differences in the regulation of orthologous genes, the formation of new genes by gene duplications, and the recruitment of genes from diverse but functionally similar enzyme families. The capacity to oxidize SOM appears to be common among ectomycorrhizal fungi. We propose that the ancestral decay mechanisms used primarily to obtain carbon have been adapted in symbiosis to scavenge nutrients instead.", "doi": "10.1111/nph.13722", "pmid": "26527297", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pmc", "key": "PMC5061094"}], "notes": [], "created": "2017-05-02T12:58:32.352Z", "modified": "2020-01-21T13:53:20.450Z"}, {"entity": "publication", "iuid": "2ad86ff014d14e63a7ea0fbd4652181e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2ad86ff014d14e63a7ea0fbd4652181e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2ad86ff014d14e63a7ea0fbd4652181e"}}, "title": "Altered DNA methylation of glycolytic and lipogenic genes in liver from obese and type 2 diabetic patients.", "authors": [{"family": "Kirchner", "given": "Henriette", "initials": "H"}, {"family": "Sinha", "given": "Indranil", "initials": "I"}, {"family": "Gao", "given": "Hui", "initials": "H"}, {"family": "Ruby", "given": "Maxwell A", "initials": "MA"}, {"family": "Sch\u00f6nke", "given": "Milena", "initials": "M"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Barr\u00e8s", "given": "Romain", "initials": "R"}, {"family": "Krook", "given": "Anna", "initials": "A"}, {"family": "N\u00e4slund", "given": "Erik", "initials": "E"}, {"family": "Dahlman-Wright", "given": "Karin", "initials": "K"}, {"family": "Zierath", "given": "Juleen R", "initials": "JR"}], "type": "journal article", "published": "2016-03-00", "journal": {"volume": "5", "issn": "2212-8778", "issue": "3", "pages": "171-183", "title": "Mol Metab", "issn-l": "2212-8778"}, "abstract": "Epigenetic modifications contribute to the etiology of type 2 diabetes.\n\nWe performed genome-wide methylome and transcriptome analysis in liver from severely obese men with or without type 2 diabetes and non-obese men to discover aberrant pathways underlying the development of insulin resistance. Results were validated by pyrosequencing.\n\nWe identified hypomethylation of genes involved in hepatic glycolysis and insulin resistance, concomitant with increased mRNA expression and protein levels. Pyrosequencing revealed the CpG-site within ATF-motifs was hypomethylated in four of these genes in liver of severely obese non-diabetic and type 2 diabetic patients, suggesting epigenetic regulation of transcription by altered ATF-DNA binding.\n\nSeverely obese non-diabetic and type 2 diabetic patients have distinct alterations in the hepatic methylome and transcriptome, with hypomethylation of several genes controlling glucose metabolism within the ATF-motif regulatory site. Obesity appears to shift the epigenetic program of the liver towards increased glycolysis and lipogenesis, which may exacerbate the development of insulin resistance.", "doi": "10.1016/j.molmet.2015.12.004", "pmid": "26977391", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2212-8778(15)00234-3"}, {"db": "pmc", "key": "PMC4770265"}], "notes": [], "created": "2017-05-03T13:00:38.522Z", "modified": "2021-07-05T12:48:15.956Z"}, {"entity": "publication", "iuid": "6e50279fe7d6427b87d96845eb20bd63", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6e50279fe7d6427b87d96845eb20bd63.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6e50279fe7d6427b87d96845eb20bd63"}}, "title": "A Multiplex Protein Panel Applied to Cerebrospinal Fluid Reveals Three New Biomarker Candidates in ALS but None in Neuropathic Pain Patients", "authors": [{"family": "Lind", "given": "Anne Li", "initials": "AL"}, {"family": "Wu", "given": "Di", "initials": "D"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Bodolea", "given": "Constantin", "initials": "C"}, {"family": "Ekegren", "given": "Titti", "initials": "T"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Gustafsson", "given": "Mats G", "initials": "MG"}, {"family": "Katila", "given": "Lenka", "initials": "L"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Gordh", "given": "Torsten", "initials": "T"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}], "type": "journal-article", "published": "2016-02-25", "journal": {"volume": "11", "issn": "1932-6203", "issue": "2", "pages": "e0149821", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": null, "doi": "10.1371/journal.pone.0149821", "pmid": "26914813", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:59:13.372Z", "modified": "2023-04-14T13:56:21.855Z"}, {"entity": "publication", "iuid": "f120a74420e14c7ab19024fa5e9b5550", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f120a74420e14c7ab19024fa5e9b5550.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f120a74420e14c7ab19024fa5e9b5550"}}, "title": "The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea.", "authors": [{"family": "Olsen", "given": "Jeanine L", "initials": "JL"}, {"family": "Rouz\u00e9", "given": "Pierre", "initials": "P"}, {"family": "Verhelst", "given": "Bram", "initials": "B"}, {"family": "Lin", "given": "Yao-Cheng", "initials": "YC"}, {"family": "Bayer", "given": "Till", "initials": "T"}, {"family": "Collen", "given": "Jonas", "initials": "J"}, {"family": "Dattolo", "given": "Emanuela", "initials": "E"}, {"family": "De Paoli", "given": "Emanuele", "initials": "E"}, {"family": "Dittami", "given": "Simon", "initials": "S"}, {"family": "Maumus", "given": "Florian", "initials": "F"}, {"family": "Michel", "given": "Gurvan", "initials": "G"}, {"family": "Kersting", "given": "Anna", "initials": "A"}, {"family": "Lauritano", "given": "Chiara", "initials": "C"}, {"family": "Lohaus", "given": "Rolf", "initials": "R"}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "Tonon", "given": "Thierry", "initials": "T"}, {"family": "Vanneste", "given": "Kevin", "initials": "K"}, {"family": "Amirebrahimi", "given": "Mojgan", "initials": "M"}, {"family": "Brakel", "given": "Janina", "initials": "J"}, {"family": "Bostr\u00f6m", "given": "Christoffer", "initials": "C"}, {"family": "Chovatia", "given": "Mansi", "initials": "M"}, {"family": "Grimwood", "given": "Jane", "initials": "J"}, {"family": "Jenkins", "given": "Jerry W", "initials": "JW"}, {"family": "Jueterbock", "given": "Alexander", "initials": "A"}, {"family": "Mraz", "given": "Amy", "initials": "A"}, {"family": "Stam", "given": "Wytze T", "initials": "WT"}, {"family": "Tice", "given": "Hope", "initials": "H"}, {"family": "Bornberg-Bauer", "given": "Erich", "initials": "E"}, {"family": "Green", "given": "Pamela J", "initials": "PJ"}, {"family": "Pearson", "given": "Gareth A", "initials": "GA"}, {"family": "Procaccini", "given": "Gabriele", "initials": "G"}, {"family": "Duarte", "given": "Carlos M", "initials": "CM"}, {"family": "Schmutz", "given": "Jeremy", "initials": "J"}, {"family": "Reusch", "given": "Thorsten B H", "initials": "TB"}, {"family": "Van de Peer", "given": "Yves", "initials": "Y"}], "type": "journal article", "published": "2016-02-18", "journal": {"volume": "530", "issn": "1476-4687", "issue": "7590", "pages": "331-335", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants.", "doi": "10.1038/nature16548", "pmid": "26814964", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "nature16548"}, {"db": "BioProject", "key": "PRJNA41721"}, {"db": "GENBANK", "key": "KG963492"}, {"db": "GENBANK", "key": "KG963493"}, {"db": "GENBANK", "key": "KG963494"}, {"db": "GENBANK", "key": "KG963495"}, {"db": "GENBANK", "key": "KG963496"}, {"db": "GENBANK", "key": "KG963497"}, {"db": "GENBANK", "key": "KG963498"}, {"db": "GENBANK", "key": "KG963499"}, {"db": "GENBANK", "key": "KG963500"}, {"db": 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"KG973423"}, {"db": "GENBANK", "key": "KG973424"}, {"db": "GENBANK", "key": "KG973425"}, {"db": "GENBANK", "key": "KG973426"}, {"db": "GENBANK", "key": "KG973427"}, {"db": "GENBANK", "key": "KG973428"}, {"db": "GENBANK", "key": "KG973429"}, {"db": "GENBANK", "key": "KG973430"}, {"db": "GENBANK", "key": "KG973431"}, {"db": "GENBANK", "key": "KG973432"}, {"db": "GENBANK", "key": "KG973433"}, {"db": "GENBANK", "key": "KG973434"}, {"db": "GENBANK", "key": "KG973435"}, {"db": "GENBANK", "key": "KG973436"}, {"db": "GENBANK", "key": "KG973437"}, {"db": "GENBANK", "key": "KG973438"}, {"db": "GENBANK", "key": "KG973439"}, {"db": "GENBANK", "key": "KG973440"}, {"db": "GENBANK", "key": "KG973441"}, {"db": "GENBANK", "key": "KG973442"}, {"db": "GENBANK", "key": "KG973443"}, {"db": "GENBANK", "key": "KG973444"}, {"db": "GENBANK", "key": "KG973445"}, {"db": "GENBANK", "key": "KG973446"}, {"db": "GENBANK", "key": "KG973447"}, {"db": "GENBANK", "key": "KG973448"}, {"db": "GENBANK", "key": "KG973449"}, {"db": "GENBANK", "key": "KG973450"}, {"db": "GENBANK", "key": "KG973451"}, {"db": "GENBANK", "key": "KG973452"}, {"db": "GENBANK", "key": "KG973453"}, {"db": "GENBANK", "key": "KG973454"}, {"db": "GENBANK", "key": "KG973455"}, {"db": "GENBANK", "key": "KG973456"}, {"db": "GENBANK", "key": "KG973457"}, {"db": "GENBANK", "key": "KG973458"}, {"db": "GENBANK", "key": "KG973459"}, {"db": "GENBANK", "key": "KG973460"}, {"db": "GENBANK", "key": "KG973461"}, {"db": "GENBANK", "key": "KG973462"}, {"db": "GENBANK", "key": "KG973463"}, {"db": "GENBANK", "key": "KG973464"}, {"db": "GENBANK", "key": "KG973465"}, {"db": "GENBANK", "key": "KG973466"}, {"db": "GENBANK", "key": "KG973467"}, {"db": "GENBANK", "key": "KG973468"}, {"db": "GENBANK", "key": "KG973469"}, {"db": "GENBANK", "key": "KG973470"}, {"db": "GENBANK", "key": "KG973471"}, {"db": "GENBANK", "key": "KG973472"}, {"db": "GENBANK", "key": "KG973473"}, {"db": "GENBANK", "key": "KG973474"}, {"db": "GENBANK", "key": "KG973475"}, {"db": "GENBANK", "key": "KG973476"}, {"db": "GENBANK", "key": "KG973477"}, {"db": "GENBANK", "key": "KG973478"}, {"db": "GENBANK", "key": "KG973479"}, {"db": "GENBANK", "key": "KG973480"}, {"db": "GENBANK", "key": "KG973481"}, {"db": "GENBANK", "key": "KG973482"}, {"db": "GENBANK", "key": "KG973483"}, {"db": "GENBANK", "key": "KG973484"}, {"db": "GENBANK", "key": "KG973485"}, {"db": "GENBANK", "key": "KG973486"}, {"db": "GENBANK", "key": "KG973487"}, {"db": "GENBANK", "key": "KG973488"}, {"db": "GENBANK", "key": "KG973489"}, {"db": "GENBANK", "key": "LFYR00000000"}], "notes": [], "created": "2017-05-03T13:00:39.525Z", "modified": "2020-01-21T13:53:21.453Z"}, {"entity": "publication", "iuid": "c1101eb867604d37b6e8ce7051cd822c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1101eb867604d37b6e8ce7051cd822c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1101eb867604d37b6e8ce7051cd822c"}}, "title": "Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development.", "authors": [{"family": "Obudulu", "given": "Ogonna", "initials": "O"}, {"family": "Bygdell", "given": "Joakim", "initials": "J"}, {"family": "Sundberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Moritz", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4258-3190", "researcher": {"href": "https://publications.scilifelab.se/researcher/95ad5b7fe48f42eda1328f54a385e097.json"}}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "Trygg", "given": "Johan", "initials": "J"}, {"family": "Wingsle", "given": "Gunnar", "initials": "G"}], "type": "journal article", "published": "2016-02-18", "journal": {"volume": "17", "issn": "1471-2164", "issue": null, "pages": "119", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Wood development is of outstanding interest both to basic research and industry due to the associated cellulose and lignin biomass production. Efforts to elucidate wood formation (which is essential for numerous aspects of both pure and applied plant science) have been made using transcriptomic analyses and/or low-resolution sampling. However, transcriptomic data do not correlate perfectly with levels of expressed proteins due to effects of post-translational modifications and variations in turnover rates. In addition, high-resolution analysis is needed to characterize key transitions. In order to identify protein profiles across the developmental region of wood formation, an in-depth and tissue specific sampling was performed.\n\nWe examined protein profiles, using an ultra-performance liquid chromatography/quadrupole time of flight mass spectrometry system, in high-resolution tangential sections spanning all wood development zones in Populus tremula from undifferentiated cambium to mature phloem and xylem, including cell expansion and cell death zones. In total, we analyzed 482 sections, 20-160 \u03bcm thick, from four 47-year-old trees growing wild in Sweden. We obtained high quality expression profiles for 3,082 proteins exhibiting consistency across the replicates, considering that the trees were growing in an uncontrolled environment. A combination of Principal Component Analysis (PCA), Orthogonal Projections to Latent Structures (OPLS) modeling and an enhanced stepwise linear modeling approach identified several major transitions in global protein expression profiles, pinpointing (for example) locations of the cambial division leading to phloem and xylem cells, and secondary cell wall formation zones. We also identified key proteins and associated pathways underlying these developmental landmarks. For example, many of the lignocellulosic related proteins were upregulated in the expansion to the early developmental xylem zone, and for laccases with a rapid decrease in early xylem zones. We observed upregulation of two forms of xylem cysteine protease (Potri.002G005700.1 and Potri.005G256000.2; Pt-XCP2.1) in early xylem and their downregulation in late maturing xylem. Our data also show that Pt-KOR1.3 (Potri.003G151700.2) exhibits an expression pattern that supports the hypothesis put forward in previous studies that this is a key xyloglucanase involved in cellulose biosynthesis in primary cell walls and reduction of cellulose crystallinity in secondary walls.\n\nOur novel multivariate approach highlights important processes and provides confirmatory insights into the molecular foundations of wood development.", "doi": "10.1186/s12864-016-2458-z", "pmid": "26887814", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-016-2458-z"}, {"db": "pmc", "key": "PMC4758094"}], "notes": [], "created": "2017-05-03T12:59:41.476Z", "modified": "2025-10-17T13:03:19.747Z"}, {"entity": "publication", "iuid": "948d8dfb2ca6423f9e87b43384490726", "links": {"self": {"href": "https://publications.scilifelab.se/publication/948d8dfb2ca6423f9e87b43384490726.json"}, "display": {"href": "https://publications.scilifelab.se/publication/948d8dfb2ca6423f9e87b43384490726"}}, "title": "Postprandial metabolomics: A pilot mass spectrometry and NMR study of the human plasma metabolome in response to a challenge meal.", "authors": [{"family": "Karimpour", "given": "Masoumeh", "initials": "M"}, {"family": "Surowiec", "given": "Izabella", "initials": "I"}, {"family": "Wu", "given": "Junfang", "initials": "J"}, {"family": "Gouveia-Figueira", "given": "Sandra", "initials": "S"}, {"family": "Pinto", "given": "Rui", "initials": "R"}, {"family": "Trygg", "given": "Johan", "initials": "J"}, {"family": "Zivkovic", "given": "Angela M", "initials": "AM"}, {"family": "Nording", "given": "Malin L", "initials": "ML"}], "type": "journal article", "published": "2016-02-18", "journal": {"volume": "908", "issn": "1873-4324", "issue": null, "pages": "121-131", "title": "Anal. Chim. Acta", "issn-l": "0003-2670"}, "abstract": "The study of postprandial metabolism is relevant for understanding metabolic diseases and characterizing personal responses to diet. We combined three analytical platforms - gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS) and nuclear magnetic resonance (NMR) - to validate a multi-platform approach for characterizing individual variation in the postprandial state. We analyzed the postprandial plasma metabolome by introducing, at three occasions, meal challenges on a usual diet, and 1.5 years later, on a modified background diet. The postprandial response was stable over time and largely independent of the background diet as revealed by all three analytical platforms. Coverage of the metabolome between NMR and GC-MS included more polar metabolites detectable only by NMR and more hydrophobic compounds detected by GC-MS. The variability across three separate testing occasions among the identified metabolites was in the range of 1.1-86% for GC-MS and 0.9-42% for NMR in the fasting state at baseline. For the LC-MS analysis, the coefficients of variation of the detected compounds in the fasting state at baseline were in the range of 2-97% for the positive and 4-69% for the negative mode. Multivariate analysis (MVA) of metabolites detected with GC-MS revealed that for both background diets, levels of postprandial amino acids and sugars increased whereas those of fatty acids decreased at 0.5 h after the meal was consumed, reflecting the expected response to the challenge meal. MVA of NMR data revealed increasing postprandial levels of amino acids and other organic acids together with decreasing levels of acetoacetate and 3-hydroxybutanoic acid, also independent of the background diet. Together these data show that the postprandial response to the same challenge meal was stable even though it was tested 1.5 years apart, and that it was largely independent of background diet. This work demonstrates the efficacy of a multi-platform metabolomics approach followed by multivariate and univariate data analysis for a broad-scale screen of the individual metabolome, particularly for studies using repeated measures to determine dietary response phenotype.", "doi": "10.1016/j.aca.2015.12.009", "pmid": "26826694", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "S0003-2670(15)30040-4"}], "notes": [], "created": "2017-05-03T12:59:37.889Z", "modified": "2025-10-17T13:03:19.757Z"}, {"entity": "publication", "iuid": "a2b236e2242f4e93b67c52cae3e1ee91", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2b236e2242f4e93b67c52cae3e1ee91.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2b236e2242f4e93b67c52cae3e1ee91"}}, "title": "Species identification of Swedish mosquitoes through DNA metabarcoding", "authors": [{"family": "Lilja", "given": "Tobias", "initials": "T"}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA", "orcid": "0000-0001-8940-456X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f54d4c39cdd74208ad03500bd22b7609.json"}}, {"family": "Troell", "given": "Karin", "initials": "K"}, {"family": "Lindstr\u00f6m", "given": "Anders", "initials": "A"}], "type": null, "published": "2016-02-16", "journal": {"volume": "35", "issn": null, "issue": null, "pages": "1-9", "title": "JOURNAL OF THE EUROPEAN MOSQUITO CONTROL ASSOCIATION", "issn-l": null}, "abstract": "DNA-barcoding utilises a fragment of the mitochondrial cytochrome oxidase subunit 1 (COI) gene to identify most animal species. Using next generation sequencing (NGS), this method can be further developed into metabarcoding processes that allow the simultaneous identification of several species from a mixed sample. We created a database of COI sequences of 27 mosquito species collected in Sweden, and combined our data with 27 additional sequences from GenBank to cover the taxa recently documented in Sweden and to include possible invasive taxa. Comparisons show that COI metabarcoding reliably identifies 41 of 54 species and the remainder to species group. Using three independent primer pairs along the COI gene, we further developed this barcoding approach to simultaneously identify Swedish mosquitoes in communities using NGS and quantify relative abundance of each mosquito species in the sample, using bioinformatics methods. We tested the accuracy of the metabarcoding method using communities assembled from morphologically identified mosquitoes, revealing 80% positive identification rate and the estimates of population structure which reflects the input sample. We conclude that metabarcoding is useful as a high throughput identification technique and for the quantification of species. Journal of the European Mosquito Control Association 35: 1-9, 2017", "doi": null, "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-01-16T09:03:24.720Z", "modified": "2025-11-17T09:36:43.363Z"}, {"entity": "publication", "iuid": "28bc8250f6bc49028fa89bf3b3bd0817", "links": {"self": {"href": "https://publications.scilifelab.se/publication/28bc8250f6bc49028fa89bf3b3bd0817.json"}, "display": {"href": "https://publications.scilifelab.se/publication/28bc8250f6bc49028fa89bf3b3bd0817"}}, "title": "Targeted Proteomics Approach for Precision Plant Breeding.", "authors": [{"family": "Chawade", "given": "Aakash", "initials": "A"}, {"family": "Alexandersson", "given": "Erik", "initials": "E"}, {"family": "Bengtsson", "given": "Therese", "initials": "T"}, {"family": "Andreasson", "given": "Erik", "initials": "E"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2016-02-05", "journal": {"volume": "15", "issn": "1535-3907", "issue": "2", "pages": "638-646", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Selected reaction monitoring (SRM) is a targeted mass spectrometry technique that enables precise quantitation of hundreds of peptides in a single run. This technique provides new opportunities for multiplexed protein biomarker measurements. For precision plant breeding, DNA-based markers have been used extensively, but the potential of protein biomarkers has not been exploited. In this work, we developed an SRM marker panel with assays for 104 potato (Solanum tuberosum) peptides selected using univariate and multivariate statistics. Thereafter, using random forest classification, the prediction markers were identified for Phytopthora infestans resistance in leaves, P. infestans resistance in tubers, and plant yield in potato leaf secretome samples. The results suggest that the marker panel has the predictive potential for three traits, two of which have no commercial DNA markers so far. Furthermore, the marker panel was also tested and found to be applicable to potato clones not used during the marker development. The proposed workflow is thus a proof-of-concept for targeted proteomics as an efficient readout in accelerated breeding for complex and agronomically important traits.", "doi": "10.1021/acs.jproteome.5b01061", "pmid": "26704985", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:38.817Z", "modified": "2020-01-21T13:53:21.247Z"}, {"entity": "publication", "iuid": "c20f0bcf05514700a52f34b7a89cd0f4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c20f0bcf05514700a52f34b7a89cd0f4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c20f0bcf05514700a52f34b7a89cd0f4"}}, "title": "Proteome-wide survey of the autoimmune target repertoire in autoimmune polyendocrine syndrome type 1", "authors": [{"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Sharon", "given": "Donald", "initials": "D"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Hallgren", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Eriksson", "given": "Daniel", "initials": "D"}, {"family": "Edqvist", "given": "Per Henrik", "initials": "PH"}, {"family": "Bensing", "given": "Sophie", "initials": "S"}, {"family": "Wahlberg", "given": "Jeanette", "initials": "J"}, {"family": "Nelson", "given": "Lawrence M", "initials": "LM"}, {"family": "Gustafsson", "given": "Jan", "initials": "J"}, {"family": "Husebye", "given": "Eystein S", "initials": "ES"}, {"family": "Anderson", "given": "Mark S", "initials": "MS"}, {"family": "Snyder", "given": "Michael", "initials": "M"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}], "type": "journal-article", "published": "2016-02-01", "journal": {"volume": "6", "issn": "2045-2322", "issue": "1", "pages": "20104", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Autoimmune polyendocrine syndrome type 1 (APS1) is a monogenic disorder that features multiple autoimmune disease manifestations. It is caused by mutations in the Autoimmune regulator (AIRE) gene, which promote thymic display of thousands of peripheral tissue antigens in a process critical for establishing central immune tolerance. We here used proteome arrays to perform a comprehensive study of autoimmune targets in APS1. Interrogation of established autoantigens revealed highly reliable detection of autoantibodies, and by exploring the full panel of more than 9000 proteins we further identified MAGEB2 and PDILT as novel major autoantigens in APS1. Our proteome-wide assessment revealed a marked enrichment for tissue-specific immune targets, mirroring AIRE's selectiveness for this category of genes. Our findings also suggest that only a very limited portion of the proteome becomes targeted by the immune system in APS1, which contrasts the broad defect of thymic presentation associated with AIRE-deficiency and raises novel questions what other factors are needed for break of tolerance.", "doi": "10.1038/srep20104", "pmid": "26830021", "labels": {"Tissue Profiling": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC4735587"}, {"db": "pii", "key": "srep20104"}], "notes": [], "created": "2017-05-03T12:59:19.123Z", "modified": "2023-06-19T09:06:28.995Z"}, {"entity": "publication", "iuid": "7bb492e04a6946d7859665496c0dcc4d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7bb492e04a6946d7859665496c0dcc4d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7bb492e04a6946d7859665496c0dcc4d"}}, "title": "Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks.", "authors": [{"family": "Huang", "given": "Yun", "initials": "Y"}, {"family": "Chain", "given": "Fr\u00e9d\u00e9ric J J", "initials": "FJ"}, {"family": "Panchal", "given": "Mahesh", "initials": "M"}, {"family": "Eizaguirre", "given": "Christophe", "initials": "C"}, {"family": "Kalbe", "given": "Martin", "initials": "M"}, {"family": "Lenz", "given": "Tobias L", "initials": "TL"}, {"family": "Samonte", "given": "Irene E", "initials": "IE"}, {"family": "Stoll", "given": "Monika", "initials": "M"}, {"family": "Bornberg-Bauer", "given": "Erich", "initials": "E"}, {"family": "Reusch", "given": "Thorsten B H", "initials": "TB"}, {"family": "Milinski", "given": "Manfred", "initials": "M"}, {"family": "Feulner", "given": "Philine G D", "initials": "PG"}], "type": "journal article", "published": "2016-02-00", "journal": {"volume": "25", "issn": "1365-294X", "issue": "4", "pages": "943-958", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "The observation of habitat-specific phenotypes suggests the action of natural selection. The three-spined stickleback (Gasterosteus aculeatus) has repeatedly colonized and adapted to diverse freshwater habitats across the northern hemisphere since the last glaciation, while giving rise to recurring phenotypes associated with specific habitats. Parapatric lake and river populations of sticklebacks harbour distinct parasite communities, a factor proposed to contribute to adaptive differentiation between these ecotypes. However, little is known about the transcriptional response to the distinct parasite pressure of those fish in a natural setting. Here, we sampled wild-caught sticklebacks across four geographical locations from lake and river habitats differing in their parasite load. We compared gene expression profiles between lake and river populations using 77 whole-transcriptome libraries from two immune-relevant tissues, the head kidney and the spleen. Differential expression analyses revealed 139 genes with habitat-specific expression patterns across the sampled population pairs. Among the 139 differentially expressed genes, eight are annotated with an immune function and 42 have been identified as differentially expressed in previous experimental studies in which fish have been immune challenged. Together, these findings reinforce the hypothesis that parasites contribute to adaptation of sticklebacks in lake and river habitats.", "doi": "10.1111/mec.13520", "pmid": "26749022", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC4790908"}, {"db": "Dryad", "key": "10.5061/dryad.HQ50S"}], "notes": [], "created": "2017-05-08T07:58:43.302Z", "modified": "2020-01-21T13:53:21.340Z"}, {"entity": "publication", "iuid": "d435f0bee53447ae9e14cabd972bdfbe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d435f0bee53447ae9e14cabd972bdfbe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d435f0bee53447ae9e14cabd972bdfbe"}}, "title": "The Story of a Hitchhiker: Population Genetic Patterns in the Invasive Barnacle Balanus(Amphibalanus) improvisus Darwin 1854.", "authors": [{"family": "Wrange", "given": "Anna-Lisa", "initials": "AL"}, {"family": "Charrier", "given": "Gregory", "initials": "G"}, {"family": "Thonig", "given": "Anne", "initials": "A"}, {"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}, {"family": "Havenhand", "given": "Jonathan N", "initials": "JN"}, {"family": "Jonsson", "given": "Per R", "initials": "PR"}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C"}], "type": "journal article", "published": "2016-01-28", "journal": {"volume": "11", "issn": "1932-6203", "issue": "1", "pages": "e0147082", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Understanding the ecological and evolutionary forces that determine the genetic structure and spread of invasive species is a key component of invasion biology. The bay barnacle, Balanus improvisus (= Amphibalanus improvisus), is one of the most successful aquatic invaders worldwide, and is characterised by broad environmental tolerance. Although the species can spread through natural larval dispersal, human-mediated transport through (primarily) shipping has almost certainly contributed to the current global distribution of this species. Despite its worldwide distribution, little is known about the phylogeography of this species. Here, we characterize the population genetic structure and model dispersal dynamics of the barnacle B. improvisus, and describe how human-mediated spreading via shipping as well as natural larval dispersal may have contributed to observed genetic variation. We used both mitochondrial DNA (cytochrome c oxidase subunit I: COI) and nuclear microsatellites to characterize the genetic structure in 14 populations of B. improvisus on a global and regional scale (Baltic Sea). Genetic diversity was high in most populations, and many haplotypes were shared among populations on a global scale, indicating that long-distance dispersal (presumably through shipping and other anthropogenic activities) has played an important role in shaping the population genetic structure of this cosmopolitan species. We could not clearly confirm prior claims that B. improvisus originates from the western margins of the Atlantic coasts; although there were indications that Argentina could be part of a native region. In addition to dispersal via shipping, we show that natural larval dispersal may play an important role for further colonisation following initial introduction.", "doi": "10.1371/journal.pone.0147082", "pmid": "26821161", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-15-22808"}, {"db": "pmc", "key": "PMC4731558"}, {"db": "Dryad", "key": "SF2V0"}], "notes": [], "created": "2017-05-03T13:00:48.005Z", "modified": "2020-01-21T13:53:21.412Z"}, {"entity": "publication", "iuid": "06a7f813e778488ca2802234eb311211", "links": {"self": {"href": "https://publications.scilifelab.se/publication/06a7f813e778488ca2802234eb311211.json"}, "display": {"href": "https://publications.scilifelab.se/publication/06a7f813e778488ca2802234eb311211"}}, "title": "Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments.", "authors": [{"family": "Thureborn", "given": "Petter", "initials": "P"}, {"family": "Franzetti", "given": "Andrea", "initials": "A"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Sj\u00f6ling", "given": "Sara", "initials": "S"}], "type": "journal article", "published": "2016-01-19", "journal": {"volume": "4", "issn": "2167-8359", "issue": null, "pages": "e1593", "title": "PeerJ", "issn-l": "2167-8359"}, "abstract": "Baltic Sea deep water and sediments hold one of the largest anthropogenically induced hypoxic areas in the world. High nutrient input and low water exchange result in eutrophication and oxygen depletion below the halocline. As a consequence at Landsort Deep, the deepest point of the Baltic Sea, anoxia in the sediments has been a persistent condition over the past decades. Given that microbial communities are drivers of essential ecosystem functions we investigated the microbial community metabolisms and functions of oxygen depleted Landsort Deep sediments by metatranscriptomics. Results show substantial expression of genes involved in protein metabolism demonstrating that the Landsort Deep sediment microbial community is active. Identified expressed gene suites of metabolic pathways with importance for carbon transformation including fermentation, dissimilatory sulphate reduction and methanogenesis were identified. The presence of transcripts for these metabolic processes suggests a potential for heterotrophic-autotrophic community synergism and indicates active mineralisation of the organic matter deposited at the sediment as a consequence of the eutrophication process. Furthermore, cyanobacteria, probably deposited from the water column, are transcriptionally active in the anoxic sediment at this depth. Results also reveal high abundance of transcripts encoding integron integrases. These results provide insight into the activity of the microbial community of the anoxic sediment at the deepest point of the Baltic Sea and its possible role in ecosystem functioning.", "doi": "10.7717/peerj.1593", "pmid": "26823996", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "1593"}, {"db": "pmc", "key": "PMC4730985"}], "notes": [], "created": "2017-05-03T13:00:51.830Z", "modified": "2020-01-21T13:56:16.842Z"}, {"entity": "publication", "iuid": "708227d54b854bada883a69b636e8610", "links": {"self": {"href": "https://publications.scilifelab.se/publication/708227d54b854bada883a69b636e8610.json"}, "display": {"href": "https://publications.scilifelab.se/publication/708227d54b854bada883a69b636e8610"}}, "title": "Using Whole-Exome Sequencing to Identify Genetic Markers for Carboplatin and Gemcitabine-Induced Toxicities.", "authors": [{"family": "Gr\u00e9en", "given": "Henrik", "initials": "H"}, {"family": "Hasmats", "given": "Johanna", "initials": "J"}, {"family": "Kupershmidt", "given": "Ilya", "initials": "I"}, {"family": "Edsg\u00e4rd", "given": "Daniel", "initials": "D"}, {"family": "de Petris", "given": "Luigi", "initials": "L"}, {"family": "Lewensohn", "given": "Rolf", "initials": "R"}, {"family": "Blackhall", "given": "Fiona", "initials": "F"}, {"family": "Vikingsson", "given": "Svante", "initials": "S"}, {"family": "Besse", "given": "Benjamin", "initials": "B"}, {"family": "Lindgren", "given": "Andrea", "initials": "A"}, {"family": "Brand\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Koyi", "given": "Hirsh", "initials": "H"}, {"family": "Peterson", "given": "Curt", "initials": "C"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2016-01-15", "journal": {"volume": "22", "issn": "1557-3265", "issue": "2", "pages": "366-373", "title": "Clin. Cancer Res.", "issn-l": "1078-0432"}, "abstract": "Chemotherapies are associated with significant interindividual variability in therapeutic effect and adverse drug reactions. In lung cancer, the use of gemcitabine and carboplatin induces grade 3 or 4 myelosuppression in about a quarter of the patients, while an equal fraction of patients is basically unaffected in terms of myelosuppressive side effects. We therefore set out to identify genetic markers for gemcitabine/carboplatin-induced myelosuppression.\n\nWe exome sequenced 32 patients that suffered extremely high neutropenia and thrombocytopenia (grade 3 or 4 after first chemotherapy cycle) or were virtually unaffected (grade 0 or 1). The genetic differences/polymorphism between the groups were compared using six different bioinformatics strategies: (i) whole-exome nonsynonymous single-nucleotide variants association analysis, (ii) deviation from Hardy-Weinberg equilibrium, (iii) analysis of genes selected by a priori biologic knowledge, (iv) analysis of genes selected from gene expression meta-analysis of toxicity datasets, (v) Ingenuity Pathway Analysis, and (vi) FunCoup network enrichment analysis.\n\nA total of 53 genetic variants that differed among these groups were validated in an additional 291 patients and were correlated to the patients' myelosuppression. In the validation, we identified rs1453542 in OR4D6 (P = 0.0008; OR, 5.2; 95% CI, 1.8-18) as a marker for gemcitabine/carboplatin-induced neutropenia and rs5925720 in DDX53 (P = 0.0015; OR, 0.36; 95% CI, 0.17-0.71) as a marker for thrombocytopenia. Patients homozygous for the minor allele of rs1453542 had a higher risk of neutropenia, and for rs5925720 the minor allele was associated with a lower risk for thrombocytopenia.\n\nWe have identified two new genetic markers with the potential to predict myelosuppression induced by gemcitabine/carboplatin chemotherapy.", "doi": "10.1158/1078-0432.CCR-15-0964", "pmid": "26378035", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "1078-0432.CCR-15-0964"}], "notes": [], "created": "2017-05-02T12:57:08.106Z", "modified": "2024-01-16T13:48:50.593Z"}, {"entity": "publication", "iuid": "a97e38c8588e41029f9414f34ea67187", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a97e38c8588e41029f9414f34ea67187.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a97e38c8588e41029f9414f34ea67187"}}, "title": "Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysis.", "authors": [{"family": "Bersani", "given": "Cinzia", "initials": "C"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Giacomello", "given": "Stefania", "initials": "S"}, {"family": "Xu", "given": "Li-Di", "initials": "LD"}, {"family": "Bianchi", "given": "Julie", "initials": "J"}, {"family": "Eriksson", "given": "Sofi", "initials": "S"}, {"family": "Jerhammar", "given": "Fredrik", "initials": "F"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Vilborg", "given": "Anna", "initials": "A"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Lui", "given": "Weng-Onn", "initials": "WO"}, {"family": "Wiman", "given": "Klas G", "initials": "KG"}], "type": "journal article", "published": "2016-01-12", "journal": {"volume": "7", "issn": "1949-2553", "issue": "2", "pages": "1895-1911", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "RNA-binding proteins (RBPs) play important roles in the regulation of gene expression through a variety of post-transcriptional mechanisms. The p53-induced RBP Wig-1 (Zmat3) binds RNA through its zinc finger domains and enhances stability of p53 and N-Myc mRNAs and decreases stability of FAS mRNA. To identify novel Wig-1-bound RNAs, we performed RNA-immunoprecipitation followed by high-throughput sequencing (RIP-Seq) in HCT116 and Saos-2 cells. We identified 286 Wig-1-bound mRNAs common between the two cell lines. Sequence analysis revealed that AU-rich elements (AREs) are highly enriched in the 3'UTR of these Wig-1-bound mRNAs. Network enrichment analysis showed that Wig-1 preferentially binds mRNAs involved in cell cycle regulation. Moreover, we identified a 2D Wig-1 binding motif in HIF1A mRNA. Our findings confirm that Wig-1 is an ARE-BP that regulates cell cycle-related processes and provide a novel view of how Wig-1 may bind mRNA through a putative structural motif. We also significantly extend the repertoire of Wig-1 target mRNAs. Since Wig-1 is a transcriptional target of the tumor suppressor p53, these results have implications for our understanding of p53-dependent stress responses and tumor suppression.", "doi": "10.18632/oncotarget.6557", "pmid": "26672765", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6557"}, {"db": "pmc", "key": "PMC4811505"}], "notes": [], "created": "2017-05-02T12:56:36.289Z", "modified": "2021-07-08T13:26:08.285Z"}, {"entity": "publication", "iuid": "ce9e7040fd814d8887d30aa861a6507d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce9e7040fd814d8887d30aa861a6507d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce9e7040fd814d8887d30aa861a6507d"}}, "title": "PGSB PlantsDB: updates to the database framework for comparative plant genome research.", "authors": [{"family": "Spannagl", "given": "Manuel", "initials": "M"}, {"family": "Nussbaumer", "given": "Thomas", "initials": "T"}, {"family": "Bader", "given": "Kai C", "initials": "KC"}, {"family": "Martis", "given": "Mihaela M", "initials": "MM"}, {"family": "Seidel", "given": "Michael", "initials": "M"}, {"family": "Kugler", "given": "Karl G", "initials": "KG"}, {"family": "Gundlach", "given": "Heidrun", "initials": "H"}, {"family": "Mayer", "given": "Klaus F X", "initials": "KF"}], "type": "journal article", "published": "2016-01-04", "journal": {"volume": "44", "issn": "1362-4962", "issue": "D1", "pages": "D1141-D1147", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "PGSB (Plant Genome and Systems Biology: formerly MIPS) PlantsDB (http://pgsb.helmholtz-muenchen.de/plant/index.jsp) is a database framework for the comparative analysis and visualization of plant genome data. The resource has been updated with new data sets and types as well as specialized tools and interfaces to address user demands for intuitive access to complex plant genome data. In its latest incarnation, we have re-worked both the layout and navigation structure and implemented new keyword search options and a new BLAST sequence search functionality. Actively involved in corresponding sequencing consortia, PlantsDB has dedicated special efforts to the integration and visualization of complex triticeae genome data, especially for barley, wheat and rye. We enhanced CrowsNest, a tool to visualize syntenic relationships between genomes, with data from the wheat sub-genome progenitor Aegilops tauschii and added functionality to the PGSB RNASeqExpressionBrowser. GenomeZipper results were integrated for the genomes of barley, rye, wheat and perennial ryegrass and interactive access is granted through PlantsDB interfaces. Data exchange and cross-linking between PlantsDB and other plant genome databases is stimulated by the transPLANT project (http://transplantdb.eu/).", "doi": "10.1093/nar/gkv1130", "pmid": "26527721", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "gkv1130"}, {"db": "pmc", "key": "PMC4702821"}], "notes": [], "created": "2017-05-02T12:57:59.386Z", "modified": "2020-01-21T13:53:20.868Z"}, {"entity": "publication", "iuid": "dfc8c13fa784413eacd98b124c06f72a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfc8c13fa784413eacd98b124c06f72a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfc8c13fa784413eacd98b124c06f72a"}}, "title": "Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax).", "authors": [{"family": "Lamichhaney", "given": "Sangeet", "initials": "S"}, {"family": "Fan", "given": "Guangyi", "initials": "G"}, {"family": "Widemo", "given": "Fredrik", "initials": "F"}, {"family": "Gunnarsson", "given": "Ulrika", "initials": "U"}, {"family": "Thalmann", "given": "Doreen Schwochow", "initials": "DS"}, {"family": "Hoeppner", "given": "Marc P", "initials": "MP"}, {"family": "Kerje", "given": "Susanne", "initials": "S", "orcid": "0000-0002-2944-9288", "researcher": {"href": "https://publications.scilifelab.se/researcher/078ca525f2cc4a68a430f2655e45efce.json"}}, {"family": "Gustafson", "given": "Ulla", "initials": "U"}, {"family": "Shi", "given": "Chengcheng", "initials": "C"}, {"family": "Zhang", "given": "He", "initials": "H"}, {"family": "Chen", "given": "Wenbin", "initials": "W"}, {"family": "Liang", "given": "Xinming", "initials": "X"}, {"family": "Huang", "given": "Leihuan", "initials": "L"}, {"family": "Wang", "given": "Jiahao", "initials": "J"}, {"family": "Liang", "given": "Enjing", "initials": "E"}, {"family": "Wu", "given": "Qiong", "initials": "Q"}, {"family": "Lee", "given": "Simon Ming-Yuen", "initials": "SM"}, {"family": "Xu", "given": "Xun", "initials": "X"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Liu", "given": "Xin", "initials": "X"}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal article", "published": "2016-01-00", "journal": {"volume": "48", "issn": "1546-1718", "issue": "1", "pages": "84-88", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "The ruff is a Palearctic wader with a spectacular lekking behavior where highly ornamented males compete for females. This bird has one of the most remarkable mating systems in the animal kingdom, comprising three different male morphs (independents, satellites and faeders) that differ in behavior, plumage color and body size. Remarkably, the satellite and faeder morphs are controlled by dominant alleles. Here we have used whole-genome sequencing and resolved the enigma of how such complex phenotypic differences can have a simple genetic basis. The Satellite and Faeder alleles are both associated with a 4.5-Mb inversion that occurred about 3.8 million years ago. We propose an evolutionary scenario where the Satellite chromosome arose by a rare recombination event about 500,000 years ago. The ruff mating system is the result of an evolutionary process in which multiple genetic changes contributing to phenotypic differences between morphs have accumulated within the inverted region.", "doi": "10.1038/ng.3430", "pmid": "26569123", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "ng.3430"}], "notes": [], "created": "2017-05-02T12:57:44.240Z", "modified": "2024-01-16T13:48:50.624Z"}, {"entity": "publication", "iuid": "bf8296e787394b88a63351bd49943daa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf8296e787394b88a63351bd49943daa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf8296e787394b88a63351bd49943daa"}}, "title": "Fat intake and breast milk fatty acid composition in farming and nonfarming women and allergy development in the offspring.", "authors": [{"family": "Jonsson", "given": "Karin", "initials": "K"}, {"family": "Barman", "given": "Malin", "initials": "M"}, {"family": "Moberg", "given": "Sara", "initials": "S"}, {"family": "Sj\u00f6berg", "given": "Agneta", "initials": "A"}, {"family": "Brekke", "given": "Hilde K", "initials": "HK"}, {"family": "Hesselmar", "given": "Bill", "initials": "B"}, {"family": "Johansen", "given": "Susanne", "initials": "S"}, {"family": "Wold", "given": "Agnes E", "initials": "AE"}, {"family": "Sandberg", "given": "Ann-Sofie", "initials": "AS"}], "type": "comparative study", "published": "2016-01-00", "journal": {"volume": "79", "issn": "1530-0447", "issue": "1-1", "pages": "114-123", "title": "Pediatr. Res.", "issn-l": "0031-3998"}, "abstract": "Children growing up on small family farms are at much lower risk of developing allergy than other children. We hypothesized that low intake of margarine and polyunsaturated fats among farming families could contribute to this protection.\n\nTwenty-eight mother-infant pairs living on small dairy farms and 37 nonfarm rural resident pairs were recruited in the FARMFLORA birth cohort. Food items expected to affect dietary fat composition were recorded by food frequency questionnaires during pregnancy and by 24-h recalls followed by 24-h food diaries during lactation. Allergy was diagnosed by doctors, using strict predefined criteria. Maternal diet and breast milk fat composition were compared between farming and nonfarming mothers and related to children's allergy at age 3 y.\n\nFarming mothers consumed more butter, whole milk, saturated fat, and total fat than nonfarming mothers, who consumed more margarine, oils, and low-fat milk. Farming mothers' breast milk contained higher proportions of saturated and lower proportions of polyunsaturated fat. Allergy was eight times more common in nonfarm children. Mothers of allergic children consumed more margarine and oils than mothers of nonallergic children.\n\nLow maternal consumption of margarine and vegetable oils might contribute to the allergy-preventive effect of growing up on small dairy farms.", "doi": "10.1038/pr.2015.187", "pmid": "26389822", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "pr2015187"}], "notes": [], "created": "2017-05-02T12:57:31.140Z", "modified": "2023-06-19T12:54:36.213Z"}, {"entity": "publication", "iuid": "b360a925eade44d1a857c91e6bf3c877", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b360a925eade44d1a857c91e6bf3c877.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b360a925eade44d1a857c91e6bf3c877"}}, "title": "Metabolic Profiling of Chicken Embryos Exposed to Perfluorooctanoic Acid (PFOA) and Agonists to Peroxisome Proliferator-Activated Receptors.", "authors": [{"family": "Mattsson", "given": "Anna", "initials": "A"}, {"family": "K\u00e4rrman", "given": "Anna", "initials": "A"}, {"family": "Pinto", "given": "Rui", "initials": "R"}, {"family": "Brunstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal article", "published": "2015-12-01", "journal": {"volume": "10", "issn": "1932-6203", "issue": "12", "pages": "e0143780", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Untargeted metabolic profiling of body fluids in experimental animals and humans exposed to chemicals may reveal early signs of toxicity and indicate toxicity pathways. Avian embryos develop separately from their mothers, which gives unique possibilities to study effects of chemicals during embryo development with minimal confounding factors from the mother. In this study we explored blood plasma and allantoic fluid from chicken embryos as matrices for revealing metabolic changes caused by exposure to chemicals during embryonic development. Embryos were exposed via egg injection on day 7 to the environmental pollutant perfluorooctanoic acid (PFOA), and effects on the metabolic profile on day 12 were compared with those caused by GW7647 and rosiglitazone, which are selective agonists to peroxisome-proliferator activated receptor \u03b1 (PPAR\u03b1) and PPAR\u03b3, respectively. Analysis of the metabolite concentrations from allantoic fluid by Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) showed clear separation between the embryos exposed to GW7647, rosiglitazone, and vehicle control, respectively. In blood plasma only GW7647 caused a significant effect on the metabolic profile. PFOA induced embryo mortality and increased relative liver weight at the highest dose. Sublethal doses of PFOA did not significantly affect the metabolic profile in either matrix, although single metabolites appeared to be altered. Neonatal mortality by PFOA in the mouse has been suggested to be mediated via activation of PPAR\u03b1. However, we found no similarity in the metabolite profile of chicken embryos exposed to PFOA with those of embryos exposed to PPAR agonists. This indicates that PFOA does not activate PPAR pathways in our model at concentrations in eggs and embryos well above those found in wild birds. The present study suggests that allantoic fluid and plasma from chicken embryos are useful and complementary matrices for exploring effects on the metabolic profile resulting from chemical exposure during embryonic development.", "doi": "10.1371/journal.pone.0143780", "pmid": "26624992", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-15-36164"}, {"db": "pmc", "key": "PMC4666608"}], "notes": [], "created": "2017-05-02T12:58:02.880Z", "modified": "2020-01-21T13:53:21.063Z"}, {"entity": "publication", "iuid": "58dcb6fc60df458ebf62a6574f7a993d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58dcb6fc60df458ebf62a6574f7a993d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58dcb6fc60df458ebf62a6574f7a993d"}}, "title": "The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.", "authors": [{"family": "Hurst", "given": "Laurence D", "initials": "LD"}, {"family": "Ghanbarian", "given": "Avazeh T", "initials": "AT"}, {"family": "Forrest", "given": "Alistair R R", "initials": "AR"}, {"family": "FANTOM consortium", "given": null, "initials": null}, {"family": "Huminiecki", "given": "Lukasz", "initials": "L"}], "type": "comparative study", "published": "2015-12-00", "journal": {"volume": "13", "issn": "1545-7885", "issue": "12", "pages": "e1002315", "title": "PLoS Biol.", "issn-l": "1544-9173"}, "abstract": "X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution.", "doi": "10.1371/journal.pbio.1002315", "pmid": "26685068", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "PBIOLOGY-D-15-00448"}, {"db": "pmc", "key": "PMC4686125"}], "notes": [], "created": "2017-05-02T12:57:21.413Z", "modified": "2020-01-21T13:53:20.516Z"}, {"entity": "publication", "iuid": "93acb4cd31914e1a856c9a41b08fd8c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/93acb4cd31914e1a856c9a41b08fd8c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/93acb4cd31914e1a856c9a41b08fd8c3"}}, "title": "Experiences with workflows for automating data-intensive bioinformatics", "authors": [{"family": "Spjuth", "given": "Ola", "initials": "O"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}, {"family": "Hern\u00e1ndez", "given": "Guillermo Carrasco", "initials": "GC"}, {"family": "Forer", "given": "Lukas", "initials": "L"}, {"family": "Giovacchini", "given": "Mario", "initials": "M"}, {"family": "Guimera", "given": "Roman Valls", "initials": "RV"}, {"family": "Kallio", "given": "Aleksi", "initials": "A"}, {"family": "Korpelainen", "given": "Eija", "initials": "E"}, {"family": "Ka\u0144du\u0142a", "given": "Maciej M", "initials": "MM"}, {"family": "Krachunov", "given": "Milko", "initials": "M"}, {"family": "Kreil", "given": "David P", "initials": "DP"}, {"family": "Kulev", "given": "Ognyan", "initials": "O"}, {"family": "\u0141abaj", "given": "Pawe\u0142 P", "initials": "PP"}, {"family": "Lampa", "given": "Samuel", "initials": "S"}, {"family": "Pireddu", "given": "Luca", "initials": "L"}, {"family": "Sch\u00f6nherr", "given": "Sebastian", "initials": "S"}, {"family": "Siretskiy", "given": "Alexey", "initials": "A"}, {"family": "Vassilev", "given": "Dimitar", "initials": "D"}], "type": "journal-article", "published": "2015-12-00", "journal": {"volume": "10", "issn": "1745-6150", "issue": "1", "pages": null, "title": "Biol. Direct", "issn-l": "1745-6150"}, "abstract": null, "doi": "10.1186/s13062-015-0071-8", "pmid": "26282399", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-02T12:58:38.115Z", "modified": "2020-01-21T13:56:16.974Z"}, {"entity": "publication", "iuid": "10824b62d1e24ae5996bfba113d94289", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10824b62d1e24ae5996bfba113d94289.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10824b62d1e24ae5996bfba113d94289"}}, "title": "Captured metagenomics: large-scale targeting of genes based on 'sequence capture' reveals functional diversity in soils.", "authors": [{"family": "Manoharan", "given": "Lokeshwaran", "initials": "L"}, {"family": "Kushwaha", "given": "Sandeep K", "initials": "SK"}, {"family": "Hedlund", "given": "Katarina", "initials": "K"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}], "type": "journal article", "published": "2015-12-00", "journal": {"volume": "22", "issn": "1756-1663", "issue": "6", "pages": "451-460", "title": "DNA Res.", "issn-l": "1340-2838"}, "abstract": "Microbial enzyme diversity is a key to understand many ecosystem processes. Whole metagenome sequencing (WMG) obtains information on functional genes, but it is costly and inefficient due to large amount of sequencing that is required. In this study, we have applied a captured metagenomics technique for functional genes in soil microorganisms, as an alternative to WMG. Large-scale targeting of functional genes, coding for enzymes related to organic matter degradation, was applied to two agricultural soil communities through captured metagenomics. Captured metagenomics uses custom-designed, hybridization-based oligonucleotide probes that enrich functional genes of interest in metagenomic libraries where only probe-bound DNA fragments are sequenced. The captured metagenomes were highly enriched with targeted genes while maintaining their target diversity and their taxonomic distribution correlated well with the traditional ribosomal sequencing. The captured metagenomes were highly enriched with genes related to organic matter degradation; at least five times more than similar, publicly available soil WMG projects. This target enrichment technique also preserves the functional representation of the soils, thereby facilitating comparative metagenomics projects. Here, we present the first study that applies the captured metagenomics approach in large scale, and this novel method allows deep investigations of central ecosystem processes by studying functional gene abundances.", "doi": "10.1093/dnares/dsv026", "pmid": "26490729", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "dsv026"}, {"db": "pmc", "key": "PMC4675713"}], "notes": [], "created": "2017-05-02T12:57:58.491Z", "modified": "2020-01-21T13:53:20.310Z"}, {"entity": "publication", "iuid": "8ffa83ee5a814a1ab0da3704d22723e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ffa83ee5a814a1ab0da3704d22723e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ffa83ee5a814a1ab0da3704d22723e9"}}, "title": "Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel.", "authors": [{"family": "Zubair", "given": "Saima", "initials": "S"}, {"family": "Fischer", "given": "Anne", "initials": "A"}, {"family": "Liljander", "given": "Anne", "initials": "A"}, {"family": "Meens", "given": "Jochen", "initials": "J"}, {"family": "Hegerman", "given": "Jan", "initials": "J"}, {"family": "Gourl\u00e9", "given": "Hadrien", "initials": "H"}, {"family": "Bishop", "given": "Richard P", "initials": "RP"}, {"family": "Roebbelen", "given": "Ina", "initials": "I"}, {"family": "Younan", "given": "Mario", "initials": "M"}, {"family": "Mustafa", "given": "Mudassir Imran", "initials": "MI"}, {"family": "Mushtaq", "given": "Mamoona", "initials": "M"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}, {"family": "Jores", "given": "Joerg", "initials": "J"}], "type": "journal article", "published": "2015-11-20", "journal": {"volume": "10", "issn": "1944-3277", "issue": null, "pages": "109", "title": "Stand Genomic Sci", "issn-l": "1944-3277"}, "abstract": "We report the genome of a Staphylococcus aureus strain (ILRI_Eymole1/1) isolated from a nasal swab of a dromedary camel (Camelus dromedarius) in North Kenya. The complete genome sequence of this strain consists of a circular chromosome of 2,874,302\u00a0bp with a GC-content of 32.88\u00a0%. In silico annotation predicted 2755 protein-encoding genes and 76 non-coding genes. This isolate belongs to MLST sequence type 30 (ST30). Phylogenetic analysis based on a subset of 283 core genes revealed that it falls within the human clonal complex 30 (CC30) S. aureus isolate cluster but is genetically distinct. About 79\u00a0% of the protein encoding genes are part of the CC30 core genome (genes common to all CC30 S. aureus isolates), ~18\u00a0% were within the variable genome (shared among multiple but not all isolates) and\u2009~\u20093\u00a0% were found only in the genome of the camel isolate. Among the 85 isolate-specific genes, 79 were located within putative phages and pathogenicity islands. Protein encoding genes associated with bacterial adhesion, and secretory proteins that are essential components of the type VII secretion system were also identified. The complete genome sequence of S. aureus strain ILRI_Eymole1/1 has been deposited in the European Nucleotide Archive under the accession no LN626917.1.", "doi": "10.1186/s40793-015-0098-6", "pmid": "26594310", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "98"}, {"db": "pmc", "key": "PMC4654806"}], "notes": [], "created": "2017-05-02T12:59:02.622Z", "modified": "2020-01-21T13:53:20.665Z"}, {"entity": "publication", "iuid": "c1ce15e64ba944d8a7c58c9f0a73a21b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1ce15e64ba944d8a7c58c9f0a73a21b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1ce15e64ba944d8a7c58c9f0a73a21b"}}, "title": "Quantitative proteogenomics of human pathogens using DIA-MS.", "authors": [{"family": "Malmstr\u00f6m", "given": "Lars", "initials": "L"}, {"family": "Bakochi", "given": "Anahita", "initials": "A"}, {"family": "Svensson", "given": "Gabriel", "initials": "G"}, {"family": "Kilsg\u00e5rd", "given": "Ola", "initials": "O"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Petersson", "given": "Ann Cathrine", "initials": "AC"}, {"family": "Hauri", "given": "Simon", "initials": "S"}, {"family": "Karlsson", "given": "Christofer", "initials": "C"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2015-11-03", "journal": {"volume": "129", "issn": "1876-7737", "issue": null, "pages": "98-107", "title": "J Proteomics", "issn-l": "1874-3919"}, "abstract": "The increasing number of bacterial genomes in combination with reproducible quantitative proteome measurements provides new opportunities to explore how genetic differences modulate proteome composition and virulence. It is challenging to combine genome and proteome data as the underlying genome influences the proteome. We present a strategy to facilitate the integration of genome data from several genetically similar bacterial strains with data-independent analysis mass spectrometry (DIA-MS) for rapid interrogation of the combined data sets. The strategy relies on the construction of a composite genome combining all genetic data in a compact format, which can accommodate the fusion with quantitative peptide and protein information determined via DIA-MS. We demonstrate the method by combining data sets from whole genome sequencing, shotgun MS and DIA-MS from 34 clinical isolates of Streptococcus pyogenes. The data structure allows for fast exploration of the data showing that undetected proteins are on average more amenable to amino acid substitution than expressed proteins. We identified several significantly differentially expressed proteins between invasive and non-invasive strains. The work underlines how integration of whole genome sequencing with accurately quantified proteomes can further advance the interpretation of the relationship between genomes, proteomes and virulence. This article is part of a Special Issue entitled: Computational Proteomics.", "doi": "10.1016/j.jprot.2015.09.012", "pmid": "26381203", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "S1874-3919(15)30129-9"}], "notes": [], "created": "2017-05-02T12:57:58.190Z", "modified": "2020-01-21T13:53:20.837Z"}, {"entity": "publication", "iuid": "eff567d480944d02a0ec33ced4c9c7aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eff567d480944d02a0ec33ced4c9c7aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eff567d480944d02a0ec33ced4c9c7aa"}}, "title": "Impact of asymmetric male and female gamete dispersal on allelic diversity and spatial genetic structure in valley oak (Quercus lobata N\u00e9e)", "authors": [{"family": "Sork", "given": "Victoria L", "initials": "VL"}, {"family": "Smouse", "given": "Peter E", "initials": "PE"}, {"family": "Grivet", "given": "Delphine", "initials": "D"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}], "type": "journal-article", "published": "2015-11-00", "journal": {"volume": "29", "issn": "0269-7653", "issue": "6", "pages": "927-945", "title": "Evol Ecol", "issn-l": null}, "abstract": null, "doi": "10.1007/s10682-015-9769-4", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-05T13:04:39.612Z", "modified": "2021-06-22T11:35:26.338Z"}, {"entity": "publication", "iuid": "757b90df89084a228cebc6c2810a72af", "links": {"self": {"href": "https://publications.scilifelab.se/publication/757b90df89084a228cebc6c2810a72af.json"}, "display": {"href": "https://publications.scilifelab.se/publication/757b90df89084a228cebc6c2810a72af"}}, "title": "Herring and Beef Meals Lead to Differences in Plasma 2-Aminoadipic Acid, \u03b2-Alanine, 4-Hydroxyproline, Cetoleic Acid, and Docosahexaenoic Acid Concentrations in Overweight Men.", "authors": [{"family": "Ross", "given": "Alastair B", "initials": "AB"}, {"family": "Svelander", "given": "Cecilia", "initials": "C"}, {"family": "Undeland", "given": "Ingrid", "initials": "I"}, {"family": "Pinto", "given": "Rui", "initials": "R"}, {"family": "Sandberg", "given": "Ann-Sofie", "initials": "AS"}], "type": "journal article", "published": "2015-11-00", "journal": {"volume": "145", "issn": "1541-6100", "issue": "11", "pages": "2456-2463", "title": "J. Nutr.", "issn-l": "0022-3166"}, "abstract": "Dietary guidelines generally recommend increasing fish intake and reducing red meat intake for better long-term health. Few studies have compared the metabolic differences between eating meat and fish.\n\nThe objective of this study was to determine whether there are differences in the postprandial plasma metabolic response to meals containing baked beef, baked herring, and pickled herring.\n\nSeventeen overweight men (BMI 25-30 kg/m(2), 41-67 y of age) were included in a randomized crossover intervention study. Subjects ate baked herring-, pickled herring-, and baked beef-based meals in a randomized order and postprandial blood plasma samples were taken over 7 h. Plasma metabolomics were measured with the use of gas chromatography-mass spectrometry and areas under the curve for detected metabolites were compared between meals.\n\nThe plasma postprandial response of 2-aminoadipic acid, a suggested marker of diabetes risk, was 1.6 times higher after the beef meal than after the baked herring meal (P < 0.001). Plasma \u03b2-alanine and 4-hydroxyproline both were markedly greater after beef intake than after herring intake (16 and 3.4 times the response of baked herring, respectively; P < 0.001). Herring intake led to a greater plasma postprandial response from docosahexaenoic acid (DHA) and cetoleic acid compared with beef (17.6 and 150 times greater, respectively; P < 0.001), whereas hippuric acid and benzoic acid were elevated after pickled herring compared with baked herring (5.4 and 43 times higher; P < 0.001).\n\nThese results in overweight men confirm that DHA and cetoleic acid reflect herring intake, whereas \u03b2-alanine and 4-hydroxyproline are potential biomarkers for beef intake. The greater postprandial rise in 2-aminoadipic acid after the beef meal, coupled to its proposed role in stimulating insulin secretion, may have importance in the context of red meat intake and increased diabetes risk. This trial was registered at clinicaltrials.gov as NCT02381613.", "doi": "10.3945/jn.115.214262", "pmid": "26400963", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "jn.115.214262"}, {"db": "ClinicalTrials.gov", "key": "NCT02381613"}], "notes": [], "created": "2017-05-02T12:58:26.502Z", "modified": "2020-01-21T13:53:20.579Z"}, {"entity": "publication", "iuid": "5e9934efa63c475ca2645fcc576fe2a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e9934efa63c475ca2645fcc576fe2a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e9934efa63c475ca2645fcc576fe2a0"}}, "title": "Early Exposure to Dogs and Farm Animals and the Risk of Childhood Asthma.", "authors": [{"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Lundholm", "given": "Cecilia", "initials": "C"}, {"family": "\u00d6rtqvist", "given": "Anne K", "initials": "AK"}, {"family": "Fall", "given": "Katja", "initials": "K"}, {"family": "Fang", "given": "Fang", "initials": "F"}, {"family": "Hedhammar", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Almqvist", "given": "Catarina", "initials": "C"}], "type": "journal article", "published": "2015-11-00", "journal": {"volume": "169", "issn": "2168-6211", "issue": "11", "pages": "e153219", "title": "JAMA Pediatr", "issn-l": "2168-6203"}, "abstract": "The association between early exposure to animals and childhood asthma is not clear, and previous studies have yielded contradictory results.\n\nTo determine whether exposure to dogs and farm animals confers a risk of asthma.\n\nIn a nationwide cohort study, the association between early exposure to dogs and farm animals and the risk of asthma was evaluated and included all children born in Sweden from January 1, 2001, to December 31, 2010 (N\u2009=\u20091,011,051), using registry data on dog and farm registration, asthma medication, diagnosis, and confounders for parents and their children. The association was assessed as the odds ratio (OR) for a current diagnosis of asthma at age 6 years for school-aged children and as the hazard ratio (HR) for incident asthma at ages 1 to 5 years for preschool-aged children. Data were analyzed from January 1, 2007, to September 30, 2012.\n\nLiving with a dog or farm animal.\n\nChildhood asthma diagnosis and medication used.\n\nOf the 1,011,051 children born during the study period, 376,638 preschool-aged (53,460 [14.2%] exposed to dogs and 1729 [0.5%] exposed to farm animals) and 276,298 school-aged children (22,629 [8.2%] exposed to dogs and 958 [0.3%] exposed to farm animals) were included in the analyses. Of these, 18,799 children (5.0%) in the preschool-aged children's cohort experienced an asthmatic event before baseline, and 28,511 cases of asthma and 906,071 years at risk were recorded during follow-up (incidence rate, 3.1 cases per 1000 years at risk). In the school-aged children's cohort, 11,585 children (4.2%) experienced an asthmatic event during the seventh year of life. Dog exposure during the first year of life was associated with a decreased risk of asthma in school-aged children (OR, 0.87; 95% CI, 0.81-0.93) and in preschool-aged children 3 years or older (HR, 0.90; 95% CI, 0.83-0.99) but not in children younger than 3 years (HR, 1.03; 95% CI, 1.00-1.07). Results were comparable when analyzing only first-born children. Farm animal exposure was associated with a reduced risk of asthma in both school-aged children and preschool-aged children (OR, 0.48; 95% CI, 0.31-0.76, and HR, 0.69; 95% CI, 0.56-0.84), respectively.\n\nIn this study, the data support the hypothesis that exposure to dogs and farm animals during the first year of life reduces the risk of asthma in children at age 6 years. This information might be helpful in decision making for families and physicians on the appropriateness and timing of early animal exposure.", "doi": "10.1001/jamapediatrics.2015.3219", "pmid": "26523822", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "2467334"}], "notes": [], "created": "2017-05-02T12:56:59.346Z", "modified": "2020-01-21T13:53:20.537Z"}, {"entity": "publication", "iuid": "f390f76260744fe79a3da0fd9756e3fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f390f76260744fe79a3da0fd9756e3fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f390f76260744fe79a3da0fd9756e3fe"}}, "title": "Assessing the Barley Genome Zipper and Genomic Resources for Breeding Purposes.", "authors": [{"family": "Silvar", "given": "Cristina", "initials": "C"}, {"family": "Martis", "given": "Mihaela M", "initials": "MM"}, {"family": "Nussbaumer", "given": "Thomas", "initials": "T"}, {"family": "Haag", "given": "Nicolai", "initials": "N"}, {"family": "Rauser", "given": "Ruben", "initials": "R"}, {"family": "Keilwagen", "given": "Jens", "initials": "J"}, {"family": "Korzun", "given": "Viktor", "initials": "V"}, {"family": "Mayer", "given": "Klaus F X", "initials": "KFX"}, {"family": "Ordon", "given": "Frank", "initials": "F"}, {"family": "Perovic", "given": "Dragan", "initials": "D"}], "type": "journal article", "published": "2015-11-00", "journal": {"volume": "8", "issn": "1940-3372", "issue": "3", "pages": "eplantgenome2015.06.0045", "title": "Plant Genome", "issn-l": "1940-3372"}, "abstract": "The aim of this study was to estimate the accuracy and convergence of newly developed barley (Hordeum vulgare L.) genomic resources, primarily genome zipper (GZ) and population sequencing (POPSEQ), at the genome-wide level and to assess their usefulness in applied barley breeding by analyzing seven known loci. Comparison of barley GZ and POPSEQ maps to a newly developed consensus genetic map constructed with data from 13 individual linkage maps yielded an accuracy of 97.8% (GZ) and 99.3% (POPSEQ), respectively, regarding the chromosome assignment. The percentage of agreement in marker position indicates that on average only 3.7% GZ and 0.7% POPSEQ positions are not in accordance with their centimorgan coordinates in the consensus map. The fine-scale comparison involved seven genetic regions on chromosomes 1H, 2H, 4H, 6H, and 7H, harboring major genes and quantitative trait loci (QTL) for disease resistance. In total, 179 GZ loci were analyzed and 64 polymorphic markers were developed. Entirely, 89.1% of these were allocated within the targeted intervals and 84.2% followed the predicted order. Forty-four markers showed a match to a POPSEQ-anchored contig, the percentage of collinearity being 93.2%, on average. Forty-four markers allowed the identification of twenty-five fingerprinted contigs (FPCs) and a more clear delimitation of the physical regions containing the traits of interest. Our results demonstrate that an increase in marker density of barley maps by using new genomic data significantly improves the accuracy of GZ. In addition, the combination of different barley genomic resources can be considered as a powerful tool to accelerate barley breeding.", "doi": "10.3835/plantgenome2015.06.0045", "pmid": "33228270", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-05T13:03:36.952Z", "modified": "2021-06-22T11:58:21.153Z"}, {"entity": "publication", "iuid": "ac412c041374424dade324b38c6e6012", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ac412c041374424dade324b38c6e6012.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ac412c041374424dade324b38c6e6012"}}, "title": "Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities.", "authors": [{"family": "Sanli", "given": "Kemal", "initials": "K"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "Blanck", "given": "Hans", "initials": "H"}, {"family": "Eriksson", "given": "Karl M", "initials": "KM"}], "type": "journal article", "published": "2015-10-30", "journal": {"volume": "6", "issn": "1664-302X", "issue": null, "pages": "1192", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "Periphyton communities are complex phototrophic, multispecies biofilms that develop on surfaces in aquatic environments. These communities harbor a large diversity of organisms comprising viruses, bacteria, algae, fungi, protozoans, and metazoans. However, thus far the total biodiversity of periphyton has not been described. In this study, we use metagenomics to characterize periphyton communities from the marine environment of the Swedish west coast. Although we found approximately ten times more eukaryotic rRNA marker gene sequences compared to prokaryotic, the whole metagenome-based similarity searches showed that bacteria constitute the most abundant phyla in these biofilms. We show that marine periphyton encompass a range of heterotrophic and phototrophic organisms. Heterotrophic bacteria, including the majority of proteobacterial clades and Bacteroidetes, and eukaryotic macro-invertebrates were found to dominate periphyton. The phototrophic groups comprise Cyanobacteria and the alpha-proteobacterial genus Roseobacter, followed by different micro- and macro-algae. We also assess the metabolic pathways that predispose these communities to an attached lifestyle. Functional indicators of the biofilm form of life in periphyton involve genes coding for enzymes that catalyze the production and degradation of extracellular polymeric substances, mainly in the form of complex sugars such as starch and glycogen-like meshes together with chitin. Genes for 278 different transporter proteins were detected in the metagenome, constituting the most abundant protein complexes. Finally, genes encoding enzymes that participate in anaerobic pathways, such as denitrification and methanogenesis, were detected suggesting the presence of anaerobic or low-oxygen micro-zones within the biofilms.", "doi": "10.3389/fmicb.2015.01192", "pmid": "26579098", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pmc", "key": "PMC4626570"}], "notes": [], "created": "2017-05-02T12:58:29.987Z", "modified": "2020-01-21T13:53:20.763Z"}, {"entity": "publication", "iuid": "7e6d084130ca43b18d68b207e950804f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7e6d084130ca43b18d68b207e950804f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7e6d084130ca43b18d68b207e950804f"}}, "title": "Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans.", "authors": [{"family": "Dumesic", "given": "Phillip A", "initials": "PA"}, {"family": "Rosenblad", "given": "Magnus A", "initials": "MA"}, {"family": "Samuelsson", "given": "Tore", "initials": "T"}, {"family": "Nguyen", "given": "Tiffany", "initials": "T"}, {"family": "Moresco", "given": "James J", "initials": "JJ"}, {"family": "Yates", "given": "John R", "initials": "JR"}, {"family": "Madhani", "given": "Hiten D", "initials": "HD"}], "type": "journal article", "published": "2015-10-15", "journal": {"volume": "43", "issn": "1362-4962", "issue": "18", "pages": "9017-9027", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "Despite conservation of the signal recognition particle (SRP) from bacteria to man, computational approaches have failed to identify SRP components from genomes of many lower eukaryotes, raising the possibility that they have been lost or altered in those lineages. We report purification and analysis of SRP in the human pathogen Cryptococcus neoformans, providing the first description of SRP in basidiomycetous yeast. The C. neoformans SRP RNA displays a predicted structure in which the universally conserved helix 8 contains an unprecedented stem-loop insertion. Guided by this sequence, we computationally identified 152 SRP RNAs throughout the phylum Basidiomycota. This analysis revealed additional helix 8 alterations including single and double stem-loop insertions as well as loop diminutions affecting RNA structural elements that are otherwise conserved from bacteria to man. Strikingly, these SRP RNA features in Basidiomycota are accompanied by phylum-specific alterations in the RNA-binding domain of Srp54, the SRP protein subunit that directly interacts with helix 8. Our findings reveal unexpected fungal SRP diversity and suggest coevolution of the two most conserved SRP features-SRP RNA helix 8 and Srp54-in basidiomycetes. Because members of this phylum include important human and plant pathogens, these noncanonical features provide new targets for antifungal compound development.", "doi": "10.1093/nar/gkv819", "pmid": "26275773", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "gkv819"}, {"db": "pmc", "key": "PMC4605306"}], "notes": [], "created": "2017-05-02T12:56:52.564Z", "modified": "2020-01-21T13:53:20.586Z"}, {"entity": "publication", "iuid": "1837468a384a4d009a692da1db915f18", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1837468a384a4d009a692da1db915f18.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1837468a384a4d009a692da1db915f18"}}, "title": "Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies).", "authors": [{"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Sundstr\u00f6m", "given": "G\u00f6rel", "initials": "G"}, {"family": "Zamani", "given": "Neda", "initials": "N"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Lin", "given": "Yao-Cheng", "initials": "YC"}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "H\u00f6ppner", "given": "Marc P", "initials": "MP"}, {"family": "Jern", "given": "Patric", "initials": "P"}, {"family": "Van de Peer", "given": "Yves", "initials": "Y"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Grabherr", "given": "Manfred G", "initials": "MG"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}], "type": "journal article", "published": "2015-09-28", "journal": {"volume": "10", "issn": "1932-6203", "issue": "9", "pages": "e0139080", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "After performing de novo transcript assembly of >1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts, indicating that these organisms were present, alive, and metabolically active. Here, we show that these serendipitously sequenced transcripts need not be considered merely as contamination, as is common, but that they provide insight into the plant's phyllosphere. Notably, we could classify these transcripts as originating predominantly from Dothideomycetes and Leotiomycetes species, with functional annotation of gene families indicating active growth and metabolism, with particular regards to glucose intake and processing, as well as gene regulation.", "doi": "10.1371/journal.pone.0139080", "pmid": "26413905", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "PONE-D-15-34536"}, {"db": "pmc", "key": "PMC4586145"}], "notes": [], "created": "2017-05-02T12:56:50.290Z", "modified": "2021-07-08T13:26:08.108Z"}, {"entity": "publication", "iuid": "1282f8e60a5b42709a9551c298359a2c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1282f8e60a5b42709a9551c298359a2c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1282f8e60a5b42709a9551c298359a2c"}}, "title": "Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis.", "authors": [{"family": "Dmitriev", "given": "Alexey A", "initials": "AA"}, {"family": "Rosenberg", "given": "Eugenia E", "initials": "EE"}, {"family": "Krasnov", "given": "George S", "initials": "GS"}, {"family": "Gerashchenko", "given": "Ganna V", "initials": "GV"}, {"family": "Gordiyuk", "given": "Vasily V", "initials": "VV"}, {"family": "Pavlova", "given": "Tatiana V", "initials": "TV"}, {"family": "Kudryavtseva", "given": "Anna V", "initials": "AV"}, {"family": "Beniaminov", "given": "Artemy D", "initials": "AD"}, {"family": "Belova", "given": "Anastasia A", "initials": "AA"}, {"family": "Bondarenko", "given": "Yuriy N", "initials": "YN"}, {"family": "Danilets", "given": "Rostislav O", "initials": "RO"}, {"family": "Glukhov", "given": "Alexander I", "initials": "AI"}, {"family": "Kondratov", "given": "Aleksandr G", "initials": "AG"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Alekseev", "given": "Boris Y", "initials": "BY"}, {"family": "Klein", "given": "George", "initials": "G"}, {"family": "Senchenko", "given": "Vera N", "initials": "VN"}, {"family": "Kashuba", "given": "Vladimir I", "initials": "VI"}], "type": "journal article", "published": "2015-09-28", "journal": {"volume": "2015", "issn": "1875-8630", "issue": null, "pages": "241301", "title": "Dis. Markers", "issn-l": "0278-0240"}, "abstract": "A significant need for reliable and accurate cancer diagnostics and prognosis compels the search for novel biomarkers that would be able to discriminate between indolent and aggressive tumors at the early stages of disease. The aim of this work was identification of potential diagnostic biomarkers for characterization of different types of prostate tumors. NotI-microarrays with 180 clones associated with chromosome 3 genes/loci were applied to determine genetic and epigenetic alterations in 33 prostate tumors. For 88 clones, aberrations were detected in more than 10% of tumors. The major types of alterations were DNA methylation and/or deletions. Frequent methylation of the discovered loci was confirmed by bisulfite sequencing on selective sampling of genes: FGF12, GATA2, and LMCD1. Three genes (BHLHE40, BCL6, and ITGA9) were tested for expression level alterations using qPCR, and downregulation associated with hypermethylation was shown in the majority of tumors. Based on these data, we proposed the set of potential biomarkers for detection of prostate cancer and discrimination between prostate tumors with different malignancy and aggressiveness: BHLHE40, FOXP1, LOC285205, ITGA9, CTDSPL, FGF12, LOC440944/SETD5, VHL, CLCN2, OSBPL10/ZNF860, LMCD1, FAM19A4, CAND2, MAP4, KY, and LRRC58. Moreover, we probabilistically estimated putative functional relations between the genes within each set using the network enrichment analysis.", "doi": "10.1155/2015/241301", "pmid": "26491211", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pmc", "key": "PMC4602334"}], "notes": [], "created": "2017-05-02T12:56:51.378Z", "modified": "2020-01-21T13:53:20.319Z"}, {"entity": "publication", "iuid": "b5bcdca266db45aeb554db7125ff761e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5bcdca266db45aeb554db7125ff761e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5bcdca266db45aeb554db7125ff761e"}}, "title": "HLA class I is most tightly linked to levels of tapasin compared with other antigen-processing proteins in glioblastoma.", "authors": [{"family": "Thuring", "given": "Camilla", "initials": "C"}, {"family": "Follin", "given": "Elna", "initials": "E"}, {"family": "Geironson", "given": "Linda", "initials": "L"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Junghans", "given": "Victoria", "initials": "V"}, {"family": "Harndahl", "given": "Mikkel", "initials": "M"}, {"family": "Buus", "given": "S\u00f8ren", "initials": "S"}, {"family": "Paulsson", "given": "Kajsa M", "initials": "KM"}], "type": "journal article", "published": "2015-09-15", "journal": {"volume": "113", "issn": "1532-1827", "issue": "6", "pages": "952-962", "title": "Br. J. Cancer", "issn-l": "0007-0920"}, "abstract": "Tumour cells can evade the immune system by dysregulation of human leukocyte antigens (HLA-I). Low quantity and/or altered quality of HLA-I cell surface expression is the result of either HLA-I alterations or dysregulations of proteins of the antigen-processing machinery (APM). Tapasin is an APM protein dedicated to the maturation of HLA-I and dysregulation of tapasin has been linked to higher malignancy in several different tumours.\n\nWe studied the expression of APM components and HLA-I, as well as HLA-I tapasin-dependency profiles in glioblastoma tissues and corresponding cell lines.\n\nTapasin displayed the strongest correlation to HLA-I heavy chain but also clustered with \u03b22-microglobulin, transporter associated with antigen processing (TAP) and LMP. Moreover, tapasin also correlated to survival of glioblastoma patients. Some APM components, for example, TAP1/TAP2 and LMP2/LMP7, showed variable but coordinated expression, whereas ERAP1/ERAP2 displayed an imbalanced expression pattern. Furthermore, analysis of HLA-I profiles revealed variable tapasin dependence of HLA-I allomorphs in glioblastoma patients.\n\nExpression of APM proteins is highly variable between glioblastomas. Tapasin stands out as the APM component strongest correlated to HLA-I expression and we proved that HLA-I profiles in glioblastoma patients include tapasin-dependent allomorphs. The level of tapasin was also correlated with patient survival time. Our results support the need for individualisation of immunotherapy protocols.", "doi": "10.1038/bjc.2015.297", "pmid": "26313662", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "bjc2015297"}, {"db": "pmc", "key": "PMC4578088"}], "notes": [], "created": "2017-05-02T12:58:46.511Z", "modified": "2020-01-21T13:53:20.802Z"}, {"entity": "publication", "iuid": "ffaff82393714a328d9e581b7583a775", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ffaff82393714a328d9e581b7583a775.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ffaff82393714a328d9e581b7583a775"}}, "title": "Auxotrophy and intrapopulation complementary in the 'interactome' of a cultivated freshwater model community.", "authors": [{"family": "Garcia", "given": "Sarahi L", "initials": "SL"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "McMahon", "given": "Katherine D", "initials": "KD"}, {"family": "Grossart", "given": "Hans-Peter", "initials": "HP"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}, {"family": "Warnecke", "given": "Falk", "initials": "F"}], "type": "journal article", "published": "2015-09-00", "journal": {"volume": "24", "issn": "1365-294X", "issue": "17", "pages": "4449-4459", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Microorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet-uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high-quality metagenome-assembled genomes (MAGs) for metabolic reconstruction. This analysis revealed the metabolic interconnectedness and niche partitioning of these naturally dominant bacteria. In particular, vitamin- and amino acid biosynthetic pathways were distributed unequally with a member of Crenarchaeota most likely being the sole producer of vitamin B12 in the mixed culture. Using coverage-based partitioning of the genes recovered from a single MAG intrapopulation metabolic complementarity was revealed pointing to 'social' interactions for the common good of populations dominating freshwater plankton. As such, our MAGs highlight the power of mixed cultures to extract naturally occurring 'interactomes' and to overcome our inability to isolate and grow the microbes dominating in nature.", "doi": "10.1111/mec.13319", "pmid": "26179741", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:57:04.286Z", "modified": "2020-01-21T13:53:21.011Z"}, {"entity": "publication", "iuid": "fe9dda67fa9940469c50f758fff3d2fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fe9dda67fa9940469c50f758fff3d2fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fe9dda67fa9940469c50f758fff3d2fe"}}, "title": "BEX1 acts as a tumor suppressor in acute myeloid leukemia.", "authors": [{"family": "Lindblad", "given": "Oscar", "initials": "O"}, {"family": "Li", "given": "Tianfeng", "initials": "T"}, {"family": "Su", "given": "Xianwei", "initials": "X"}, {"family": "Sun", "given": "Jianmin", "initials": "J"}, {"family": "Kabir", "given": "Nuzhat N", "initials": "NN"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Zhao", "given": "Hui", "initials": "H"}, {"family": "Lu", "given": "Gang", "initials": "G"}, {"family": "R\u00f6nnstrand", "given": "Lars", "initials": "L"}, {"family": "Kazi", "given": "Julhash U", "initials": "JU"}], "type": "journal article", "published": "2015-08-28", "journal": {"volume": "6", "issn": "1949-2553", "issue": "25", "pages": "21395-21405", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "Acute myeloid leukemia (AML) is a heterogeneous disease of the myeloid lineage. About 35% of AML patients carry an oncogenic FLT3 mutant making FLT3 an attractive target for treatment of AML. Major problems in the development of FLT3 inhibitors include lack of specificity, poor response and development of a resistant phenotype upon treatment. Further understanding of FLT3 signaling and discovery of novel regulators will therefore help to determine additional pharmacological targets in FLT3-driven AML. In this report, we identified BEX1 as a novel regulator of oncogenic FLT3-ITD-driven AML. We showed that BEX1 expression was down-regulated in a group of AML patients carrying FLT3-ITD. Loss of BEX1 expression resulted in poor overall survival (hazard ratio, HR = 2.242, p = 0.0011). Overexpression of BEX1 in mouse pro-B and myeloid cells resulted in decreased FLT3-ITD-dependent cell proliferation, colony and tumor formation, and in increased apoptosis in vitro and in vivo. BEX1 localized to the cytosolic compartment of cells and significantly decreased FLT3-ITD-induced AKT phosphorylation without affecting ERK1/2 or STAT5 phosphorylation. Our data suggest that the loss of BEX1 expression in FLT3-ITD driven AML potentiates oncogenic signaling and leads to decreased overall survival of the patients.", "doi": "10.18632/oncotarget.4095", "pmid": "26046670", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "4095"}, {"db": "pmc", "key": "PMC4673273"}], "notes": [], "created": "2017-05-02T12:57:49.633Z", "modified": "2020-01-21T13:53:21.005Z"}, {"entity": "publication", "iuid": "bdca11793f0f486da3f109cc4468c7ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bdca11793f0f486da3f109cc4468c7ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bdca11793f0f486da3f109cc4468c7ad"}}, "title": "The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution.", "authors": [{"family": "Zuccolo", "given": "Andrea", "initials": "A"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "De Paoli", "given": "Emanuele", "initials": "E"}, {"family": "Morgante", "given": "Michele", "initials": "M"}], "type": "journal article", "published": "2015-08-15", "journal": {"volume": "568", "issn": "1879-0038", "issue": "1", "pages": "89-99", "title": "Gene", "issn-l": "0378-1119"}, "abstract": "Long Terminal Repeat retroelements (LTR-RTs) are a major component of many plant genomes. Although well studied and described in angiosperms, their features and dynamics are poorly understood in gymnosperms. Representative complete copies of a Ty1-copia element isolate in Picea abies and named PARTC were identified in six other conifer species (Picea glauca, Pinus sylvestris, Pinus taeda, Abies sibirica, Taxus baccata and Juniperus communis) covering more than 200 million years of evolution. Here we characterized the structure of this element, assessed its abundance across conifers, studied the modes and timing of its amplification, and evaluated the degree of conservation of its extant copies at nucleotide level over distant species. We demonstrated that the element is ancient, abundant, widespread and its paralogous copies are present in the genera Picea, Pinus and Abies as an LTR-RT family. The amplification leading to the extant copies of PARTC occurred over long evolutionary times spanning 10s of MY and mostly took place after the speciation of the conifers analyzed. The level of conservation of PARTC is striking and may be explained by low substitution rates and limited removal mechanisms for LTR-RTs. These PARTC features and dynamics are representative of a more general scenario for LTR-RTs in gymnosperms quite different from that characterizing the vast majority of LTR-RT elements in angiosperms.", "doi": "10.1016/j.gene.2015.05.028", "pmid": "25982862", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "S0378-1119(15)00586-7"}], "notes": [], "created": "2017-05-02T12:59:02.923Z", "modified": "2020-01-21T13:53:20.832Z"}, {"entity": "publication", "iuid": "a70aaaa7899f4e879e6ae51fb735c04a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a70aaaa7899f4e879e6ae51fb735c04a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a70aaaa7899f4e879e6ae51fb735c04a"}}, "title": "Identifying and Assessing Interesting Subgroups in a Heterogeneous Population.", "authors": [{"family": "Lee", "given": "Woojoo", "initials": "W"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15f303cb2044cfa81719700137e3603.json"}}, {"family": "Guegan", "given": "Justine", "initials": "J"}, {"family": "Dessen", "given": "Philippe", "initials": "P"}, {"family": "Lazar", "given": "Vladimir", "initials": "V"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}], "type": "journal article", "published": "2015-08-03", "journal": {"volume": "2015", "issn": "2314-6141", "issue": null, "pages": "462549", "title": "Biomed Res Int", "issn-l": "2314-6133"}, "abstract": "Biological heterogeneity is common in many diseases and it is often the reason for therapeutic failures. Thus, there is great interest in classifying a disease into subtypes that have clinical significance in terms of prognosis or therapy response. One of the most popular methods to uncover unrecognized subtypes is cluster analysis. However, classical clustering methods such as k-means clustering or hierarchical clustering are not guaranteed to produce clinically interesting subtypes. This could be because the main statistical variability--the basis of cluster generation--is dominated by genes not associated with the clinical phenotype of interest. Furthermore, a strong prognostic factor might be relevant for a certain subgroup but not for the whole population; thus an analysis of the whole sample may not reveal this prognostic factor. To address these problems we investigate methods to identify and assess clinically interesting subgroups in a heterogeneous population. The identification step uses a clustering algorithm and to assess significance we use a false discovery rate- (FDR-) based measure. Under the heterogeneity condition the standard FDR estimate is shown to overestimate the true FDR value, but this is remedied by an improved FDR estimation procedure. As illustrations, two real data examples from gene expression studies of lung cancer are provided.", "doi": "10.1155/2015/462549", "pmid": "26339613", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pmc", "key": "PMC4539210"}], "notes": [], "created": "2017-05-02T12:57:46.628Z", "modified": "2021-07-08T11:36:54.648Z"}, {"entity": "publication", "iuid": "2f8df27edfb14ac7b9eeddf216394a87", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f8df27edfb14ac7b9eeddf216394a87.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f8df27edfb14ac7b9eeddf216394a87"}}, "title": "Representation of selected-reaction monitoring data in the mzQuantML data standard.", "authors": [{"family": "Qi", "given": "Da", "initials": "D"}, {"family": "Lawless", "given": "Craig", "initials": "C"}, {"family": "Teleman", "given": "Johan", "initials": "J"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Holman", "given": "Stephen W", "initials": "SW"}, {"family": "Hubbard", "given": "Simon", "initials": "S"}, {"family": "Jones", "given": "Andrew R", "initials": "AR"}], "type": "journal article", "published": "2015-08-00", "journal": {"volume": "15", "issn": "1615-9861", "issue": "15", "pages": "2592-2596", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "The mzQuantML data standard was designed to capture the output of quantitative software in proteomics, to support submissions to public repositories, development of visualization software and pipeline/modular approaches. The standard is designed around a common core that can be extended to support particular types of technique through the release of semantic rules that are checked by validation software. The first release of mzQuantML supported four quantitative proteomics techniques via four sets of semantic rules: (i) intensity-based (MS(1) ) label free, (ii) MS(1) label-based (such as SILAC or N(15) ), (iii) MS(2) tag-based (iTRAQ or tandem mass tags), and (iv) spectral counting. We present an update to mzQuantML for supporting SRM techniques. The update includes representing the quantitative measurements, and associated meta-data, for SRM transitions, the mechanism for inferring peptide-level or protein-level quantitative values, and support for both label-based or label-free SRM protocols, through the creation of semantic rules and controlled vocabulary terms. We have updated the specification document for mzQuantML (version 1.0.1) and the mzQuantML validator to ensure that consistent files are produced by different exporters. We also report the capabilities for production of mzQuantML files from popular SRM software packages, such as Skyline and Anubis.", "doi": "10.1002/pmic.201400281", "pmid": "25884107", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pmc", "key": "PMC4692094"}], "notes": [], "created": "2017-05-02T12:58:20.628Z", "modified": "2020-01-21T13:53:20.419Z"}, {"entity": "publication", "iuid": "7fb91ebe96624c79b2949d7397a0e3c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7fb91ebe96624c79b2949d7397a0e3c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7fb91ebe96624c79b2949d7397a0e3c3"}}, "title": "Inbreeding Affects Gene Expression Differently in Two Self-Incompatible Arabidopsis lyrata Populations with Similar Levels of Inbreeding Depression.", "authors": [{"family": "Menzel", "given": "Mandy", "initials": "M"}, {"family": "Sletvold", "given": "Nina", "initials": "N"}, {"family": "\u00c5gren", "given": "Jon", "initials": "J"}, {"family": "Hansson", "given": "Bengt", "initials": "B"}], "type": "journal article", "published": "2015-08-00", "journal": {"volume": "32", "issn": "1537-1719", "issue": "8", "pages": "2036-2047", "title": "Mol. Biol. Evol.", "issn-l": "0737-4038"}, "abstract": "Knowledge of which genes and pathways are affected by inbreeding may help understanding the genetic basis of inbreeding depression, the potential for purging (selection against deleterious recessive alleles), and the transition from outcrossing to selfing. Arabidopsis lyrata is a predominantly self-incompatible perennial plant, closely related to the selfing model species A. thaliana. To examine how inbreeding affects gene expression, we compared the transcriptome of experimentally selfed and outcrossed A. lyrata originating from two Scandinavian populations that express similar inbreeding depression for fitness (\u2202 \u2248 0.80). The number of genes significantly differentially expressed between selfed and outcrossed individuals were 2.5 times higher in the Norwegian population (\u2248 500 genes) than in the Swedish population (\u2248 200 genes). In both populations, a majority of genes were upregulated on selfing (\u2248 80%). Functional annotation analysis of the differentially expressed genes showed that selfed offspring were characterized by 1) upregulation of stress-related genes in both populations and 2) upregulation of photosynthesis-related genes in Sweden but downregulation in Norway. Moreover, we found that reproduction- and pollination-related genes were affected by inbreeding only in Norway. We conclude that inbreeding causes both general and population-specific effects. The observed common effects suggest that inbreeding generally upregulates rather than downregulates gene expression and affects genes associated with stress response and general metabolic activity. Population differences in the number of affected genes and in effects on the expression of photosynthesis-related genes show that the genetic basis of inbreeding depression can differ between populations with very similar levels of inbreeding depression.", "doi": "10.1093/molbev/msv086", "pmid": "25855783", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "msv086"}, {"db": "pmc", "key": "PMC4833072"}], "notes": [], "created": "2017-05-02T12:58:03.771Z", "modified": "2020-01-21T13:53:20.593Z"}, {"entity": "publication", "iuid": "601e012dd7aa4584a4aa14787aa91773", "links": {"self": {"href": "https://publications.scilifelab.se/publication/601e012dd7aa4584a4aa14787aa91773.json"}, "display": {"href": "https://publications.scilifelab.se/publication/601e012dd7aa4584a4aa14787aa91773"}}, "title": "Identification of New Potential Interaction Partners for Human Cytoplasmic Copper Chaperone Atox1: Roles in Gene Regulation?", "authors": [{"family": "\u00d6hrvik", "given": "Helena", "initials": "H"}, {"family": "Wittung-Stafshede", "given": "Pernilla", "initials": "P", "orcid": "0000-0003-1058-1964", "researcher": {"href": "https://publications.scilifelab.se/researcher/9016aa00d62f439fb15532a1f4ba814e.json"}}], "type": "journal article", "published": "2015-07-23", "journal": {"volume": "16", "issn": "1422-0067", "issue": "8", "pages": "16728-16739", "title": "Int J Mol Sci", "issn-l": null}, "abstract": "The human copper (Cu) chaperone Atox1 delivers Cu to P1B type ATPases in the Golgi network, for incorporation into essential Cu-dependent enzymes. Atox1 homologs are found in most organisms; it is a 68-residue ferredoxin-fold protein that binds Cu in a conserved surface-exposed Cys-X-X-Cys (CXXC) motif. In addition to its well-documented cytoplasmic chaperone function, in 2008 Atox1 was suggested to have functionality in the nucleus. To identify new interactions partners of Atox1, we performed a yeast two-hybrid screen with a large human placenta library of cDNA fragments using Atox1 as bait. Among 98 million fragments investigated, 25 proteins were found to be confident interaction partners. Nine of these were uncharacterized proteins, and the remaining 16 proteins were analyzed by bioinformatics with respect to cell localization, tissue distribution, function, sequence motifs, three-dimensional structures and interaction networks. Several of the hits were eukaryotic-specific proteins interacting with DNA or RNA implying that Atox1 may act as a modulator of gene regulation. Notably, because many of the identified proteins contain CXXC motifs, similarly to the Cu transport reactions, interactions between these and Atox1 may be mediated by Cu.", "doi": "10.3390/ijms160816728", "pmid": "26213915", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "ijms160816728"}, {"db": "pmc", "key": "PMC4581165"}], "notes": [], "created": "2017-05-02T12:58:13.795Z", "modified": "2021-06-16T16:16:13.344Z"}, {"entity": "publication", "iuid": "edc4228d642b4f87a72a1da844100488", "links": {"self": {"href": "https://publications.scilifelab.se/publication/edc4228d642b4f87a72a1da844100488.json"}, "display": {"href": "https://publications.scilifelab.se/publication/edc4228d642b4f87a72a1da844100488"}}, "title": "Cell periphery-related proteins as major genomic targets behind the adaptive evolution of an industrial Saccharomyces cerevisiae strain to combined heat and hydrolysate stress.", "authors": [{"family": "Wallace-Salinas", "given": "Valeria", "initials": "V"}, {"family": "Brink", "given": "Daniel P", "initials": "DP"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Gorwa-Grauslund", "given": "Marie F", "initials": "MF"}], "type": "comparative study", "published": "2015-07-09", "journal": {"volume": "16", "issn": "1471-2164", "issue": null, "pages": "514", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Laboratory evolution is an important tool for developing robust yeast strains for bioethanol production since the biological basis behind combined tolerance requires complex alterations whose proper regulation is difficult to achieve by rational metabolic engineering. Previously, we reported on the evolved industrial Saccharomyces cerevisiae strain ISO12 that had acquired improved tolerance to grow and ferment in the presence of lignocellulose-derived inhibitors at high temperature (39 \u00b0C). In the current study, we used comparative genomics to uncover the extent of the genomic alterations that occurred during the evolution process and investigated possible associations between the mutations and the phenotypic traits in ISO12.\r\n\r\nThrough whole-genome sequencing and variant calling we identified a high number of strain-unique SNPs and INDELs in both ISO12 and the parental strain Ethanol Red. The variants were predicted to have 760 non-synonymous effects in both strains combined and were significantly enriched in Gene Ontology terms related to cell periphery, membranes and cell wall. Eleven genes, including MTL1, FLO9/FLO11, and CYC3 were found to be under positive selection in ISO12. Additionally, the FLO genes exhibited changes in copy number, and the alterations to this gene family were correlated with experimental results of multicellularity and invasive growth in the adapted strain. An independent lipidomic analysis revealed further differences between the strains in the content of nine lipid species. Finally, ISO12 displayed improved viability in undiluted spruce hydrolysate that was unrelated to reduction of inhibitors and changes in cell wall integrity, as shown by HPLC and lyticase assays.\r\n\r\nTogether, the results of the sequence comparison and the physiological characterisations indicate that cell-periphery proteins (e.g. extracellular sensors such as MTL1) and peripheral lipids/membranes are important evolutionary targets in the process of adaptation to the combined stresses. The capacity of ISO12 to develop complex colony formation also revealed multicellularity as a possible evolutionary strategy to improve competitiveness and tolerance to environmental stresses (also reflected by the FLO genes). Although a panel of altered genes with high relevance to the novel phenotype was detected, this study also demonstrates that the observed long-term molecular effects of thermal and inhibitor stress have polygenetic basis.", "doi": "10.1186/s12864-015-1737-4", "pmid": "26156140", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-015-1737-4"}, {"db": "pmc", "key": "PMC4496855"}], "notes": [], "created": "2017-05-02T12:58:54.149Z", "modified": "2020-01-21T13:53:21.644Z"}, {"entity": "publication", "iuid": "0ac23564d9bc4d0ebe7f129ac923224a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0ac23564d9bc4d0ebe7f129ac923224a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0ac23564d9bc4d0ebe7f129ac923224a"}}, "title": "The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides.", "authors": [{"family": "Tsirigos", "given": "Konstantinos D", "initials": "KD"}, {"family": "Peters", "given": "Christoph", "initials": "C"}, {"family": "Shu", "given": "Nanjiang", "initials": "N"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2015-07-01", "journal": {"volume": "43", "issn": "1362-4962", "issue": "W1", "pages": "W401-W407", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "TOPCONS (http://topcons.net/) is a widely used web server for consensus prediction of membrane protein topology. We hereby present a major update to the server, with some substantial improvements, including the following: (i) TOPCONS can now efficiently separate signal peptides from transmembrane regions. (ii) The server can now differentiate more successfully between globular and membrane proteins. (iii) The server now is even slightly faster, although a much larger database is used to generate the multiple sequence alignments. For most proteins, the final prediction is produced in a matter of seconds. (iv) The user-friendly interface is retained, with the additional feature of submitting batch files and accessing the server programmatically using standard interfaces, making it thus ideal for proteome-wide analyses. Indicatively, the user can now scan the entire human proteome in a few days. (v) For proteins with homology to a known 3D structure, the homology-inferred topology is also displayed. (vi) Finally, the combination of methods currently implemented achieves an overall increase in performance by 4% as compared to the currently available best-scoring methods and TOPCONS is the only method that can identify signal peptides and still maintain a state-of-the-art performance in topology predictions.", "doi": "10.1093/nar/gkv485", "pmid": "25969446", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "gkv485"}, {"db": "pmc", "key": "PMC4489233"}], "notes": [], "created": "2017-05-02T12:58:48.007Z", "modified": "2020-01-21T13:53:21.865Z"}, {"entity": "publication", "iuid": "9f2f8be71cb04b10bd23d217e3118645", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f2f8be71cb04b10bd23d217e3118645.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f2f8be71cb04b10bd23d217e3118645"}}, "title": "Proteomics for the detection of indirect markers of steroids treatment in bovine muscle.", "authors": [{"family": "Stella", "given": "Roberto", "initials": "R"}, {"family": "Biancotto", "given": "Giancarlo", "initials": "G"}, {"family": "Arrigoni", "given": "Giorgio", "initials": "G"}, {"family": "Barrucci", "given": "Federica", "initials": "F"}, {"family": "Angeletti", "given": "Roberto", "initials": "R"}, {"family": "James", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2015-07-00", "journal": {"volume": "15", "issn": "1615-9861", "issue": "13", "pages": "2332-2341", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "Despite the ban by the European Union, anabolic steroids might still be illicitly employed in bovine meat production. The surveillance of misuse of such potentially harmful molecules is necessary to guarantee consumers' health. Analytical methods for drug residue control are based on LC-MS/MS, but their efficacy can be hindered due to undetectable residual concentrations as a result of low-dosage treatments. Screening methods based on the recognition of indirect biological effects of growth promoters' administration, such as the alteration of protein expression, can improve the efficacy of surveillance. The present study was aimed at identifying modifications in the muscle protein expression pattern between bulls treated with an ear implant (Revalor-XS\u00ae) containing trenbolone acetate (200 mg) and estradiol (40 mg), and untreated animals. The analysis of skeletal muscle was carried out using a tandem mass tags shotgun proteomics approach. We defined 28 candidate protein markers with a significantly altered expression induced by steroids administration. A subset of 18 candidate markers was validated by SRM and allowed to build a predictive model based on partial least square discriminant analysis. Our findings confirm the effectiveness of the proteomics approach as potential tool to overcome analytical limitations of drug residue monitoring.", "doi": "10.1002/pmic.201400468", "pmid": "25757884", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:58:40.910Z", "modified": "2020-01-21T13:53:20.704Z"}, {"entity": "publication", "iuid": "8675b169b6f3458eafcce15f23e8fb9f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8675b169b6f3458eafcce15f23e8fb9f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8675b169b6f3458eafcce15f23e8fb9f"}}, "title": "Global Multilocus Sequence Type Analysis of Chlamydia trachomatis Strains from 16 Countries.", "authors": [{"family": "Herrmann", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Isaksson", "given": "Jenny", "initials": "J"}, {"family": "Ryberg", "given": "Martin", "initials": "M"}, {"family": "T\u00e5ngrot", "given": "Jeanette", "initials": "J"}, {"family": "Saleh", "given": "Isam", "initials": "I"}, {"family": "Versteeg", "given": "Bart", "initials": "B"}, {"family": "Gravningen", "given": "Kirsten", "initials": "K"}, {"family": "Bruisten", "given": "Sylvia", "initials": "S"}], "type": "journal article", "published": "2015-07-00", "journal": {"volume": "53", "issn": "1098-660X", "issue": "7", "pages": "2172-2179", "title": "J. Clin. Microbiol.", "issn-l": "0095-1137"}, "abstract": "The Uppsala University Chlamydia trachomatis multilocus sequence type (MLST) database (http://mlstdb.bmc.uu.se) is based on five target regions (non-housekeeping genes) and the ompA gene. Each target has various numbers of alleles-hctB, 89; CT058, 51; CT144, 30; CT172, 38; and pbpB, 35-derived from 13 studies. Our aims were to perform an overall analysis of all C. trachomatis MLST sequence types (STs) in the database, examine STs with global spread, and evaluate the phylogenetic capability by using the five targets. A total of 415 STs were recognized from 2,089 specimens. The addition of 49 ompA gene variants created 459 profiles. ST variation and their geographical distribution were characterized using eBURST and minimum spanning tree analyses. There were 609 samples from men having sex with men (MSM), with 4 predominating STs detected in this group, comprising 63% of MSM cases. Four other STs predominated among 1,383 heterosexual cases comprising, 31% of this group. The diversity index in ocular trachoma cases was significantly lower than in sexually transmitted chlamydia infections. Predominating STs were identified in 12 available C. trachomatis whole genomes which were compared to 22 C. trachomatis full genomes without predominating STs. No specific gene in the 12 genomes with predominating STs could be linked to successful spread of certain STs. Phylogenetic analysis showed that MLST targets provide a tree similar to trees based on whole-genome analysis. The presented MLST scheme identified C. trachomatis strains with global spread. It provides a tool for epidemiological investigations and is useful for phylogenetic analyses.", "doi": "10.1128/JCM.00249-15", "pmid": "25926497", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "JCM.00249-15"}, {"db": "pmc", "key": "PMC4473235"}], "notes": [], "created": "2017-05-02T12:57:16.596Z", "modified": "2020-01-21T13:53:20.644Z"}, {"entity": "publication", "iuid": "13e9767b644d400b8d43ca9de8e4ab29", "links": {"self": {"href": "https://publications.scilifelab.se/publication/13e9767b644d400b8d43ca9de8e4ab29.json"}, "display": {"href": "https://publications.scilifelab.se/publication/13e9767b644d400b8d43ca9de8e4ab29"}}, "title": "Ebf1 heterozygosity results in increased DNA damage in pro-B cells and their synergistic transformation by Pax5 haploinsufficiency.", "authors": [{"family": "Prasad", "given": "Mahadesh A J", "initials": "MA"}, {"family": "Ungerb\u00e4ck", "given": "Jonas", "initials": "J"}, {"family": "\u00c5hsberg", "given": "Josefine", "initials": "J"}, {"family": "Somasundaram", "given": "Rajesh", "initials": "R"}, {"family": "Strid", "given": "Tobias", "initials": "T", "orcid": "0000-0002-2166-5170", "researcher": {"href": "https://publications.scilifelab.se/researcher/8294f89150574803a12bc1944714d12b.json"}}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "M\u00e5nsson", "given": "Robert", "initials": "R"}, {"family": "De Paepe", "given": "Ayla", "initials": "A"}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H"}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}, {"family": "Hagman", "given": "James", "initials": "J"}, {"family": "Sigvardsson", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2015-06-25", "journal": {"volume": "125", "issn": "1528-0020", "issue": "26", "pages": "4052-4059", "title": "Blood", "issn-l": "0006-4971"}, "abstract": "Early B-cell factor 1 (Ebf1) is a transcription factor with documented dose-dependent functions in normal and malignant B-lymphocyte development. To understand more about the roles of Ebf1 in malignant transformation, we investigated the impact of reduced functional Ebf1 dosage on mouse B-cell progenitors. Gene expression analysis suggested that Ebf1 was involved in the regulation of genes important for DNA repair and cell survival. Investigation of the DNA damage in steady state, as well as after induction of DNA damage by UV light, confirmed that pro-B cells lacking 1 functional allele of Ebf1 display signs of increased DNA damage. This correlated to reduced expression of DNA repair genes including Rad51, and chromatin immunoprecipitation data suggested that Rad51 is a direct target for Ebf1. Although reduced dosage of Ebf1 did not significantly increase tumor formation in mice, a dramatic increase in the frequency of pro-B cell leukemia was observed in mice with combined heterozygous mutations in the Ebf1 and Pax5 genes, revealing a synergistic effect of combined dose reduction of these proteins. Our data suggest that Ebf1 controls DNA repair in a dose-dependent manner providing a possible explanation to the frequent involvement of EBF1 gene loss in human leukemia.", "doi": "10.1182/blood-2014-12-617282", "pmid": "25838350", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "S0006-4971(20)31508-1"}, {"db": "pmc", "key": "PMC4481594"}], "notes": [], "created": "2017-05-02T12:58:20.029Z", "modified": "2021-07-06T15:41:35.261Z"}, {"entity": "publication", "iuid": "da36b659341b4fb4b845415d63d65ca7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da36b659341b4fb4b845415d63d65ca7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da36b659341b4fb4b845415d63d65ca7"}}, "title": "Confrontation of fibroblasts with cancer cells in vitro: gene network analysis of transcriptome changes and differential capacity to inhibit tumor growth.", "authors": [{"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Alkasalias", "given": "Twana", "initials": "T"}, {"family": "Pavlova", "given": "Tatiana", "initials": "T"}, {"family": "Szekely", "given": "Laszlo", "initials": "L"}, {"family": "Kashuba", "given": "Vladimir", "initials": "V"}, {"family": "Rundqvist", "given": "Helene", "initials": "H"}, {"family": "Wiklund", "given": "Peter", "initials": "P"}, {"family": "Egevad", "given": "Lars", "initials": "L"}, {"family": "Csermely", "given": "Peter", "initials": "P"}, {"family": "Korcsmaros", "given": "Tamas", "initials": "T"}, {"family": "Guven", "given": "Hayrettin", "initials": "H"}, {"family": "Klein", "given": "George", "initials": "G"}], "type": "journal article", "published": "2015-06-18", "journal": {"volume": "34", "issn": "1756-9966", "issue": null, "pages": "62", "title": "J. Exp. Clin. Cancer Res.", "issn-l": "1756-9966"}, "abstract": "There is growing evidence that emerging malignancies in solid tissues might be kept under control by physical intercellular contacts with normal fibroblasts.\n\nHere we characterize transcriptional landscapes of fibroblasts that confronted cancer cells. We studied four pairs of in vitro and ex vivo fibroblast lines which, within each pair, differed in their capacity to inhibit cancer cells. The natural process was modeled in vitro by confronting the fibroblasts with PC-3 cancer cells. Fibroblast transcriptomes were recorded by Affymetrix microarrays and then investigated using network analysis.\n\nThe network enrichment analysis allowed us to separate confrontation- and inhibition-specific components of the fibroblast transcriptional response. Confrontation-specific differences were stronger and were characterized by changes in a number of pathways, including Rho, the YAP/TAZ cascade, NF-kB, and TGF-beta signaling, as well as the transcription factor RELA. Inhibition-specific differences were more subtle and characterized by involvement of Rho signaling at the pathway level and by potential individual regulators such as IL6, MAPK8, MAP2K4, PRKCA, JUN, STAT3, and STAT5A.\n\nWe investigated the interaction between cancer cells and fibroblasts in order to shed light on the potential mechanisms and explain the differential inhibitory capacity of the latter, which enabled both a holistic view on the process and details at the gene/protein level. The combination of our methods pointed to proteins, such as members of the Rho pathway, pro-inflammatory signature and the YAP1/TAZ cascade, that warrant further investigation via tools of experimental perturbation. We also demonstrated functional congruence between the in vitro and ex vivo models. The microarray data are made available via the Gene Expression Omnibus as GSE57199.", "doi": "10.1186/s13046-015-0178-x", "pmid": "26081588", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "10.1186/s13046-015-0178-x"}, {"db": "pmc", "key": "PMC4472614"}, {"db": "GEO", "key": "GSE57199"}], "notes": [], "created": "2017-05-02T12:56:30.176Z", "modified": "2020-01-21T13:53:20.909Z"}, {"entity": "publication", "iuid": "110f4581854a476b9c6f6e1d9b01a259", "links": {"self": {"href": "https://publications.scilifelab.se/publication/110f4581854a476b9c6f6e1d9b01a259.json"}, "display": {"href": "https://publications.scilifelab.se/publication/110f4581854a476b9c6f6e1d9b01a259"}}, "title": "Transglutaminase 4 as a prostate autoantigen in male subfertility", "authors": [{"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Sharon", "given": "Donald", "initials": "D"}, {"family": "Shum", "given": "Anthony K", "initials": "AK"}, {"family": "Khan", "given": "Imran S", "initials": "IS"}, {"family": "Fasano", "given": "Kayla J", "initials": "KJ"}, {"family": "Hallgren", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Ardesj\u00f6-Lundgren", "given": "Brita", "initials": "B"}, {"family": "Alimohammadi", "given": "Mohammad", "initials": "M"}, {"family": "Rathsman", "given": "Sandra", "initials": "S"}, {"family": "Ludvigsson", "given": "Jonas F", "initials": "JF"}, {"family": "Lundh", "given": "Dan", "initials": "D"}, {"family": "Motrich", "given": "Ruben", "initials": "R"}, {"family": "Rivero", "given": "Virginia", "initials": "V"}, {"family": "Fong", "given": "Lawrence", "initials": "L"}, {"family": "Giwercman", "given": "Aleksander", "initials": "A"}, {"family": "Gustafsson", "given": "Jan", "initials": "J"}, {"family": "Perheentupa", "given": "Jaakko", "initials": "J"}, {"family": "Husebye", "given": "Eystein S", "initials": "ES"}, {"family": "Anderson", "given": "Mark S", "initials": "MS"}, {"family": "Snyder", "given": "Michael", "initials": "M"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}], "type": "journal-article", "published": "2015-06-17", "journal": {"volume": "7", "issn": "1946-6234", "issue": "292", "pages": "292ra101", "title": "Sci. Transl. Med.", "issn-l": "1946-6234"}, "abstract": "Autoimmune polyendocrine syndrome type 1 (APS1), a monogenic disorder caused by AIRE gene mutations, features multiple autoimmune disease components. Infertility is common in both males and females with APS1. Although female infertility can be explained by autoimmune ovarian failure, the mechanisms underlying male infertility have remained poorly understood. We performed a proteome-wide autoantibody screen in APS1 patient sera to assess the autoimmune response against the male reproductive organs. By screening human protein arrays with male and female patient sera and by selecting for gender-imbalanced autoantibody signals, we identified transglutaminase 4 (TGM4) as a male-specific autoantigen. Notably, TGM4 is a prostatic secretory molecule with critical role in male reproduction. TGM4 autoantibodies were detected in most of the adult male APS1 patients but were absent in all the young males. Consecutive serum samples further revealed that TGM4 autoantibodies first presented during pubertal age and subsequent to prostate maturation. We assessed the animal model for APS1, the Aire-deficient mouse, and found spontaneous development of TGM4 autoantibodies specifically in males. Aire-deficient mice failed to present TGM4 in the thymus, consistent with a defect in central tolerance for TGM4. In the mouse, we further link TGM4 immunity with a destructive prostatitis and compromised secretion of TGM4. Collectively, our findings in APS1 patients and Aire-deficient mice reveal prostate autoimmunity as a major manifestation of APS1 with potential role in male subfertility.", "doi": "10.1126/scitranslmed.aaa9186", "pmid": "26084804", "labels": {"Bioinformatics Support and Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "Autoimmunity and Serology Profiling": "Service", "PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Service", "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "7/292/292ra101"}], "notes": [], "created": "2017-05-02T12:57:44.848Z", "modified": "2023-06-19T09:06:56.580Z"}, {"entity": "publication", "iuid": "ba403f45bd534ed4bb05220c498f685c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba403f45bd534ed4bb05220c498f685c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba403f45bd534ed4bb05220c498f685c"}}, "title": "Whiteboard: a framework for the programmatic visualization of complex biological analyses.", "authors": [{"family": "Sundstr\u00f6m", "given": "G\u00f6rel", "initials": "G"}, {"family": "Zamani", "given": "Neda", "initials": "N"}, {"family": "Grabherr", "given": "Manfred G", "initials": "MG"}, {"family": "Mauceli", "given": "Evan", "initials": "E"}], "type": "journal article", "published": "2015-06-15", "journal": {"volume": "31", "issn": "1367-4811", "issue": "12", "pages": "2054-2055", "title": "Bioinformatics", "issn-l": "1367-4803"}, "abstract": "Whiteboard is a class library implemented in C++ that enables visualization to be tightly coupled with computation when analyzing large and complex datasets.\n\nthe C++ source code, coding samples and documentation are freely available under the Lesser General Public License from http://whiteboard-class.sourceforge.net/.", "doi": "10.1093/bioinformatics/btv078", "pmid": "25661541", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "btv078"}], "notes": [], "created": "2017-05-02T12:58:42.929Z", "modified": "2020-01-21T13:53:20.820Z"}, {"entity": "publication", "iuid": "213a771d07904e0697738317d50322be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/213a771d07904e0697738317d50322be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/213a771d07904e0697738317d50322be"}}, "title": "A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data.", "authors": [{"family": "Siretskiy", "given": "Alexey", "initials": "A"}, {"family": "Sundqvist", "given": "Tore", "initials": "T"}, {"family": "Voznesenskiy", "given": "Mikhail", "initials": "M"}, {"family": "Spjuth", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2015-06-04", "journal": {"volume": "4", "issn": "2047-217X", "issue": null, "pages": "26", "title": "Gigascience", "issn-l": "2047-217X"}, "abstract": "New high-throughput technologies, such as massively parallel sequencing, have transformed the life sciences into a data-intensive field. The most common e-infrastructure for analyzing this data consists of batch systems that are based on high-performance computing resources; however, the bioinformatics software that is built on this platform does not scale well in the general case. Recently, the Hadoop platform has emerged as an interesting option to address the challenges of increasingly large datasets with distributed storage, distributed processing, built-in data locality, fault tolerance, and an appealing programming methodology.\n\nIn this work we introduce metrics and report on a quantitative comparison between Hadoop and a single node of conventional high-performance computing resources for the tasks of short read mapping and variant calling. We calculate efficiency as a function of data size and observe that the Hadoop platform is more efficient for biologically relevant data sizes in terms of computing hours for both split and un-split data files. We also quantify the advantages of the data locality provided by Hadoop for NGS problems, and show that a classical architecture with network-attached storage will not scale when computing resources increase in numbers. Measurements were performed using ten datasets of different sizes, up to 100 gigabases, using the pipeline implemented in Crossbow. To make a fair comparison, we implemented an improved preprocessor for Hadoop with better performance for splittable data files. For improved usability, we implemented a graphical user interface for Crossbow in a private cloud environment using the CloudGene platform. All of the code and data in this study are freely available as open source in public repositories.\n\nFrom our experiments we can conclude that the improved Hadoop pipeline scales better than the same pipeline on high-performance computing resources, we also conclude that Hadoop is an economically viable option for the common data sizes that are currently used in massively parallel sequencing. Given that datasets are expected to increase over time, Hadoop is a framework that we envision will have an increasingly important role in future biological data analysis.", "doi": "10.1186/s13742-015-0058-5", "pmid": "26045962", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "58"}, {"db": "pmc", "key": "PMC4455317"}], "notes": [], "created": "2017-05-02T12:58:34.234Z", "modified": "2020-01-21T13:53:20.379Z"}, {"entity": "publication", "iuid": "e006ef50a921485094f14198c96adcd4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e006ef50a921485094f14198c96adcd4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e006ef50a921485094f14198c96adcd4"}}, "title": "Circulating microRNA expression pattern separates patients with anti-neutrophil cytoplasmic antibody associated vasculitis from healthy controls.", "authors": [{"family": "Skoglund", "given": "C", "initials": "C"}, {"family": "Carlsen", "given": "A L", "initials": "AL"}, {"family": "Weiner", "given": "M", "initials": "M"}, {"family": "Kurz", "given": "T", "initials": "T"}, {"family": "Hellmark", "given": "Thomas", "initials": "T", "orcid": "0000-0002-2952-1155", "researcher": {"href": "https://publications.scilifelab.se/researcher/13f4a44a5f0d4c69a7eb1da54a15a677.json"}}, {"family": "Eriksson", "given": "P", "initials": "P"}, {"family": "Heegaard", "given": "N H H", "initials": "NH"}, {"family": "Segelmark", "given": "M", "initials": "M"}], "type": "journal article", "published": "2015-05-26", "journal": {"volume": "33", "issn": "0392-856X", "issue": "2 Suppl 89", "pages": "S-64-71", "title": "Clin. Exp. Rheumatol.", "issn-l": null}, "abstract": "Antineutrophil cytoplasmic antibody associated vasculitis (AAV) has an unpredictable course and better biomarkers are needed. Micro-RNAs in body fluids are protected from degradation and might be used as biomarkers for diagnosis and prognosis, here we explore the potential in AAV.\n\nPlasma samples from two AAV cohorts (n=67 and 38) were compared with samples from healthy controls (n=27 and 45) and disease controls (n=20). A panel of 32 miRNAs was measured using a microfluidic quantitative real-time PCR system, and results were compared with clinical data.\n\nSeven individual miRNAs were differently expressed compared to controls in both cohorts; miR-29a, -34a, -142-3p and -383 were up-regulated and miR-20a, -92a and -221 were down-regulated. Cluster analysis as well as principal component analysis (PCA) indicated that patterns of miRNA expression differentiate AAV patients from healthy subjects as well as from renal transplant recipients. Loadings plots indicated similar contribution of the same miRNAs in both cohorts to the PCA. Renal engagement was important for miRNA expression but consistent correlations between estimated glomerular filtration rate and miRNA levels were not found. We found no significant correlation between treatment regimens and circulating miRNA levels.\n\nIn this first study ever on circulating miRNA profiles in AAV, we find clear indication of their potential as biomarkers for diagnosis and classification, but more studies are needed to identify the best markers as well as the mechanisms responsible for variations.", "doi": null, "pmid": "26016752", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "8520"}], "notes": [], "created": "2017-05-02T12:58:35.998Z", "modified": "2025-11-17T09:37:39.724Z"}, {"entity": "publication", "iuid": "81ec6acf68314f978983a9af465f56b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/81ec6acf68314f978983a9af465f56b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/81ec6acf68314f978983a9af465f56b9"}}, "title": "Phylogeny, evolution and classification of gall wasps: the plot thickens.", "authors": [{"family": "Ronquist", "given": "Fredrik", "initials": "F"}, {"family": "Nieves-Aldrey", "given": "Jos\u00e9-Luis", "initials": "JL"}, {"family": "Buffington", "given": "Matthew L", "initials": "ML"}, {"family": "Liu", "given": "Zhiwei", "initials": "Z"}, {"family": "Liljeblad", "given": "Johan", "initials": "J"}, {"family": "Nylander", "given": "Johan A A", "initials": "JA"}], "type": "journal article", "published": "2015-05-20", "journal": {"volume": "10", "issn": "1932-6203", "issue": "5", "pages": "e0123301", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Gall wasps (Cynipidae) represent the most spectacular radiation of gall-inducing insects. In addition to true gall formers, gall wasps also include phytophagous inquilines, which live inside the galls induced by gall wasps or other insects. Here we present the first comprehensive molecular and total-evidence analyses of higher-level gall wasp relationships. We studied more than 100 taxa representing a rich selection of outgroups and the majority of described cynipid genera outside the diverse oak gall wasps (Cynipini), which were more sparsely sampled. About 5 kb of nucleotide data from one mitochondrial (COI) and four nuclear (28S, LWRh, EF1alpha F1, and EF1alpha F2) markers were analyzed separately and in combination with morphological and life-history data. According to previous morphology-based studies, gall wasps evolved in the Northern Hemisphere and were initially herb gallers. Inquilines originated once from gall inducers that lost the ability to initiate galls. Our results, albeit not conclusive, suggest a different scenario. The first gall wasps were more likely associated with woody host plants, and there must have been multiple origins of gall inducers, inquilines or both. One possibility is that gall inducers arose independently from inquilines in several lineages. Except for these surprising results, our analyses are largely consistent with previous studies. They confirm that gall wasps are conservative in their host-plant preferences, and that herb-galling lineages have radiated repeatedly onto the same set of unrelated host plants. We propose a revised classification of the family into twelve tribes, which are strongly supported as monophyletic across independent datasets. Four are new: Aulacideini, Phanacidini, Diastrophini and Ceroptresini. We present a key to the tribes and discuss their morphological and biological diversity. Until the relationships among the tribes are resolved, the origin and early evolution of gall wasps will remain elusive.", "doi": "10.1371/journal.pone.0123301", "pmid": "25993346", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-14-21986"}, {"db": "pmc", "key": "PMC4439057"}], "notes": [], "created": "2017-05-02T12:58:25.610Z", "modified": "2020-01-21T13:53:20.600Z"}, {"entity": "publication", "iuid": "0a87e15a24134172b31a8ce9ed2a3b37", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a87e15a24134172b31a8ce9ed2a3b37.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a87e15a24134172b31a8ce9ed2a3b37"}}, "title": "Is label-free LC-MS/MS ready for biomarker discovery?", "authors": [{"family": "Sandin", "given": "Marianne", "initials": "M"}, {"family": "Chawade", "given": "Aakash", "initials": "A"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2015-04-00", "journal": {"volume": "9", "issn": "1862-8354", "issue": "3-4", "pages": "289-294", "title": "Proteomics Clin Appl", "issn-l": "1862-8346"}, "abstract": "Label-free LC-MS methods are attractive for high-throughput quantitative proteomics, as the sample processing is straightforward and can be scaled to a large number of samples. Label-free methods therefore facilitate biomarker discovery in studies involving dozens of clinical samples. However, despite the increased popularity of label-free workflows, there is a hesitance in the research community to use it in clinical proteomics studies. Therefore, we here discuss pros and cons of label-free LC-MS/MS for biomarker discovery, and delineate the main prerequisites for its successful employment. Furthermore, we cite studies where label-free LC-MS/MS was successfully used to identify novel biomarkers, and foresee an increased acceptance of label-free techniques by the proteomics community in the near future.", "doi": "10.1002/prca.201400202", "pmid": "25656266", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [], "notes": [], "created": "2017-05-02T12:58:29.693Z", "modified": "2020-01-21T13:53:20.283Z"}, {"entity": "publication", "iuid": "5574a7cc0c2044bf9d9d7afdffd09a4e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5574a7cc0c2044bf9d9d7afdffd09a4e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5574a7cc0c2044bf9d9d7afdffd09a4e"}}, "title": "Site-specific programming of the host epithelial transcriptome by the gut microbiota.", "authors": [{"family": "Sommer", "given": "Felix", "initials": "F"}, {"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Sommer", "given": "Nina", "initials": "N"}, {"family": "Fogelstrand", "given": "Per", "initials": "P"}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2015-03-28", "journal": {"volume": "16", "issn": "1474-760X", "issue": null, "pages": "62", "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "The intestinal epithelium separates us from the microbiota but also interacts with it and thus affects host immune status and physiology. Previous studies investigated microbiota-induced responses in the gut using intact tissues or unfractionated epithelial cells, thereby limiting conclusions about regional differences in the epithelium. Here, we sought to investigate microbiota-induced transcriptional responses in specific fractions of intestinal epithelial cells. To this end, we used microarray analysis of laser capture microdissection (LCM)-harvested ileal and colonic tip and crypt epithelial fractions from germ-free and conventionally raised mice and from mice during the time course of colonization.\n\nWe found that about 10% of the host's transcriptome was microbially regulated, mainly including genes annotated with functions in immunity, cell proliferation, and metabolism. The microbial impact on host gene expression was highly site specific, as epithelial responses to the microbiota differed between cell fractions. Specific transcriptional regulators were enriched in each fraction. In general, the gut microbiota induced a more rapid response in the colon than in the ileum.\n\nOur study indicates that the microbiota engage different regulatory networks to alter host gene expression in a particular niche. Understanding host-microbiota interactions on a cellular level may facilitate signaling pathways that contribute to health and disease and thus provide new therapeutic strategies.", "doi": "10.1186/s13059-015-0614-4", "pmid": "25887251", "labels": {"Array and Analysis Facility": null, "Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "10.1186/s13059-015-0614-4"}, {"db": "pmc", "key": "PMC4404278"}], "notes": [], "created": "2017-05-02T12:58:36.919Z", "modified": "2020-01-21T13:53:20.495Z"}, {"entity": "publication", "iuid": "fdc11bd62f0e43b4af5a4f3b1ccef537", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fdc11bd62f0e43b4af5a4f3b1ccef537.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fdc11bd62f0e43b4af5a4f3b1ccef537"}}, "title": "Discovery of molecular markers to discriminate corneal endothelial cells in the human body.", "authors": [{"family": "Yoshihara", "given": "Masahito", "initials": "M"}, {"family": "Ohmiya", "given": "Hiroko", "initials": "H"}, {"family": "Hara", "given": "Susumu", "initials": "S"}, {"family": "Kawasaki", "given": "Satoshi", "initials": "S"}, {"family": "FANTOM consortium", "given": null, "initials": null}, {"family": "Hayashizaki", "given": "Yoshihide", "initials": "Y"}, {"family": "Itoh", "given": "Masayoshi", "initials": "M"}, {"family": "Kawaji", "given": "Hideya", "initials": "H"}, {"family": "Tsujikawa", "given": "Motokazu", "initials": "M"}, {"family": "Nishida", "given": "Kohji", "initials": "K"}], "type": "journal article", "published": "2015-03-25", "journal": {"volume": "10", "issn": "1932-6203", "issue": "3", "pages": "e0117581", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The corneal endothelium is a monolayer of hexagonal corneal endothelial cells (CECs) on the inner surface of the cornea. CECs are critical in maintaining corneal transparency through their barrier and pump functions. CECs in vivo have a limited capacity in proliferation, and loss of a significant number of CECs results in corneal edema called bullous keratopathy which can lead to severe visual loss. Corneal transplantation is the most effective method to treat corneal endothelial dysfunction, where it suffers from donor shortage. Therefore, regeneration of CECs from other cell types attracts increasing interests, and specific markers of CECs are crucial to identify actual CECs. However, the currently used markers are far from satisfactory because of their non-specific expression in other cell types. Here, we explored molecular markers to discriminate CECs from other cell types in the human body by integrating the published RNA-seq data of CECs and the FANTOM5 atlas representing diverse range of cell types based on expression patterns. We identified five genes, CLRN1, MRGPRX3, HTR1D, GRIP1 and ZP4 as novel markers of CECs, and the specificities of these genes were successfully confirmed by independent experiments at both the RNA and protein levels. Notably none of them have been documented in the context of CEC function. These markers could be useful for the purification of actual CECs, and also available for the evaluation of the products derived from other cell types. Our results demonstrate an effective approach to identify molecular markers for CECs and open the door for the regeneration of CECs in vitro.", "doi": "10.1371/journal.pone.0117581", "pmid": "25807145", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-14-40332"}, {"db": "pmc", "key": "PMC4373821"}], "notes": [], "created": "2017-05-02T12:58:59.941Z", "modified": "2020-01-21T13:53:20.999Z"}, {"entity": "publication", "iuid": "b75cb0615d7548be838de2ae09115840", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b75cb0615d7548be838de2ae09115840.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b75cb0615d7548be838de2ae09115840"}}, "title": "Comparative proteomic analysis of hyphae and germinating cysts of Phytophthora pisi and Phytophthora sojae.", "authors": [{"family": "Hosseini", "given": "S", "initials": "S"}, {"family": "Resj\u00f6", "given": "S", "initials": "S"}, {"family": "Liu", "given": "Yongfeng", "initials": "Y"}, {"family": "Durling", "given": "M", "initials": "M"}, {"family": "Heyman", "given": "F", "initials": "F"}, {"family": "Levander", "given": "F", "initials": "F"}, {"family": "Liu", "given": "Yanhong", "initials": "Y"}, {"family": "Elfstrand", "given": "M", "initials": "M"}, {"family": "Funck Jensen", "given": "D", "initials": "D"}, {"family": "Andreasson", "given": "E", "initials": "E"}, {"family": "Karlsson", "given": "M", "initials": "M"}], "type": "comparative study", "published": "2015-03-18", "journal": {"volume": "117", "issn": "1876-7737", "issue": null, "pages": "24-40", "title": "J Proteomics", "issn-l": "1874-3919"}, "abstract": "The recently described oomycete pathogen Phytophthora pisi causes root rot on pea and faba bean, while the closely related Phytophthora sojae is the causal agent of soybean root and stem rot. Differences in the pathogenicity factor repertoires that enable the two species to have distinct host specificity towards pea and soybean, were studied using tandem mass spectrometry in a global proteome study of hyphae and germinating cysts in P. pisi and P. sojae. In total 2775 proteins from P. pisi and 2891 proteins from P. sojae were identified. Fifty-eight orthologous proteins were more abundant in germinated cysts of both pathogens and thus identified as candidate proteins for the infective stage. Several of these proteins were associated with lipid transport and metabolism, and energy production. Twenty-three orthologous proteins were more abundant in hyphae of both pathogens and thus identified as candidate proteins for vegetative growth. Proteins uniquely present in germinating cysts of either P. pisi or P. sojae were considered as candidates for species-specific pathogenicity factors that may be involved in host specificity. Among these proteins were serine proteases, membrane transporters and a berberine-like protein. These results significantly expand the knowledge of the expressed proteome in P. pisi and P. sojae.\n\nP. sojae and P. pisi are closely related species that specifically cause root rot on soybean and pea, respectively. The pathogenicity factors contributing to their host specificity remained unknown. We carried out a comparative large-scale proteome analysis of vegetative (hyphae) and infective (germinating cysts) life stages in P. pisi and P. sojae. This study provides knowledge of the common factors and mechanism involved in initiation of infection and species-specific proteins that may contribute to the host specificity of these pathogens. This knowledge will lead to a better understanding of the infection biology of these pathogens, allowing new possibilities towards developing alternative and effective plant protection measures.", "doi": "10.1016/j.jprot.2015.01.006", "pmid": "25613045", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "S1874-3919(15)00014-7"}], "notes": [], "created": "2017-05-02T12:57:18.438Z", "modified": "2020-01-21T13:53:20.814Z"}, {"entity": "publication", "iuid": "fc128150f0c649cfb1173c27c2b6bb58", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fc128150f0c649cfb1173c27c2b6bb58.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fc128150f0c649cfb1173c27c2b6bb58"}}, "title": "Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis.", "authors": [{"family": "Vigil-Stenman", "given": "Theoden", "initials": "T"}, {"family": "Larsson", "given": "John", "initials": "J"}, {"family": "Nylander", "given": "Johan A A", "initials": "JA"}, {"family": "Bergman", "given": "Birgitta", "initials": "B"}], "type": "journal article", "published": "2015-03-17", "journal": {"volume": "16", "issn": "1471-2164", "issue": null, "pages": "193", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Insertion sequences (ISs) are approximately 1 kbp long \"jumping\" genes found in prokaryotes. ISs encode the protein Transposase, which facilitates the excision and reinsertion of ISs in genomes, making these sequences a type of class I (\"cut-and-paste\") Mobile Genetic Elements. ISs are proposed to be involved in the reductive evolution of symbiotic prokaryotes. Our previous sequencing of the genome of the cyanobacterium 'Nostoc azollae' 0708, living in a tight perpetual symbiotic association with a plant (the water fern Azolla), revealed the presence of an eroding genome, with a high number of insertion sequences (ISs) together with an unprecedented large proportion of pseudogenes. To investigate the role of ISs in the reductive evolution of 'Nostoc azollae' 0708, and potentially in the formation of pseudogenes, a bioinformatic investigation of the IS identities and positions in 47 cyanobacterial genomes was conducted. To widen the scope, the IS contents were analysed qualitatively and quantitatively in 20 other genomes representing both free-living and symbiotic bacteria.\n\nInsertion Sequences were not randomly distributed in the bacterial genomes and were found to transpose short distances from their original location (\"local hopping\") and pseudogenes were enriched in the vicinity of IS elements. In general, symbiotic organisms showed higher densities of IS elements and pseudogenes than non-symbiotic bacteria. A total of 1108 distinct repeated sequences over 500\u00a0bp were identified in the 67 genomes investigated. In the genome of 'Nostoc azollae' 0708, IS elements were apparent at 970 locations (14.3%), with 428 being full-length. Morphologically complex cyanobacteria with large genomes showed higher frequencies of IS elements, irrespective of life style.\n\nThe apparent co-location of IS elements and pseudogenes found in prokaryotic genomes implies earlier IS transpositions into genes. As transpositions tend to be local rather than genome wide this likely explains the proximity between IS elements and pseudogenes. These findings suggest that ISs facilitate the reductive evolution in for instance in the symbiotic cyanobacterium 'Nostoc azollae' 0708 and in other obligate prokaryotic symbionts.", "doi": "10.1186/s12864-015-1386-7", "pmid": "25885210", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-015-1386-7"}, {"db": "pmc", "key": "PMC4369082"}], "notes": [], "created": "2017-05-02T12:58:51.466Z", "modified": "2020-01-21T13:53:20.988Z"}, {"entity": "publication", "iuid": "de4b6eb652804a01a00ed66e7f961b23", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de4b6eb652804a01a00ed66e7f961b23.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de4b6eb652804a01a00ed66e7f961b23"}}, "title": "FGF2 as a potential prognostic biomarker for proneural glioma patients.", "authors": [{"family": "Sooman", "given": "Linda", "initials": "L"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Jaiswal", "given": "Archita", "initials": "A"}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Tchougounova", "given": "Elena", "initials": "E"}, {"family": "Smits", "given": "Anja", "initials": "A"}, {"family": "Elsir", "given": "Tamador", "initials": "T"}, {"family": "Gullbo", "given": "Joachim", "initials": "J"}, {"family": "Lennartsson", "given": "Johan", "initials": "J"}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Ekman", "given": "Simon", "initials": "S"}], "type": "journal article", "published": "2015-03-00", "journal": {"volume": "54", "issn": "1651-226X", "issue": "3", "pages": "385-394", "title": "Acta Oncol", "issn-l": "0284-186X"}, "abstract": "The survival of high-grade glioma patients is poor and the treatment of these patients can cause severe side effects. This fosters the necessity to identify prognostic biomarkers, in order to optimize treatment and diminish unnecessary suffering of patients. The aim of this study was to identify prognostic biomarkers for high-grade glioma patients.\n\nEleven proteins were selected for analysis due to their suggested importance for survival of patients with other types of cancers and due to a high variation in protein levels between glioma patients (according to the Human Protein Atlas, www.proteinatlas.org). Protein expression patterns of these 11 proteins were analyzed by immunohistochemistry in tumor samples from 97 high-grade glioma patients. The prognostic values of the proteins were analyzed with univariate and multivariate Cox regression analyses for the high-grade glioma patients, including subgroup analyses of histological subtypes and immunohistochemically defined molecular subtypes.\n\nThe proteins with the most significant (univariate and multivariate p<0.05) correlations were analyzed further with cross-validated Kaplan-Meier analyses for the possibility of predicting survival based on the protein expression pattern of the corresponding candidate. Random Forest classification with variable subset selection was used to analyze if a protein signature consisting of any combination of the 11 proteins could predict survival for the high-grade glioma patients and the subgroup with glioblastoma patients. The proteins which correlated most significantly (univariate and multivariate p<0.05) to survival in the Cox regression analyses were Myc for all high-grade gliomas and FGF2, CA9 and CD44 for the subgroup of proneural gliomas, with FGF2 having a strong negative predictive value for survival. No prognostic signature of the proteins could be found.\n\nFGF2 is a potential prognostic biomarker for proneural glioma patients, and warrants further investigation.", "doi": "10.3109/0284186X.2014.951492", "pmid": "25263081", "labels": {"Tissue Profiling": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:58:37.514Z", "modified": "2020-01-21T13:53:20.922Z"}, {"entity": "publication", "iuid": "fb9e062df2d940768c112d913d87c1a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb9e062df2d940768c112d913d87c1a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb9e062df2d940768c112d913d87c1a0"}}, "title": "MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics.", "authors": [{"family": "Kushwaha", "given": "Sandeep K", "initials": "SK"}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L"}, {"family": "Meerupati", "given": "Tejashwari", "initials": "T"}, {"family": "Hedlund", "given": "Katarina", "initials": "K"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}], "type": "journal article", "published": "2015-02-28", "journal": {"volume": "16", "issn": "1471-2105", "issue": null, "pages": "65", "title": "BMC Bioinformatics", "issn-l": "1471-2105"}, "abstract": "Massive sequencing of genes from different environments has evolved metagenomics as central to enhancing the understanding of the wide diversity of micro-organisms and their roles in driving ecological processes. Reduced cost and high throughput sequencing has made large-scale projects achievable to a wider group of researchers, though complete metagenome sequencing is still a daunting task in terms of sequencing as well as the downstream bioinformatics analyses. Alternative approaches such as targeted amplicon sequencing requires custom PCR primer generation, and is not scalable to thousands of genes or gene families.\n\nIn this study, we are presenting a web-based tool called MetCap that circumvents the limitations of amplicon sequencing of multiple genes by designing probes that are suitable for large-scale targeted metagenomics sequencing studies. MetCap provides a novel approach to target thousands of genes and genomic regions that could be used in targeted metagenomics studies. Automatic analysis of user-defined sequences is performed, and probes specifically designed for metagenome studies are generated. To illustrate the advantage of a targeted metagenome approach, we have generated more than 400,000 probes that match more than 300,000 [corrected] publicly available sequences related to carbon degradation, and used these probes for target sequencing in a soil metagenome study. The results show high enrichment of target genes and a successful capturing of the majority of gene families. MetCap is freely available to users from: http://soilecology.biol.lu.se/metcap/ .\n\nMetCap is facilitating probe-based target enrichment as an easy and efficient alternative tool compared to complex primer-based enrichment for large-scale investigations of metagenomes. Our results have shown efficient large-scale target enrichment through MetCap-designed probes for a soil metagenome. The web service is suitable for any targeted metagenomics project that aims to study several genes simultaneously. The novel bioinformatics approach taken by the web service will enable researchers in microbial ecology to tap into the vast diversity of microbial communities using targeted metagenomics as a cost-effective alternative to whole metagenome sequencing.", "doi": "10.1186/s12859-015-0501-8", "pmid": "25880302", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "10.1186/s12859-015-0501-8"}, {"db": "pmc", "key": "PMC4355349"}], "notes": [], "created": "2017-05-02T12:57:40.699Z", "modified": "2020-01-21T13:53:20.982Z"}, {"entity": "publication", "iuid": "192848cea52249de9869fe68a50dcf31", "links": {"self": {"href": "https://publications.scilifelab.se/publication/192848cea52249de9869fe68a50dcf31.json"}, "display": {"href": "https://publications.scilifelab.se/publication/192848cea52249de9869fe68a50dcf31"}}, "title": "Data processing has major impact on the outcome of quantitative label-free LC-MS analysis.", "authors": [{"family": "Chawade", "given": "Aakash", "initials": "A"}, {"family": "Sandin", "given": "Marianne", "initials": "M"}, {"family": "Teleman", "given": "Johan", "initials": "J"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2015-02-06", "journal": {"volume": "14", "issn": "1535-3907", "issue": "2", "pages": "676-687", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "High-throughput multiplexed protein quantification using mass spectrometry is steadily increasing in popularity, with the two major techniques being data-dependent acquisition (DDA) and targeted acquisition using selected reaction monitoring (SRM). However, both techniques involve extensive data processing, which can be performed by a multitude of different software solutions. Analysis of quantitative LC-MS/MS data is mainly performed in three major steps: processing of raw data, normalization, and statistical analysis. To evaluate the impact of data processing steps, we developed two new benchmark data sets, one each for DDA and SRM, with samples consisting of a long-range dilution series of synthetic peptides spiked in a total cell protein digest. The generated data were processed by eight different software workflows and three postprocessing steps. The results show that the choice of the raw data processing software and the postprocessing steps play an important role in the final outcome. Also, the linear dynamic range of the DDA data could be extended by an order of magnitude through feature alignment and a charge state merging algorithm proposed here. Furthermore, the benchmark data sets are made publicly available for further benchmarking and software developments.", "doi": "10.1021/pr500665j", "pmid": "25407311", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [], "notes": [], "created": "2017-05-02T12:56:44.389Z", "modified": "2020-01-21T13:53:20.346Z"}, {"entity": "publication", "iuid": "c2a7d6add2784a56baf3f80c90b065eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2a7d6add2784a56baf3f80c90b065eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2a7d6add2784a56baf3f80c90b065eb"}}, "title": "Multi-omic data analysis using Galaxy.", "authors": [{"family": "Boekel", "given": "Jorrit", "initials": "J"}, {"family": "Chilton", "given": "John M", "initials": "JM"}, {"family": "Cooke", "given": "Ira R", "initials": "IR"}, {"family": "Horvatovich", "given": "Peter L", "initials": "PL"}, {"family": "Jagtap", "given": "Pratik D", "initials": "PD"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Lukasse", "given": "Pieter", "initials": "P"}, {"family": "Moerland", "given": "Perry D", "initials": "PD"}, {"family": "Griffin", "given": "Timothy J", "initials": "TJ"}], "type": "journal article", "published": "2015-02-00", "journal": {"volume": "33", "issn": "1546-1696", "issue": "2", "pages": "137-139", "title": "Nat. Biotechnol.", "issn-l": "1087-0156"}, "abstract": null, "doi": "10.1038/nbt.3134", "pmid": "25658277", "labels": {"Clinical Proteomics Mass spectrometry": null, "Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "nbt.3134"}], "notes": [], "created": "2017-05-02T12:56:37.598Z", "modified": "2021-07-08T11:36:15.267Z"}, {"entity": "publication", "iuid": "5682a631ed244850a303f6e70f78fafb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5682a631ed244850a303f6e70f78fafb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5682a631ed244850a303f6e70f78fafb"}}, "title": "Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date.", "authors": [{"family": "Leong", "given": "Su-Lin L", "initials": "SL"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Pettersson", "given": "Olga V", "initials": "OV"}, {"family": "Frisvad", "given": "Jens C", "initials": "JC"}, {"family": "Thrane", "given": "Ulf", "initials": "U"}, {"family": "Heipieper", "given": "Hermann J", "initials": "HJ"}, {"family": "Dijksterhuis", "given": "Jan", "initials": "J"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Pettersson", "given": "Mats", "initials": "M"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Schn\u00fcrer", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2015-02-00", "journal": {"volume": "17", "issn": "1462-2920", "issue": "2", "pages": "496-513", "title": "Environ. Microbiol.", "issn-l": "1462-2912"}, "abstract": "Xeromyces bisporus can grow on sugary substrates down to 0.61, an extremely low water activity. Its genome size is approximately 22\u2009Mb. Gene clusters encoding for secondary metabolites were conspicuously absent; secondary metabolites were not detected experimentally. Thus, in its 'dry' but nutrient-rich environment, X.\u2009bisporus appears to have relinquished abilities for combative interactions. Elements to sense/signal osmotic stress, e.g. HogA pathway, were present in X.\u2009bisporus. However, transcriptomes at optimal (\u223c\u20090.89) versus low aw (0.68) revealed differential expression of only a few stress-related genes; among these, certain (not all) steps for glycerol synthesis were upregulated. Xeromyces bisporus increased glycerol production during hypo- and hyper-osmotic stress, and much of its wet weight comprised water and rinsable solutes; leaked solutes may form a protective slime. Xeromyces bisporus and other food-borne moulds increased membrane fatty acid saturation as water activity decreased. Such modifications did not appear to be transcriptionally regulated in X.\u2009bisporus; however, genes modulating sterols, phospholipids and the cell wall were differentially expressed. Xeromyces bisporus was previously proposed to be a 'chaophile', preferring solutes that disorder biomolecular structures. Both X.\u2009bisporus and the closely related xerophile, Xerochrysium xerophilum, with low membrane unsaturation indices, could represent a phylogenetic cluster of 'chaophiles'.", "doi": "10.1111/1462-2920.12596", "pmid": "25142400", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": null, "Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null, "National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:57:46.930Z", "modified": "2020-01-21T13:56:16.749Z"}, {"entity": "publication", "iuid": "422ac06b69a9438ab2116ba55bd587c7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/422ac06b69a9438ab2116ba55bd587c7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/422ac06b69a9438ab2116ba55bd587c7"}}, "title": "The statistical geometry of transcriptome divergence in cell-type evolution and cancer.", "authors": [{"family": "Liang", "given": "Cong", "initials": "C"}, {"family": "FANTOM Consortium", "given": null, "initials": null}, {"family": "Forrest", "given": "Alistair R R", "initials": "AR"}, {"family": "Wagner", "given": "G\u00fcnter P", "initials": "GP"}], "type": "journal article", "published": "2015-01-14", "journal": {"volume": "6", "issn": "2041-1723", "issue": null, "pages": "6066", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "In evolution, body plan complexity increases due to an increase in the number of individualized cell types. Yet, there is very little understanding of the mechanisms that produce this form of organismal complexity. One model for the origin of novel cell types is the sister cell-type model. According to this model, each cell type arises together with a sister cell type through specialization from an ancestral cell type. A key prediction of the sister cell-type model is that gene expression profiles of cell types exhibit tree structure. Here we present a statistical model for detecting tree structure in transcriptomic data and apply it to transcriptomes from ENCODE and FANTOM5. We show that transcriptomes of normal cells harbour substantial amounts of hierarchical structure. In contrast, cancer cell lines have less tree structure, suggesting that the emergence of cancer cells follows different principles from that of evolutionary cell-type origination.", "doi": "10.1038/ncomms7066", "pmid": "25585899", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "ncomms7066"}], "notes": [], "created": "2017-05-02T12:57:47.832Z", "modified": "2020-01-21T13:53:20.481Z"}, {"entity": "publication", "iuid": "b2c465bc09a64bf0be44207444dc79b4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b2c465bc09a64bf0be44207444dc79b4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b2c465bc09a64bf0be44207444dc79b4"}}, "title": "A Machine Learning Approach to Explain Drug Selectivity to Soluble and Membrane Protein Targets.", "authors": [{"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Gustafsson", "given": "Mats G", "initials": "MG"}, {"family": "Str\u00f6mbergsson", "given": "Helena", "initials": "H"}], "type": "journal article", "published": "2015-01-00", "journal": {"volume": "34", "issn": "1868-1751", "issue": "1", "pages": "44-52", "title": "Mol Inform", "issn-l": "1868-1743"}, "abstract": "Improved understanding of the forces that determine drug specificity to their targets is important for drug design and discovery, as well as for gaining knowledge about molecular recognition. Here, we present a machine learning approach that includes all approved drugs with a known protein target. The drugs were characterized using easily interpretable physico-chemical descriptors. Employing the Random Forest method, we were able to predict whether a drug binds to a soluble or membrane protein with an average accuracy of 84\u2009% and an average area under curve of 0.91. The high average performance suggests that there exist some general physico-chemical differences between drugs that bind to membrane and soluble protein targets. Variable importance measures in combination with permutation tests were used to find the most influential descriptors. This resulted in six outstanding descriptors, that all involve drug flexibility and lipophilicity, suggesting that drugs binding to membrane protein targets are in general more flexible and lipophilic, and conversely, drugs binding to soluble protein targets are more rigid and hydrophilic. With the notion that ligands in general are blueprints of their protein pockets, we may also draw general conclusions about the protein-pocket properties which may add to the understanding of molecular recognition.", "doi": "10.1002/minf.201400121", "pmid": "27490861", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:57:02.813Z", "modified": "2020-01-21T13:53:20.776Z"}, {"entity": "publication", "iuid": "9f6f40b4f94f4367ab6a011bb905a4eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f6f40b4f94f4367ab6a011bb905a4eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f6f40b4f94f4367ab6a011bb905a4eb"}}, "title": "Inhibition of tumor cell proliferation and motility by fibroblasts is both contact and soluble factor dependent.", "authors": [{"family": "Alkasalias", "given": "Twana", "initials": "T"}, {"family": "Flaberg", "given": "Emilie", "initials": "E"}, {"family": "Kashuba", "given": "Vladimir", "initials": "V"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Pavlova", "given": "Tatiana", "initials": "T"}, {"family": "Savchenko", "given": "Andrii", "initials": "A"}, {"family": "Szekely", "given": "Laszlo", "initials": "L"}, {"family": "Klein", "given": "George", "initials": "G"}, {"family": "Guven", "given": "Hayrettin", "initials": "H"}], "type": "journal article", "published": "2014-12-02", "journal": {"volume": "111", "issn": "1091-6490", "issue": "48", "pages": "17188-17193", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Normal human and murine fibroblasts can inhibit proliferation of tumor cells when cocultured in vitro. The inhibitory capacity varies depending on the donor and the site of origin of the fibroblast. We showed previously that effective inhibition requires formation of a morphologically intact fibroblast monolayer before seeding of the tumor cells. Here we show that inhibition is extended to motility of tumor cells and we dissect the factors responsible for these inhibitory functions. We find that inhibition is due to two different sets of molecules: (i) the extracellular matrix (ECM) and other surface proteins of the fibroblasts, which are responsible for contact-dependent inhibition of tumor cell proliferation; and (ii) soluble factors secreted by fibroblasts when confronted with tumor cells (confronted conditioned media, CCM) contribute to inhibition of tumor cell proliferation and motility. However, conditioned media (CM) obtained from fibroblasts alone (nonconfronted conditioned media, NCM) did not inhibit tumor cell proliferation and motility. In addition, quantitative PCR (Q-PCR) data show up-regulation of proinflammatory genes. Moreover, comparison of CCM and NCM with an antibody array for 507 different soluble human proteins revealed differential expression of growth differentiation factor 15, dickkopf-related protein 1, endothelial-monocyte-activating polypeptide II, ectodysplasin A2, Galectin-3, chemokine (C-X-C motif) ligand 2, Nidogen1, urokinase, and matrix metalloproteinase 3.", "doi": "10.1073/pnas.1419554111", "pmid": "25404301", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "1419554111"}, {"db": "pmc", "key": "PMC4260581"}, {"db": "GEO", "key": "GSE56832"}], "notes": [], "created": "2017-05-04T14:56:34.078Z", "modified": "2020-01-21T13:53:20.711Z"}, {"entity": "publication", "iuid": "53b5880c43c0494ba6f1db70c623fd0a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/53b5880c43c0494ba6f1db70c623fd0a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/53b5880c43c0494ba6f1db70c623fd0a"}}, "title": "High opsin diversity in a non-visual infaunal brittle star.", "authors": [{"family": "Delroisse", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Ullrich-L\u00fcter", "given": "Esther", "initials": "E"}, {"family": "Ortega-Martinez", "given": "Olga", "initials": "O"}, {"family": "Dupont", "given": "Sam", "initials": "S"}, {"family": "Arnone", "given": "Maria-Ina", "initials": "MI"}, {"family": "Mallefet", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Flammang", "given": "Patrick", "initials": "P"}], "type": "journal article", "published": "2014-11-28", "journal": {"volume": "15", "issn": "1471-2164", "issue": null, "pages": "1035", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "In metazoans, opsins are photosensitive proteins involved in both vision and non-visual photoreception. Echinoderms have no well-defined eyes but several opsin genes were found in the purple sea urchin (Strongylocentrotus purpuratus) genome. Molecular data are lacking for other echinoderm classes although many species are known to be light sensitive.\n\nIn this study focused on the European brittle star Amphiura filiformis, we first highlighted a blue-green light sensitivity using a behavioural approach. We then identified 13 new putative opsin genes against eight bona fide opsin genes in the genome of S. purpuratus. Six opsins were included in the rhabdomeric opsin group (r-opsins). In addition, one putative ciliary opsin (c-opsin), showing high similarity with the c-opsin of S. purpuratus (Sp-opsin 1), one Go opsin similar to Sp-opsins 3.1 and 3.2, two basal-branch opsins similar to Sp-opsins 2 and 5, and two neuropsins similar to Sp-opsin 8, were identified. Finally, two sequences from one putative RGR opsin similar to Sp-opsin 7 were also detected. Adult arm transcriptome analysis pinpointed opsin mRNAs corresponding to one r-opsin, one neuropsin and the homologue of Sp-opsin 2. Opsin phylogeny was determined by maximum likelihood and Bayesian analyses. Using antibodies designed against c- and r-opsins from S. purpuratus, we detected putative photoreceptor cells mainly in spines and tube feet of A. filiformis, respectively. The r-opsin expression pattern is similar to the one reported in S. purpuratus with cells labelled at the tip and at the base of the tube feet. In addition, r-opsin positive cells were also identified in the radial nerve of the arm. C-opsins positive cells, expressed in pedicellariae, spines, tube feet and epidermis in S. purpuratus were observed at the level of the spine stroma in the brittle star.\n\nLight perception in A. filiformis seems to be mediated by opsins (c- and r-) in, at least, spines, tube feet and in the radial nerve cord. Other non-visual opsin types could participate to the light perception process indicating a complex expression pattern of opsins in this infaunal brittle star.", "doi": "10.1186/1471-2164-15-1035", "pmid": "25429842", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "1471-2164-15-1035"}, {"db": "pmc", "key": "PMC4289182"}], "notes": [], "created": "2017-11-01T12:55:01.631Z", "modified": "2020-01-21T13:53:21.662Z"}, {"entity": "publication", "iuid": "3376814cf7dd4225a0d37524a179501e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3376814cf7dd4225a0d37524a179501e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3376814cf7dd4225a0d37524a179501e"}}, "title": "Leachability and desorption of PCBs from soil and their dependency on pH and dissolved organic matter.", "authors": [{"family": "Badea", "given": "Silviu-Laurentiu", "initials": "SL"}, {"family": "Mustafa", "given": "Majid", "initials": "M"}, {"family": "Lundstedt", "given": "Staffan", "initials": "S"}, {"family": "Tysklind", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2014-11-15", "journal": {"volume": "499", "issn": "1879-1026", "issue": null, "pages": "220-227", "title": "Sci. Total Environ.", "issn-l": "0048-9697"}, "abstract": "pH affects both soil-water partitioning coefficient (Kd) of polychlorinated biphenyls (PCBs) and dissolved organic matter (DOM), thereby influencing PCBs' leachability from contaminated soils. To explore these incompletely understood interactions, the leachability of 11 selected PCBs in a naturally aged soil was investigated in pH static leaching tests spanning a wide pH range (2 to 9). The K(d) was calculated for each of the PCBs, based on their observed concentrations in the soil and leachates obtained from each test. The concentration and composition of DOM in each leachate were also determined, the latter using FTIR spectroscopy. Correlations between the DOM's FTIR spectra and K(d) values were investigated by orthogonal projections to latent structures. The log K(d)-values varied among the PCB congeners and were most variable at low pH, but the values for all studied congeners decreased with increasing pH, by up to 3 log units (for PCB 187). In the pH 5-7 interval, an abrupt decrease in log K(d) values with increases in pH was observed, although the total organic carbon content remained relatively stable. The FTIR data indicate that fulvic and humic acids in DOM partially deprotonate as the pH rises from 5 to 7.", "doi": "10.1016/j.scitotenv.2014.08.031", "pmid": "25192928", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "S0048-9697(14)01198-X"}], "notes": [], "created": "2017-05-04T14:56:35.297Z", "modified": "2020-01-21T13:53:20.435Z"}, {"entity": "publication", "iuid": "a2d87d94b9184e6288bb985c1b453bf1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2d87d94b9184e6288bb985c1b453bf1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2d87d94b9184e6288bb985c1b453bf1"}}, "title": "Multimodal fluorescence microscopy of prion strain specific PrP deposits stained by thiophene-based amyloid ligands.", "authors": [{"family": "Magnusson", "given": "Karin", "initials": "K"}, {"family": "Simon", "given": "Rozalyn", "initials": "R"}, {"family": "Sj\u00f6lander", "given": "Daniel", "initials": "D"}, {"family": "Sigurdson", "given": "Christina J", "initials": "CJ"}, {"family": "Hammarstr\u00f6m", "given": "Per", "initials": "P"}, {"family": "Nilsson", "given": "K Peter R", "initials": "KP"}], "type": "journal article", "published": "2014-11-01", "journal": {"volume": "8", "issn": "1933-690X", "issue": "4", "pages": "319-329", "title": "Prion", "issn-l": "1933-6896"}, "abstract": "The disease-associated prion protein (PrP) forms aggregates which vary in structural conformation yet share an identical primary sequence. These variations in PrP conformation are believed to manifest in prion strains exhibiting distinctly different periods of disease incubation as well as regionally specific aggregate deposition within the brain. The anionic luminescent conjugated polythiophene (LCP), polythiophene acetic acid (PTAA) has previously been used to distinguish PrP deposits associated with distinct mouse adapted strains via distinct fluorescence emission profiles from the dye. Here, we employed PTAA and 3 structurally related chemically defined luminescent conjugated oligothiophenes (LCOs) to stain brain tissue sections from mice inoculated with 2 distinct prion strains. Our results showed that in addition to emission spectra, excitation, and fluorescence lifetime imaging microscopy (FLIM) can fruitfully be assessed for optical distinction of PrP deposits associated with distinct prion strains. Our findings support the theory that alterations in LCP/LCO fluorescence are due to distinct conformational restriction of the thiophene backbone upon interaction with PrP aggregates associated with distinct prion strains. We foresee that LCP and LCO staining in combination with multimodal fluorescence microscopy might aid in detecting structural differences among discrete protein aggregates and in linking protein conformational features with disease phenotypes for a variety of neurodegenerative proteinopathies.", "doi": "10.4161/pri.29239", "pmid": "25495506", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pmc", "key": "PMC4601348"}], "notes": [], "created": "2017-05-04T14:56:34.999Z", "modified": "2020-01-21T13:53:20.731Z"}, {"entity": "publication", "iuid": "2d9a5bba203442a68bdf3dbbf96f4fe7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2d9a5bba203442a68bdf3dbbf96f4fe7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2d9a5bba203442a68bdf3dbbf96f4fe7"}}, "title": "Binning metagenomic contigs by coverage and composition.", "authors": [{"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Bjarnason", "given": "Brynjar Sm\u00e1ri", "initials": "BS"}, {"family": "de Bruijn", "given": "Ino", "initials": "I"}, {"family": "Schirmer", "given": "Melanie", "initials": "M"}, {"family": "Quick", "given": "Joshua", "initials": "J"}, {"family": "Ijaz", "given": "Umer Z", "initials": "UZ"}, {"family": "Lahti", "given": "Leo", "initials": "L"}, {"family": "Loman", "given": "Nicholas J", "initials": "NJ"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Quince", "given": "Christopher", "initials": "C"}], "type": "journal article", "published": "2014-11-00", "journal": {"volume": "11", "issn": "1548-7105", "issue": "11", "pages": "1144-1146", "title": "Nat. Methods", "issn-l": "1548-7091"}, "abstract": "Shotgun sequencing enables the reconstruction of genomes from complex microbial communities, but because assembly does not reconstruct entire genomes, it is necessary to bin genome fragments. Here we present CONCOCT, a new algorithm that combines sequence composition and coverage across multiple samples, to automatically cluster contigs into genomes. We demonstrate high recall and precision on artificial as well as real human gut metagenome data sets.", "doi": "10.1038/nmeth.3103", "pmid": "25218180", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "nmeth.3103"}], "notes": [], "created": "2017-05-04T14:56:33.177Z", "modified": "2020-01-21T13:53:20.403Z"}, {"entity": "publication", "iuid": "19ea34d312ad497faaf55ebe93f27a63", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19ea34d312ad497faaf55ebe93f27a63.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19ea34d312ad497faaf55ebe93f27a63"}}, "title": "Melanoma patient-derived xenografts accurately model the disease and develop fast enough to guide treatment decisions.", "authors": [{"family": "Einarsdottir", "given": "Berglind O", "initials": "BO"}, {"family": "Bagge", "given": "Roger Olofsson", "initials": "RO"}, {"family": "Bhadury", "given": "Joydeep", "initials": "J"}, {"family": "Jespersen", "given": "Henrik", "initials": "H"}, {"family": "Mattsson", "given": "Jan", "initials": "J"}, {"family": "Nilsson", "given": "Lisa M", "initials": "LM"}, {"family": "Truv\u00e9", "given": "Katarina", "initials": "K"}, {"family": "L\u00f3pez", "given": "Marcela D\u00e1vila", "initials": "MD"}, {"family": "Naredi", "given": "Peter", "initials": "P"}, {"family": "Nilsson", "given": "Ola", "initials": "O"}, {"family": "Stierner", "given": "Ulrika", "initials": "U"}, {"family": "Ny", "given": "Lars", "initials": "L"}, {"family": "Nilsson", "given": "Jonas A", "initials": "JA"}], "type": "case reports", "published": "2014-10-30", "journal": {"volume": "5", "issn": "1949-2553", "issue": "20", "pages": "9609-9618", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "The development of novel therapies against melanoma would benefit from individualized tumor models to ensure the rapid and accurate identification of biomarkers of therapy response. Previous studies have suggested that patient-derived xenografts (PDXes) could be useful. However, the utility of PDXes in guiding real-time treatment decisions has only been reported in anecdotal forms. Here tumor biopsies from patients with stage III and IV metastatic malignant melanoma were transplanted into immunocompromised mice to generate PDXes. 23/26 melanoma biopsies generated serially transplantable PDX models, and their histology, mutation status and expression profile resembled their corresponding patient biopsy. The potential treatment for one patient was revealed by an in vitro drug screen and treating PDXes with the MEK inhibitor trametinib. In another patient, the BRAF mutation predicted the response of both the patient and its corresponding PDXes to MAPK-targeted therapy. Importantly, in this unselected group of patients, the time from biopsy for generation of PDXes until death was significantly longer than the time required to reach the treatment phase of the PDXes. Thus, it could be clinically meaningful to use this type of platform for melanoma patients as a pre-selection tool in clinical trials.", "doi": "10.18632/oncotarget.2445", "pmid": "25228592", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "2445"}, {"db": "pmc", "key": "PMC4259423"}], "notes": [], "created": "2017-05-04T14:56:33.778Z", "modified": "2020-01-21T13:53:20.354Z"}, {"entity": "publication", "iuid": "0a5dbff5e2254b4da19a43ae855f86ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a5dbff5e2254b4da19a43ae855f86ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a5dbff5e2254b4da19a43ae855f86ce"}}, "title": "Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis.", "authors": [{"family": "Merid", "given": "Simon Kebede", "initials": "SK"}, {"family": "Goranskaya", "given": "Daria", "initials": "D"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}], "type": "journal article", "published": "2014-09-19", "journal": {"volume": "15", "issn": "1471-2105", "issue": null, "pages": "308", "title": "BMC Bioinformatics", "issn-l": "1471-2105"}, "abstract": "In somatic cancer genomes, delineating genuine driver mutations against a background of multiple passenger events is a challenging task. The difficulty of determining function from sequence data and the low frequency of mutations are increasingly hindering the search for novel, less common cancer drivers. The accumulation of extensive amounts of data on somatic point and copy number alterations necessitates the development of systematic methods for driver mutation analysis.\n\nWe introduce a framework for detecting driver mutations via functional network analysis, which is applied to individual genomes and does not require pooling multiple samples. It probabilistically evaluates 1) functional network links between different mutations in the same genome and 2) links between individual mutations and known cancer pathways. In addition, it can employ correlations of mutation patterns in pairs of genes. The method was used to analyze genomic alterations in two TCGA datasets, one for glioblastoma multiforme and another for ovarian carcinoma, which were generated using different approaches to mutation profiling. The proportions of drivers among the reported de novo point mutations in these cancers were estimated to be 57.8% and 16.8%, respectively. The both sets also included extended chromosomal regions with synchronous duplications or losses of multiple genes. We identified putative copy number driver events within many such segments. Finally, we summarized seemingly disparate mutations and discovered a functional network of collagen modifications in the glioblastoma. In order to select the most efficient network for use with this method, we used a novel, ROC curve-based procedure for benchmarking different network versions by their ability to recover pathway membership.\n\nThe results of our network-based procedure were in good agreement with published gold standard sets of cancer genes and were shown to complement and expand frequency-based driver analyses. On the other hand, three sequence-based methods applied to the same data yielded poor agreement with each other and with our results. We review the difference in driver proportions discovered by different sequencing approaches and discuss the functional roles of novel driver mutations. The software used in this work and the global network of functional couplings are publicly available at http://research.scilifelab.se/andrej_alexeyenko/downloads.html.", "doi": "10.1186/1471-2105-15-308", "pmid": "25236784", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "1471-2105-15-308"}, {"db": "pmc", "key": "PMC4262241"}], "notes": [], "created": "2017-05-04T14:56:28.896Z", "modified": "2020-01-21T13:53:20.274Z"}, {"entity": "publication", "iuid": "aab88baf82cb4f46a382a588d0809a37", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aab88baf82cb4f46a382a588d0809a37.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aab88baf82cb4f46a382a588d0809a37"}}, "title": "Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "Molin", "given": "Mikael", "initials": "M"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2014-09-01", "journal": {"volume": "15", "issn": "1471-2164", "issue": null, "pages": "749", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Environmental shotgun sequencing (metagenomics) provides a new way to study communities in microbial ecology. We here use sequence data from the Global Ocean Sampling (GOS) expedition to investigate toxicant selection pressures revealed by the presence of detoxification genes in marine bacteria. To capture a broad range of potential toxicants we selected detoxification protein families representing systems protecting microorganisms from a variety of stressors, such as metals, organic compounds, antibiotics and oxygen radicals.\n\nUsing a bioinformatics procedure based on comparative analysis to finished bacterial genomes we found that the amount of detoxification genes present in marine microorganisms seems surprisingly small. The underrepresentation is particularly evident for toxicant transporters and proteins involved in detoxifying metals. Exceptions are enzymes involved in oxidative stress defense where peroxidase enzymes are more abundant in marine bacteria compared to bacteria in general. In contrast, catalases are almost completely absent from the open ocean environment, suggesting that peroxidases and peroxiredoxins constitute a core line of defense against reactive oxygen species (ROS) in the marine milieu.\n\nWe found no indication that detoxification systems would be generally more abundant close to the coast compared to the open ocean. On the contrary, for several of the protein families that displayed a significant geographical distribution, like peroxidase, penicillin binding transpeptidase and divalent ion transport protein, the open ocean samples showed the highest abundance. Along the same lines, the abundance of most detoxification proteins did not increase with estimated pollution. The low level of detoxification systems in marine bacteria indicate that the majority of marine bacteria have a low capacity to adapt to increased pollution. Our study exemplifies the use of metagenomics data in ecotoxicology, and in particular how anthropogenic consequences on life in the sea can be examined.", "doi": "10.1186/1471-2164-15-749", "pmid": "25179155", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-15-749"}, {"db": "pmc", "key": "PMC4161860"}], "notes": [], "created": "2017-05-04T14:56:30.100Z", "modified": "2020-01-21T13:53:20.757Z"}, {"entity": "publication", "iuid": "9b3132abbae844bc95f381f228b343ed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b3132abbae844bc95f381f228b343ed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b3132abbae844bc95f381f228b343ed"}}, "title": "Do the same genes underlie parallel phenotypic divergence in different Littorina saxatilis populations?", "authors": [{"family": "Westram", "given": "A M", "initials": "AM"}, {"family": "Galindo", "given": "J", "initials": "J"}, {"family": "Alm Rosenblad", "given": "M", "initials": "M"}, {"family": "Grahame", "given": "J W", "initials": "JW"}, {"family": "Panova", "given": "M", "initials": "M"}, {"family": "Butlin", "given": "R K", "initials": "RK"}], "type": "journal article", "published": "2014-09-00", "journal": {"volume": "23", "issn": "1365-294X", "issue": "18", "pages": "4603-4616", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Parallel patterns of adaptive divergence and speciation are cited as powerful evidence for the role of selection driving these processes. However, it is often not clear whether parallel phenotypic divergence is underlain by parallel genetic changes. Here, we asked about the genetic basis of parallel divergence in the marine snail Littorina saxatilis, which has repeatedly evolved coexisting ecotypes adapted to either crab predation or wave action. We sequenced the transcriptome of snails of both ecotypes from three distant geographical locations (Spain, Sweden and United Kingdom) and mapped the reads to the L. saxatilis reference genome. We identified genomic regions potentially under divergent selection between ecotypes within each country, using an outlier approach based on F(ST) values calculated per locus. In line with previous studies indicating that gene reuse is generally common, we expected to find extensive sharing of outlier loci due to recent shared ancestry and gene flow between at least two of the locations in our study system. Contrary to our expectations, we found that most outliers were country specific, suggesting that much of the genetic basis of divergence is not shared among locations. However, we did find that more outliers were shared than expected by chance and that differentiation of shared outliers is often generated by the same SNPs. We discuss two mechanisms potentially explaining the limited amount of sharing we observed. First, a polygenic basis of divergent traits might allow for multiple distinct molecular mechanisms generating the same phenotypic patterns. Second, additional, location-specific axes of selection that we did not focus on in this study may produce distinct patterns of genetic divergence within each site.", "doi": "10.1111/mec.12883", "pmid": "25113130", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pmc", "key": "PMC4285301"}, {"db": "Dryad", "key": "21PF0"}], "notes": [], "created": "2017-05-04T14:56:32.875Z", "modified": "2020-01-21T13:56:16.771Z"}, {"entity": "publication", "iuid": "d58d90e1b5b54964b9aa5becd6d9e2d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d58d90e1b5b54964b9aa5becd6d9e2d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d58d90e1b5b54964b9aa5becd6d9e2d6"}}, "title": "Species and gene divergence in Littorina snails detected by array comparative genomic hybridization.", "authors": [{"family": "Panova", "given": "Marina", "initials": "M"}, {"family": "Johansson", "given": "Tomas", "initials": "T"}, {"family": "Canb\u00e4ck", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Bentzer", "given": "Johan", "initials": "J"}, {"family": "Rosenblad", "given": "Magnus Alm", "initials": "MA"}, {"family": "Johannesson", "given": "Kerstin", "initials": "K"}, {"family": "Tunlid", "given": "Anders", "initials": "A"}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C"}], "type": "journal article", "published": "2014-08-18", "journal": {"volume": "15", "issn": "1471-2164", "issue": null, "pages": "687", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Array comparative genomic hybridization (aCGH) is commonly used to screen different types of genetic variation in humans and model species. Here, we performed aCGH using an oligonucleotide gene-expression array for a non-model species, the intertidal snail Littorina saxatilis. First, we tested what types of genetic variation can be detected by this method using direct re-sequencing and comparison to the Littorina genome draft. Secondly, we performed a genome-wide comparison of four closely related Littorina species: L. fabalis, L. compressa, L. arcana and L. saxatilis and of populations of L. saxatilis found in Spain, Britain and Sweden. Finally, we tested whether we could identify genetic variation underlying \"Crab\" and \"Wave\" ecotypes of L. saxatilis.\n\nWe could reliably detect copy number variations, deletions and high sequence divergence (i.e. above 3%), but not single nucleotide polymorphisms. The overall hybridization pattern and number of significantly diverged genes were in close agreement with earlier phylogenetic reconstructions based on single genes. The trichotomy of L. arcana, L. compressa and L. saxatilis could not be resolved and we argue that these divergence events have occurred recently and very close in time. We found evidence for high levels of segmental duplication in the Littorina genome (10% of the transcripts represented on the array and up to 23% of the analyzed genomic fragments); duplicated genes and regions were mostly the same in all analyzed species. Finally, this method discriminated geographically distant populations of L. saxatilis, but we did not detect any significant genome divergence associated with ecotypes of L. saxatilis.\n\nThe present study provides new information on the sensitivity and the potential use of oligonucleotide arrays for genotyping of non-model organisms. Applying this method to Littorina species yields insights into genome evolution following the recent species radiation and supports earlier single-gene based phylogenies. Genetic differentiation of L. saxatilis ecotypes was not detected in this study, despite pronounced innate phenotypic differences. The reason may be that these differences are due to single-nucleotide polymorphisms.", "doi": "10.1186/1471-2164-15-687", "pmid": "25135785", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-15-687"}, {"db": "pmc", "key": "PMC4148934"}, {"db": "GEO", "key": "GSE59825"}], "notes": [], "created": "2017-05-04T14:56:30.407Z", "modified": "2020-01-21T13:56:16.790Z"}, {"entity": "publication", "iuid": "9759aa95cd6e4785b8089751ab8f89a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9759aa95cd6e4785b8089751ab8f89a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9759aa95cd6e4785b8089751ab8f89a3"}}, "title": "A universal genomic coordinate translator for comparative genomics.", "authors": [{"family": "Zamani", "given": "Neda", "initials": "N"}, {"family": "Sundstr\u00f6m", "given": "G\u00f6rel", "initials": "G"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JR"}, {"family": "H\u00f6ppner", "given": "Marc P", "initials": "MP"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Haas", "given": "Brian J", "initials": "BJ"}, {"family": "Grabherr", "given": "Manfred G", "initials": "MG"}], "type": "journal article", "published": "2014-06-30", "journal": {"volume": "15", "issn": "1471-2105", "issue": null, "pages": "227", "title": "BMC Bioinformatics", "issn-l": "1471-2105"}, "abstract": "Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N.\n\nHere, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of expression levels across species.\n\nKraken is a computational genome coordinate translator that facilitates cross-species comparisons, distinguishes orthologs from paralogs, and does not require costly all-to-all whole genome mappings. Kraken is freely available under LPGL from http://github.com/nedaz/kraken.", "doi": "10.1186/1471-2105-15-227", "pmid": "24976580", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "1471-2105-15-227"}, {"db": "pmc", "key": "PMC4086997"}], "notes": [], "created": "2017-05-04T14:56:29.197Z", "modified": "2020-01-21T13:53:20.678Z"}, {"entity": "publication", "iuid": "a3889680f65b459997a465f1fe5999e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3889680f65b459997a465f1fe5999e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3889680f65b459997a465f1fe5999e5"}}, "title": "Large tilts in transmembrane helices can be induced during tertiary structure formation.", "authors": [{"family": "Virkki", "given": "Minttu", "initials": "M"}, {"family": "Boekel", "given": "Carolina", "initials": "C"}, {"family": "Illerg\u00e5rd", "given": "Kristoffer", "initials": "K"}, {"family": "Peters", "given": "Christoph", "initials": "C"}, {"family": "Shu", "given": "Nanjiang", "initials": "N"}, {"family": "Tsirigos", "given": "Konstantinos D", "initials": "KD"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}, {"family": "von Heijne", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-4490-8569", "researcher": {"href": "https://publications.scilifelab.se/researcher/f663c0a9e9e1455cbbf8e6aea13af4a9.json"}}, {"family": "Nilsson", "given": "IngMarie", "initials": "I"}], "type": "journal article", "published": "2014-06-26", "journal": {"volume": "426", "issn": "1089-8638", "issue": "13", "pages": "2529-2538", "title": "J. Mol. Biol.", "issn-l": "0022-2836"}, "abstract": "While early structural models of helix-bundle integral membrane proteins posited that the transmembrane \u03b1-helices [transmembrane helices (TMHs)] were orientated more or less perpendicular to the membrane plane, there is now ample evidence from high-resolution structures that many TMHs have significant tilt angles relative to the membrane. Here, we address the question whether the tilt is an intrinsic property of the TMH in question or if it is imparted on the TMH during folding of the protein. Using a glycosylation mapping technique, we show that four highly tilted helices found in multi-spanning membrane proteins all have much shorter membrane-embedded segments when inserted by themselves into the membrane than seen in the high-resolution structures. This suggests that tilting can be induced by tertiary packing interactions within the protein, subsequent to the initial membrane-insertion step.", "doi": "10.1016/j.jmb.2014.04.020", "pmid": "24793448", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "S0022-2836(14)00204-6"}], "notes": [], "created": "2017-05-04T14:56:31.665Z", "modified": "2021-06-16T15:23:33.399Z"}, {"entity": "publication", "iuid": "5a66bf267f774256b9ca3a08b8a2d86a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a66bf267f774256b9ca3a08b8a2d86a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a66bf267f774256b9ca3a08b8a2d86a"}}, "title": "Normalyzer: a tool for rapid evaluation of normalization methods for omics data sets.", "authors": [{"family": "Chawade", "given": "Aakash", "initials": "A"}, {"family": "Alexandersson", "given": "Erik", "initials": "E"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2014-06-06", "journal": {"volume": "13", "issn": "1535-3907", "issue": "6", "pages": "3114-3120", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "High-throughput omics data often contain systematic biases introduced during various steps of sample processing and data generation. As the source of these biases is usually unknown, it is difficult to select an optimal normalization method for a given data set. To facilitate this process, we introduce the open-source tool \"Normalyzer\". It normalizes the data with 12 different normalization methods and generates a report with several quantitative and qualitative plots for comparative evaluation of different methods. The usefulness of Normalyzer is demonstrated with three different case studies from quantitative proteomics and transcriptomics. The results from these case studies show that the choice of normalization method strongly influences the outcome of downstream quantitative comparisons. Normalyzer is an R package and can be used locally or through the online implementation at http://quantitativeproteomics.org/normalyzer .", "doi": "10.1021/pr401264n", "pmid": "24766612", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pmc", "key": "PMC4053077"}], "notes": [], "created": "2017-05-04T14:56:31.965Z", "modified": "2020-01-21T13:53:20.523Z"}, {"entity": "publication", "iuid": "062de5b535954abc89347c8dfaaaf44b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/062de5b535954abc89347c8dfaaaf44b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/062de5b535954abc89347c8dfaaaf44b"}}, "title": "Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools.", "authors": [{"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Sherwood", "given": "Ellen", "initials": "E", "orcid": "0000-0003-3158-9957", "researcher": {"href": "https://publications.scilifelab.se/researcher/f17cb04d51c24494b9eab42010fd1a04.json"}}, {"family": "Ye", "given": "Rosa", "initials": "R"}, {"family": "Knudsen", "given": "Bjarne", "initials": "B"}, {"family": "Simonsen", "given": "Martin", "initials": "M"}, {"family": "Turner", "given": "Benjamin", "initials": "B"}, {"family": "de Jong", "given": "Pieter", "initials": "P"}, {"family": "Wu", "given": "Cheng-Cang", "initials": "CC"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2014-06-06", "journal": {"volume": "15", "issn": "1471-2164", "issue": null, "pages": "439", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Sampling genomes with Fosmid vectors and sequencing of pooled Fosmid libraries on the Illumina platform for massive parallel sequencing is a novel and promising approach to optimizing the trade-off between sequencing costs and assembly quality.\n\nIn order to sequence the genome of Norway spruce, which is of great size and complexity, we developed and applied a new technology based on the massive production, sequencing, and assembly of Fosmid pools (FP). The spruce chromosomes were sampled with ~40,000 bp Fosmid inserts to obtain around two-fold genome coverage, in parallel with traditional whole genome shotgun sequencing (WGS) of haploid and diploid genomes. Compared to the WGS results, the contiguity and quality of the FP assemblies were high, and they allowed us to fill WGS gaps resulting from repeats, low coverage, and allelic differences. The FP contig sets were further merged with WGS data using a novel software package GAM-NGS.\n\nBy exploiting FP technology, the first published assembly of a conifer genome was sequenced entirely with massively parallel sequencing. Here we provide a comprehensive report on the different features of the approach and the optimization of the process.We have made public the input data (FASTQ format) for the set of pools used in this study:ftp://congenie.org/congenie/Nystedt_2013/Assembly/ProcessedData/FosmidPools/.(alternatively accessible via http://congenie.org/downloads).The software used for running the assembly process is available at http://research.scilifelab.se/andrej_alexeyenko/downloads/fpools/.", "doi": "10.1186/1471-2164-15-439", "pmid": "24906298", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "1471-2164-15-439"}, {"db": "pmc", "key": "PMC4070561"}], "notes": [], "created": "2017-05-04T14:56:29.797Z", "modified": "2021-07-08T13:26:08.069Z"}, {"entity": "publication", "iuid": "2bcb991386854aaeba941d3457c9380a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2bcb991386854aaeba941d3457c9380a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2bcb991386854aaeba941d3457c9380a"}}, "title": "Numerical compression schemes for proteomics mass spectrometry data.", "authors": [{"family": "Teleman", "given": "Johan", "initials": "J"}, {"family": "Dowsey", "given": "Andrew W", "initials": "AW"}, {"family": "Gonzalez-Galarza", "given": "Faviel F", "initials": "FF"}, {"family": "Perkins", "given": "Simon", "initials": "S"}, {"family": "Pratt", "given": "Brian", "initials": "B"}, {"family": "R\u00f6st", "given": "Hannes L", "initials": "HL"}, {"family": "Malmstr\u00f6m", "given": "Lars", "initials": "L"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Jones", "given": "Andrew R", "initials": "AR"}, {"family": "Deutsch", "given": "Eric W", "initials": "EW"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2014-06-00", "journal": {"volume": "13", "issn": "1535-9484", "issue": "6", "pages": "1537-1542", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "The open XML format mzML, used for representation of MS data, is pivotal for the development of platform-independent MS analysis software. Although conversion from vendor formats to mzML must take place on a platform on which the vendor libraries are available (i.e. Windows), once mzML files have been generated, they can be used on any platform. However, the mzML format has turned out to be less efficient than vendor formats. In many cases, the na\u00efve mzML representation is fourfold or even up to 18-fold larger compared with the original vendor file. In disk I/O limited setups, a larger data file also leads to longer processing times, which is a problem given the data production rates of modern mass spectrometers. In an attempt to reduce this problem, we here present a family of numerical compression algorithms called MS-Numpress, intended for efficient compression of MS data. To facilitate ease of adoption, the algorithms target the binary data in the mzML standard, and support in main proteomics tools is already available. Using a test set of 10 representative MS data files we demonstrate typical file size decreases of 90% when combined with traditional compression, as well as read time decreases of up to 50%. It is envisaged that these improvements will be beneficial for data handling within the MS community.", "doi": "10.1074/mcp.O114.037879", "pmid": "24677029", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "O114.037879"}, {"db": "pmc", "key": "PMC4047472"}], "notes": [], "created": "2017-05-04T14:56:32.571Z", "modified": "2020-01-21T13:53:20.395Z"}, {"entity": "publication", "iuid": "f2b37f297e674bd59ee4fa8b88976193", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f2b37f297e674bd59ee4fa8b88976193.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f2b37f297e674bd59ee4fa8b88976193"}}, "title": "miR-20b regulates expression of proteinase-activated receptor-1 (PAR-1) thrombin receptor in melanoma cells.", "authors": [{"family": "Saleiban", "given": "Amina", "initials": "A"}, {"family": "Fax\u00e4lv", "given": "Lars", "initials": "L"}, {"family": "Claesson", "given": "Kjersti", "initials": "K"}, {"family": "J\u00f6nsson", "given": "Jan-Ingvar", "initials": "JI", "orcid": "0000-0003-4814-978X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcc87190783c48229913c2a35a2782c8.json"}}, {"family": "Osman", "given": "Abdimajid", "initials": "A"}], "type": "journal article", "published": "2014-05-00", "journal": {"volume": "27", "issn": "1755-148X", "issue": "3", "pages": "431-441", "title": "Pigment Cell Melanoma Res", "issn-l": "1755-1471"}, "abstract": "The proteinase-activated receptor 1 (PAR-1) plays a central role in melanoma progression and its expression level is believed to correlate with the degree of cancer invasiveness. Here, we show that PAR-1 is post-transcriptionally regulated by miR-20b microRNA in human melanoma cells. PAR-1 was found to be expressed in metastatic melanoma cells but was barely detectable in primary melanoma. By transducing primary melanoma cells with a lentivirus containing a 3'-UTR construct of PAR-1 mRNA, we could show that endogenous melanoma microRNAs interacted with PAR-1 3'-UTR and silenced a fused luciferase reporter. Transfection of an inhibitor against miR-20b into primary melanoma cells reversed this process. Finally, transfection of miR-20b mimic into metastatic melanoma cells caused downregulation of the luciferase reporter. We conclude that miR-20b regulates expression of melanoma PAR-1 receptor, which may explain the differential expression of PAR-1 observed in human melanoma.", "doi": "10.1111/pcmr.12217", "pmid": "24405508", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:34.377Z", "modified": "2021-07-08T09:31:31.596Z"}, {"entity": "publication", "iuid": "2100a7328f9e41eba90b9521a8230c62", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2100a7328f9e41eba90b9521a8230c62.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2100a7328f9e41eba90b9521a8230c62"}}, "title": "Quantitative label-free phosphoproteomics of six different life stages of the late blight pathogen Phytophthora infestans reveals abundant phosphorylation of members of the CRN effector family.", "authors": [{"family": "Resj\u00f6", "given": "Svante", "initials": "S"}, {"family": "Ali", "given": "Ashfaq", "initials": "A"}, {"family": "Meijer", "given": "Harold J G", "initials": "HJ"}, {"family": "Seidl", "given": "Michael F", "initials": "MF"}, {"family": "Snel", "given": "Berend", "initials": "B"}, {"family": "Sandin", "given": "Marianne", "initials": "M"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Govers", "given": "Francine", "initials": "F"}, {"family": "Andreasson", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2014-04-04", "journal": {"volume": "13", "issn": "1535-3907", "issue": "4", "pages": "1848-1859", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "The oomycete Phytophthora infestans is the causal agent of late blight in potato and tomato. Since the underlying processes that govern pathogenicity and development in P. infestans are largely unknown, we have performed a large-scale phosphoproteomics study of six different P. infestans life stages. We have obtained quantitative data for 2922 phosphopeptides and compared their abundance. Life-stage-specific phosphopeptides include ATP-binding cassette transporters and a kinase that only occurs in appressoria. In an extended data set, we identified 2179 phosphorylation sites and deduced 22 phosphomotifs. Several of the phosphomotifs matched consensus sequences of kinases that occur in P. infestans but not Arabidopsis. In addition, we detected tyrosine phosphopeptides that are potential targets of kinases resembling mammalian tyrosine kinases. Among the phosphorylated proteins are members of the RXLR and Crinkler effector families. The latter are phosphorylated in several life stages and at multiple positions, in sites that are conserved between different members of the Crinkler family. This indicates that proteins in the Crinkler family have functions beyond their putative role as (necrosis-inducing) effectors. This phosphoproteomics data will be instrumental for studies on oomycetes and host-oomycete interactions. The data sets have been deposited to ProteomeXchange (identifier PXD000433).", "doi": "10.1021/pr4009095", "pmid": "24588563", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:32.265Z", "modified": "2020-01-21T13:53:20.371Z"}, {"entity": "publication", "iuid": "9a77ab7989a14c33ada831caaf15fd9f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9a77ab7989a14c33ada831caaf15fd9f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9a77ab7989a14c33ada831caaf15fd9f"}}, "title": "An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.", "authors": [{"family": "Brownstein", "given": "Catherine A", "initials": "CA"}, {"family": "Beggs", "given": "Alan H", "initials": "AH"}, {"family": "Homer", "given": "Nils", "initials": "N"}, {"family": "Merriman", "given": "Barry", "initials": "B"}, {"family": "Yu", "given": "Timothy W", "initials": "TW"}, {"family": "Flannery", "given": "Katherine C", "initials": "KC"}, {"family": "DeChene", "given": "Elizabeth T", "initials": "ET"}, {"family": "Towne", "given": "Meghan C", "initials": "MC"}, {"family": "Savage", "given": "Sarah K", "initials": "SK"}, {"family": "Price", "given": "Emily N", "initials": "EN"}, {"family": "Holm", "given": "Ingrid A", "initials": "IA"}, {"family": "Luquette", "given": "Lovelace J", "initials": "LJ"}, {"family": "Lyon", "given": "Elaine", "initials": "E"}, {"family": "Majzoub", "given": "Joseph", "initials": "J"}, {"family": "Neupert", "given": "Peter", "initials": "P"}, {"family": "McCallie", "given": "David", "initials": "D"}, {"family": "Szolovits", "given": "Peter", "initials": "P"}, {"family": "Willard", "given": "Huntington F", "initials": "HF"}, {"family": "Mendelsohn", "given": "Nancy J", "initials": "NJ"}, {"family": "Temme", "given": "Renee", "initials": "R"}, {"family": "Finkel", "given": "Richard S", "initials": "RS"}, {"family": "Yum", "given": "Sabrina W", "initials": "SW"}, {"family": "Medne", "given": "Livija", "initials": "L"}, {"family": "Sunyaev", "given": "Shamil R", "initials": "SR"}, {"family": "Adzhubey", "given": "Ivan", "initials": "I"}, {"family": "Cassa", "given": "Christopher A", "initials": "CA"}, {"family": "de Bakker", "given": "Paul I W", "initials": "PI"}, {"family": "Duzkale", "given": "Hatice", "initials": "H"}, {"family": "Dworzy\u0144ski", "given": "Piotr", "initials": "P"}, {"family": "Fairbrother", "given": "William", "initials": "W"}, {"family": "Francioli", "given": "Laurent", "initials": "L"}, {"family": "Funke", "given": "Birgit H", "initials": "BH"}, {"family": "Giovanni", "given": "Monica A", "initials": "MA"}, {"family": "Handsaker", "given": "Robert E", "initials": "RE"}, {"family": "Lage", "given": "Kasper", "initials": "K"}, {"family": "Lebo", "given": "Matthew S", "initials": "MS"}, {"family": "Lek", "given": "Monkol", "initials": "M"}, {"family": "Leshchiner", "given": "Ignaty", "initials": "I"}, {"family": "MacArthur", "given": "Daniel G", "initials": "DG"}, {"family": "McLaughlin", "given": "Heather M", "initials": "HM"}, {"family": "Murray", "given": "Michael F", "initials": "MF"}, {"family": "Pers", "given": "Tune H", "initials": "TH"}, {"family": "Polak", "given": "Paz P", "initials": "PP"}, {"family": "Raychaudhuri", "given": "Soumya", "initials": "S"}, {"family": "Rehm", "given": "Heidi L", "initials": "HL"}, {"family": "Soemedi", "given": "Rachel", "initials": "R"}, {"family": "Stitziel", "given": "Nathan O", "initials": "NO"}, {"family": "Vestecka", "given": "Sara", "initials": "S"}, {"family": "Supper", "given": "Jochen", "initials": "J"}, {"family": "Gugenmus", "given": "Claudia", "initials": "C"}, {"family": "Klocke", "given": "Bernward", "initials": "B"}, {"family": "Hahn", "given": "Alexander", "initials": "A"}, {"family": "Schubach", "given": "Max", "initials": "M"}, {"family": "Menzel", "given": "Mortiz", "initials": "M"}, {"family": "Biskup", "given": "Saskia", "initials": "S"}, {"family": "Freisinger", "given": "Peter", "initials": "P"}, {"family": "Deng", "given": "Mario", "initials": "M"}, {"family": "Braun", "given": "Martin", "initials": "M"}, {"family": "Perner", "given": "Sven", "initials": "S"}, {"family": "Smith", "given": "Richard J H", "initials": "RJ"}, {"family": "Andorf", "given": "Janeen L", "initials": "JL"}, {"family": "Huang", "given": "Jian", "initials": "J"}, {"family": "Ryckman", "given": "Kelli", "initials": "K"}, {"family": "Sheffield", "given": "Val C", "initials": "VC"}, {"family": "Stone", "given": "Edwin M", "initials": "EM"}, {"family": "Bair", "given": "Thomas", "initials": "T"}, {"family": "Black-Ziegelbein", "given": "E Ann", "initials": "EA"}, {"family": "Braun", "given": "Terry A", "initials": "TA"}, {"family": "Darbro", "given": "Benjamin", "initials": "B"}, {"family": "DeLuca", "given": "Adam P", "initials": "AP"}, {"family": "Kolbe", "given": "Diana L", "initials": "DL"}, {"family": "Scheetz", "given": "Todd E", "initials": "TE"}, {"family": "Shearer", "given": "Aiden E", "initials": "AE"}, {"family": "Sompallae", "given": "Rama", "initials": "R"}, {"family": "Wang", "given": "Kai", "initials": "K"}, {"family": "Bassuk", "given": "Alexander G", "initials": "AG"}, {"family": "Edens", "given": "Erik", "initials": "E"}, {"family": "Mathews", "given": "Katherine", "initials": "K"}, {"family": "Moore", "given": "Steven A", "initials": "SA"}, {"family": "Shchelochkov", "given": "Oleg A", "initials": "OA"}, {"family": "Trapane", "given": "Pamela", "initials": "P"}, {"family": "Bossler", "given": "Aaron", "initials": "A"}, {"family": "Campbell", "given": "Colleen A", "initials": "CA"}, {"family": "Heusel", "given": "Jonathan W", "initials": "JW"}, {"family": "Kwitek", "given": "Anne", "initials": "A"}, {"family": "Maga", "given": "Tara", "initials": "T"}, {"family": "Panzer", "given": "Karin", "initials": "K"}, {"family": "Wassink", "given": "Thomas", "initials": "T"}, {"family": "Van Daele", "given": "Douglas", "initials": "D"}, {"family": "Azaiez", "given": "Hela", "initials": "H"}, {"family": "Booth", "given": "Kevin", "initials": "K"}, {"family": "Meyer", "given": "Nic", "initials": "N"}, {"family": "Segal", "given": "Michael M", "initials": "MM"}, {"family": "Williams", "given": "Marc S", "initials": "MS"}, {"family": "Tromp", "given": "Gerard", "initials": "G"}, {"family": "White", "given": "Peter", "initials": "P"}, {"family": "Corsmeier", "given": "Donald", "initials": "D"}, {"family": "Fitzgerald-Butt", "given": "Sara", "initials": "S"}, {"family": "Herman", "given": "Gail", "initials": "G"}, {"family": "Lamb-Thrush", "given": "Devon", "initials": "D"}, {"family": "McBride", "given": "Kim L", "initials": "KL"}, {"family": "Newsom", "given": "David", "initials": "D"}, {"family": "Pierson", "given": "Christopher R", "initials": "CR"}, {"family": "Rakowsky", "given": "Alexander T", "initials": "AT"}, {"family": "Maver", "given": "Ale\u0161", "initials": "A"}, {"family": "Lovre\u010di\u0107", "given": "Luca", "initials": "L"}, {"family": "Palanda\u010di\u0107", "given": "Anja", "initials": "A"}, {"family": "Peterlin", "given": "Borut", "initials": "B"}, {"family": "Torkamani", "given": "Ali", "initials": "A"}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Magnusson", "given": "M\u00e5ns", "initials": "M"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "Gilissen", "given": "Christian", "initials": "C"}, {"family": "Hoischen", "given": "Alexander", "initials": "A"}, {"family": "van Bon", "given": "Bregje", "initials": "B"}, {"family": "Yntema", "given": "Helger", "initials": "H"}, {"family": "Nelen", "given": "Marcel", "initials": "M"}, {"family": "Zhang", "given": "Weidong", "initials": "W"}, {"family": "Sager", "given": "Jason", "initials": "J"}, {"family": "Zhang", "given": "Lu", "initials": "L"}, {"family": "Blair", "given": "Kathryn", "initials": "K"}, {"family": "Kural", "given": "Deniz", "initials": "D"}, {"family": "Cariaso", "given": "Michael", "initials": "M"}, {"family": "Lennon", "given": "Greg G", "initials": "GG"}, {"family": "Javed", "given": "Asif", "initials": "A"}, {"family": "Agrawal", "given": "Saloni", "initials": "S"}, {"family": "Ng", "given": "Pauline C", "initials": "PC"}, {"family": "Sandhu", "given": "Komal S", "initials": "KS"}, {"family": "Krishna", "given": "Shuba", "initials": "S"}, {"family": "Veeramachaneni", "given": "Vamsi", "initials": "V"}, {"family": "Isakov", "given": "Ofer", "initials": "O"}, {"family": "Halperin", "given": "Eran", "initials": "E"}, {"family": "Friedman", "given": "Eitan", "initials": "E"}, {"family": "Shomron", "given": "Noam", "initials": "N"}, {"family": "Glusman", "given": "Gustavo", "initials": "G"}, {"family": "Roach", "given": "Jared C", "initials": "JC"}, {"family": "Caballero", "given": "Juan", "initials": "J"}, {"family": "Cox", "given": "Hannah C", "initials": "HC"}, {"family": "Mauldin", "given": "Denise", "initials": "D"}, {"family": "Ament", "given": "Seth A", "initials": "SA"}, {"family": "Rowen", "given": "Lee", "initials": "L"}, {"family": "Richards", "given": "Daniel R", "initials": "DR"}, {"family": "San Lucas", "given": "F Anthony", "initials": "FA"}, {"family": "Gonzalez-Garay", "given": "Manuel L", "initials": "ML"}, {"family": "Caskey", "given": "C Thomas", "initials": "CT"}, {"family": "Bai", "given": "Yu", "initials": "Y"}, {"family": "Huang", "given": "Ying", "initials": "Y"}, {"family": "Fang", "given": "Fang", "initials": "F"}, {"family": "Zhang", "given": "Yan", "initials": "Y"}, {"family": "Wang", "given": "Zhengyuan", "initials": "Z"}, {"family": "Barrera", "given": "Jorge", "initials": "J"}, {"family": "Garcia-Lobo", "given": "Juan M", "initials": "JM"}, {"family": "Gonz\u00e1lez-Lamu\u00f1o", "given": "Domingo", "initials": "D"}, {"family": "Llorca", "given": "Javier", "initials": "J"}, {"family": "Rodriguez", "given": "Maria C", "initials": "MC"}, {"family": "Varela", "given": "Ignacio", "initials": "I"}, {"family": "Reese", "given": "Martin G", "initials": "MG"}, {"family": "De La Vega", "given": "Francisco M", "initials": "FM"}, {"family": "Kiruluta", "given": "Edward", "initials": "E"}, {"family": "Cargill", "given": "Michele", "initials": "M"}, {"family": "Hart", "given": "Reece K", "initials": "RK"}, {"family": "Sorenson", "given": "Jon M", "initials": "JM"}, {"family": "Lyon", "given": "Gholson J", "initials": "GJ"}, {"family": "Stevenson", "given": "David A", "initials": "DA"}, {"family": "Bray", "given": "Bruce E", "initials": "BE"}, {"family": "Moore", "given": "Barry M", "initials": "BM"}, {"family": "Eilbeck", "given": "Karen", "initials": "K"}, {"family": "Yandell", "given": "Mark", "initials": "M"}, {"family": "Zhao", "given": "Hongyu", "initials": "H"}, {"family": "Hou", "given": "Lin", "initials": "L"}, {"family": "Chen", "given": "Xiaowei", "initials": "X"}, {"family": "Yan", "given": "Xiting", "initials": "X"}, {"family": "Chen", "given": "Mengjie", "initials": "M"}, {"family": "Li", "given": "Cong", "initials": "C"}, {"family": "Yang", "given": "Can", "initials": "C"}, {"family": "Gunel", "given": "Murat", "initials": "M"}, {"family": "Li", "given": "Peining", "initials": "P"}, {"family": "Kong", "given": "Yong", "initials": "Y"}, {"family": "Alexander", "given": "Austin C", "initials": "AC"}, {"family": "Albertyn", "given": "Zayed I", "initials": "ZI"}, {"family": "Boycott", "given": "Kym M", "initials": "KM"}, {"family": "Bulman", "given": "Dennis E", "initials": "DE"}, {"family": "Gordon", "given": "Paul M K", "initials": "PM"}, {"family": "Innes", "given": "A Micheil", "initials": "AM"}, {"family": "Knoppers", "given": "Bartha M", "initials": "BM"}, {"family": "Majewski", "given": "Jacek", "initials": "J"}, {"family": "Marshall", "given": "Christian R", "initials": "CR"}, {"family": "Parboosingh", "given": "Jillian S", "initials": "JS"}, {"family": "Sawyer", "given": "Sarah L", "initials": "SL"}, {"family": "Samuels", "given": "Mark E", "initials": "ME"}, {"family": "Schwartzentruber", "given": "Jeremy", "initials": "J"}, {"family": "Kohane", "given": "Isaac S", "initials": "IS"}, {"family": "Margulies", "given": "David M", "initials": "DM"}], "type": "journal article", "published": "2014-03-25", "journal": {"volume": "15", "issn": "1474-760X", "issue": "3", "pages": "R53", "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance.\n\nA total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization.\n\nThe CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.", "doi": "10.1186/gb-2014-15-3-r53", "pmid": "24667040", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "gb-2014-15-3-r53"}, {"db": "pmc", "key": "PMC4073084"}], "notes": [], "created": "2017-05-04T14:56:31.024Z", "modified": "2021-07-05T12:48:16.023Z"}, {"entity": "publication", "iuid": "e0bf412e7b65470aa17c3e0bc106b686", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0bf412e7b65470aa17c3e0bc106b686.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0bf412e7b65470aa17c3e0bc106b686"}}, "title": "On the biogeography of Centipeda: a species-tree diffusion approach.", "authors": [{"family": "Nylinder", "given": "Stephan", "initials": "S"}, {"family": "Lemey", "given": "Philippe", "initials": "P"}, {"family": "De Bruyn", "given": "Mark", "initials": "M"}, {"family": "Suchard", "given": "Marc A", "initials": "MA"}, {"family": "Pfeil", "given": "Bernard E", "initials": "BE"}, {"family": "Walsh", "given": "Neville", "initials": "N"}, {"family": "Anderberg", "given": "Arne A", "initials": "AA"}], "type": "journal article", "published": "2014-03-00", "journal": {"volume": "63", "issn": "1076-836X", "issue": "2", "pages": "178-191", "title": "Syst. Biol.", "issn-l": "1063-5157"}, "abstract": "Reconstructing the biogeographic history of groups present in continuous arid landscapes is challenging due to the difficulties in defining discrete areas for analyses, and even more so when species largely overlap both in terms of geography and habitat preference. In this study, we use a novel approach to estimate ancestral areas for the small plant genus Centipeda. We apply continuous diffusion of geography by a relaxed random walk where each species is sampled from its extant distribution on an empirical distribution of time-calibrated species-trees. Using a distribution of previously published substitution rates of the internal transcribed spacer (ITS) for Asteraceae, we show how the evolution of Centipeda correlates with the temporal increase of aridity in the arid zone since the Pliocene. Geographic estimates of ancestral species show a consistent pattern of speciation of early lineages in the Lake Eyre region, with a division in more northerly and southerly groups since \u223c840 ka. Summarizing the geographic slices of species-trees at the time of the latest speciation event (\u223c20 ka), indicates no presence of the genus in Australia west of the combined desert belt of the Nullabor Plain, the Great Victoria Desert, the Gibson Desert, and the Great Sandy Desert, or beyond the main continental shelf of Australia. The result indicates all western occurrences of the genus to be a result of recent dispersal rather than ancient vicariance. This study contributes to our understanding of the spatiotemporal processes shaping the flora of the arid zone, and offers a significant improvement in inference of ancestral areas for any organismal group distributed where it remains difficult to describe geography in terms of discrete areas.", "doi": "10.1093/sysbio/syt102", "pmid": "24335493", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "syt102"}, {"db": "pmc", "key": "PMC3926304"}], "notes": [], "created": "2017-05-04T14:56:35.814Z", "modified": "2020-01-21T13:53:20.934Z"}, {"entity": "publication", "iuid": "c71dc7a07b0e4a3a86b069c73ed1711f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c71dc7a07b0e4a3a86b069c73ed1711f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c71dc7a07b0e4a3a86b069c73ed1711f"}}, "title": "Functional tradeoffs underpin salinity-driven divergence in microbial community composition.", "authors": [{"family": "Dupont", "given": "Chris L", "initials": "CL"}, {"family": "Larsson", "given": "John", "initials": "J"}, {"family": "Yooseph", "given": "Shibu", "initials": "S"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}, {"family": "Goll", "given": "Johannes", "initials": "J"}, {"family": "Asplund-Samuelsson", "given": "Johannes", "initials": "J"}, {"family": "McCrow", "given": "John P", "initials": "JP"}, {"family": "Celepli", "given": "Narin", "initials": "N"}, {"family": "Allen", "given": "Lisa Zeigler", "initials": "LZ"}, {"family": "Ekman", "given": "Martin", "initials": "M"}, {"family": "Lucas", "given": "Andrew J", "initials": "AJ"}, {"family": "Hagstr\u00f6m", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Thiagarajan", "given": "Mathangi", "initials": "M"}, {"family": "Brindefalk", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Richter", "given": "Alexander R", "initials": "AR"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Tenney", "given": "Aaron", "initials": "A"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Tovchigrechko", "given": "Andrey", "initials": "A"}, {"family": "Nylander", "given": "Johan A A", "initials": "JA"}, {"family": "Brami", "given": "Daniel", "initials": "D"}, {"family": "Badger", "given": "Jonathan H", "initials": "JH"}, {"family": "Allen", "given": "Andrew E", "initials": "AE"}, {"family": "Rusch", "given": "Douglas B", "initials": "DB"}, {"family": "Hoffman", "given": "Jeff", "initials": "J"}, {"family": "Norrby", "given": "Erling", "initials": "E"}, {"family": "Friedman", "given": "Robert", "initials": "R"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Venter", "given": "J Craig", "initials": "JC"}, {"family": "Bergman", "given": "Birgitta", "initials": "B"}], "type": "journal article", "published": "2014-02-27", "journal": {"volume": "9", "issn": "1932-6203", "issue": "2", "pages": "e89549", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.", "doi": "10.1371/journal.pone.0089549", "pmid": "24586863", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-46808"}, {"db": "pmc", "key": "PMC3937345"}], "notes": [], "created": "2017-05-04T14:56:34.688Z", "modified": "2020-01-21T13:56:16.779Z"}, {"entity": "publication", "iuid": "315cc4ca75894903b5c88ba14a8365e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/315cc4ca75894903b5c88ba14a8365e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/315cc4ca75894903b5c88ba14a8365e3"}}, "title": "Intraclonal variations among Streptococcus pneumoniae isolates influence the likelihood of invasive disease in children.", "authors": [{"family": "Browall", "given": "Sarah", "initials": "S"}, {"family": "Norman", "given": "Martin", "initials": "M"}, {"family": "T\u00e5ngrot", "given": "Jeanette", "initials": "J"}, {"family": "Galanis", "given": "Ilias", "initials": "I"}, {"family": "Sj\u00f6str\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Dagerhamn", "given": "Jessica", "initials": "J"}, {"family": "Hellberg", "given": "Christel", "initials": "C"}, {"family": "Pathak", "given": "Anuj", "initials": "A"}, {"family": "Spadafina", "given": "Tiziana", "initials": "T"}, {"family": "Sandgren", "given": "Andreas", "initials": "A"}, {"family": "B\u00e4ttig", "given": "Patrick", "initials": "P"}, {"family": "Franz\u00e9n", "given": "Oscar", "initials": "O"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "\u00d6rtqvist", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Normark", "given": "Staffan", "initials": "S"}, {"family": "Henriques-Normark", "given": "Birgitta", "initials": "B"}], "type": "journal article", "published": "2014-02-01", "journal": {"volume": "209", "issn": "1537-6613", "issue": "3", "pages": "377-388", "title": "J. Infect. Dis.", "issn-l": "0022-1899"}, "abstract": "Pneumococcal serotypes are represented by a varying number of clonal lineages with different genetic contents, potentially affecting invasiveness. However, genetic variation within the same genetic lineage may be larger than anticipated.\n\nA total of 715 invasive and carriage isolates from children in the same region and during the same period were compared using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. Bacterial genome sequencing, functional assays, and in vivo virulence mice studies were performed.\n\nClonal types of the same serotype but also intraclonal variants within clonal complexes (CCs) showed differences in invasive-disease potential. CC138, a common CC, was divided into several PFGE patterns, partly explained by number, location, and type of temperate bacteriophages. Whole-genome sequencing of 4 CC138 isolates representing PFGE clones with different invasive-disease potentials revealed intraclonal sequence variations of the virulence-associated proteins pneumococcal surface protein A (PspA) and pneumococcal choline-binding protein C (PspC). A carrier isolate lacking PcpA exhibited decreased virulence in mice, and there was a differential binding of human factor H, depending on invasiveness.\n\nPneumococcal clonal types but also intraclonal variants exhibited different invasive-disease potentials in children. Intraclonal variants, reflecting different prophage contents, showed differences in major surface antigens. This suggests ongoing immune selection, such as that due to PspC-mediated complement resistance through varied human factor H binding, that may affect invasiveness in children.", "doi": "10.1093/infdis/jit481", "pmid": "24009156", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "jit481"}, {"db": "pmc", "key": "PMC4014860"}], "notes": [], "created": "2017-05-04T14:56:31.363Z", "modified": "2020-01-21T13:56:16.724Z"}, {"entity": "publication", "iuid": "9faa5e6eecf842d68a5653375fe59ee3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9faa5e6eecf842d68a5653375fe59ee3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9faa5e6eecf842d68a5653375fe59ee3"}}, "title": "Lipid mediator profiles differ between lung compartments in asthmatic and healthy humans.", "authors": [{"family": "Larsson", "given": "Nirina", "initials": "N"}, {"family": "Lundstr\u00f6m", "given": "Susanna L", "initials": "SL"}, {"family": "Pinto", "given": "Rui", "initials": "R"}, {"family": "Rankin", "given": "Gregory", "initials": "G"}, {"family": "Karimpour", "given": "Masoumeh", "initials": "M"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}, {"family": "Sandstr\u00f6m", "given": "Thomas", "initials": "T"}, {"family": "Pourazar", "given": "Jamshid", "initials": "J"}, {"family": "Trygg", "given": "Johan", "initials": "J"}, {"family": "Behndig", "given": "Annelie F", "initials": "AF"}, {"family": "Wheelock", "given": "Craig E", "initials": "CE"}, {"family": "Nording", "given": "Malin L", "initials": "ML"}], "type": "comparative study", "published": "2014-02-00", "journal": {"volume": "43", "issn": "1399-3003", "issue": "2", "pages": "453-463", "title": "Eur. Respir. J.", "issn-l": "0903-1936"}, "abstract": "Oxylipins are oxidised fatty acids that can exert lipid mediator functions in inflammation, and several oxylipins derived from arachidonic acid are linked to asthma. This study quantified oxylipin profiles in different regions of the lung to obtain a broad-scale characterisation of the allergic asthmatic inflammation in relation to healthy individuals. Bronchoalveolar lavage fluid (BALF), bronchial wash fluid and endobronchial mucosal biopsies were collected from 16 healthy and 16 mildly allergic asthmatic individuals. Inflammatory cell counts, immunohistochemical staining and oxylipin profiling were performed. Univariate and multivariate statistics were employed to evaluate compartment-dependent and diagnosis-dependent oxylipin profiles in relation to other measured parameters. Multivariate modelling showed significantly different bronchial wash fluid and BALF oxylipin profiles in both groups (R(2)Y[cum]=0.822 and Q(2)[cum]=0.759). Total oxylipin concentrations and five individual oxylipins, primarily from the lipoxygenase (LOX) pathway of arachidonic and linoleic acid, were elevated in bronchial wash fluid from asthmatics compared to that from healthy controls, supported by immunohistochemical staining of 15-LOX-1 in the bronchial epithelium. No difference between the groups was found among BALF oxylipins. In conclusion, bronchial wash fluid and BALF contain distinct oxylipin profiles, which may have ramifications for the study of respiratory diseases. Specific protocols for sampling proximal and distal airways separately should be employed for lipid mediator studies.", "doi": "10.1183/09031936.00209412", "pmid": "24036245", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "09031936.00209412"}], "notes": [], "created": "2017-05-04T14:56:30.705Z", "modified": "2020-01-21T13:53:20.718Z"}, {"entity": "publication", "iuid": "42302ed840ee429b92fda660d9ee7bea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42302ed840ee429b92fda660d9ee7bea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42302ed840ee429b92fda660d9ee7bea"}}, "title": "Dating the diversification of the major lineages of Passeriformes (Aves).", "authors": [{"family": "Ericson", "given": "Per G P", "initials": "PG"}, {"family": "Klopfstein", "given": "Seraina", "initials": "S"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Nguyen", "given": "Jacqueline M T", "initials": "JM"}, {"family": "Nylander", "given": "Johan A A", "initials": "JA"}], "type": "journal article", "published": "2014-01-15", "journal": {"volume": "14", "issn": "1471-2148", "issue": null, "pages": "8", "title": "BMC Evol. Biol.", "issn-l": "1471-2148"}, "abstract": "The avian Order Passeriformes is an enormously species-rich group, which comprises almost 60% of all living bird species. This diverse order is believed to have originated before the break-up of Gondwana in the late Cretaceous. However, previous molecular dating studies have relied heavily on the geological split between New Zealand and Antarctica, assumed to have occurred 85-82 Mya, for calibrating the molecular clock and might thus be circular in their argument.\n\nThis study provides a time-scale for the evolution of the major clades of passerines using seven nuclear markers, five taxonomically well-determined passerine fossils, and an updated interpretation of the New Zealand split from Antarctica 85-52 Mya in a Bayesian relaxed-clock approach. We also assess how different interpretations of the New Zealand-Antarctica vicariance event influence our age estimates. Our results suggest that the diversification of Passeriformes began in the late Cretaceous or early Cenozoic. Removing the root calibration for the New Zealand-Antarctica vicariance event (85-52 Mya) dramatically increases the 95% credibility intervals and leads to unrealistically old age estimates. We assess the individual characteristics of the seven nuclear genes analyzed in our study. Our analyses provide estimates of divergence times for the major groups of passerines, which can be used as secondary calibration points in future molecular studies.\n\nOur analysis takes recent paleontological and geological findings into account and provides the best estimate of the passerine evolutionary time-scale currently available. This time-scale provides a temporal framework for further biogeographical, ecological, and co-evolutionary studies of the largest bird radiation, and adds to the growing support for a Cretaceous origin of Passeriformes.", "doi": "10.1186/1471-2148-14-8", "pmid": "24422673", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "1471-2148-14-8"}, {"db": "pmc", "key": "PMC3917694"}], "notes": [], "created": "2017-05-04T14:56:29.498Z", "modified": "2020-01-21T13:53:20.488Z"}, {"entity": "publication", "iuid": "f5ae0bcb00e84e21ab0bdf4d81044a0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5ae0bcb00e84e21ab0bdf4d81044a0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5ae0bcb00e84e21ab0bdf4d81044a0c"}}, "title": "HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.", "authors": [{"family": "Branca", "given": "Rui M M", "initials": "RM", "orcid": "0000-0003-3890-6476", "researcher": {"href": "https://publications.scilifelab.se/researcher/87d6256540174d3da581d4572f9d182a.json"}}, {"family": "Orre", "given": "Lukas M", "initials": "LM", "orcid": "0000-0002-0384-1003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b4e49a93b0143db88059c4d1e9fdc59.json"}}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ", "orcid": "0000-0003-4729-4205", "researcher": {"href": "https://publications.scilifelab.se/researcher/18aebf211fa640f48a7c8d860c168e5a.json"}}, {"family": "Granholm", "given": "Viktor", "initials": "V"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "P\u00e9rez-Bercoff", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Forshed", "given": "Jenny", "initials": "J"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c9f4444f83e43d79c4772a430ca3969.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}], "type": "journal article", "published": "2014-01-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "11", "issue": "1", "pages": "59-62", "issn-l": "1548-7091"}, "abstract": "We present a liquid chromatography-mass spectrometry (LC-MS)-based method permitting unbiased (gene prediction-independent) genome-wide discovery of protein-coding loci in higher eukaryotes. Using high-resolution isoelectric focusing (HiRIEF) at the peptide level in the 3.7-5.0 pH range and accurate peptide isoelectric point (pI) prediction, we probed the six-reading-frame translation of the human and mouse genomes and identified 98 and 52 previously undiscovered protein-coding loci, respectively. The method also enabled deep proteome coverage, identifying 13,078 human and 10,637 mouse proteins.", "doi": "10.1038/nmeth.2732", "pmid": "24240322", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "nmeth.2732"}], "notes": [], "created": "2023-06-16T12:47:04.864Z", "modified": "2023-06-16T12:47:27.234Z"}, {"entity": "publication", "iuid": "d3162e61d4ce4afb9b8b0254b9f21ab1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d3162e61d4ce4afb9b8b0254b9f21ab1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d3162e61d4ce4afb9b8b0254b9f21ab1"}}, "title": "Data processing methods and quality control strategies for label-free LC-MS protein quantification.", "authors": [{"family": "Sandin", "given": "Marianne", "initials": "M"}, {"family": "Teleman", "given": "Johan", "initials": "J"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2014-01-00", "journal": {"volume": "1844", "issn": "0006-3002", "issue": "1 Pt A", "pages": "29-41", "title": "Biochim. Biophys. Acta", "issn-l": null}, "abstract": "Protein quantification using different LC-MS techniques is becoming a standard practice. However, with a multitude of experimental setups to choose from, as well as a wide array of software solutions for subsequent data processing, it is non-trivial to select the most appropriate workflow for a given biological question. In this review, we highlight different issues that need to be addressed by software for quantitative LC-MS experiments and describe different approaches that are available. With focus on label-free quantification, examples are discussed both for LC-MS/MS and LC-SRM data processing. We further elaborate on current quality control methodology for performing accurate protein quantification experiments. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.", "doi": "10.1016/j.bbapap.2013.03.026", "pmid": "23567904", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "S1570-9639(13)00139-8"}], "notes": [], "created": "2017-05-04T14:56:28.593Z", "modified": "2020-01-21T13:53:20.886Z"}, {"entity": "publication", "iuid": "d757e4ec2c9645bf9b2e900d4b22d853", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d757e4ec2c9645bf9b2e900d4b22d853.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d757e4ec2c9645bf9b2e900d4b22d853"}}, "title": "Automated quality control system for LC-SRM setups.", "authors": [{"family": "Teleman", "given": "Johan", "initials": "J"}, {"family": "Waldemarson", "given": "Sofia", "initials": "S"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2013-12-16", "journal": {"volume": "95", "issn": "1876-7737", "issue": null, "pages": "77-83", "title": "J Proteomics", "issn-l": "1874-3919"}, "abstract": "Selected reaction monitoring (SRM) is emerging as a standard tool for high-throughput protein quantification. For reliable and reproducible SRM protein quantification it is essential that system performance is stable. We present here a quality control workflow that is based on repeated analysis of a standard sample to allow insight into the stability of the key properties of a SRM setup. This is supported by automated software to monitor system performance and display information like signal intensities and retention time stability over time, and alert upon deviations from expected metrics. Utilising the software to evaluate 407 repeated injections of a standard sample during half a year, outliers in relative peptide signal intensities and relative peptide fragment ratios are identified, indicating the need for instrument maintenance. We therefore believe that the software could be a vital and powerful tool for any lab regularly performing SRM, increasing the reliability and quality of the SRM platform.\n\nSelected reaction monitoring (SRM) mass spectrometry is becoming established as a standard technique for accurate protein quantification. However, to achieve the required quantification reproducibility of the liquid chromatography (LC)-SRM setup, system performance needs to be monitored over time. Here we introduce a workflow with associated software to enable automated monitoring of LC-SRM setups. We believe that usage of the presented concepts will further strengthen the role of SRM as a reliable tool for protein quantification. This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics.", "doi": "10.1016/j.jprot.2013.03.029", "pmid": "23584149", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "S1874-3919(13)00176-0"}], "notes": [], "created": "2017-05-04T14:56:24.885Z", "modified": "2020-01-21T13:53:20.898Z"}, {"entity": "publication", "iuid": "1d3d7629f89949b7a615689e384b642a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d3d7629f89949b7a615689e384b642a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d3d7629f89949b7a615689e384b642a"}}, "title": "Linkage analysis in familial non-Lynch syndrome colorectal cancer families from Sweden.", "authors": [{"family": "Kontham", "given": "Vinaykumar", "initials": "V"}, {"family": "von Holst", "given": "Susanna", "initials": "S"}, {"family": "Lindblom", "given": "Annika", "initials": "A"}], "type": "clinical trial", "published": "2013-12-11", "journal": {"volume": "8", "issn": "1932-6203", "issue": "12", "pages": "e83936", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Family history is a major risk factor for colorectal cancer and many families segregate the disease as a seemingly monogenic trait. A minority of familial colorectal cancer could be explained by known monogenic genes and genetic loci. Familial polyposis and Lynch syndrome are two syndromes where the predisposing genes are known but numerous families have been tested without finding the predisposing gene. We performed a genome wide linkage analysis in 121 colorectal families with an increased risk of colorectal cancer. The families were ascertained from the department of clinical genetics at the Karolinska University Hospital in Stockholm, Sweden and were considered negative for Familial Polyposis and Lynch syndrome. In total 600 subjects were genotyped using single nucleotide polymorphism array chips. Parametric- and non-parametric linkage analyses were computed using MERLIN in all and subsets of families. No statistically significant result was seen, however, there were suggestive positive HLODs above two in parametric linkage analysis. This was observed in a recessive model for high-risk families, at locus 9q31.1 (HLOD=2.2, rs1338121) and for moderate-risk families, at locus Xp22.33 (LOD=2.2 and HLOD=2.5, rs2306737). Using families with early-onset, recessive analysis suggested one locus on 4p16.3 (LOD=2.2, rs920683) and one on 17p13.2 (LOD/HLOD=2.0, rs884250). No NPL score above two was seen for any of the families. Our linkage study provided additional support for the previously suggested region on chromosome 9 and suggested additional loci to be involved in colorectal cancer risk. Sequencing of genes in the regions will be done in future studies.", "doi": "10.1371/journal.pone.0083936", "pmid": "24349560", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-40988"}, {"db": "pmc", "key": "PMC3859667"}], "notes": [], "created": "2017-05-04T14:56:27.482Z", "modified": "2020-01-21T13:56:16.717Z"}, {"entity": "publication", "iuid": "c4b3d70c6f7544148e5ab0eb59554e42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c4b3d70c6f7544148e5ab0eb59554e42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c4b3d70c6f7544148e5ab0eb59554e42"}}, "title": "Protein expansion is primarily due to indels in intrinsically disordered regions.", "authors": [{"family": "Light", "given": "Sara", "initials": "S"}, {"family": "Sagit", "given": "Rauan", "initials": "R"}, {"family": "Sachenkova", "given": "Oxana", "initials": "O"}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2013-12-00", "journal": {"volume": "30", "issn": "1537-1719", "issue": "12", "pages": "2645-2653", "title": "Mol. Biol. Evol.", "issn-l": "0737-4038"}, "abstract": "Proteins evolve not only through point mutations but also by insertion and deletion events, which affect the length of the protein. It is well known that such indel events most frequently occur in surface-exposed loops. However, detailed analysis of indel events in distantly related and fast-evolving proteins is hampered by the difficulty involved in correctly aligning such sequences. Here, we circumvent this problem by first only analyzing homologous proteins based on length variation rather than pairwise alignments. Using this approach, we find a surprisingly strong relationship between difference in length and difference in the number of intrinsically disordered residues, where up to three quarters of the length variation can be explained by changes in the number of intrinsically disordered residues. Further, we find that disorder is common in both insertions and deletions. A more detailed analysis reveals that indel events do not induce disorder but rather that already disordered regions accrue indels, suggesting that there is a lowered selective pressure for indels to occur within intrinsically disordered regions.", "doi": "10.1093/molbev/mst157", "pmid": "24037790", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "mst157"}], "notes": [], "created": "2017-05-04T14:56:25.405Z", "modified": "2020-01-21T13:53:20.855Z"}, {"entity": "publication", "iuid": "0e3e7d2669db4343813208ec913c4d7c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e3e7d2669db4343813208ec913c4d7c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e3e7d2669db4343813208ec913c4d7c"}}, "title": "Early B-cell factor 1 regulates the expansion of B-cell progenitors in a dose-dependent manner.", "authors": [{"family": "\u00c5hsberg", "given": "Josefine", "initials": "J"}, {"family": "Ungerb\u00e4ck", "given": "Jonas", "initials": "J"}, {"family": "Strid", "given": "Tobias", "initials": "T", "orcid": "0000-0002-2166-5170", "researcher": {"href": "https://publications.scilifelab.se/researcher/8294f89150574803a12bc1944714d12b.json"}}, {"family": "Welinder", "given": "Eva", "initials": "E"}, {"family": "Stjernberg", "given": "Jenny", "initials": "J"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Qian", "given": "Hong", "initials": "H"}, {"family": "Sigvardsson", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2013-11-15", "journal": {"volume": "288", "issn": "1083-351X", "issue": "46", "pages": "33449-33461", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Transcription factor doses are of importance for normal and malignant B-lymphocyte development; however, the understanding of underlying mechanisms and functional consequences of reduced transcription factor levels is limited. We have analyzed progenitor and B-lineage compartments in mice carrying heterozygote mutations in the E2a, Ebf1, or Pax5 gene. Although lymphoid progenitors from Ebf1 or Pax5 heterozygote mice were specified and lineage-restricted in a manner comparable with Wt progenitors, this process was severely impaired in E2a heterozygote mutant mice. This defect was not significantly enhanced upon combined deletion of E2a with Ebf1 or Pax5. Analysis of the pre-B-cell compartment in Ebf1 heterozygote mice revealed a reduction in cell numbers. These cells expressed Pax5 and other B-lineage-associated genes, and global gene expression analysis suggested that the reduction of the pre-B-cell compartment was a result of impaired pre-B-cell expansion. This idea was supported by a reduction in IL2R\u03b1-expressing late pre-B-cells as well as by cell cycle analysis and by the finding that the complexity of the VDJ rearrangement patterns was comparable in Wt and Ebf1(+/-) pre-B-cells, although the number of progenitors was reduced. Heterozygote deletion of Ebf1 resulted in impaired response to IL7 in vitro and reduced expression levels of pre-BCR on the cell surface, providing possible explanations for the observed stage-specific reduction in cellular expansion. Thus, transcription factor doses are critical for specification as well as expansion of B-lymphoid progenitors, providing increased insight into the molecular regulation of B-cell development.", "doi": "10.1074/jbc.M113.506261", "pmid": "24078629", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "S0021-9258(19)54468-4"}, {"db": "pmc", "key": "PMC3829190"}], "notes": [], "created": "2017-05-04T14:56:24.274Z", "modified": "2021-07-06T15:17:27.838Z"}, {"entity": "publication", "iuid": "5eec2eb4880c440a81bb8c33a7186826", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5eec2eb4880c440a81bb8c33a7186826.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5eec2eb4880c440a81bb8c33a7186826"}}, "title": "Genomic mechanisms accounting for the adaptation to parasitism in nematode-trapping fungi.", "authors": [{"family": "Meerupati", "given": "Tejashwari", "initials": "T"}, {"family": "Andersson", "given": "Karl-Magnus", "initials": "KM"}, {"family": "Friman", "given": "Eva", "initials": "E"}, {"family": "Kumar", "given": "Dharmendra", "initials": "D"}, {"family": "Tunlid", "given": "Anders", "initials": "A"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}], "type": "journal article", "published": "2013-11-00", "journal": {"volume": "9", "issn": "1553-7404", "issue": "11", "pages": "e1003909", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Orbiliomycetes is one of the earliest diverging branches of the filamentous ascomycetes. The class contains nematode-trapping fungi that form unique infection structures, called traps, to capture and kill free-living nematodes. The traps have evolved differently along several lineages and include adhesive traps (knobs, nets or branches) and constricting rings. We show, by genome sequencing of the knob-forming species Monacrosporium haptotylum and comparison with the net-forming species Arthrobotrys oligospora, that two genomic mechanisms are likely to have been important for the adaptation to parasitism in these fungi. Firstly, the expansion of protein domain families and the large number of species-specific genes indicated that gene duplication followed by functional diversification had a major role in the evolution of the nematode-trapping fungi. Gene expression indicated that many of these genes are important for pathogenicity. Secondly, gene expression of orthologs between the two fungi during infection indicated that differential regulation was an important mechanism for the evolution of parasitism in nematode-trapping fungi. Many of the highly expressed and highly upregulated M. haptotylum transcripts during the early stages of nematode infection were species-specific and encoded small secreted proteins (SSPs) that were affected by repeat-induced point mutations (RIP). An active RIP mechanism was revealed by lack of repeats, dinucleotide bias in repeats and genes, low proportion of recent gene duplicates, and reduction of recent gene family expansions. The high expression and rapid divergence of SSPs indicate a striking similarity in the infection mechanisms of nematode-trapping fungi and plant and insect pathogens from the crown groups of the filamentous ascomycetes (Pezizomycotina). The patterns of gene family expansions in the nematode-trapping fungi were more similar to plant pathogens than to insect and animal pathogens. The observation of RIP activity in the Orbiliomycetes suggested that this mechanism was present early in the evolution of the filamentous ascomycetes.", "doi": "10.1371/journal.pgen.1003909", "pmid": "24244185", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-13-01003"}, {"db": "pmc", "key": "PMC3828140"}], "notes": [], "created": "2017-05-04T14:56:27.183Z", "modified": "2020-01-21T13:53:20.545Z"}, {"entity": "publication", "iuid": "85f6c19f555c4c98970dbe95b129cc87", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85f6c19f555c4c98970dbe95b129cc87.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85f6c19f555c4c98970dbe95b129cc87"}}, "title": "Proteins of novel lactic acid bacteria from Apis mellifera mellifera: an insight into the production of known extra-cellular proteins during microbial stress.", "authors": [{"family": "Butler", "given": "\u00c8ile", "initials": "\u00c8"}, {"family": "Alsterfjord", "given": "Magnus", "initials": "M"}, {"family": "Olofsson", "given": "Tobias C", "initials": "TC"}, {"family": "Karlsson", "given": "Christofer", "initials": "C"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "V\u00e1squez", "given": "Alejandra", "initials": "A"}], "type": "journal article", "published": "2013-10-22", "journal": {"volume": "13", "issn": "1471-2180", "issue": null, "pages": "235", "title": "BMC Microbiol.", "issn-l": "1471-2180"}, "abstract": "Lactic acid bacteria (LAB) has been considered a beneficial bacterial group, found as part of the microbiota of diverse hosts, including humans and various animals. However, the mechanisms of how hosts and LAB interact are still poorly understood. Previous work demonstrates that 13 species of Lactobacillus and Bifidobacterium from the honey crop in bees function symbiotically with the honeybee. They protect each other, their hosts, and the surrounding environment against severe bee pathogens, bacteria, and yeasts. Therefore, we hypothesized that these LAB under stress, i.e. in their natural niche in the honey crop, are likely to produce bioactive substances with antimicrobial activity.\n\nThe genomic analysis of the LAB demonstrated varying genome sizes ranging from 1.5 to 2.2 mega-base pairs (Mbps) which points out a clear difference within the protein gene content, as well as specialized functions in the honeybee microbiota and their adaptation to their host. We demonstrate a clear variation between the secreted proteins of the symbiotic LAB when subjected to microbial stressors. We have identified that 10 of the 13 LAB produced extra-cellular proteins of known or unknown function in which some are arranged in interesting putative operons that may be involved in antimicrobial action, host interaction, or biofilm formation. The most common known extra-cellular proteins secreted were enzymes, DNA chaperones, S-layer proteins, bacteriocins, and lysozymes. A new bacteriocin may have been identified in one of the LAB symbionts while many proteins with unknown functions were produced which must be investigated further.\n\nThe 13 LAB symbionts likely play different roles in their natural environment defending their niche and their host and participating in the honeybee's food production. These roles are partly played through producing extracellular proteins on exposure to microbial stressors widely found in natural occurring flowers. Many of these secreted proteins may have a putative antimicrobial function. In the future, understanding these processes in this complicated environment may lead to novel applications of honey crop LAB proteins.", "doi": "10.1186/1471-2180-13-235", "pmid": "24148670", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "1471-2180-13-235"}, {"db": "pmc", "key": "PMC4015849"}, {"db": "GENBANK", "key": "KC776061"}, {"db": "GENBANK", "key": "KC776062"}, {"db": "GENBANK", "key": "KC776063"}, {"db": "GENBANK", "key": "KC776064"}, {"db": "GENBANK", "key": "KC776065"}, {"db": "GENBANK", "key": "KC776066"}, {"db": "GENBANK", "key": "KC776067"}, {"db": "GENBANK", "key": "KC776068"}, {"db": "GENBANK", "key": "KC776069"}, {"db": "GENBANK", "key": "KC776070"}, {"db": "GENBANK", "key": "KC776071"}, {"db": "GENBANK", "key": "KC776073"}, {"db": "GENBANK", "key": "KC776074"}, {"db": "GENBANK", "key": "KC776075"}, {"db": "GENBANK", "key": "KC776076"}, {"db": "GENBANK", "key": "KC776077"}, {"db": "GENBANK", "key": "KC776078"}, {"db": "GENBANK", "key": "KC776079"}, {"db": "GENBANK", "key": "KC776080"}, {"db": "GENBANK", "key": "KC776081"}, {"db": "GENBANK", "key": "KC776082"}, {"db": "GENBANK", "key": "KC776083"}, {"db": "GENBANK", "key": "KC776084"}, {"db": "GENBANK", "key": "KC776085"}, {"db": "GENBANK", "key": "KC776086"}, {"db": "GENBANK", "key": "KC776087"}, {"db": "GENBANK", "key": "KC776088"}, {"db": "GENBANK", "key": "KC776089"}, {"db": "GENBANK", "key": "KC776090"}, {"db": "GENBANK", "key": "KC776091"}, {"db": "GENBANK", "key": "KC776092"}, {"db": "GENBANK", "key": "KC776093"}, {"db": "GENBANK", "key": "KC776094"}, {"db": "GENBANK", "key": "KC776095"}, {"db": "GENBANK", "key": "KC776096"}, {"db": "GENBANK", "key": "KC776097"}, {"db": "GENBANK", "key": "KC776098"}, {"db": "GENBANK", "key": "KC776099"}, {"db": "GENBANK", "key": "KC776100"}, {"db": "GENBANK", "key": "KC776101"}, {"db": "GENBANK", "key": "KC776102"}, {"db": "GENBANK", "key": "KC776103"}, {"db": "GENBANK", "key": "KC776104"}, {"db": "GENBANK", "key": "KC776105"}, {"db": "GENBANK", "key": "KC776106"}, {"db": "GENBANK", "key": "KC776107"}, {"db": "GENBANK", "key": "KC776108"}, {"db": "GENBANK", "key": "KC776109"}, {"db": "GENBANK", "key": "KC776110"}, {"db": "GENBANK", "key": "KC776111"}, {"db": "GENBANK", "key": "KC789963"}, {"db": "GENBANK", "key": "KC789964"}, {"db": "GENBANK", "key": "KC789965"}, {"db": "GENBANK", "key": "KC789966"}, {"db": "GENBANK", "key": "KC789967"}, {"db": "GENBANK", "key": "KC789968"}, {"db": "GENBANK", "key": "KC789969"}, {"db": "GENBANK", "key": "KC789970"}, {"db": "GENBANK", "key": "KC789971"}, {"db": "GENBANK", "key": "KC789972"}, {"db": "GENBANK", "key": "KC789973"}, {"db": "GENBANK", "key": "KC789974"}, {"db": "GENBANK", "key": "KC789975"}, {"db": "GENBANK", "key": "KC789976"}, {"db": "GENBANK", "key": "KC789977"}, {"db": "GENBANK", "key": "KC789978"}, {"db": "GENBANK", "key": "KC789979"}, {"db": "GENBANK", "key": "KC789980"}, {"db": "GENBANK", "key": "KC789981"}, {"db": "GENBANK", "key": "KC789982"}, {"db": "GENBANK", "key": "KC789983"}, {"db": "GENBANK", "key": "KC789984"}, {"db": "GENBANK", "key": "KC789985"}, {"db": "GENBANK", "key": "KC789986"}, {"db": "GENBANK", "key": "KC789987"}, {"db": "GENBANK", "key": "KC789988"}, {"db": "GENBANK", "key": "KC789989"}, {"db": "GENBANK", "key": "KC789990"}, {"db": "GENBANK", "key": "KC789991"}, {"db": "GENBANK", "key": "KC789992"}, {"db": "GENBANK", "key": "KC789993"}, {"db": "GENBANK", "key": "KC789994"}, {"db": "GENBANK", "key": "KC789995"}, {"db": "GENBANK", "key": "KC789996"}, {"db": "GENBANK", "key": "KC789997"}, {"db": "GENBANK", "key": "KC789998"}, {"db": "GENBANK", "key": "KC789999"}, {"db": "GENBANK", "key": "KC790000"}, {"db": "GENBANK", "key": "KC790001"}, {"db": "GENBANK", "key": "KC790002"}, {"db": "GENBANK", "key": "KC790003"}, {"db": "GENBANK", "key": "KC790004"}, {"db": "GENBANK", "key": "KC790005"}, {"db": "GENBANK", "key": "KC790006"}, {"db": "GENBANK", "key": "KC790007"}, {"db": "GENBANK", "key": "KC790008"}, {"db": "GENBANK", "key": "KC790009"}, {"db": "GENBANK", "key": "KC790010"}, {"db": "GENBANK", "key": "KC790011"}, {"db": "GENBANK", "key": "KC790012"}, {"db": "GENBANK", "key": "KC790013"}, {"db": "GENBANK", "key": "KC790014"}, {"db": "GENBANK", "key": "KC790015"}, {"db": "GENBANK", "key": "KC790016"}, {"db": "GENBANK", "key": "KC790017"}, {"db": "GENBANK", "key": "KC790018"}, {"db": "GENBANK", "key": "KC801035"}], "notes": [], "created": "2017-05-04T14:56:21.844Z", "modified": "2020-01-21T13:53:20.622Z"}, {"entity": "publication", "iuid": "21a96555ec1b4b9faeb9d22a4c6c6c25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/21a96555ec1b4b9faeb9d22a4c6c6c25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/21a96555ec1b4b9faeb9d22a4c6c6c25"}}, "title": "Transcriptome signatures in Helicobacter pylori-infected mucosa identifies acidic mammalian chitinase loss as a corpus atrophy marker.", "authors": [{"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Thorell", "given": "Kaisa", "initials": "K"}, {"family": "Worah", "given": "Kuntal", "initials": "K"}, {"family": "Wang", "given": "Shugui", "initials": "S"}, {"family": "Hibberd", "given": "Martin Lloyd", "initials": "ML"}, {"family": "Sj\u00f6vall", "given": "Henrik", "initials": "H"}, {"family": "Pettersson", "given": "Sven", "initials": "S"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Lundin", "given": "Samuel B", "initials": "SB"}], "type": "journal article", "published": "2013-10-11", "journal": {"volume": "6", "issn": "1755-8794", "issue": null, "pages": "41", "title": "BMC Med Genomics", "issn-l": "1755-8794"}, "abstract": "The majority of gastric cancer cases are believed to be caused by chronic infection with the bacterium Helicobacter pylori, and atrophic corpus gastritis is a predisposing condition to gastric cancer development. We aimed to increase understanding of the molecular details of atrophy by performing a global transcriptome analysis of stomach tissue.\n\nBiopsies from patients with different stages of H. pylori infection were taken from both the antrum and corpus mucosa and analyzed on microarrays. The stages included patients without current H. pylori infection, H. pylori-infected without corpus atrophy and patients with current or past H. pylori-infection with corpus-predominant atrophic gastritis.\n\nUsing clustering and integrated analysis, we found firm evidence for antralization of the corpus mucosa of atrophy patients. This antralization harbored gain of gastrin expression, as well as loss of expression of corpus-related genes, such as genes associated with acid production, energy metabolism and blood clotting. The analyses provided detailed molecular evidence for simultaneous intestinal metaplasia (IM) and spasmolytic polypeptide expressing metaplasia (SPEM) in atrophic corpus tissue. Finally, acidic mammalian chitinase, a chitin-degrading enzyme produced by chief cells, was shown to be strongly down-regulated in corpus atrophy.\n\nTranscriptome analysis revealed several gene groups which are related to development of corpus atrophy, some of which were increased also in H. pylori-infected non-atrophic patients. Furthermore, loss of acidic chitinase expression is a promising marker for corpus atrophy.", "doi": "10.1186/1755-8794-6-41", "pmid": "24119614", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "1755-8794-6-41"}, {"db": "pmc", "key": "PMC4015281"}], "notes": [], "created": "2017-05-04T14:56:21.543Z", "modified": "2021-07-05T13:05:37.549Z"}, {"entity": "publication", "iuid": "dc5fe3e123854fb6b55ca080222083e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc5fe3e123854fb6b55ca080222083e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc5fe3e123854fb6b55ca080222083e0"}}, "title": "Molecular characterization of the \u03b1-subunit of Na\u207a/K\u207a ATPase from the euryhaline barnacle Balanus improvisus reveals multiple genes and differential expression of alternative splice variants.", "authors": [{"family": "Lind", "given": "Ulrika", "initials": "U"}, {"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "Wrange", "given": "Anna-Lisa", "initials": "AL"}, {"family": "Sundell", "given": "Kristina S", "initials": "KS"}, {"family": "Jonsson", "given": "Per R", "initials": "PR"}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C"}, {"family": "Havenhand", "given": "Jonathan", "initials": "J"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2013-10-09", "journal": {"volume": "8", "issn": "1932-6203", "issue": "10", "pages": "e77069", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The euryhaline bay barnacle Balanus improvisus has one of the broadest salinity tolerances of any barnacle species. It is able to complete its life cycle in salinities close to freshwater (3 PSU) up to fully marine conditions (35 PSU) and is regarded as one of few truly brackish-water species. Na\u207a/K\u207a ATPase (NAK) has been shown to be important for osmoregulation when marine organisms are challenged by changing salinities, and we therefore cloned and examined the expression of different NAKs from B. improvisus. We found two main gene variants, NAK1 and NAK2, which were approximately 70% identical at the protein level. The NAK1 mRNA existed in a long and short variant with the encoded proteins differing only by 27 N-terminal amino acids. This N-terminal stretch was coded for by a separate exon, and the two variants of NAK1 mRNAs appeared to be created by alternative splicing. We furthermore showed that the two NAK1 isoforms were differentially expressed in different life stages and in various tissues of adult barnacle, i.e the long isoform was predominant in cyprids and in adult cirri. In barnacle cyprid larvae that were exposed to a combination of different salinities and pCO2 levels, the expression of the long NAK1 mRNA increased relative to the short in low salinities. We suggest that the alternatively spliced long variant of the Nak1 protein might be of importance for osmoregulation in B. improvisus in low salinity conditions.", "doi": "10.1371/journal.pone.0077069", "pmid": "24130836", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-40484"}, {"db": "pmc", "key": "PMC3793950"}, {"db": "GENBANK", "key": "KC357568"}, {"db": "GENBANK", "key": "KC357569"}, {"db": "GENBANK", "key": "KC357570"}], "notes": [], "created": "2017-05-04T14:56:27.783Z", "modified": "2020-01-21T13:53:20.916Z"}, {"entity": "publication", "iuid": "0a743e63bdd2424f925baf5c563bbc0d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a743e63bdd2424f925baf5c563bbc0d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a743e63bdd2424f925baf5c563bbc0d"}}, "title": "Structural diversity of signal recognition particle RNAs in plastids.", "authors": [{"family": "Rosenblad", "given": "Magnus Alm", "initials": "MA"}, {"family": "Tr\u00e4ger", "given": "Chantal", "initials": "C"}, {"family": "Sch\u00fcnemann", "given": "Danja", "initials": "D"}], "type": "journal article", "published": "2013-10-00", "journal": {"volume": "8", "issn": "1559-2324", "issue": "10", "pages": "doi: 10.4161/psb.26848", "title": "Plant Signal Behav", "issn-l": "1559-2316"}, "abstract": "One of the pathways for protein targeting to the plasma membrane in bacteria utilizes the co-translationally acting signal recognition particle (SRP), a universally conserved ribonucleoprotein complex consisting of a 54 kDa protein and a functional RNA. An interesting exception is the higher plant chloroplast SRP, which lacks the otherwise essential RNA component. Furthermore, green plant chloroplasts have an additional post-translational SRP-dependent transport system in which the chloroplast-specific cpSRP43 protein binds to imported substrate proteins and to the conserved 54 kDa SRP subunit (cpSRP54). While homologs to the bacterial SRP protein and RNA component previously have been identified in genome sequences of red algae and diatoms, a recent study investigated the evolution of the green plant SRP system.1 Analysis of hundreds of plastid and nuclear genomes showed a surprising pattern of multiple losses of the plastid SRP RNA during evolution and a widespread presence in all non-spermatophyte plants and green algae. Contrary to expectations, all green organisms that have an identified cpSRP RNA also contain a cpSRP43. Notably, the structure of the plastid SRP RNAs is much more diverse than that of bacterial SRP RNAs. The apical GNRA tetraloop is only conserved in organisms of the red lineage and basal organisms of the green lineage, whereas further chloroplast SRP RNAs are characterized by atypical, mostly enlarged apical loops.", "doi": "10.4161/psb.26848", "pmid": "24494244", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:26.872Z", "modified": "2020-01-21T13:53:21.747Z"}, {"entity": "publication", "iuid": "8d3ee82789cd475d9bf3c5b4a32d3dd2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d3ee82789cd475d9bf3c5b4a32d3dd2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d3ee82789cd475d9bf3c5b4a32d3dd2"}}, "title": "Improved production of membrane proteins in Escherichia coli by selective codon substitutions.", "authors": [{"family": "N\u00f8rholm", "given": "Morten H H", "initials": "MH"}, {"family": "Toddo", "given": "Stephen", "initials": "S"}, {"family": "Virkki", "given": "Minttu T I", "initials": "MT"}, {"family": "Light", "given": "Sara", "initials": "S"}, {"family": "von Heijne", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-4490-8569", "researcher": {"href": "https://publications.scilifelab.se/researcher/f663c0a9e9e1455cbbf8e6aea13af4a9.json"}}, {"family": "Daley", "given": "Daniel O", "initials": "DO"}], "type": "journal article", "published": "2013-08-02", "journal": {"volume": "587", "issn": "1873-3468", "issue": "15", "pages": "2352-2358", "title": "FEBS Lett.", "issn-l": "0014-5793"}, "abstract": "Membrane proteins are extremely challenging to produce in sufficient quantities for biochemical and structural analysis and there is a growing demand for solutions to this problem. In this study we attempted to improve expression of two difficult-to-express coding sequences (araH and narK) for membrane transporters. For both coding sequences, synonymous codon substitutions in the region adjacent to the AUG start led to significant improvements in expression, whereas multi-parameter sequence optimization of codons throughout the coding sequence failed. We conclude that coding sequences can be re-wired for high-level protein expression by selective engineering of the 5' coding sequence with synonymous codons, thus circumventing the need to consider whole sequence optimization.", "doi": "10.1016/j.febslet.2013.05.063", "pmid": "23769986", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "S0014-5793(13)00442-0"}], "notes": [], "created": "2017-05-04T14:56:23.649Z", "modified": "2021-06-16T15:21:58.662Z"}, {"entity": "publication", "iuid": "f8642f169e964e94bb3ea82333586b5d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8642f169e964e94bb3ea82333586b5d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8642f169e964e94bb3ea82333586b5d"}}, "title": "Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum.", "authors": [{"family": "Andersson", "given": "Karl-Magnus", "initials": "KM"}, {"family": "Meerupati", "given": "Tejashwari", "initials": "T"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Friman", "given": "Eva", "initials": "E"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Tunlid", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2013-08-00", "journal": {"volume": "79", "issn": "1098-5336", "issue": "16", "pages": "4993-5004", "title": "Appl. Environ. Microbiol.", "issn-l": "0099-2240"}, "abstract": "Many nematophagous fungi use morphological structures called traps to capture nematodes by adhesion or mechanically. To better understand the cellular functions of adhesive traps, the trap cell proteome of the fungus Monacrosporium haptotylum was characterized. The trap of M. haptotylum consists of a unicellular structure called a knob that develops at the apex of a hypha. Proteins extracted from knobs and mycelia were analyzed using SDS-PAGE and liquid chromatography-tandem mass spectrometry (LC-MS-MS). The peptide sequences were matched against predicted gene models from the recently sequenced M. haptotylum genome. In total, 336 proteins were identified, with 54 expressed at significantly higher levels in the knobs than in the mycelia. The upregulated knob proteins included peptidases, small secreted proteins with unknown functions, and putative cell surface adhesins containing carbohydrate-binding domains, including the WSC domain. Phylogenetic analysis showed that all upregulated WSC domain proteins belonged to a large, expanded cluster of paralogs in M. haptotylum. Several peptidases and homologs of experimentally verified proteins in other pathogenic fungi were also upregulated in the knob proteome. Complementary profiling of gene expression at the transcriptome level showed poor correlation between the upregulation of knob proteins and their corresponding transcripts. We propose that the traps of M. haptotylum contain many of the proteins needed in the early stages of infection and that the trap cells can tightly control the translation and degradation of these proteins to minimize the cost of protein synthesis.", "doi": "10.1128/AEM.01390-13", "pmid": "23770896", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "AEM.01390-13"}, {"db": "pmc", "key": "PMC3754708"}], "notes": [], "created": "2017-05-04T14:56:20.335Z", "modified": "2020-01-21T13:53:20.969Z"}, {"entity": "publication", "iuid": "ae438fb9b85c4feab4abc585bcd67553", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae438fb9b85c4feab4abc585bcd67553.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae438fb9b85c4feab4abc585bcd67553"}}, "title": "Response of Acidithiobacillus\u00a0caldus toward suboptimal pH conditions.", "authors": [{"family": "Mangold", "given": "Stefanie", "initials": "S"}, {"family": "Rao Jonna", "given": "Venkateswara", "initials": "V"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2013-07-00", "journal": {"volume": "17", "issn": "1433-4909", "issue": "4", "pages": "689-696", "title": "Extremophiles", "issn-l": "1431-0651"}, "abstract": "Maintenance of a circumneutral intracellular pH is important for any organism. Acidophilic microorganisms thrive at low pH while maintaining their intracellular pH around 6.5. However, the mechanisms contributing to acidophile pH homeostasis are not well characterized. The authors investigated the proteomic response and cytoplasmic membrane fatty acid profiles of Acidithiobacillus caldus toward three pH values: 1.1, 2.5, and 4.0. Major rearrangements were observed but lower pH elicited larger changes. Differentially expressed transcription factors suggested tight transcriptional control of pH induced genes. Enzymes involved in sulfur metabolism were up-regulated at pH 1.1 suggesting either that: (1) cells required more energy for maintenance or (2) increased metabolic activity was a specific acid stress response to export intracellular protons via 1\u00b0 electron transport proton pumps. Furthermore, glutamate decarboxylase, an important enzyme in Escherichia coli acid resistance, was uniquely expressed at pH 1.1. Other proteins previously shown to be involved in neutrophilic acid response, such as spermidine synthase, PspA, and toluene tolerance protein, were differentially expressed in At. caldus but require further investigation to show a direct link to pH homeostasis. Their roles in acidophilic organisms are discussed. Active modulation of fatty acid profiles was detected and suggested a more rigid membrane at low pH.", "doi": "10.1007/s00792-013-0553-5", "pmid": "23712908", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:23.349Z", "modified": "2020-01-21T13:53:20.770Z"}, {"entity": "publication", "iuid": "ef809a1996704838a59705082f7f5b37", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef809a1996704838a59705082f7f5b37.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef809a1996704838a59705082f7f5b37"}}, "title": "Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data.", "authors": [{"family": "Lampa", "given": "Samuel", "initials": "S"}, {"family": "Dahl\u00f6", "given": "Martin", "initials": "M"}, {"family": "Olason", "given": "Pall I", "initials": "PI"}, {"family": "Hagberg", "given": "Jonas", "initials": "J"}, {"family": "Spjuth", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2013-06-25", "journal": {"volume": "2", "issn": "2047-217X", "issue": "1", "pages": "9", "title": "Gigascience", "issn-l": "2047-217X"}, "abstract": ": Analyzing and storing data and results from next-generation sequencing (NGS) experiments is a challenging task, hampered by ever-increasing data volumes and frequent updates of analysis methods and tools. Storage and computation have grown beyond the capacity of personal computers and there is a need for suitable e-infrastructures for processing. Here we describe UPPNEX, an implementation of such an infrastructure, tailored to the needs of data storage and analysis of NGS data in Sweden serving various labs and multiple instruments from the major sequencing technology platforms. UPPNEX comprises resources for high-performance computing, large-scale and high-availability storage, an extensive bioinformatics software suite, up-to-date reference genomes and annotations, a support function with system and application experts as well as a web portal and support ticket system. UPPNEX applications are numerous and diverse, and include whole genome-, de novo- and exome sequencing, targeted resequencing, SNP discovery, RNASeq, and methylation analysis. There are over 300 projects that utilize UPPNEX and include large undertakings such as the sequencing of the flycatcher and Norwegian spruce. We describe the strategic decisions made when investing in hardware, setting up maintenance and support, allocating resources, and illustrate major challenges such as managing data growth. We conclude with summarizing our experiences and observations with UPPNEX to date, providing insights into the successful and less successful decisions made.", "doi": "10.1186/2047-217X-2-9", "pmid": "23800020", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "2047-217X-2-9"}, {"db": "pmc", "key": "PMC3704847"}], "notes": [], "created": "2017-05-04T14:56:23.957Z", "modified": "2020-01-21T13:53:20.946Z"}, {"entity": "publication", "iuid": "bbbb90a3332e4601827c71c44bfacee9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bbbb90a3332e4601827c71c44bfacee9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bbbb90a3332e4601827c71c44bfacee9"}}, "title": "Vandetanib combined with a p38 MAPK inhibitor synergistically reduces glioblastoma cell survival.", "authors": [{"family": "Sooman", "given": "Linda", "initials": "L"}, {"family": "Lennartsson", "given": "Johan", "initials": "J"}, {"family": "Gullbo", "given": "Joachim", "initials": "J"}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Tsakonas", "given": "Georgios", "initials": "G"}, {"family": "Johansson", "given": "Fredrik", "initials": "F"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Jaiswal", "given": "Archita", "initials": "A"}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Alafuzoff", "given": "Irina", "initials": "I"}, {"family": "Popova", "given": "Svetlana", "initials": "S"}, {"family": "Blomquist", "given": "Erik", "initials": "E"}, {"family": "Ekman", "given": "Simon", "initials": "S"}], "type": "journal article", "published": "2013-06-20", "journal": {"volume": "30", "issn": "1559-131X", "issue": "3", "pages": "638", "title": "Med. Oncol.", "issn-l": "1357-0560"}, "abstract": "The survival for patients with high-grade glioma is poor, and only a limited number of patients respond to the therapy. The aim of this study was to analyze the significance of using p38 MAPK phosphorylation as a prognostic marker in high-grade glioma patients and as a therapeutic target in combination chemotherapy with vandetanib. p38 MAPK phosphorylation was analyzed with immunohistochemistry in 90 high-grade glioma patients. Correlation between p38 MAPK phosphorylation and overall survival was analyzed with Mann-Whitney U test analysis. The effects on survival of glioblastoma cells of combining vandetanib with the p38 MAPK inhibitor SB 203580 were analyzed in vitro with the median-effect method with the fluorometric microculture cytotoxicity assay. Two patients had phosphorylated p38 MAPK in both the cytoplasm and nucleus, and these two presented with worse survival than patients with no detectable p38 MAPK phosphorylation or phosphorylated p38 MAPK only in the nucleus. This was true for both high-grade glioma patients (WHO grade III and IV, n = 90, difference in median survival: 6.1 months, 95 % CI [0.20, 23], p = 0.039) and for the subgroup with glioblastoma patients (WHO grade IV, n = 70, difference in median survival: 6.1 months, 95 % CI [0.066, 23], p = 0.043). The combination of vandetanib and the p38 MAPK inhibitor SB 203580 had synergistic effects on cell survival for glioblastoma-derived cells in vitro. In conclusion, p38 MAPK phosphorylation may be a prognostic marker for high-grade glioma patients, and vandetanib combined with a p38 MAPK inhibitor may be useful combination chemotherapy for glioma patients.", "doi": "10.1007/s12032-013-0638-0", "pmid": "23783486", "labels": {"Tissue Profiling": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:00.970Z", "modified": "2020-01-21T13:53:20.826Z"}, {"entity": "publication", "iuid": "d124b89b92db4a0c8b4ec14ab8bb8485", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d124b89b92db4a0c8b4ec14ab8bb8485.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d124b89b92db4a0c8b4ec14ab8bb8485"}}, "title": "The impact of splicing on protein domain architecture.", "authors": [{"family": "Light", "given": "Sara", "initials": "S"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "23", "issn": "1879-033X", "issue": "3", "pages": "451-458", "title": "Curr. Opin. Struct. Biol.", "issn-l": "0959-440X"}, "abstract": "Many proteins are composed of protein domains, functional units of common descent. Multidomain forms are common in all eukaryotes making up more than half of the proteome and the evolution of novel domain architecture has been accelerated in metazoans. It is also becoming increasingly clear that alternative splicing is prevalent among vertebrates. Given that protein domains are defined as structurally, functionally and evolutionarily distinct units, one may speculate that some alternative splicing events may lead to clean excisions of protein domains, thus generating a number of different domain architectures from one gene template. However, recent findings indicate that smaller alternative splicing events, in particular in disordered regions, might be more prominent than domain architectural changes. The problem of identifying protein isoforms is, however, still not resolved. Clearly, many splice forms identified through detection of mRNA sequences appear to produce 'nonfunctional' proteins, such as proteins with missing internal secondary structure elements. Here, we review the state of the art methods for identification of functional isoforms and present a summary of what is known, thus far, about alternative splicing with regard to protein domain architectures.", "doi": "10.1016/j.sbi.2013.02.013", "pmid": "23562110", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "S0959-440X(13)00043-2"}], "notes": [], "created": "2017-05-04T14:56:22.753Z", "modified": "2020-01-21T13:53:20.880Z"}, {"entity": "publication", "iuid": "c403f99f84324b52bc5e13ce42920772", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c403f99f84324b52bc5e13ce42920772.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c403f99f84324b52bc5e13ce42920772"}}, "title": "The Norway spruce genome sequence and conifer genome evolution.", "authors": [{"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Wetterbom", "given": "Anna", "initials": "A"}, {"family": "Zuccolo", "given": "Andrea", "initials": "A"}, {"family": "Lin", "given": "Yao-Cheng", "initials": "YC"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Giacomello", "given": "Stefania", "initials": "S"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Vicedomini", "given": "Riccardo", "initials": "R"}, {"family": "Sahlin", "given": "Kristoffer", "initials": "K"}, {"family": "Sherwood", "given": "Ellen", "initials": "E", "orcid": "0000-0003-3158-9957", "researcher": {"href": "https://publications.scilifelab.se/researcher/f17cb04d51c24494b9eab42010fd1a04.json"}}, {"family": "Elfstrand", "given": "Malin", "initials": "M"}, {"family": "Gramzow", "given": "Lydia", "initials": "L"}, {"family": "Holmberg", "given": "Kristina", "initials": "K"}, {"family": "H\u00e4llman", "given": "Jimmie", "initials": "J"}, {"family": "Keech", "given": "Olivier", "initials": "O"}, {"family": "Klasson", "given": "Lisa", "initials": "L"}, {"family": "Koriabine", "given": "Maxim", "initials": "M"}, {"family": "Kucukoglu", "given": "Melis", "initials": "M"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Luthman", "given": "Johannes", "initials": "J"}, {"family": "Lysholm", "given": "Fredrik", "initials": "F"}, {"family": "Niittyl\u00e4", "given": "Totte", "initials": "T"}, {"family": "Olson", "given": "Ake", "initials": "A"}, {"family": "Rilakovic", "given": "Nemanja", "initials": "N"}, {"family": "Ritland", "given": "Carol", "initials": "C"}, {"family": "Rossell\u00f3", "given": "Josep A", "initials": "JA"}, {"family": "Sena", "given": "Juliana", "initials": "J"}, {"family": "Svensson", "given": "Thomas", "initials": "T", "orcid": "0000-0002-9190-2979", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc636683ece84dc4ac3e4d10df0c7a49.json"}}, {"family": "Talavera-L\u00f3pez", "given": "Carlos", "initials": "C"}, {"family": "Thei\u00dfen", "given": "G\u00fcnter", "initials": "G"}, {"family": "Tuominen", "given": "Hannele", "initials": "H"}, {"family": "Vanneste", "given": "Kevin", "initials": "K"}, {"family": "Wu", "given": "Zhi-Qiang", "initials": "ZQ"}, {"family": "Zhang", "given": "Bo", "initials": "B"}, {"family": "Zerbe", "given": "Philipp", "initials": "P"}, {"family": "Arvestad", "given": "Lars", "initials": "L"}, {"family": "Bhalerao", "given": "Rishikesh", "initials": "R"}, {"family": "Bohlmann", "given": "Joerg", "initials": "J"}, {"family": "Bousquet", "given": "Jean", "initials": "J"}, {"family": "Garcia Gil", "given": "Rosario", "initials": "R"}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "de Jong", "given": "Pieter", "initials": "P"}, {"family": "MacKay", "given": "John", "initials": "J"}, {"family": "Morgante", "given": "Michele", "initials": "M"}, {"family": "Ritland", "given": "Kermit", "initials": "K"}, {"family": "Sundberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Thompson", "given": "Stacey Lee", "initials": "SL"}, {"family": "Van de Peer", "given": "Yves", "initials": "Y"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Jansson", "given": "Stefan", "initials": "S"}], "type": "journal article", "published": "2013-05-30", "journal": {"volume": "497", "issn": "1476-4687", "issue": "7451", "pages": "579-584", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.", "doi": "10.1038/nature12211", "pmid": "23698360", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support for Computational Resources": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "nature12211"}], "notes": [], "created": "2017-05-04T14:56:13.625Z", "modified": "2024-01-16T13:48:50.828Z"}, {"entity": "publication", "iuid": "582a8c67757947af8da206b409f290b2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/582a8c67757947af8da206b409f290b2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/582a8c67757947af8da206b409f290b2"}}, "title": "Membrane protein shaving with thermolysin can be used to evaluate topology predictors.", "authors": [{"family": "Bendz", "given": "Maria", "initials": "M"}, {"family": "Skwark", "given": "Marcin", "initials": "M"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Granholm", "given": "Viktor", "initials": "V"}, {"family": "Cristobal", "given": "Susana", "initials": "S"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2013-05-00", "journal": {"volume": "13", "issn": "1615-9861", "issue": "9", "pages": "1467-1480", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "Topology analysis of membrane proteins can be obtained by enzymatic shaving in combination with MS identification of peptides. Ideally, such analysis could provide quite detailed information about the membrane spanning regions. Here, we examine the ability of some shaving enzymes to provide large-scale analysis of membrane proteome topologies. To compare different shaving enzymes, we first analyzed the detected peptides from two over-expressed proteins. Second, we analyzed the peptides from non-over-expressed Escherichia coli membrane proteins with known structure to evaluate the shaving methods. Finally, the identified peptides were used to test the accuracy of a number of topology predictors. At the end we suggest that the usage of thermolysin, an enzyme working at the natural pH of the cell for membrane shaving, is superior because: (i) we detect a similar number of peptides and proteins using thermolysin and trypsin; (ii) thermolysin shaving can be run at a natural pH and (iii) the incubation time is quite short. (iv) Fewer detected peptides from thermolysin shaving originate from the transmembrane regions. Using thermolysin shaving we can also provide a clear separation between the best and the less accurate topology predictors, indicating that using data from shaving can provide valuable information when developing new topology predictors.", "doi": "10.1002/pmic.201200517", "pmid": "23512833", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:28.081Z", "modified": "2020-01-21T13:53:20.509Z"}, {"entity": "publication", "iuid": "a011177aefea4d8dbac7e0bc51c6509f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a011177aefea4d8dbac7e0bc51c6509f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a011177aefea4d8dbac7e0bc51c6509f"}}, "title": "Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins.", "authors": [{"family": "Light", "given": "Sara", "initials": "S"}, {"family": "Sagit", "given": "Rauan", "initials": "R"}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2013-05-00", "journal": {"volume": "1834", "issn": "0006-3002", "issue": "5", "pages": "890-897", "title": "Biochim. Biophys. Acta", "issn-l": null}, "abstract": "Proteins evolve through point mutations as well as by insertions and deletions (indels). During the last decade it has become apparent that protein regions that do not fold into three-dimensional structures, i.e. intrinsically disordered regions, are quite common. Here, we have studied the relationship between protein disorder and indels using HMM-HMM pairwise alignments in two sets of orthologous eukaryotic protein pairs. First, we show that disordered residues are much more frequent among indel residues than among aligned residues and, also are more prevalent among indels than in coils. Second, we observed that disordered residues are particularly common in longer indels. Disordered indels of short-to-medium size are prevalent in the non-terminal regions of proteins while the longest indels, ordered and disordered alike, occur toward the termini of the proteins where new structural units are comparatively well tolerated. Finally, while disordered regions often evolve faster than ordered regions and disorder is common in indels, there are some previously recognized protein families where the disordered region is more conserved than the ordered region. We find that these rare proteins are often involved in information processes, such as RNA processing and translation. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.", "doi": "10.1016/j.bbapap.2013.01.002", "pmid": "23333420", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "S1570-9639(13)00007-1"}], "notes": [], "created": "2017-05-04T14:56:20.632Z", "modified": "2020-01-21T13:53:20.724Z"}, {"entity": "publication", "iuid": "401ede1efc9b4c878a4b77f8ca000c4a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/401ede1efc9b4c878a4b77f8ca000c4a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/401ede1efc9b4c878a4b77f8ca000c4a"}}, "title": "An adaptive alignment algorithm for quality-controlled label-free LC-MS.", "authors": [{"family": "Sandin", "given": "Marianne", "initials": "M"}, {"family": "Ali", "given": "Ashfaq", "initials": "A"}, {"family": "Hansson", "given": "Karin", "initials": "K"}, {"family": "M\u00e5nsson", "given": "Olle", "initials": "O"}, {"family": "Andreasson", "given": "Erik", "initials": "E"}, {"family": "Resj\u00f6", "given": "Svante", "initials": "S"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}], "type": "comparative study", "published": "2013-05-00", "journal": {"volume": "12", "issn": "1535-9484", "issue": "5", "pages": "1407-1420", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Label-free quantification using precursor-based intensities is a versatile workflow for large-scale proteomics studies. The method however requires extensive computational analysis and is therefore in need of robust quality control during the data mining stage. We present a new label-free data analysis workflow integrated into a multiuser software platform. A novel adaptive alignment algorithm has been developed to minimize the possible systematic bias introduced into the analysis. Parameters are estimated on the fly from the data at hand, producing a user-friendly analysis suite. Quality metrics are output in every step of the analysis as well as actively incorporated into the parameter estimation. We furthermore show the improvement of this system by comprehensive comparison to classical label-free analysis methodology as well as current state-of-the-art software.", "doi": "10.1074/mcp.O112.021907", "pmid": "23306530", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "O112.021907"}, {"db": "pmc", "key": "PMC3650348"}], "notes": [], "created": "2017-05-04T14:56:25.730Z", "modified": "2020-01-21T13:53:20.466Z"}, {"entity": "publication", "iuid": "3ba82d89aad14984be5a0cbac09383b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ba82d89aad14984be5a0cbac09383b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ba82d89aad14984be5a0cbac09383b5"}}, "title": "A phylogeny of the highly diverse cup-fungus family Pyronemataceae (Pezizomycetes, Ascomycota) clarifies relationships and evolution of selected life history traits.", "authors": [{"family": "Hansen", "given": "Karen", "initials": "K"}, {"family": "Perry", "given": "Brian A", "initials": "BA"}, {"family": "Dranginis", "given": "Andrew W", "initials": "AW"}, {"family": "Pfister", "given": "Donald H", "initials": "DH"}], "type": "journal article", "published": "2013-05-00", "journal": {"volume": "67", "issn": "1095-9513", "issue": "2", "pages": "311-335", "title": "Mol. Phylogenet. Evol.", "issn-l": "1055-7903"}, "abstract": "Pyronemataceae is the largest and most heterogeneous family of Pezizomycetes. It is morphologically and ecologically highly diverse, comprising saprobic, ectomycorrhizal, bryosymbiotic and parasitic species, occurring in a broad range of habitats (on soil, burnt ground, debris, wood, dung and inside living bryophytes, plants and lichens). To assess the monophyly of Pyronemataceae and provide a phylogenetic hypothesis of the group, we compiled a four-gene dataset including one nuclear ribosomal and three protein-coding genes for 132 distinct Pezizomycetes species (4437 nucleotides with all markers available for 80% of the total 142 included taxa). This is the most comprehensive molecular phylogeny of Pyronemataceae, and Pezizomycetes, to date. Three hundred ninety-four new sequences were generated during this project, with the following numbers for each gene: RPB1 (124), RPB2 (99), EF-1\u03b1 (120) and LSU rDNA (51). The dataset includes 93 unique species from 40 genera of Pyronemataceae, and 34 species from 25 genera representing an additional 12 families of the class. Parsimony, maximum likelihood and Bayesian analyses suggest that Pyronemataceae is paraphyletic due to the nesting of both Ascodesmidaceae and Glaziellaceae within the family. Four lineages with taxa currently classified in the family, the Boubovia, Geopyxis, Pseudombrophila and Pulvinula lineages, form a monophyletic group with Ascodesmidaceae and Glaziellaceae. We advocate the exclusion of these four lineages in order to recognize a monophyletic Pyronemataceae. The genus Coprotus (Thelebolales, Leotiomycetes) is shown to belong to Pezizomycetes, forming a strongly supported monophyletic group with Boubovia. Ten strongly supported lineages are identified within Pyronemataceae s. str. Of these, the Pyropyxis and Otidea lineages are identified as successive sister lineages to the rest of Pyronemataceae s. str. The highly reduced (gymnohymenial) Monascella is shown to belong to Pezizomycetes and is for the first time suggested to be closely related to the cleistothecial Warcupia, as a sister group to the primarily apothecial Otidea. None of the lineages of pyronemataceous taxa identified here correspond to previous families or subfamily classifications. Ancestral character state reconstructions (ASR) using a Bayesian approach support that the ancestors of Pezizomycetes and Pyronemataceae were soil inhabiting and saprobic. Ectomycorrhizae have arisen within both lineages A, B and C of Pezizomycetes and are suggested to have evolved independently seven to eight times within Pyronemataceae s. l., whereas an obligate bryosymbiotic lifestyle has arisen only twice. No reversals to a free-living, saprobic lifestyle have happened from symbiotic or parasitic Pyronemataceae. Specializations to various substrates (e.g. burnt ground and dung) are suggested to have occurred several times in mainly saprobic lineages. Although carotenoids in the apothecia are shown to have arisen at least four times in Pezizomycetes, the ancestor of Pyronemataceae s. str., excluding the Pyropyxis and Otidea lineages, most likely produced carotenoids, which were then subsequently lost in some clades (- and possibly gained again). Excipular hairs were found with a high probability to be absent from apothecia in the deepest nodes of Pezizomycetes and in the ancestor of Pyronemataceae s. str. True hairs are restricted to the core group of Pyronemataceae s. str., but are also found in Lasiobolus (Ascodesmidaceae), the Pseudombrophila lineage and the clade of Chorioactidaceae, Sarcoscyphaceae and Sarcosomataceae. The number of gains and losses of true hairs within Pyronemataceae s. str., however, remains uncertain. The ASR of ascospore guttulation under binary coding (present or absent) indicates that this character is fast evolving and prone to shifts.", "doi": "10.1016/j.ympev.2013.01.014", "pmid": "23403226", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "S1055-7903(13)00051-1"}], "notes": [], "created": "2017-05-04T14:56:26.029Z", "modified": "2020-01-21T13:53:20.458Z"}, {"entity": "publication", "iuid": "84a80a4059fd4217ba39d3a1321ed220", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84a80a4059fd4217ba39d3a1321ed220.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84a80a4059fd4217ba39d3a1321ed220"}}, "title": "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.", "authors": [{"family": "Mayer", "given": "Gerhard", "initials": "G"}, {"family": "Montecchi-Palazzi", "given": "Luisa", "initials": "L"}, {"family": "Ovelleiro", "given": "David", "initials": "D"}, {"family": "Jones", "given": "Andrew R", "initials": "AR"}, {"family": "Binz", "given": "Pierre-Alain", "initials": "PA"}, {"family": "Deutsch", "given": "Eric W", "initials": "EW"}, {"family": "Chambers", "given": "Matthew", "initials": "M"}, {"family": "Kallhardt", "given": "Marius", "initials": "M"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Shofstahl", "given": "James", "initials": "J"}, {"family": "Orchard", "given": "Sandra", "initials": "S"}, {"family": "Vizca\u00edno", "given": "Juan Antonio", "initials": "JA"}, {"family": "Hermjakob", "given": "Henning", "initials": "H"}, {"family": "Stephan", "given": "Christian", "initials": "C"}, {"family": "Meyer", "given": "Helmut E", "initials": "HE"}, {"family": "Eisenacher", "given": "Martin", "initials": "M"}, {"family": "HUPO-PSI Group", "given": null, "initials": null}], "type": "journal article", "published": "2013-03-12", "journal": {"volume": "2013", "issn": "1758-0463", "issue": null, "pages": "bat009", "title": "Database (Oxford)", "issn-l": "1758-0463"}, "abstract": "Controlled vocabularies (CVs), i.e. a collection of predefined terms describing a modeling domain, used for the semantic annotation of data, and ontologies are used in structured data formats and databases to avoid inconsistencies in annotation, to have a unique (and preferably short) accession number and to give researchers and computer algorithms the possibility for more expressive semantic annotation of data. The Human Proteome Organization (HUPO)-Proteomics Standards Initiative (PSI) makes extensive use of ontologies/CVs in their data formats. The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. Owing to the range of topics covered by the CV, collaborative development across several PSI working groups, including proteomics research groups, instrument manufacturers and software vendors, was necessary. In this article, we describe the overall structure of the CV, the process by which it has been developed and is maintained and the dependencies on other ontologies. Database URL: http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo.", "doi": "10.1093/database/bat009", "pmid": "23482073", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "bat009"}, {"db": "pmc", "key": "PMC3594986"}], "notes": [], "created": "2017-05-04T14:56:23.051Z", "modified": "2020-01-21T13:53:20.615Z"}, {"entity": "publication", "iuid": "60def3883784449d9884f29e78eccdc6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/60def3883784449d9884f29e78eccdc6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/60def3883784449d9884f29e78eccdc6"}}, "title": "Origin and evolution of medium chain alcohol dehydrogenases.", "authors": [{"family": "J\u00f6rnvall", "given": "Hans", "initials": "H"}, {"family": "Hedlund", "given": "Joel", "initials": "J"}, {"family": "Bergman", "given": "Tomas", "initials": "T"}, {"family": "Kallberg", "given": "Yvonne", "initials": "Y"}, {"family": "Cederlund", "given": "Ella", "initials": "E"}, {"family": "Persson", "given": "Bengt", "initials": "B", "orcid": "0000-0003-3165-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f116ef0ed146419cb18e742c270c4a.json"}}], "type": "journal article", "published": "2013-02-25", "journal": {"volume": "202", "issn": "1872-7786", "issue": "1-3", "pages": "91-96", "title": "Chem. Biol. Interact.", "issn-l": "0009-2797"}, "abstract": "Different lines of alcohol dehydrogenases (ADHs) have separate superfamily origins, already recognized but now extended and re-evaluated by re-screening of the latest databank update. The short-chain form (SDR) is still the superfamily with most abundant occurrence, most multiple divergence, most prokaryotic emphasis, and most non-complicated architecture. This pattern is compatible with an early appearance at the time of the emergence of prokaryotic cellular life. The medium-chain form (MDR) is also old but second in terms of all the parameters above, and therefore compatible with a second emergence. However, this step appears seemingly earlier than previously considered, and may indicate sub-stages of early emergences at the increased resolution available from the now greater number of data entries. The Zn-MDR origin constitutes a third stage, possibly compatible with the transition to oxidative conditions on earth. Within all these three lines, repeated enzymogeneses gave the present divergence. MDR-ADH origin(s), at a fourth stage, may also be further resolved in multiple or extended modes, but the classical liver MDR-ADH of the liver type can still be traced to a gene duplication ~550 MYA (million years ago), at the early vertebrate radiation, compatible with the post-eon-shift, \"Cambrian explosion\". Classes and isozymes correspond to subsequent and recent duplicatory events, respectively. They illustrate a peculiar pattern with functional and emerging evolutionary distinctions between parent and emerging lines, suggesting a parallelism between duplicatory and mutational events, now also visible at separate sub-stages. Combined, all forms show distinctive patterns at different levels and illustrate correlations with global events. They further show that simple molecular observations on patterns, multiplicities and occurrence give much information, suggesting common divergence rules not much disturbed by horizontal gene transfers after the initial origins.", "doi": "10.1016/j.cbi.2012.11.008", "pmid": "23200944", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "S0009-2797(12)00252-9"}], "notes": [], "created": "2017-05-04T14:56:22.149Z", "modified": "2021-07-05T12:34:46.003Z"}, {"entity": "publication", "iuid": "90ae156bc11f447fb7decb8223931d4f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/90ae156bc11f447fb7decb8223931d4f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/90ae156bc11f447fb7decb8223931d4f"}}, "title": "Classification and nomenclature of the superfamily of short-chain dehydrogenases/reductases (SDRs).", "authors": [{"family": "Persson", "given": "Bengt", "initials": "B", "orcid": "0000-0003-3165-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f116ef0ed146419cb18e742c270c4a.json"}}, {"family": "Kallberg", "given": "Yvonne", "initials": "Y"}], "type": "journal article", "published": "2013-02-25", "journal": {"volume": "202", "issn": "1872-7786", "issue": "1-3", "pages": "111-115", "title": "Chem. Biol. Interact.", "issn-l": "0009-2797"}, "abstract": "The short-chain dehydrogenases/reductases (SDRs) constitute one of the largest protein superfamilies known today. The members are distantly related with typically 20-30% residue identity in pair-wise comparisons. Still, all hitherto structurally known SDRs present a common three-dimensional structure consisting of a Rossmann fold with a parallel beta sheet flanked by three helices on each side. Using hidden Markov models (HMMs), we have developed a semi-automated subclassification system for this huge family. Currently, 75% of all SDR forms have been assigned to one of the 464 families totalling 122,940 proteins. There are 47 human SDR families, corresponding to 75 genes. Most human SDR families (35 families) have only one gene, while 12 have between 2 and 8 genes. For more than half of the human SDR families, the three-dimensional fold is known. The number of SDR members increases considerably every year, but the number of SDR families now starts to converge. The classification method has paved the ground for a sustainable and expandable nomenclature system. Information on the SDR superfamily is continuously updated at http://sdr-enzymes.org/.", "doi": "10.1016/j.cbi.2012.11.009", "pmid": "23200746", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "S0009-2797(12)00253-0"}], "notes": [], "created": "2017-05-04T14:56:22.458Z", "modified": "2021-07-05T12:34:46.037Z"}, {"entity": "publication", "iuid": "82d52b73bd3b4b62839f8b5f7a6d957f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/82d52b73bd3b4b62839f8b5f7a6d957f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/82d52b73bd3b4b62839f8b5f7a6d957f"}}, "title": "Evolution of sperm structure and energetics in passerine birds.", "authors": [{"family": "Rowe", "given": "Melissah", "initials": "M"}, {"family": "Laskemoen", "given": "Terje", "initials": "T"}, {"family": "Johnsen", "given": "Arild", "initials": "A"}, {"family": "Lifjeld", "given": "Jan T", "initials": "JT"}], "type": "journal article", "published": "2013-02-22", "journal": {"volume": "280", "issn": "1471-2954", "issue": "1753", "pages": "20122616", "title": "Proc. Biol. Sci.", "issn-l": "0962-8452"}, "abstract": "Spermatozoa exhibit considerable interspecific variability in size and shape. Our understanding of the adaptive significance of this diversity, however, remains limited. Determining how variation in sperm structure translates into variation in sperm performance will contribute to our understanding of the evolutionary diversification of sperm form. Here, using data from passerine birds, we test the hypothesis that longer sperm swim faster because they have more available energy. We found that sperm with longer midpieces have higher levels of intracellular adenosine triphosphate (ATP), but that greater energy reserves do not translate into faster-swimming sperm. Additionally, we found that interspecific variation in sperm ATP concentration is not associated with the level of sperm competition faced by males. Finally, using Bayesian methods, we compared the evolutionary trajectories of sperm morphology and ATP content, and show that both traits have undergone directional evolutionary change. However, in contrast to recent suggestions in other taxa, we show that changes in ATP are unlikely to have preceded changes in morphology in passerine sperm. These results suggest that variable selective pressures are likely to have driven the evolution of sperm traits in different taxa, and highlight fundamental biological differences between taxa with internal and external fertilization, as well as those with and without sperm storage.", "doi": "10.1098/rspb.2012.2616", "pmid": "23282997", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "rspb.2012.2616"}, {"db": "pmc", "key": "PMC3574354"}], "notes": [], "created": "2017-05-04T14:56:26.554Z", "modified": "2020-01-21T13:53:20.608Z"}, {"entity": "publication", "iuid": "b49daef208484f799d58336b9e5235cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b49daef208484f799d58336b9e5235cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b49daef208484f799d58336b9e5235cb"}}, "title": "FANTOM: Functional and taxonomic analysis of metagenomes.", "authors": [{"family": "Sanli", "given": "Kemal", "initials": "K"}, {"family": "Karlsson", "given": "Fredrik H", "initials": "FH"}, {"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2013-02-01", "journal": {"volume": "14", "issn": "1471-2105", "issue": null, "pages": "38", "title": "BMC Bioinformatics", "issn-l": "1471-2105"}, "abstract": "Interpretation of quantitative metagenomics data is important for our understanding of ecosystem functioning and assessing differences between various environmental samples. There is a need for an easy to use tool to explore the often complex metagenomics data in taxonomic and functional context.\n\nHere we introduce FANTOM, a tool that allows for exploratory and comparative analysis of metagenomics abundance data integrated with metadata information and biological databases. Importantly, FANTOM can make use of any hierarchical database and it comes supplied with NCBI taxonomic hierarchies as well as KEGG Orthology, COG, PFAM and TIGRFAM databases.\n\nThe software is implemented in Python, is platform independent, and is available at http://www.sysbio.se/Fantom.", "doi": "10.1186/1471-2105-14-38", "pmid": "23375020", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "1471-2105-14-38"}, {"db": "pmc", "key": "PMC3566963"}], "notes": [], "created": "2017-05-04T14:56:21.245Z", "modified": "2021-07-05T13:05:37.732Z"}, {"entity": "publication", "iuid": "752ae511ee974720af3eb8a3ba277f87", "links": {"self": {"href": "https://publications.scilifelab.se/publication/752ae511ee974720af3eb8a3ba277f87.json"}, "display": {"href": "https://publications.scilifelab.se/publication/752ae511ee974720af3eb8a3ba277f87"}}, "title": "Adipose tissue resting energy expenditure and expression of genes involved in mitochondrial function are higher in women than in men.", "authors": [{"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Svensson", "given": "Per-Arne", "initials": "PA"}, {"family": "Jacobson", "given": "Peter", "initials": "P"}, {"family": "Jern\u00e5s", "given": "Margareta", "initials": "M"}, {"family": "Taube", "given": "Magdalena", "initials": "M"}, {"family": "Larsson", "given": "Ingrid", "initials": "I"}, {"family": "Andersson-Assarsson", "given": "Johanna C", "initials": "JC"}, {"family": "Sj\u00f6str\u00f6m", "given": "Lars", "initials": "L"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Walley", "given": "Andrew", "initials": "A"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Carlsson", "given": "Lena M S", "initials": "LM"}], "type": "journal article", "published": "2013-02-00", "journal": {"volume": "98", "issn": "1945-7197", "issue": "2", "pages": "E370-E378", "title": "J. Clin. Endocrinol. Metab.", "issn-l": "0021-972X"}, "abstract": "Men and women differ in body fat distribution and adipose tissue metabolism as well as in obesity comorbidities and their response to obesity treatment.\n\nThe objective of the study was a search for sex differences in adipose tissue function.\n\nThis was an exploratory study performed at a university hospital.\n\nResting metabolic rate (RMR), body composition, and sc adipose tissue genome-wide expression were measured in the SOS Sib Pair study (n = 732).\n\nThe relative contribution of fat mass to RMR and the metabolic rate per kilogram adipose tissue was higher in women than in men (P value for sex by fat mass interaction = .0019). Women had increased expression of genes involved in mitochondrial function, here referred to as a mitochondrial gene signature. Analysis of liver, muscle, and blood showed that the pronounced mitochondrial gene signature in women was specific for adipose tissue. Brown adipocytes are dense in mitochondria, and the expression of the brown adipocyte marker uncoupling protein 1 was 5-fold higher in women compared with men in the SOS Sib Pair Study (P = 7.43 \u00d7 10(-7)), and this was confirmed in a cross-sectional, population-based study (n = 83, 6-fold higher in women, P = .00256).\n\nThe increased expression of the brown adipocyte marker uncoupling protein 1 in women indicates that the higher relative contribution of the fat mass to RMR in women is in part explained by an increased number of brown adipocytes.", "doi": "10.1210/jc.2012-2764", "pmid": "23264395", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "jc.2012-2764"}, {"db": "pmc", "key": "PMC3633773"}], "notes": [], "created": "2017-05-04T14:56:24.579Z", "modified": "2021-07-05T13:05:37.674Z"}, {"entity": "publication", "iuid": "8612a29d126645759788621e019e0ea4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8612a29d126645759788621e019e0ea4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8612a29d126645759788621e019e0ea4"}}, "title": "A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.", "authors": [{"family": "Teschendorff", "given": "Andrew E", "initials": "AE"}, {"family": "Marabita", "given": "Francesco", "initials": "F"}, {"family": "Lechner", "given": "Matthias", "initials": "M"}, {"family": "Bartlett", "given": "Thomas", "initials": "T"}, {"family": "Tegner", "given": "Jesper", "initials": "J"}, {"family": "Gomez-Cabrero", "given": "David", "initials": "D"}, {"family": "Beck", "given": "Stephan", "initials": "S"}], "type": "journal article", "published": "2013-01-15", "journal": {"volume": "29", "issn": "1367-4811", "issue": "2", "pages": "189-196", "title": "Bioinformatics", "issn-l": "1367-4803"}, "abstract": "The Illumina Infinium 450 k DNA Methylation Beadchip is a prime candidate technology for Epigenome-Wide Association Studies (EWAS). However, a difficulty associated with these beadarrays is that probes come in two different designs, characterized by widely different DNA methylation distributions and dynamic range, which may bias downstream analyses. A key statistical issue is therefore how best to adjust for the two different probe designs.\n\nHere we propose a novel model-based intra-array normalization strategy for 450 k data, called BMIQ (Beta MIxture Quantile dilation), to adjust the beta-values of type2 design probes into a statistical distribution characteristic of type1 probes. The strategy involves application of a three-state beta-mixture model to assign probes to methylation states, subsequent transformation of probabilities into quantiles and finally a methylation-dependent dilation transformation to preserve the monotonicity and continuity of the data. We validate our method on cell-line data, fresh frozen and paraffin-embedded tumour tissue samples and demonstrate that BMIQ compares favourably with two competing methods. Specifically, we show that BMIQ improves the robustness of the normalization procedure, reduces the technical variation and bias of type2 probe values and successfully eliminates the type1 enrichment bias caused by the lower dynamic range of type2 probes. BMIQ will be useful as a preprocessing step for any study using the Illumina Infinium 450 k platform.\n\nBMIQ is freely available from http://code.google.com/p/bmiq/.\n\na.teschendorff@ucl.ac.uk\n\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/bts680", "pmid": "23175756", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "bts680"}, {"db": "pmc", "key": "PMC3546795"}], "notes": [], "created": "2017-05-04T14:56:20.940Z", "modified": "2020-01-21T13:53:20.630Z"}, {"entity": "publication", "iuid": "b56c38a501824beda4557d1adbf34863", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b56c38a501824beda4557d1adbf34863.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b56c38a501824beda4557d1adbf34863"}}, "title": "Evolution from the prokaryotic to the higher plant chloroplast signal recognition particle: the signal recognition particle RNA is conserved in plastids of a wide range of photosynthetic organisms.", "authors": [{"family": "Tr\u00e4ger", "given": "Chantal", "initials": "C"}, {"family": "Rosenblad", "given": "Magnus Alm", "initials": "MA"}, {"family": "Ziehe", "given": "Dominik", "initials": "D"}, {"family": "Garcia-Petit", "given": "Christel", "initials": "C"}, {"family": "Schrader", "given": "Lukas", "initials": "L"}, {"family": "Kock", "given": "Klaus", "initials": "K"}, {"family": "Richter", "given": "Christine Vera", "initials": "CV"}, {"family": "Klinkert", "given": "Birgit", "initials": "B"}, {"family": "Narberhaus", "given": "Franz", "initials": "F"}, {"family": "Herrmann", "given": "Christian", "initials": "C"}, {"family": "Hofmann", "given": "Eckhard", "initials": "E"}, {"family": "Aronsson", "given": "Henrik", "initials": "H"}, {"family": "Sch\u00fcnemann", "given": "Danja", "initials": "D"}], "type": "journal article", "published": "2012-12-00", "journal": {"volume": "24", "issn": "1532-298X", "issue": "12", "pages": "4819-4836", "title": "Plant Cell", "issn-l": "1040-4651"}, "abstract": "The protein targeting signal recognition particle (SRP) pathway in chloroplasts of higher plants has undergone dramatic evolutionary changes. It disposed of its RNA, which is an essential SRP component in bacteria, and uses a unique chloroplast-specific protein cpSRP43. Nevertheless, homologs of the conserved SRP54 and the SRP receptor, FtsY, are present in higher plant chloroplasts. In this study, we analyzed the phylogenetic distribution of SRP components in photosynthetic organisms to elucidate the evolution of the SRP system. We identified conserved plastid SRP RNAs within all nonspermatophyte land plant lineages and in all chlorophyte branches. Furthermore, we show the simultaneous presence of cpSRP43 in these organisms. The function of this novel SRP system was biochemically and structurally characterized in the moss Physcomitrella patens. We show that P. patens chloroplast SRP (cpSRP) RNA binds cpSRP54 but has lost the ability to significantly stimulate the GTPase cycle of SRP54 and FtsY. Furthermore, the crystal structure at 1.8-\u00c5 resolution and the nucleotide specificity of P. patens cpFtsY was determined and compared with bacterial FtsY and higher plant chloroplast FtsY. Our data lead to the view that the P. patens cpSRP system occupies an intermediate position in the evolution from bacterial-type SRP to higher plant-type cpSRP system.", "doi": "10.1105/tpc.112.102996", "pmid": "23275580", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "tpc.112.102996"}, {"db": "pmc", "key": "PMC3556960"}], "notes": [], "created": "2017-05-04T14:56:19.415Z", "modified": "2020-01-21T13:53:20.795Z"}, {"entity": "publication", "iuid": "c42b4df6aa6a4db9a6b82b4a3a73fd10", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c42b4df6aa6a4db9a6b82b4a3a73fd10.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c42b4df6aa6a4db9a6b82b4a3a73fd10"}}, "title": "Epitope-specificity of recombinant antibodies reveals promiscuous peptide-binding properties.", "authors": [{"family": "Olsson", "given": "Niclas", "initials": "N"}, {"family": "Wallin", "given": "Stefan", "initials": "S"}, {"family": "James", "given": "Peter", "initials": "P"}, {"family": "Borrebaeck", "given": "Carl A K", "initials": "CA"}, {"family": "Wingren", "given": "Christer", "initials": "C"}], "type": "journal article", "published": "2012-12-00", "journal": {"volume": "21", "issn": "1469-896X", "issue": "12", "pages": "1897-1910", "title": "Protein Sci.", "issn-l": "0961-8368"}, "abstract": "Protein-peptide interactions are a common occurrence and essential for numerous cellular processes, and frequently explored in broad applications within biology, medicine, and proteomics. Therefore, understanding the molecular mechanism(s) of protein-peptide recognition, specificity, and binding interactions will be essential. In this study, we report the first detailed analysis of antibody-peptide interaction characteristics, by combining large-scale experimental peptide binding data with the structural analysis of eight human recombinant antibodies and numerous peptides, targeting tryptic mammalian and eukaryote proteomes. The results consistently revealed that promiscuous peptide-binding interactions, that is, both specific and degenerate binding, were exhibited by all antibodies, and the discovery was corroborated by orthogonal data, indicating that this might be a general phenomenon for low-affinity antibody-peptide interactions. The molecular mechanism for the degenerate peptide-binding specificity appeared to be executed through the use of 2-3 semi-conserved anchor residues in the C-terminal part of the peptides, in analogue to the mechanism utilized by the major histocompatibility complex-peptide complexes. In the long-term, this knowledge will be instrumental for advancing our fundamental understanding of protein-peptide interactions, as well as for designing, generating, and applying peptide specific antibodies, or peptide-binding proteins in general, in various biotechnical and medical applications.", "doi": "10.1002/pro.2173", "pmid": "23034898", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pmc", "key": "PMC3575919"}], "notes": [], "created": "2017-05-04T14:56:20.027Z", "modified": "2020-01-21T13:53:20.850Z"}, {"entity": "publication", "iuid": "a2e31bb0de974a24a0767b2b43be5e9e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2e31bb0de974a24a0767b2b43be5e9e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2e31bb0de974a24a0767b2b43be5e9e"}}, "title": "The plant short-chain dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns.", "authors": [{"family": "Moummou", "given": "Hanane", "initials": "H"}, {"family": "Kallberg", "given": "Yvonne", "initials": "Y"}, {"family": "Tonfack", "given": "Libert Brice", "initials": "LB"}, {"family": "Persson", "given": "Bengt", "initials": "B", "orcid": "0000-0003-3165-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f116ef0ed146419cb18e742c270c4a.json"}}, {"family": "van der Rest", "given": "Beno\u00eet", "initials": "B"}], "type": "journal article", "published": "2012-11-20", "journal": {"volume": "12", "issn": "1471-2229", "issue": null, "pages": "219", "title": "BMC Plant Biol.", "issn-l": "1471-2229"}, "abstract": "Short-chain dehydrogenases/reductases (SDRs) form one of the largest and oldest NAD(P)(H) dependent oxidoreductase families. Despite a conserved 'Rossmann-fold' structure, members of the SDR superfamily exhibit low sequence similarities, which constituted a bottleneck in terms of identification. Recent classification methods, relying on hidden-Markov models (HMMs), improved identification and enabled the construction of a nomenclature. However, functional annotations of plant SDRs remain scarce.\n\nWide-scale analyses were performed on ten plant genomes. The combination of hidden Markov model (HMM) based analyses and similarity searches led to the construction of an exhaustive inventory of plant SDR. With 68 to 315 members found in each analysed genome, the inventory confirmed the over-representation of SDRs in plants compared to animals, fungi and prokaryotes. The plant SDRs were first classified into three major types - 'classical', 'extended' and 'divergent' - but a minority (10% of the predicted SDRs) could not be classified into these general types ('unknown' or 'atypical' types). In a second step, we could categorize the vast majority of land plant SDRs into a set of 49 families. Out of these 49 families, 35 appeared early during evolution since they are commonly found through all the Green Lineage. Yet, some SDR families - tropinone reductase-like proteins (SDR65C), 'ABA2-like'-NAD dehydrogenase (SDR110C), 'salutaridine/menthone-reductase-like' proteins (SDR114C), 'dihydroflavonol 4-reductase'-like proteins (SDR108E) and 'isoflavone-reductase-like' (SDR460A) proteins - have undergone significant functional diversification within vascular plants since they diverged from Bryophytes. Interestingly, these diversified families are either involved in the secondary metabolism routes (terpenoids, alkaloids, phenolics) or participate in developmental processes (hormone biosynthesis or catabolism, flower development), in opposition to SDR families involved in primary metabolism which are poorly diversified.\n\nThe application of HMMs to plant genomes enabled us to identify 49 families that encompass all Angiosperms ('higher plants') SDRs, each family being sufficiently conserved to enable simpler analyses based only on overall sequence similarity. The multiplicity of SDRs in plant kingdom is mainly explained by the diversification of large families involved in different secondary metabolism pathways, suggesting that the chemical diversification that accompanied the emergence of vascular plants acted as a driving force for SDR evolution.", "doi": "10.1186/1471-2229-12-219", "pmid": "23167570", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "1471-2229-12-219"}, {"db": "pmc", "key": "PMC3541173"}], "notes": [], "created": "2017-05-04T14:56:15.150Z", "modified": "2021-07-05T12:34:46.044Z"}, {"entity": "publication", "iuid": "0dc2a140d296454ea162ebc52988e560", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0dc2a140d296454ea162ebc52988e560.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0dc2a140d296454ea162ebc52988e560"}}, "title": "A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.", "authors": [{"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Papini", "given": "Marta", "initials": "M"}, {"family": "Pornputtapong", "given": "Natapol", "initials": "N"}, {"family": "Scalcinati", "given": "Gionata", "initials": "G"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Matthias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "comparative study", "published": "2012-11-01", "journal": {"volume": "40", "issn": "1362-4962", "issue": "20", "pages": "10084-10097", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "RNA-seq, has recently become an attractive method of choice in the studies of transcriptomes, promising several advantages compared with microarrays. In this study, we sought to assess the contribution of the different analytical steps involved in the analysis of RNA-seq data generated with the Illumina platform, and to perform a cross-platform comparison based on the results obtained through Affymetrix microarray. As a case study for our work we, used the Saccharomyces cerevisiae strain CEN.PK 113-7D, grown under two different conditions (batch and chemostat). Here, we asses the influence of genetic variation on the estimation of gene expression level using three different aligners for read-mapping (Gsnap, Stampy and TopHat) on S288c genome, the capabilities of five different statistical methods to detect differential gene expression (baySeq, Cuffdiff, DESeq, edgeR and NOISeq) and we explored the consistency between RNA-seq analysis using reference genome and de novo assembly approach. High reproducibility among biological replicates (correlation\u22650.99) and high consistency between the two platforms for analysis of gene expression levels (correlation\u22650.91) are reported. The results from differential gene expression identification derived from the different statistical methods, as well as their integrated analysis results based on gene ontology annotation are in good agreement. Overall, our study provides a useful and comprehensive comparison between the two platforms (RNA-seq and microrrays) for gene expression analysis and addresses the contribution of the different steps involved in the analysis of RNA-seq data.", "doi": "10.1093/nar/gks804", "pmid": "22965124", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "gks804"}, {"db": "pmc", "key": "PMC3488244"}, {"db": "GDB", "key": "SRR453566"}, {"db": "GDB", "key": "SRR453567"}, {"db": "GDB", "key": "SRR453568"}, {"db": "GDB", "key": "SRR453569"}, {"db": "GDB", "key": "SRR453570"}, {"db": "GDB", "key": "SRR453571"}, {"db": "GDB", "key": "SRR453578"}, {"db": "GDB", "key": "SRS307298"}, {"db": "GEO", "key": "GSE37599"}, {"db": "SRA", "description": "Yeast RNA-seq", "key": "SRP012047"}], "notes": [], "created": "2017-05-04T14:56:19.115Z", "modified": "2021-07-08T13:44:33.019Z"}, {"entity": "publication", "iuid": "b2e6addab2f24f72a5f8964b5587a900", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b2e6addab2f24f72a5f8964b5587a900.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b2e6addab2f24f72a5f8964b5587a900"}}, "title": "Strategy for minimizing between-study variation of large-scale phenotypic experiments using multivariate analysis.", "authors": [{"family": "Pinto", "given": "Rui C", "initials": "RC"}, {"family": "Gerber", "given": "Lorenz", "initials": "L"}, {"family": "Eliasson", "given": "Mattias", "initials": "M"}, {"family": "Sundberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Trygg", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2012-10-16", "journal": {"volume": "84", "issn": "1520-6882", "issue": "20", "pages": "8675-8681", "title": "Anal. Chem.", "issn-l": "0003-2700"}, "abstract": "We have developed a multistep strategy that integrates data from several large-scale experiments that suffer from systematic between-experiment variation. This strategy removes such variation that would otherwise mask differences of interest. It was applied to the evaluation of wood chemical analysis of 736 hybrid aspen trees: wild-type controls and transgenic trees potentially involved in wood formation. The trees were grown in four different greenhouse experiments imposing significant variation between experiments. Pyrolysis coupled to gas chromatography/mass spectrometry (Py-GC/MS) was used as a high throughput-screening platform for fingerprinting of wood chemotype. Our proposed strategy includes quality control, outlier detection, gene specific classification, and consensus analysis. The orthogonal projections to latent structures discriminant analysis (OPLS-DA) method was used to generate the consensus chemotype profiles for each transgenic line. These were thereafter compiled to generate a global dataset. Multivariate analysis and cluster analysis techniques revealed a drastic reduction in between-experiment variation that enabled a global analysis of all transgenic lines from the four independent experiments. Information from in-depth analysis of specific transgenic lines and independent peak identification validated our proposed strategy.", "doi": "10.1021/ac301869p", "pmid": "22978754", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:14.540Z", "modified": "2020-01-21T13:53:20.782Z"}, {"entity": "publication", "iuid": "36aa2c1a1e004c4581aec22ec50609dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36aa2c1a1e004c4581aec22ec50609dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36aa2c1a1e004c4581aec22ec50609dd"}}, "title": "Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae.", "authors": [{"family": "Papini", "given": "Marta", "initials": "M"}, {"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2012-10-09", "journal": {"volume": "11", "issn": "1475-2859", "issue": null, "pages": "136", "title": "Microb. Cell Fact.", "issn-l": "1475-2859"}, "abstract": "Scheffersomyces stipitis is a Crabtree negative yeast, commonly known for its capacity to ferment pentose sugars. Differently from Crabtree positive yeasts such as Saccharomyces cerevisiae, the onset of fermentation in S. stipitis is not dependent on the sugar concentration, but is regulated by a decrease in oxygen levels. Even though S. stipitis has been extensively studied due to its potential application in pentoses fermentation, a limited amount of information is available about its metabolism during aerobic growth on glucose. Here, we provide a systems biology based comparison between the two yeasts, uncovering the metabolism of S. stipitis during aerobic growth on glucose under batch and chemostat cultivations.\n\nStarting from the analysis of physiological data, we confirmed through 13C-based flux analysis the fully respiratory metabolism of S. stipitis when growing both under glucose limited or glucose excess conditions. The patterns observed showed similarity to the fully respiratory metabolism observed for S. cerevisiae under chemostat cultivations however, intracellular metabolome analysis uncovered the presence of several differences in metabolite patterns. To describe gene expression levels under the two conditions, we performed RNA sequencing and the results were used to quantify transcript abundances of genes from the central carbon metabolism and compared with those obtained with S. cerevisiae. Interestingly, genes involved in central pathways showed different patterns of expression, suggesting different regulatory networks between the two yeasts. Efforts were focused on identifying shared and unique families of transcription factors between the two yeasts through in silico transcription factors analysis, suggesting a different regulation of glycolytic and glucoenogenic pathways.\n\nThe work presented addresses the impact of high-throughput methods in describing and comparing the physiology of Crabtree positive and Crabtree negative yeasts. Based on physiological data and flux analysis we identified the presence of one metabolic condition for S. stipitis under aerobic batch and chemostat cultivations, which shows similarities to the oxidative metabolism observed for S. cerevisiae under chemostat cultivations. Through metabolome analysis and genome-wide transcriptomic analysis several differences were identified. Interestingly, in silico analysis of transciption factors was useful to address a different regulation of mRNAs of genes involved in the central carbon metabolism. To our knowledge, this is the first time that the metabolism of S. stiptis is investigated in details and is compared to S. cerevisiae. Our study provides useful results and allows for the possibility to incorporate these data into recently developed genome-scaled metabolic, thus contributing to improve future industrial applications of S. stipitis as cell factory.", "doi": "10.1186/1475-2859-11-136", "pmid": "23043429", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "1475-2859-11-136"}, {"db": "pmc", "key": "PMC3528450"}], "notes": [], "created": "2017-05-04T14:56:17.576Z", "modified": "2021-07-08T13:44:33.145Z"}, {"entity": "publication", "iuid": "fd5339728a92423293ad65afe5cbdb19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd5339728a92423293ad65afe5cbdb19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd5339728a92423293ad65afe5cbdb19"}}, "title": "Evolutionary conservation of the ribosomal biogenesis factor Rbm19/Mrd1: implications for function.", "authors": [{"family": "Kallberg", "given": "Yvonne", "initials": "Y"}, {"family": "Segerstolpe", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Lackmann", "given": "Fredrik", "initials": "F"}, {"family": "Persson", "given": "Bengt", "initials": "B", "orcid": "0000-0003-3165-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f116ef0ed146419cb18e742c270c4a.json"}}, {"family": "Wieslander", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2012-09-12", "journal": {"volume": "7", "issn": "1932-6203", "issue": "9", "pages": "e43786", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Ribosome biogenesis in eukaryotes requires coordinated folding and assembly of a pre-rRNA into sequential pre-rRNA-protein complexes in which chemical modifications and RNA cleavages occur. These processes require many small nucleolar RNAs (snoRNAs) and proteins. Rbm19/Mrd1 is one such protein that is built from multiple RNA-binding domains (RBDs). We find that Rbm19/Mrd1 with five RBDs is present in all branches of the eukaryotic phylogenetic tree, except in animals and Choanoflagellates, that instead have a version with six RBDs and Microsporidia which have a minimal Rbm19/Mrd1 protein with four RBDs. Rbm19/Mrd1 therefore evolved as a multi-RBD protein very early in eukaryotes. The linkers between the RBDs have conserved properties; they are disordered, except for linker 3, and position the RBDs at conserved relative distances from each other. All but one of the RBDs have conserved properties for RNA-binding and each RBD has a specific consensus sequence and a conserved position in the protein, suggesting a functionally important modular design. The patterns of evolutionary conservation provide information for experimental analyses of the function of Rbm19/Mrd1. In vivo mutational analysis confirmed that a highly conserved loop 5-\u03b24-strand in RBD6 is essential for function.", "doi": "10.1371/journal.pone.0043786", "pmid": "22984444", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-14217"}, {"db": "pmc", "key": "PMC3440411"}], "notes": [], "created": "2017-05-04T14:56:19.726Z", "modified": "2021-07-05T12:34:46.059Z"}, {"entity": "publication", "iuid": "b659c386f09242aca02397820ed956c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b659c386f09242aca02397820ed956c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b659c386f09242aca02397820ed956c9"}}, "title": "Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences", "authors": [{"family": "Nilsson", "given": "R Henrik", "initials": "RH"}, {"family": "Tedersoo", "given": "Leho", "initials": "L"}, {"family": "Abarenkov", "given": "Kessy", "initials": "K"}, {"family": "Ryberg", "given": "Martin", "initials": "M"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Hartmann", "given": "Martin", "initials": "M"}, {"family": "Schoch", "given": "Conrad L", "initials": "CL"}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA"}, {"family": "Bergsten", "given": "Johannes", "initials": "J"}, {"family": "Porter", "given": "Teresita M", "initials": "TM"}, {"family": "Jumpponen", "given": "Ari", "initials": "A"}, {"family": "Vaishampayan", "given": "Parag", "initials": "P"}, {"family": "Ovaskainen", "given": "Otso", "initials": "O"}, {"family": "Hallenberg", "given": "Nils", "initials": "N"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Eriksson", "given": "K Martin", "initials": "KM"}, {"family": "Larsson", "given": "Karl Henrik", "initials": "KH"}, {"family": "Larsson", "given": "Ellen", "initials": "E"}, {"family": "K\u00f5ljalg", "given": "Urmas", "initials": "U"}], "type": "journal-article", "published": "2012-09-05", "journal": {"volume": "4", "issn": "1314-4049", "issue": null, "pages": "37-63", "title": "MycoKeys", "issn-l": null}, "abstract": null, "doi": "10.3897/mycokeys.4.3606", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:18.543Z", "modified": "2021-06-22T12:06:26.068Z"}, {"entity": "publication", "iuid": "8ac40d6bdf594ad68f2c6a1b5740ee67", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ac40d6bdf594ad68f2c6a1b5740ee67.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ac40d6bdf594ad68f2c6a1b5740ee67"}}, "title": "The evolution of filamin-a protein domain repeat perspective.", "authors": [{"family": "Light", "given": "Sara", "initials": "S"}, {"family": "Sagit", "given": "Rauan", "initials": "R"}, {"family": "Ithychanda", "given": "Sujay S", "initials": "SS"}, {"family": "Qin", "given": "Jun", "initials": "J"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2012-09-00", "journal": {"volume": "179", "issn": "1095-8657", "issue": "3", "pages": "289-298", "title": "J. Struct. Biol.", "issn-l": "1047-8477"}, "abstract": "Particularly in higher eukaryotes, some protein domains are found in tandem repeats, performing broad functions often related to cellular organization. For instance, the eukaryotic protein filamin interacts with many proteins and is crucial for the cytoskeleton. The functional properties of long repeat domains are governed by the specific properties of each individual domain as well as by the repeat copy number. To provide better understanding of the evolutionary and functional history of repeating domains, we investigated the mode of evolution of the filamin domain in some detail. Among the domains that are common in long repeat proteins, sushi and spectrin domains evolve primarily through cassette tandem duplications while scavenger and immunoglobulin repeats appear to evolve through clustered tandem duplications. Additionally, immunoglobulin and filamin repeats exhibit a unique pattern where every other domain shows high sequence similarity. This pattern may be the result of tandem duplications, serve to avert aggregation between adjacent domains or it is the result of functional constraints. In filamin, our studies confirm the presence of interspersed integrin binding domains in vertebrates, while invertebrates exhibit more varied patterns, including more clustered integrin binding domains. The most notable case is leech filamin, which contains a 20 repeat expansion and exhibits unique dimerization topology. Clearly, invertebrate filamins are varied and contain examples of similar adjacent integrin-binding domains. Given that invertebrate integrin shows more similarity to the weaker filamin binder, integrin \u03b23, it is possible that the distance between integrin-binding domains is not as crucial for invertebrate filamins as for vertebrates.", "doi": "10.1016/j.jsb.2012.02.010", "pmid": "22414427", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "S1047-8477(12)00063-9"}, {"db": "pmc", "key": "PMC3728663"}, {"db": "mid", "key": "NIHMS470530"}], "notes": [], "created": "2017-05-04T14:56:17.274Z", "modified": "2020-01-21T13:53:20.651Z"}, {"entity": "publication", "iuid": "2e8a48c6bcb0435e81f13645120db225", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e8a48c6bcb0435e81f13645120db225.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e8a48c6bcb0435e81f13645120db225"}}, "title": "Proteomic screen reveals Fbw7 as a modulator of the NF-\u03baB pathway.", "authors": [{"family": "Arabi", "given": "Azadeh", "initials": "A"}, {"family": "Ullah", "given": "Karim", "initials": "K"}, {"family": "Branca", "given": "Rui M M", "initials": "RM"}, {"family": "Johansson", "given": "Johan", "initials": "J"}, {"family": "Bandarra", "given": "Daniel", "initials": "D"}, {"family": "Haneklaus", "given": "Moritz", "initials": "M"}, {"family": "Fu", "given": "Jing", "initials": "J"}, {"family": "Ari\u00ebs", "given": "Ingrid", "initials": "I"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Den Boer", "given": "Monique L", "initials": "ML"}, {"family": "Pokrovskaja", "given": "Katja", "initials": "K"}, {"family": "Grand\u00e9r", "given": "Dan", "initials": "D"}, {"family": "Xiao", "given": "Gutian", "initials": "G"}, {"family": "Rocha", "given": "Sonia", "initials": "S"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Sangfelt", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2012-08-07", "journal": {"volume": "3", "issn": "2041-1723", "issue": null, "pages": "976", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Fbw7 is a ubiquitin-ligase that targets several oncoproteins for proteolysis, but the full range of Fbw7 substrates is not known. Here we show that by performing quantitative proteomics combined with degron motif searches, we effectively screened for a more complete set of Fbw7 targets. We identify 89 putative Fbw7 substrates, including several disease-associated proteins. The transcription factor NF-\u03baB2 (p100/p52) is one of the candidate Fbw7 substrates. We show that Fbw7 interacts with p100 via a conserved degron and that it promotes degradation of p100 in a GSK3\u03b2 phosphorylation-dependent manner. Fbw7 inactivation increases p100 levels, which in the presence of NF-\u03baB pathway stimuli, leads to increased p52 levels and activity. Accordingly, the apoptotic threshold can be increased by loss of Fbw7 in a p100-dependent manner. In conclusion, Fbw7-mediated destruction of p100 is a regulatory component restricting the response to NF-\u03baB2 pathway stimulation.", "doi": "10.1038/ncomms1975", "pmid": "22864569", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "ncomms1975"}, {"db": "pmc", "key": "PMC4354031"}], "notes": [], "created": "2017-05-04T14:56:18.815Z", "modified": "2021-07-08T11:36:15.152Z"}, {"entity": "publication", "iuid": "5b6f8762d73149dbb537f991932a7fbc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b6f8762d73149dbb537f991932a7fbc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b6f8762d73149dbb537f991932a7fbc"}}, "title": "Quantitative proteomics targeting classes of motif-containing peptides using immunoaffinity-based mass spectrometry.", "authors": [{"family": "Olsson", "given": "Niclas", "initials": "N"}, {"family": "James", "given": "Peter", "initials": "P"}, {"family": "Borrebaeck", "given": "Carl A K", "initials": "CA"}, {"family": "Wingren", "given": "Christer", "initials": "C"}], "type": "journal article", "published": "2012-08-00", "journal": {"volume": "11", "issn": "1535-9484", "issue": "8", "pages": "342-354", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "The development of high-performance technology platforms for generating detailed protein expression profiles, or protein atlases, is essential. Recently, we presented a novel platform that we termed global proteome survey, where we combined the best features of affinity proteomics and mass spectrometry, to probe any proteome in a species independent manner while still using a limited set of antibodies. We used so called context-independent-motif-specific antibodies, directed against short amino acid motifs. This enabled enrichment of motif-containing peptides from a digested proteome, which then were detected and identified by mass spectrometry. In this study, we have demonstrated the quantitative capability, reproducibility, sensitivity, and coverage of the global proteome survey technology by targeting stable isotope labeling with amino acids in cell culture-labeled yeast cultures cultivated in glucose or ethanol. The data showed that a wide range of motif-containing peptides (proteins) could be detected, identified, and quantified in a highly reproducible manner. On average, each of six different motif-specific antibodies was found to target about 75 different motif-containing proteins. Furthermore, peptides originating from proteins spanning in abundance from over a million down to less than 50 copies per cell, could be targeted. It is worth noting that a significant set of peptides previously not reported in the PeptideAtlas database was among the profiled targets. The quantitative data corroborated well with the corresponding data generated after conventional strong cation exchange fractionation of the same samples. Finally, several differentially expressed proteins, with both known and unknown functions, many relevant for the central carbon metabolism, could be detected in the glucose- versus ethanol-cultivated yeast. Taken together, the study demonstrated the potential of our immunoaffinity-based mass spectrometry platform for reproducible quantitative proteomics targeting classes of motif-containing peptides.", "doi": "10.1074/mcp.M111.016238", "pmid": "22543061", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "M111.016238"}, {"db": "pmc", "key": "PMC3412966"}], "notes": [], "created": "2017-05-04T14:56:17.870Z", "modified": "2020-01-21T13:53:20.530Z"}, {"entity": "publication", "iuid": "867161b23dec4def849ff5da517f7aae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/867161b23dec4def849ff5da517f7aae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/867161b23dec4def849ff5da517f7aae"}}, "title": "Polyploidy and the evolution of complex traits.", "authors": [{"family": "Huminiecki", "given": "Lukasz", "initials": "L"}, {"family": "Conant", "given": "Gavin C", "initials": "GC"}], "type": "journal article", "published": "2012-07-30", "journal": {"volume": "2012", "issn": "2090-052X", "issue": null, "pages": "292068", "title": "Int J Evol Biol", "issn-l": null}, "abstract": "We explore how whole-genome duplications (WGDs) may have given rise to complex innovations in cellular networks, innovations that could not have evolved through sequential single-gene duplications. We focus on two classical WGD events, one in bakers' yeast and the other at the base of vertebrates (i.e., two rounds of whole-genome duplication: 2R-WGD). Two complex adaptations are discussed in detail: aerobic ethanol fermentation in yeast and the rewiring of the vertebrate developmental regulatory network through the 2R-WGD. These two examples, derived from diverged branches on the eukaryotic tree, boldly underline the evolutionary potential of WGD in facilitating major evolutionary transitions. We close by arguing that the evolutionary importance of WGD may require updating certain aspects of modern evolutionary theory, perhaps helping to synthesize a new evolutionary systems biology.", "doi": "10.1155/2012/292068", "pmid": "22900230", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pmc", "key": "PMC3413983"}], "notes": [], "created": "2017-05-04T14:56:15.763Z", "modified": "2020-01-21T13:53:20.637Z"}, {"entity": "publication", "iuid": "cf46f4fc293f4987b7abe9996f9626c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf46f4fc293f4987b7abe9996f9626c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf46f4fc293f4987b7abe9996f9626c9"}}, "title": "Automated selected reaction monitoring software for accurate label-free protein quantification.", "authors": [{"family": "Teleman", "given": "Johan", "initials": "J"}, {"family": "Karlsson", "given": "Christofer", "initials": "C"}, {"family": "Waldemarson", "given": "Sofia", "initials": "S"}, {"family": "Hansson", "given": "Karin", "initials": "K"}, {"family": "James", "given": "Peter", "initials": "P"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2012-07-06", "journal": {"volume": "11", "issn": "1535-3907", "issue": "7", "pages": "3766-3773", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Selected reaction monitoring (SRM) is a mass spectrometry method with documented ability to quantify proteins accurately and reproducibly using labeled reference peptides. However, the use of labeled reference peptides becomes impractical if large numbers of peptides are targeted and when high flexibility is desired when selecting peptides. We have developed a label-free quantitative SRM workflow that relies on a new automated algorithm, Anubis, for accurate peak detection. Anubis efficiently removes interfering signals from contaminating peptides to estimate the true signal of the targeted peptides. We evaluated the algorithm on a published multisite data set and achieved results in line with manual data analysis. In complex peptide mixtures from whole proteome digests of Streptococcus pyogenes we achieved a technical variability across the entire proteome abundance range of 6.5-19.2%, which was considerably below the total variation across biological samples. Our results show that the label-free SRM workflow with automated data analysis is feasible for large-scale biological studies, opening up new possibilities for quantitative proteomics and systems biology.", "doi": "10.1021/pr300256x", "pmid": "22658081", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pmc", "key": "PMC3426189"}], "notes": [], "created": "2017-05-04T14:56:16.974Z", "modified": "2020-01-21T13:53:20.874Z"}, {"entity": "publication", "iuid": "ede8b83029ae429f9d2c02612ae27f3d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ede8b83029ae429f9d2c02612ae27f3d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ede8b83029ae429f9d2c02612ae27f3d"}}, "title": "Which sequencing depth is sufficient to describe patterns in bacterial \u03b1- and \u03b2-diversity?", "authors": [{"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Severin", "given": "Ina", "initials": "I"}, {"family": "Logue", "given": "J\u00fcrg Brendan", "initials": "JB"}, {"family": "Ostman", "given": "Orjan", "initials": "O"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES"}], "type": "journal article", "published": "2012-06-00", "journal": {"volume": "4", "issn": "1758-2229", "issue": "3", "pages": "367-372", "title": "Environ Microbiol Rep", "issn-l": "1758-2229"}, "abstract": "The vastness of microbial diversity implies that an almost infinite number of individuals needs to be identified to accurately describe such communities. Practical and economical constraints may therefore prevent appropriate study designs. However, for many questions in ecology it is not essential to know the actual diversity but rather the trends among samples thereof. It is, hence, important to know to what depth microbial communities need to be sampled to accurately measure trends in diversity. We used three data sets of freshwater and sediment bacteria, where diversity was explored using 454 pyrosequencing. Each data set contained 6-15 communities from which 15\u2003000-20\u2003000 16S rRNA gene sequences each were obtained. These data sets were subsampled repeatedly to 10 different depths down to 200 sequences per community. Diversity estimates varied with sequencing depth, yet, trends in diversity among samples were less sensitive. We found that 1000 denoised sequences per sample explained to 90% the trends in \u03b2-diversity (Bray-Curtis index) among samples observed for 15\u2003000-20\u2003000 sequences. Similarly, 5000 denoised sequences were sufficient to describe trends in \u03b1-diversity (Shannon index) with the same accuracy. Further, 5000 denoised sequences captured to more than 80% the trends in Chao1 richness and Pielou's evenness.", "doi": "10.1111/j.1758-2229.2012.00345.x", "pmid": "23760801", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:15.460Z", "modified": "2020-01-21T13:53:20.940Z"}, {"entity": "publication", "iuid": "f9228292f20d4e1995524fc30991b78e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9228292f20d4e1995524fc30991b78e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9228292f20d4e1995524fc30991b78e"}}, "title": "Multimodel pathway enrichment methods for functional evaluation of expression regulation.", "authors": [{"family": "Kirik", "given": "Ufuk", "initials": "U"}, {"family": "Cifani", "given": "Paolo", "initials": "P"}, {"family": "Albrekt", "given": "Ann-Sofie", "initials": "AS"}, {"family": "Lindstedt", "given": "Malin", "initials": "M"}, {"family": "Heyden", "given": "Anders", "initials": "A"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2012-05-04", "journal": {"volume": "11", "issn": "1535-3907", "issue": "5", "pages": "2955-2967", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Functional analysis of quantitative expression data is becoming common practice within the proteomics and transcriptomics fields; however, a gold standard for this type of analysis has yet not emerged. To grasp the systemic changes in biological systems, efficient and robust methods are needed for data analysis following expression regulation experiments. We discuss several conceptual and practical challenges potentially hindering the emergence of such methods and present a novel method, called FEvER, that utilizes two enrichment models in parallel. We also present analysis of three disparate differential expression data sets using our method and compare our results to other established methods. With many useful features such as pathway hierarchy overview, we believe the FEvER method and its software implementation will provide a useful tool for peers in the field of proteomics. Furthermore, we show that the method is also applicable to other types of expression data.", "doi": "10.1021/pr300038b", "pmid": "22471554", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:16.365Z", "modified": "2020-01-21T13:53:20.975Z"}, {"entity": "publication", "iuid": "0dbbf8978547434d8ec6c1926d36edeb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0dbbf8978547434d8ec6c1926d36edeb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0dbbf8978547434d8ec6c1926d36edeb"}}, "title": "Manipulating the genetic code for membrane protein production: what have we learnt so far?", "authors": [{"family": "N\u00f8rholm", "given": "Morten H H", "initials": "MH"}, {"family": "Light", "given": "Sara", "initials": "S"}, {"family": "Virkki", "given": "Minttu T I", "initials": "MT"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}, {"family": "von Heijne", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-4490-8569", "researcher": {"href": "https://publications.scilifelab.se/researcher/f663c0a9e9e1455cbbf8e6aea13af4a9.json"}}, {"family": "Daley", "given": "Daniel O", "initials": "DO"}], "type": "journal article", "published": "2012-04-00", "journal": {"volume": "1818", "issn": "0006-3002", "issue": "4", "pages": "1091-1096", "title": "Biochim. Biophys. Acta", "issn-l": null}, "abstract": "With synthetic gene services, molecular cloning is as easy as ordering a pizza. However choosing the right RNA code for efficient protein production is less straightforward, more akin to deciding on the pizza toppings. The possibility to choose synonymous codons in the gene sequence has ignited a discussion that dates back 50 years: Does synonymous codon use matter? Recent studies indicate that replacement of particular codons for synonymous codons can improve expression in homologous or heterologous hosts, however it is not always successful. Furthermore it is increasingly apparent that membrane protein biogenesis can be codon-sensitive. Single synonymous codon substitutions can influence mRNA stability, mRNA structure, translational initiation, translational elongation and even protein folding. Synonymous codon substitutions therefore need to be carefully evaluated when membrane proteins are engineered for higher production levels and further studies are needed to fully understand how to select the codons that are optimal for higher production. This article is part of a Special Issue entitled: Protein Folding in Membranes.", "doi": "10.1016/j.bbamem.2011.08.018", "pmid": "21884679", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "S0005-2736(11)00280-X"}, {"db": "pmc", "key": "PMC3288168"}, {"db": "mid", "key": "NIHMS328986"}], "notes": [], "created": "2017-05-04T14:56:14.844Z", "modified": "2021-06-16T15:21:58.633Z"}, {"entity": "publication", "iuid": "6435cce794dd4d8bbeb5a4dc74edbc9c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6435cce794dd4d8bbeb5a4dc74edbc9c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6435cce794dd4d8bbeb5a4dc74edbc9c"}}, "title": "A dimerized single-chain variable fragment system for the assessment of neutralizing activity of phage display-selected antibody fragments specific for cytomegalovirus.", "authors": [{"family": "Carlsson", "given": "Fredrika", "initials": "F"}, {"family": "Trilling", "given": "Mirko", "initials": "M"}, {"family": "Perez", "given": "Franck", "initials": "F"}, {"family": "Ohlin", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2012-02-28", "journal": {"volume": "376", "issn": "1872-7905", "issue": "1-2", "pages": "69-78", "title": "J. Immunol. Methods", "issn-l": "0022-1759"}, "abstract": "Cytomegalovirus (CMV) causes severe sequelae in congenitally infected newborns and may cause life-threatening disease in immuno-deficient patients. Recent findings demonstrate the possibility to alleviate the disease by infusing intravenous immunoglobulin G (IgG) preparations, indicating that antibodies are an effective therapeutic option. Modern molecular methodologies, like phage display, allow for the development of specific antibodies targeting virtually any antigen, including those of CMV. However, such methodologies do not in general result in products that by themselves mediate biological activity. To facilitate a semi-high-throughput approach for functional screening in future efforts to develop efficacious antibodies against CMV, we have integrated two different approaches to circumvent potential bottlenecks in such efforts. Firstly, we explored an approach that permits easy transfer of antibody fragment encoding genes from commonly used phage display vectors into vectors for the production of divalent immunoglobulins. Secondly, we demonstrate that such proteins can be applied in a novel reporter-based neutralization assay to establish a proof-of-concept workflow for the generation of neutralizing antibodies against CMV. We validated our approach by showing that divalent antibodies raised against the antigenic domain (AD)-2 region of gB effectively neutralized three different CMV strains (AD169, Towne and TB40/E), whereas two antibodies against the AD-1 region of gB displayed minor neutralizing capabilities. In conclusion, the methods investigated in this proof-of-concept study enables for a semi-high-throughput workflow in the screening and investigation of biological active antibodies.", "doi": "10.1016/j.jim.2011.11.010", "pmid": "22154743", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "S0022-1759(11)00316-4"}], "notes": [], "created": "2017-05-04T14:56:16.057Z", "modified": "2020-01-21T13:53:20.565Z"}, {"entity": "publication", "iuid": "d790487ea34c4b10bdd4b71b2e32c46f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d790487ea34c4b10bdd4b71b2e32c46f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d790487ea34c4b10bdd4b71b2e32c46f"}}, "title": "Characterization of the lipid droplet proteome of a clonal insulin-producing \u03b2-cell line (INS-1 832/13).", "authors": [{"family": "Larsson", "given": "Sara", "initials": "S"}, {"family": "Resj\u00f6", "given": "Svante", "initials": "S"}, {"family": "Gomez", "given": "Maria F", "initials": "MF"}, {"family": "James", "given": "Peter", "initials": "P"}, {"family": "Holm", "given": "Cecilia", "initials": "C"}], "type": "journal article", "published": "2012-02-03", "journal": {"volume": "11", "issn": "1535-3907", "issue": "2", "pages": "1264-1273", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Lipids are known to play a crucial role both in the normal control of insulin release and in the deterioration of \u03b2-cell function, as observed in type 2 diabetes. Despite this established dual role of lipids, little is known about lipid storage and handling in \u03b2-cells. Here, we isolated lipid droplets from oleate-incubated INS-1 832/13 cells and characterized the lipid droplet proteome. In a total of four rounds of droplet isolation and proteomic analysis by HPLC-MS/MS, we identified 96 proteins that were specific to droplets. The proteins fall into six categories based on function or previously observed localization: metabolism, endoplasmic reticulum/ribosomes, mitochondria, vesicle formation and transport, signaling, and miscellaneous. The protein profile reinforces the emerging picture of the lipid droplet as an active and dynamic organelle involved in lipid homeostasis and intracellular trafficking. Proteins belonging to the category mitochondria were highly represented, suggesting that the \u03b2-cell mitochondria and lipid droplets form a metabolic unit of potential relevance for insulin secretion.", "doi": "10.1021/pr200957p", "pmid": "22268682", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:16.669Z", "modified": "2020-01-21T13:53:20.903Z"}]}