{"entity": "researcher", "timestamp": "2026-04-20T22:01:37.091Z", "family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG", "orcid": "0000-0002-7392-1746", "affiliations": ["Department of Cell and Molecular Biology, BMC, Box 596, Uppsala Universitet, SE-751 24 Uppsala, Sweden"], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/b01942d70ef84a1db3aaccab65af9c57.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/b01942d70ef84a1db3aaccab65af9c57"}}, "publications": [{"entity": "publication", "iuid": "97a9599da59641ebb05e5b7a8fe6ad45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/97a9599da59641ebb05e5b7a8fe6ad45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/97a9599da59641ebb05e5b7a8fe6ad45"}}, "title": "The expanded genome of Hexamita inflata, a free-living diplomonad.", "authors": [{"family": "Akdeniz", "given": "Zeynep", "initials": "Z", "orcid": "0000-0002-5279-6077", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b6a7222e2d3487db2b50842f74e173e.json"}}, {"family": "Havelka", "given": "Michal", "initials": "M"}, {"family": "Stoklasa", "given": "Michal", "initials": "M"}, {"family": "Jim\u00e9nez-Gonz\u00e1lez", "given": "Alejandro", "initials": "A", "orcid": "0000-0003-3493-4154", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c6b93b731741018637733969c308a6.json"}}, {"family": "\u017d\u00e1rsk\u00fd", "given": "Vojt\u011bch", "initials": "V"}, {"family": "Xu", "given": "Feifei", "initials": "F", "orcid": "0000-0003-1946-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c51ec60768479f851e29ebc804f547.json"}}, {"family": "Stairs", "given": "Courtney W", "initials": "CW", "orcid": "0000-0001-6650-0970", "researcher": {"href": "https://publications.scilifelab.se/researcher/618e83e896494c7bb6cbe06350baf0a5.json"}}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J", "orcid": "0000-0002-7992-7970", "researcher": {"href": "https://publications.scilifelab.se/researcher/622d380bca244d738f5551cbed742b3e.json"}}, {"family": "Kol\u00edsko", "given": "Martin", "initials": "M"}, {"family": "Provazn\u00edk", "given": "Jan", "initials": "J"}, {"family": "Sv\u00e4rd", "given": "Staffan", "initials": "S", "orcid": "0000-0002-7392-1746", "researcher": {"href": "https://publications.scilifelab.se/researcher/b01942d70ef84a1db3aaccab65af9c57.json"}}, {"family": "Andersson", "given": "Jan O", "initials": "JO", "orcid": "0000-0002-3075-4896", "researcher": {"href": "https://publications.scilifelab.se/researcher/489ed7f61a7b49a3a7ebd9ee3c391f5b.json"}}, {"family": "Tachezy", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2025-02-01", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "12", "issue": "1", "pages": "192", "issn-l": "2052-4463"}, "abstract": "Diplomonads are anaerobic, flagellated protists, being part of the Metamonada group of Eukaryotes. Diplomonads either live as endobionts (parasites and commensals) of animals or free-living in low-oxygen environments. Genomic information is available for parasitic diplomonads like Giardia intestinalis and Spironucleus salmonicida, while little is known about the genomic arrangements of free-living diplomonads. We have generated the first reference genome of a free-living diplomonad, Hexamita inflata. The final version of the genome assembly is fragmented (1241 contigs) but substantially larger (142 Mbp) than the parasitic diplomonad genomes (9.8-14.7 Mbp). It encodes 79,341 proteins; 29,874 have functional annotations and 49,467 are hypothetical proteins. Interspersed repeats comprise 34% of the genome (9617 Retroelements, 2676 DNA transposons). The large expansion of protein-encoding capacity and the interspersed repeats are the major reasons for the large genome size. This genome from a free-living diplomonad will be the basis for further studies of the Diplomonadida lineage and the evolution of parasitism-free living style transitions.", "doi": "10.1038/s41597-025-04514-x", "pmid": "39893204", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11787283"}, {"db": "pii", "key": "10.1038/s41597-025-04514-x"}], "notes": [], "created": "2025-03-07T09:59:16.550Z", "modified": "2025-04-03T08:27:54.918Z"}, {"entity": "publication", "iuid": "63814c2828f14ee58cef696374d723d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63814c2828f14ee58cef696374d723d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63814c2828f14ee58cef696374d723d9"}}, "title": "Trophozoite fitness dictates the intestinal epithelial cell response to Giardia intestinalis infection.", "authors": [{"family": "Gr\u00fcttner", "given": "Jana", "initials": "J", "orcid": "0000-0002-2507-3375", "researcher": {"href": "https://publications.scilifelab.se/researcher/28fb027f36d94b85afb5e1325fd0ed7b.json"}}, {"family": "van Rijn", "given": "Jorik M", "initials": "JM", "orcid": "0000-0003-2865-4455", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f2defce179d4632a4e7d60666417ab2.json"}}, {"family": "Geiser", "given": "Petra", "initials": "P", "orcid": "0000-0003-2785-4201", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0bf10f41dc4698b19288809bae2dd6.json"}}, {"family": "Florbrant", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-1630-4442", "researcher": {"href": "https://publications.scilifelab.se/researcher/360f8004f9394dabb68f1f9e0725e42c.json"}}, {"family": "Webb", "given": "Dominic-Luc", "initials": "DL", "orcid": "0000-0002-6979-9194", "researcher": {"href": "https://publications.scilifelab.se/researcher/868fca24b48f440eb2417acdb04e73d3.json"}}, {"family": "Hellstr\u00f6m", "given": "Per M", "initials": "PM", "orcid": "0000-0001-8428-0772", "researcher": {"href": "https://publications.scilifelab.se/researcher/e85863b505f34d7e95a23ac127b9d6dc.json"}}, {"family": "Sundbom", "given": "Magnus", "initials": "M", "orcid": "0000-0002-6243-2859", "researcher": {"href": "https://publications.scilifelab.se/researcher/a54316faa45947bd92615d27a38c2b87.json"}}, {"family": "Sellin", "given": "Mikael E", "initials": "ME", "orcid": "0000-0002-8355-0803", "researcher": {"href": "https://publications.scilifelab.se/researcher/f797357bcd3d4447bff96c20873dd500.json"}}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG", "orcid": "0000-0002-7392-1746", "researcher": {"href": "https://publications.scilifelab.se/researcher/b01942d70ef84a1db3aaccab65af9c57.json"}}], "type": "journal article", "published": "2023-05-00", "journal": {"title": "PLoS Pathog.", "issn": "1553-7374", "volume": "19", "issue": "5", "pages": "e1011372", "issn-l": "1553-7366"}, "abstract": "Giardia intestinalis is a non-invasive, protozoan parasite infecting the upper small intestine of most mammals. Symptomatic infections cause the diarrhoeal disease giardiasis in humans and animals, but at least half of the infections are asymptomatic. However, the molecular underpinnings of these different outcomes of the infection are still poorly defined. Here, we studied the early transcriptional response to G. intestinalis trophozoites, the disease-causing life-cycle stage, in human enteroid-derived, 2-dimensional intestinal epithelial cell (IEC) monolayers. Trophozoites preconditioned in media that maximise parasite fitness triggered only neglectable inflammatory transcription in the IECs during the first hours of co-incubation. By sharp contrast, \"non-fit\" or lysed trophozoites induced a vigorous IEC transcriptional response, including high up-regulation of many inflammatory cytokines and chemokines. Furthermore, \"fit\" trophozoites could even suppress the stimulatory effect of lysed trophozoites in mixed infections, suggesting active G. intestinalis suppression of the IEC response. By dual-species RNA-sequencing, we defined the IEC and G. intestinalis gene expression programs associated with these differential outcomes of the infection. Taken together, our results inform on how G. intestinalis infection can lead to such highly variable effects on the host, and pinpoints trophozoite fitness as a key determinant of the IEC response to this common parasite.", "doi": "10.1371/journal.ppat.1011372", "pmid": "37141303", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10187934"}, {"db": "pii", "key": "PPATHOGENS-D-22-02213"}], "notes": [], "created": "2023-05-22T07:22:26.525Z", "modified": "2023-05-22T07:22:26.821Z"}, {"entity": "publication", "iuid": "ba8e61b15fdf4091b7ee12bca3608e26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba8e61b15fdf4091b7ee12bca3608e26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba8e61b15fdf4091b7ee12bca3608e26"}}, "title": "The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites.", "authors": [{"family": "Xu", "given": "Feifei", "initials": "F", "orcid": "0000-0003-1946-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c51ec60768479f851e29ebc804f547.json"}}, {"family": "Jim\u00e9nez-Gonz\u00e1lez", "given": "Alejandro", "initials": "A", "orcid": "0000-0003-3493-4154", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c6b93b731741018637733969c308a6.json"}}, {"family": "Einarsson", "given": "Elin", "initials": "E", "orcid": "0000-0002-1242-5263", "researcher": {"href": "https://publications.scilifelab.se/researcher/be89fa4c7f9d484c858a0bf385f06c61.json"}}, {"family": "\u00c1stvaldsson", "given": "\u00c1sgeir", "initials": "\u00c1", "orcid": "0000-0002-0320-6974", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a3d973dc6d246b48426d2063eef8934.json"}}, {"family": "Peirasmaki", "given": "Dimitra", "initials": "D", "orcid": "0000-0001-5376-626X", "researcher": {"href": "https://publications.scilifelab.se/researcher/94231cbd0cab4644b42c3fab58cea9aa.json"}}, {"family": "Eckmann", "given": "Lars", "initials": "L"}, {"family": "Andersson", "given": "Jan O", "initials": "JO", "orcid": "0000-0002-3075-4896", "researcher": {"href": "https://publications.scilifelab.se/researcher/489ed7f61a7b49a3a7ebd9ee3c391f5b.json"}}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG", "orcid": "0000-0002-7392-1746", "researcher": {"href": "https://publications.scilifelab.se/researcher/b01942d70ef84a1db3aaccab65af9c57.json"}}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J", "orcid": "0000-0002-7992-7970", "researcher": {"href": "https://publications.scilifelab.se/researcher/622d380bca244d738f5551cbed742b3e.json"}}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "Microb Genom", "issn": "2057-5858", "volume": "6", "issue": "8", "issn-l": null}, "abstract": "Diplomonad parasites of the genus Giardia have adapted to colonizing different hosts, most notably the intestinal tract of mammals. The human-pathogenic Giardia species, Giardia intestinalis, has been extensively studied at the genome and gene expression level, but no such information is available for other Giardia species. Comparative data would be particularly valuable for Giardia muris, which colonizes mice and is commonly used as a prototypic in vivo model for investigating host responses to intestinal parasitic infection. Here we report the draft-genome of G. muris. We discovered a highly streamlined genome, amongst the most densely encoded ever described for a nuclear eukaryotic genome. G. muris and G. intestinalis share many known or predicted virulence factors, including cysteine proteases and a large repertoire of cysteine-rich surface proteins involved in antigenic variation. Different to G. intestinalis, G. muris maintains tandem arrays of pseudogenized surface antigens at the telomeres, whereas intact surface antigens are present centrally in the chromosomes. The two classes of surface antigens engage in genetic exchange. Reconstruction of metabolic pathways from the G. muris genome suggest significant metabolic differences to G. intestinalis. Additionally, G. muris encodes proteins that might be used to modulate the prokaryotic microbiota. The responsible genes have been introduced in the Giardia genus via lateral gene transfer from prokaryotic sources. Our findings point to important evolutionary steps in the Giardia genus as it adapted to different hosts and it provides a powerful foundation for mechanistic exploration of host-pathogen interaction in the G. muris-mouse pathosystem.", "doi": "10.1099/mgen.0.000402", "pmid": "32618561", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7641422"}], "notes": [], "created": "2021-01-08T16:29:45.383Z", "modified": "2021-11-10T12:48:32.906Z"}]}