{"entity": "journal", "iuid": "500235128de94f828b8045983283a2f9", "timestamp": "2026-08-09T07:30:38.903Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/J.%20Exp.%20Bot..json"}, "display": {"href": "https://publications.scilifelab.se/journal/J.%20Exp.%20Bot."}}, "title": "J. Exp. Bot.", "issn": "1460-2431", "issn-l": "0022-0957", "publications_count": 11, "publications": [{"entity": "publication", "iuid": "8ed2bc92c9ef4a80aab66db3bcbdb8b1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ed2bc92c9ef4a80aab66db3bcbdb8b1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ed2bc92c9ef4a80aab66db3bcbdb8b1"}}, "title": "Wood-specific modification of glucuronoxylan can enhance growth in Populus.", "authors": [{"family": "Urbancsok", "given": "J\u00e1nos", "initials": "J", "orcid": "0000-0003-3237-6806", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab6f0e25417543f49060959d3af92967.json"}}, {"family": "Donev", "given": "Evgeniy N", "initials": "EN", "orcid": "0000-0002-7279-0481", "researcher": {"href": "https://publications.scilifelab.se/researcher/26467c84e2664b4980a4ed04335860ad.json"}}, {"family": "Derba-Maceluch", "given": "Marta", "initials": "M", "orcid": "0000-0002-8034-3630", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5be452cef9048e19a08fa8043b74329.json"}}, {"family": "Sivan", "given": "Pramod", "initials": "P", "orcid": "0000-0001-5297-2221", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bed5958298d4ca08df06860c94a3878.json"}}, {"family": "Barbut", "given": "F\u00e9lix R", "initials": "FR", "orcid": "0000-0001-5395-6776", "researcher": {"href": "https://publications.scilifelab.se/researcher/8df5c17bbf0440fd8be22761c2df9a6f.json"}}, {"family": "Mitra", "given": "Madhusree", "initials": "M", "orcid": "0000-0002-8653-8770", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c1827f45c7f4853888f15d857b7e414.json"}}, {"family": "Yassin", "given": "Zakiya", "initials": "Z", "orcid": "0000-0001-6878-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/53cd7ddc17274c0c9eabb07ae4e6c8e0.json"}}, {"family": "Cermanov\u00e1", "given": "Kate\u0159ina", "initials": "K"}, {"family": "\u0160imura", "given": "Jan", "initials": "J", "orcid": "0000-0002-1567-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac1674ad68434ab19f17056e7824c932.json"}}, {"family": "Karady", "given": "Michal", "initials": "M", "orcid": "0000-0002-5603-706X", "researcher": {"href": "https://publications.scilifelab.se/researcher/114911ccd31849e1a7584b5a52e9eb14.json"}}, {"family": "Scheepers", "given": "Gerhard", "initials": "G", "orcid": "0000-0002-5630-1377", "researcher": {"href": "https://publications.scilifelab.se/researcher/60a566216ee146d1bba50d7f8779a6f8.json"}}, {"family": "Mellerowicz", "given": "Ewa J", "initials": "EJ", "orcid": "0000-0001-6817-1031", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9bf45f4790e4360b19ec021469cfad2.json"}}], "type": "journal article", "published": "2025-08-23", "journal": {"title": "J. Exp. Bot.", "issn": "1460-2431", "issn-l": "0022-0957"}, "abstract": "Xylem cells are surrounded by primary and secondary cell walls. Formation of primary walls is regulated by the cell wall integrity surveillance system, but it is unclear if the deposition of secondary walls is similarly regulated. To study this question, we introduced to aspen three different enzymes cleaving cell wall-localized xylan and we suppressed xylan synthase components either ubiquitously or specifically during secondary wall formation using Populus trichocarpa GT43B promoter. When xylan was ubiquitously altered, 95% of lines showed reduced growth, whereas when it was altered during secondary wall deposition, 30% of lines grew better with the rest having no growth impairment, suggesting opposite effects of primary and secondary wall disturbances. To detect mechanism of growth stimulation by disturbed deposition of secondary wall, we analyzed changes in wood quality traits, chemistry, transcriptomics, metabolomics and hormonomics in transgenic lines. We found increased tension wood production, reduced S- and H-lignin, and changes in several metabolites in common in these lines. Remorin REM1.3 and NRL2 (NPH3 family) transcripts increased and changes in jasmonates, ABA and SA occurred in secondary wall-forming xylem suggesting their involvement in secondary wall integrity surveyance and signaling. The data indicate that a unique program mediates responses to secondary wall impairment that induces growth.", "doi": "10.1093/jxb/eraf364", "pmid": "40847653", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "8240116"}], "notes": [], "created": "2025-11-18T12:16:27.291Z", "modified": "2025-11-18T12:16:27.407Z"}, {"entity": "publication", "iuid": "82da1c79ab3d480f8ef86647b089b801", "links": {"self": {"href": "https://publications.scilifelab.se/publication/82da1c79ab3d480f8ef86647b089b801.json"}, "display": {"href": "https://publications.scilifelab.se/publication/82da1c79ab3d480f8ef86647b089b801"}}, "title": "Aberrant growth and expansion in Penium margaritaceum triggered by disruption of microtubules and the cell wall.", "authors": [{"family": "LoRicco", "given": "Josephine G", "initials": "JG", "orcid": "0000-0002-1550-2463", "researcher": {"href": "https://publications.scilifelab.se/researcher/edbbb3add76a4370b4037d1aaa8132dc.json"}}, {"family": "Malone", "given": "Stuart", "initials": "S"}, {"family": "Becker", "given": "Abigail", "initials": "A"}, {"family": "Xue", "given": "Nichole", "initials": "N"}, {"family": "Bagdan", "given": "Kaylee", "initials": "K", "orcid": "0000-0002-5060-4270", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f069d44c6094291a5452952b4209e66.json"}}, {"family": "Eastman", "given": "Anika", "initials": "A"}, {"family": "Sgambettera", "given": "Gabriel", "initials": "G"}, {"family": "Winegrad", "given": "Aaron", "initials": "A"}, {"family": "Gibeau", "given": "Benjamin", "initials": "B"}, {"family": "Bauer", "given": "Lindsay", "initials": "L"}, {"family": "Epstein", "given": "Ruby", "initials": "R"}, {"family": "Domozych", "given": "David S", "initials": "DS", "orcid": "0000-0001-8800-0061", "researcher": {"href": "https://publications.scilifelab.se/researcher/389412e319244f48955e4aeeac9ec616.json"}}], "type": "journal article", "published": "2025-02-25", "journal": {"title": "J. Exp. Bot.", "issn": "1460-2431", "volume": "76", "issue": "4", "pages": "961-979", "issn-l": "0022-0957"}, "abstract": "Penium margaritaceum, a unicellular zygnematophyte (Streptophyta), was employed to elucidate changes in cell expansion when cells were challenged with the fungal pectinolytic enzyme, pectate lyase, and/or the microtubule-disrupting agent, amiprophos-methyl (APM). Microtubule disruption by APM resulted in significant swelling at expansion zones. These swollen zones provided an easy marker for the location of expansion zones, particularly in cells with altered cell wall pectin. Short-term treatment with pectate lyase showed pectin degradation primarily at the isthmus expansion zone and two satellite bands, corresponding to the location of future expansion in daughter cells. When the homogalacturonan lattice of the cell wall was removed by treatment with pectate lyase during long treatments, cell division was maintained, but daughter cell products were considerably smaller. Treatment of cells with a mixture of both pectate lyase and APM resulted in a distinct phenotype, consisting of 'dumbbell'-shaped cells, as APM-induced swelling occurs at the novel expansion centers exposed by pectate lyase treatment. These cells also presented other curious alterations, including an extensive, chloroplast-free cytoplasmic zone at the center of the cell, a septum containing \u03b2-glycan, arabinogalactan and homogalacturonan epitopes, unique stacks of endoplasmic reticulum, displaced Golgi bodies, and an extensive network of vacuoles. These results provide insight into the importance of cell wall integrity in defining the location of cell growth and division in P. margaritaceum. Understanding these processes in a unicellular zygnematophyte may provide insights into steps involved in the evolution of land plants.", "doi": "10.1093/jxb/erae387", "pmid": "39269031", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "7756302"}], "notes": [], "created": "2024-11-15T12:08:05.360Z", "modified": "2025-11-05T13:54:08.964Z"}, {"entity": "publication", "iuid": "f41b7e4ccde445e8a64194739a57ed51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f41b7e4ccde445e8a64194739a57ed51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f41b7e4ccde445e8a64194739a57ed51"}}, "title": "Comparison of plastid proteomes points towards a higher plastidial redox turnover in vascular tissues than in mesophyll cells.", "authors": [{"family": "Boussardon", "given": "Cl\u00e9ment", "initials": "C", "orcid": "0000-0001-8313-3535", "researcher": {"href": "https://publications.scilifelab.se/researcher/63dace73d3684bf3b48c13b58c5f777f.json"}}, {"family": "Carrie", "given": "Chris", "initials": "C", "orcid": "0000-0002-4240-4674", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a9f440fc0e94cbe956b35046cc13287.json"}}, {"family": "Keech", "given": "Olivier", "initials": "O", "orcid": "0000-0002-0546-7721", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbfa829eb0b74b67aed7865dda0e15d3.json"}}], "type": "journal article", "published": "2023-08-03", "journal": {"title": "J. Exp. Bot.", "issn": "1460-2431", "volume": "74", "issue": "14", "pages": "4110-4124", "issn-l": "0022-0957"}, "abstract": "Plastids are complex organelles that vary in size and function depending on the cell type. Accordingly, they can be referred to as amyloplasts, chloroplasts, chromoplasts, etioplasts, or proplasts, to only cite a few. Over the past decades, methods based on density gradients and differential centrifugation have been extensively used for the purification of plastids. However, these methods need large amounts of starting material, and hardly provide a tissue-specific resolution. Here, we applied our IPTACT (Isolation of Plastids TAgged in specific Cell Types) method, which involves the biotinylation of plastids in vivo using one-shot transgenic lines expressing the Translocon of the Outer Membrane 64 (TOC64) gene coupled with a biotin ligase receptor particle and the BirA biotin ligase, to isolate plastids from mesophyll and companion cells of Arabidopsis using tissue specific pCAB3 and pSUC2 promoters, respectively. Subsequently, a proteome profiling was performed, which allowed the identification of 1672 proteins, among which 1342 were predicted to be plastidial, and 705 were fully confirmed according to the SUBA5 database. Interestingly, although 92% of plastidial proteins were equally distributed between the two tissues, we observed an accumulation of proteins associated with jasmonic acid biosynthesis, plastoglobuli (e.g. NAD(P)H dehydrogenase C1, vitamin E deficient 1, plastoglobulin of 34 kDa, ABC1-like kinase 1) and cyclic electron flow in plastids originating from vascular tissue. Besides demonstrating the technical feasibility of isolating plastids in a tissue-specific manner, our work provides strong evidence that plastids from vascular tissue have a higher redox turnover to ensure optimal functioning, notably under high solute strength as encountered in vascular cells.", "doi": "10.1093/jxb/erad133", "pmid": "37026385", "labels": {"Global Proteomics and Proteogenomics": "Service", "Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10400147"}, {"db": "pii", "key": "7110727"}], "notes": [], "created": "2023-06-07T19:03:18.674Z", "modified": "2023-11-29T13:24:39.668Z"}, {"entity": "publication", "iuid": "32a294f52192486aabddd5b6dcb69cc8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/32a294f52192486aabddd5b6dcb69cc8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/32a294f52192486aabddd5b6dcb69cc8"}}, "title": "A MITE insertion abolishes the AP3-3 self-maintenance regulatory loop in apetalous flowers of Nigella damascena.", "authors": [{"family": "Conde E Silva", "given": "Natalia", "initials": "N", "orcid": "0000-0003-2435-9184", "researcher": {"href": "https://publications.scilifelab.se/researcher/bdec1fbe4d50482198c6759f4c47e462.json"}}, {"family": "Leguilloux", "given": "Martine", "initials": "M"}, {"family": "Bellec", "given": "Arnaud", "initials": "A", "orcid": "0000-0002-7608-9537", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9c2cdea0dd645209766bf96deb930a5.json"}}, {"family": "Rodde", "given": "Nathalie", "initials": "N", "orcid": "0000-0003-3361-4730", "researcher": {"href": "https://publications.scilifelab.se/researcher/950d614a328b44fbb3d7ac18b1b1e2ae.json"}}, {"family": "Aubert", "given": "Juliette", "initials": "J", "orcid": "0000-0001-6136-3815", "researcher": {"href": "https://publications.scilifelab.se/researcher/a60f9a06e785408e9db43e2a55b533de.json"}}, {"family": "Manicacci", "given": "Domenica", "initials": "D", "orcid": "0000-0002-6779-113X", "researcher": {"href": "https://publications.scilifelab.se/researcher/37f4aa92f5dc43d28a6795113ed48ad4.json"}}, {"family": "Damerval", "given": "Catherine", "initials": "C", "orcid": "0000-0002-7317-4971", "researcher": {"href": "https://publications.scilifelab.se/researcher/a48c5646210742ff92a211d82e35c0d7.json"}}, {"family": "Berges", "given": "Helene", "initials": "H", "orcid": "0000-0002-5492-1062", "researcher": {"href": "https://publications.scilifelab.se/researcher/728be2338bd2407980d11b8850d85d9c.json"}}, {"family": "Deveaux", "given": "Yves", "initials": "Y", "orcid": "0000-0002-3297-1317", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ef27480c1c94cc9a5d742d0dd3c1d12.json"}}], "type": "journal article", "published": "2023-03-13", "journal": {"title": "J. Exp. Bot.", "issn": "1460-2431", "volume": "74", "issue": "5", "pages": "1448-1459", "issn-l": "0022-0957"}, "abstract": "MADS-box transcription factors are important regulators of floral organ identity through their binding to specific motifs, termed CArG, in the promoter of their target genes. Petal initiation and development depend on class A and B genes, but MADS-box genes of the APETALA3 (AP3) clade are key regulators of this process. In the early diverging eudicot Nigella damascena, an apetalous [T] morph is characterized by the lack of expression of the NdAP3-3 gene, with its expression being petal-specific in the wild-type [P] morph. All [T] morph plants are homozygous for an NdAP3-3 allele with a Miniature Inverted-repeat Transposable Element (MITE) insertion in the second intron of the gene. Here, we investigated to which extent the MITE insertion impairs regulation of the NdAP3-3 gene. We found that expression of NdAP3-3 is initiated in the [T] morph, but the MITE insertion prevents its positive self-maintenance by affecting the correct splicing of the mRNA. We also found specific CArG features in the promoter of the NdAP3-3 genes with petal-specific expression. However, they are not sufficient to drive expression only in petals of transgenic Arabidopsis, highlighting the existence of Nigella-specific cis/trans-acting factors in regulating AP3 paralogs.", "doi": "10.1093/jxb/erac489", "pmid": "36512646", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "6895535"}], "notes": [], "created": "2023-08-15T07:02:42.318Z", "modified": "2023-08-15T07:02:42.621Z"}, {"entity": "publication", "iuid": "08ce6b64bfcb41c7ba2ac0cbd0821f5f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/08ce6b64bfcb41c7ba2ac0cbd0821f5f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/08ce6b64bfcb41c7ba2ac0cbd0821f5f"}}, "title": "Intramolecular carbon isotope signals reflect metabolite allocation in plants.", "authors": [{"family": "Wieloch", "given": "Thomas", "initials": "T", "orcid": "0000-0001-9162-2291", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae51002869054ad981fde0c6b4d9d047.json"}}, {"family": "Sharkey", "given": "Thomas David", "initials": "TD", "orcid": "0000-0002-4423-3223", "researcher": {"href": "https://publications.scilifelab.se/researcher/5cf989a87cfd49228ebdf3cb1043bf29.json"}}, {"family": "Werner", "given": "Roland Anton", "initials": "RA"}, {"family": "Schleucher", "given": "J\u00fcrgen", "initials": "J"}], "type": "journal article", "published": "2022-01-27", "journal": {"title": "J. Exp. Bot.", "issn": "1460-2431", "issn-l": "0022-0957"}, "abstract": "Stable isotopes at natural abundance are key tools to study physiological processes occurring outside the temporal scope of manipulation and monitoring experiments. Whole-molecule carbon isotope ratios ( 13C/ 12C) enable assessments of plant carbon uptake yet conceal information about carbon allocation. Here, we identify an intramolecular 13C/ 12C signal at tree-ring glucose C-5 and C-6 and develop experimentally testable theories on its origin. More specifically, we assess the potential of processes within C3 metabolism for signal introduction based (inter alia) on constraints on signal propagation posed by metabolic networks. We propose that the intramolecular signal reports carbon allocation into major metabolic pathways in actively photosynthesising leaf cells including the anaplerotic, shikimate, and non-mevalonate pathway. We support our theoretical framework by linking it to previously reported whole-molecule 13C/ 12C increases in cellulose of ozone-treated Betula pendula and a highly significant relationship between the intramolecular signal and tropospheric ozone concentration. Our theory postulates a pronounced preference of leaf-cytosolic triose-phosphate isomerase to catalyse the forward reaction in vivo (dihydroxyacetone phosphate to glyceraldehyde 3-phosphate). In conclusion, intramolecular 13C/ 12C analysis resolves information about carbon uptake and allocation enabling more comprehensive assessments of carbon metabolism than whole-molecule 13C/ 12C analysis.", "doi": "10.1093/jxb/erac028", "pmid": "35084456", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6515905"}], "notes": [], "created": "2022-03-22T13:21:48.006Z", "modified": "2025-10-17T13:03:55.109Z"}, {"entity": "publication", "iuid": "a99daae53bd54387a514643b88a96846", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a99daae53bd54387a514643b88a96846.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a99daae53bd54387a514643b88a96846"}}, "title": "Carbon flux around leaf-cytosolic glyceraldehyde-3-phosphate dehydrogenase introduces a 13C signal in plant glucose.", "authors": [{"family": "Wieloch", "given": "Thomas", "initials": "T", "orcid": "0000-0001-9162-2291", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae51002869054ad981fde0c6b4d9d047.json"}}, {"family": "Werner", "given": "Roland Anton", "initials": "RA"}, {"family": "Schleucher", "given": "J\u00fcrgen", "initials": "J"}], "type": "journal article", "published": "2021-10-26", "journal": {"title": "J. Exp. Bot.", "issn": "1460-2431", "volume": "72", "issue": "20", "pages": "7136-7144", "issn-l": "0022-0957"}, "abstract": "Within the plant and Earth sciences, stable isotope analysis is a versatile tool conveying information (inter alia) about plant physiological and paleoclimate variability across scales. Here, we identify a 13C signal (i.e. systematic 13C/12C variation) at tree-ring glucose C-4 and report an experimentally testable theory on its origin. We propose the signal is introduced by glyceraldehyde-3-phosphate dehydrogenases in the cytosol of leaves. It conveys two kinds of (potentially convoluted) information: (i) commitment of glyceraldehyde 3-phosphate to 3-phosphoglycerate versus fructose 1,6-bisphosphate metabolism; and (ii) the contribution of non-phosphorylating versus phosphorylating glyceraldehyde-3-phosphate dehydrogenase to catalysing the glyceraldehyde 3-phosphate to 3-phosphoglycerate forward reaction of glycolysis. The theory is supported by 13C fractionation modelling. Modelling results provide the first evidence in support of the cytosolic oxidation-reduction (COR) cycle, a carbon-neutral mechanism supplying NADPH at the expense of ATP and NADH, which may help to maintain leaf-cytosolic redox balances. In line with expectations related to COR cycling, we found a positive correlation between air vapour pressure deficit and 13C discrimination at glucose C-4. Overall, 13C-4 signal analysis may enable an improved understanding of leaf carbon and energy metabolism.", "doi": "10.1093/jxb/erab316", "pmid": "34223885", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6315293"}, {"db": "pmc", "key": "PMC8547152"}], "notes": [], "created": "2021-12-05T14:23:28.515Z", "modified": "2025-10-17T13:03:55.409Z"}, {"entity": "publication", "iuid": "3d6084989c4c436bb04585ec88b5f5f5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3d6084989c4c436bb04585ec88b5f5f5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3d6084989c4c436bb04585ec88b5f5f5"}}, "title": "Polycomb Repressive Complex 2-mediated histone modification H3K27me3 is associated with embryogenic potential in Norway spruce.", "authors": [{"family": "Nakamura", "given": "Miyuki", "initials": "M", "orcid": "0000-0002-8153-7293", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa9f227109b54fa9a1457a1f7af197af.json"}}, {"family": "Batista", "given": "Rita A", "initials": "RA"}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}, {"family": "Hennig", "given": "Lars", "initials": "L", "orcid": "0000-0002-6645-1862", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b350e5d9ba74c27bf1709ff0457e605.json"}}], "type": "journal article", "published": "2020-10-22", "journal": {"title": "J. Exp. Bot.", "issn": "1460-2431", "volume": "71", "issue": "20", "pages": "6366-6378", "issn-l": "0022-0957"}, "abstract": "Epigenetic reprogramming during germ cell formation is essential to gain pluripotency and thus embryogenic potential. The histone modification H3K27me3, which is catalysed by the Polycomb repressive complex 2 (PRC2), regulates important developmental processes in both plants and animals, and defects in PRC2 components cause pleiotropic developmental abnormalities. Nevertheless, the role of H3K27me3 in determining embryogenic potential in gymnosperms is still elusive. To address this, we generated H3K27me3 profiles of Norway spruce (Picea abies) embryonic callus and non-embryogenic callus using CUT&RUN, which is a powerful method for chromatin profiling. Here, we show that H3K27me3 mainly accumulated in genic regions in the Norway spruce genome, similarly to what is observed in other plant species. Interestingly, H3K27me3 levels in embryonic callus were much lower than those in the other examined tissues, but markedly increased upon embryo induction. These results show that H3K27me3 levels are associated with the embryogenic potential of a given tissue, and that the early phase of somatic embryogenesis is accompanied by changes in H3K27me3 levels. Thus, our study provides novel insights into the role of this epigenetic mark in spruce embryogenesis and reinforces the importance of PRC2 as a key regulator of cell fate determination across different plant species.", "doi": "10.1093/jxb/eraa365", "pmid": "32894759", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "5902563"}, {"db": "pmc", "key": "PMC7586741"}], "notes": [], "created": "2020-11-16T09:34:27.793Z", "modified": "2021-11-10T12:46:16.725Z"}, {"entity": "publication", "iuid": "dad2c2d54faa4a46a778b12fa7f53f4a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dad2c2d54faa4a46a778b12fa7f53f4a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dad2c2d54faa4a46a778b12fa7f53f4a"}}, "title": "Ultra-rapid auxin metabolite profiling for high-throughput mutant screening in Arabidopsis.", "authors": [{"family": "Penc\u00edk", "given": "Ale\u0161", "initials": "A"}, {"family": "Casanova-S\u00e1ez", "given": "Rub\u00e9n", "initials": "R"}, {"family": "Pilarov\u00e1", "given": "Veronika", "initials": "V"}, {"family": "\u017dukauskaite", "given": "Asta", "initials": "A"}, {"family": "Pinto", "given": "Rui", "initials": "R"}, {"family": "Micol", "given": "Jos\u00e9 Luis", "initials": "JL", "orcid": "0000-0002-0396-1750", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9fed6e5b83447ea8954d666f0f2c1a1.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Nov\u00e1k", "given": "Ondrej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}], "type": "journal article", "published": "2018-04-27", "journal": {"title": "J. Exp. Bot.", "issn": "1460-2431", "volume": "69", "issue": "10", "pages": "2569-2579", "issn-l": "0022-0957"}, "abstract": "Auxin (indole-3-acetic acid, IAA) plays fundamental roles as a signalling molecule during numerous plant growth and development processes. The formation of local auxin gradients and auxin maxima/minima, which is very important for these processes, is regulated by auxin metabolism (biosynthesis, degradation, and conjugation) as well as transport. When studying auxin metabolism pathways it is crucial to combine data obtained from genetic investigations with the identification and quantification of individual metabolites. Thus, to facilitate efforts to elucidate auxin metabolism and its roles in plants, we have developed a high-throughput method for simultaneously quantifying IAA and its key metabolites in minute samples (<10 mg FW) of Arabidopsis thaliana tissues by in-tip micro solid-phase extraction and fast LC-tandem MS. As a proof of concept, we applied the method to a collection of Arabidopsis mutant lines and identified lines with altered IAA metabolite profiles using multivariate data analysis. Finally, we explored the correlation between IAA metabolite profiles and IAA-related phenotypes. The developed rapid analysis of large numbers of samples (>100 samples d-1) is a valuable tool to screen for novel regulators of auxin metabolism and homeostasis among large collections of genotypes.", "doi": "10.1093/jxb/ery084", "pmid": "29514302", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "4919650"}, {"db": "pmc", "key": "PMC5920284"}], "notes": [], "created": "2019-01-10T11:22:35.140Z", "modified": "2025-10-17T13:03:18.202Z"}, {"entity": "publication", "iuid": "963fc811ecd04e45bee0fe127479ecb2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/963fc811ecd04e45bee0fe127479ecb2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/963fc811ecd04e45bee0fe127479ecb2"}}, "title": "Transcriptional stimulation of rate-limiting components of the autophagic pathway improves plant fitness.", "authors": [{"family": "Minina", "given": "Elena A", "initials": "EA", "orcid": "0000-0002-2619-1859", "researcher": {"href": "https://publications.scilifelab.se/researcher/63cb7fc5ae9348ea97ce21d5f86ad623.json"}}, {"family": "Moschou", "given": "Panagiotis N", "initials": "PN"}, {"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Sanchez-Vera", "given": "Victoria", "initials": "V"}, {"family": "Cardoso", "given": "Catarina", "initials": "C"}, {"family": "Liu", "given": "Qinsong", "initials": "Q"}, {"family": "Elander", "given": "Pernilla H", "initials": "PH"}, {"family": "Dalman", "given": "Kerstin", "initials": "K"}, {"family": "Beganovic", "given": "Mirela", "initials": "M"}, {"family": "Lindberg Yilmaz", "given": "Jenny", "initials": "J"}, {"family": "Marmon", "given": "Sofia", "initials": "S"}, {"family": "Shabala", "given": "Lana", "initials": "L"}, {"family": "Suarez", "given": "Maria F", "initials": "MF"}, {"family": "Ljung", "given": "Karin", "initials": "K"}, {"family": "Nov\u00e1k", "given": "Ondrej", "initials": "O"}, {"family": "Shabala", "given": "Sergey", "initials": "S"}, {"family": "Stymne", "given": "Sten", "initials": "S"}, {"family": "Hofius", "given": "Daniel", "initials": "D"}, {"family": "Bozhkov", "given": "Peter V", "initials": "PV"}], "type": "journal article", "published": "2018-03-14", "journal": {"title": "J. Exp. Bot.", "issn": "1460-2431", "volume": "69", "issue": "6", "pages": "1415-1432", "issn-l": "0022-0957"}, "abstract": "Autophagy is a major catabolic process whereby autophagosomes deliver cytoplasmic content to the lytic compartment for recycling. Autophagosome formation requires two ubiquitin-like systems conjugating Atg12 with Atg5, and Atg8 with lipid phosphatidylethanolamine (PE), respectively. Genetic suppression of these systems causes autophagy-deficient phenotypes with reduced fitness and longevity. We show that Atg5 and the E1-like enzyme, Atg7, are rate-limiting components of Atg8-PE conjugation in Arabidopsis. Overexpression of ATG5 or ATG7 stimulates Atg8 lipidation, autophagosome formation, and autophagic flux. It also induces transcriptional changes opposite to those observed in atg5 and atg7 mutants, favoring stress resistance and growth. As a result, ATG5- or ATG7-overexpressing plants exhibit increased resistance to necrotrophic pathogens and oxidative stress, delayed aging and enhanced growth, seed set, and seed oil content. This work provides an experimental paradigm and mechanistic insight into genetic stimulation of autophagy in planta and shows its efficiency for improving plant productivity.", "doi": "10.1093/jxb/ery010", "pmid": "29365132", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "4818325"}, {"db": "pmc", "key": "PMC6019011"}], "notes": [], "created": "2019-01-10T11:21:10.106Z", "modified": "2025-10-17T13:03:18.283Z"}, {"entity": "publication", "iuid": "fa592b5a2d9c4e64b66d41327a9a6fb4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa592b5a2d9c4e64b66d41327a9a6fb4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa592b5a2d9c4e64b66d41327a9a6fb4"}}, "title": "Reduced mitochondrial malate dehydrogenase activity has a strong effect on photorespiratory metabolism as revealed by 13C labelling.", "authors": [{"family": "Lind\u00e9n", "given": "Pernilla", "initials": "P"}, {"family": "Keech", "given": "Olivier", "initials": "O"}, {"family": "Stenlund", "given": "Hans", "initials": "H"}, {"family": "Gardestr\u00f6m", "given": "Per", "initials": "P"}, {"family": "Moritz", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4258-3190", "researcher": {"href": "https://publications.scilifelab.se/researcher/95ad5b7fe48f42eda1328f54a385e097.json"}}], "type": "journal article", "published": "2016-05-00", "journal": {"title": "J. Exp. Bot.", "issn": "1460-2431", "issn-l": "0022-0957", "volume": "67", "issue": "10", "pages": "3123-3135"}, "abstract": "Mitochondrial malate dehydrogenase (mMDH) catalyses the interconversion of malate and oxaloacetate (OAA) in the tricarboxylic acid (TCA) cycle. Its activity is important for redox control of the mitochondrial matrix, through which it may participate in regulation of TCA cycle turnover. In Arabidopsis, there are two isoforms of mMDH. Here, we investigated to which extent the lack of the major isoform, mMDH1 accounting for about 60% of the activity, affected leaf metabolism. In air, rosettes of mmdh1 plants were only slightly smaller than wild type plants although the fresh weight was decreased by about 50%. In low CO2 the difference was much bigger, with mutant plants accumulating only 14% of fresh weight as compared to wild type. To investigate the metabolic background to the differences in growth, we developed a (13)CO2 labelling method, using a custom-built chamber that enabled simultaneous treatment of sets of plants under controlled conditions. The metabolic profiles were analysed by gas- and liquid- chromatography coupled to mass spectrometry to investigate the metabolic adjustments between wild type and mmdh1 The genotypes responded similarly to high CO2 treatment both with respect to metabolite pools and (13)C incorporation during a 2-h treatment. However, under low CO2 several metabolites differed between the two genotypes and, interestingly most of these were closely associated with photorespiration. We found that while the glycine/serine ratio increased, a concomitant altered glutamine/glutamate/\u03b1-ketoglutarate relation occurred. Taken together, our results indicate that adequate mMDH activity is essential to shuttle reductants out from the mitochondria to support the photorespiratory flux, and strengthen the idea that photorespiration is tightly intertwined with peripheral metabolic reactions.", "doi": "10.1093/jxb/erw030", "pmid": "26889011", "labels": {"Swedish Metabolomics Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "erw030"}, {"db": "pmc", "key": "PMC4867893"}], "notes": [], "created": "2017-05-03T12:59:39.973Z", "modified": "2025-10-17T13:03:19.568Z"}, {"entity": "publication", "iuid": "dd23902bae6b4016a2757ea2928c5499", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd23902bae6b4016a2757ea2928c5499.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd23902bae6b4016a2757ea2928c5499"}}, "title": "Plant-mediated gene silencing restricts growth of the potato late blight pathogen Phytophthora infestans.", "authors": [{"family": "Jahan", "given": "Sultana N", "initials": "SN"}, {"family": "\u00c5sman", "given": "Anna K M", "initials": "AK"}, {"family": "Corcoran", "given": "P\u00e1draic", "initials": "P"}, {"family": "Fogelqvist", "given": "Johan", "initials": "J"}, {"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2015-05-00", "journal": {"volume": "66", "issn": "1460-2431", "issue": "9", "pages": "2785-2794", "title": "J. Exp. Bot.", "issn-l": "0022-0957"}, "abstract": "Phytophthora infestans is an oomycete that causes severe damage to potato, and is well known for its ability to evolve rapidly in order to overcome resistant potato varieties. An RNA silencing strategy was evaluated here to clarify if small interfering RNA homologous to selected genes in P. infestans could be targeted from the plant host to reduce the magnitude of the infection. As a proof-of-concept, a hairpin RNA (hp-RNA) construct using the GFP marker gene was designed and introduced in potato. At 72 hpi, a 55-fold reduction of the signal intensity of a corresponding GFP expressing P. infestans strain on leaf samples of transgenic plants, compared with wild-type potato, was detected. This suggests that an RNA interference construct in the potato host could be processed and target a transcript of the pathogen. Three genes important in the infection process of P. infestans, PiGPB1, PiCESA2, and PiPEC, together with PiGAPDH taking part in basic cell maintenance were subsequently tested using an analogous transgenic strategy. Out of these gene candidates, the hp-PiGPB1 targeting the G protein \u03b2-subunit (PiGPB1) important for pathogenicity resulted in most restricted disease progress. Further, Illumina sequencing of inoculated transgenic potato leaves revealed sRNAs of 24/25 nt size homologous to the PiGPB1 gene in the transgenic plants indicating post-transcriptional silencing of the target gene. The work demonstrates that a host-induced gene-silencing approach is functional against P. infestans but is highly dependent on target gene for a successful outcome. This finding broadens the arsenal of control strategies to this important plant disease.", "doi": "10.1093/jxb/erv094", "pmid": "25788734", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "erv094"}, {"db": "pmc", "key": "PMC4986879"}], "notes": [], "created": "2017-05-02T12:57:24.967Z", "modified": "2020-01-21T13:56:05.653Z"}], "created": "2017-05-09T09:12:14.025Z", "modified": "2020-11-27T13:14:02.968Z"}