{"entity": "researcher", "timestamp": "2026-06-09T03:10:08.456Z", "family": "Van Aken", "given": "Olivier", "initials": "O", "orcid": "0000-0003-4024-968X", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/4f8174aa4d9e4031822ea281b6f0f9dd.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/4f8174aa4d9e4031822ea281b6f0f9dd"}}, "publications": [{"entity": "publication", "iuid": "d822f5357c6a448b82142e0a1e71bdac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d822f5357c6a448b82142e0a1e71bdac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d822f5357c6a448b82142e0a1e71bdac"}}, "title": "Evolved and Plastic Gene Expression in Adaptation of a Specialist Fly to a Novel Niche.", "authors": [{"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}}, {"family": "Ortega Gim\u00e9nez", "given": "Jes\u00fas", "initials": "J", "orcid": "0000-0001-6599-1675", "researcher": {"href": "https://publications.scilifelab.se/researcher/e60538dadc0a4ee9ade7bc0015d67491.json"}}, {"family": "Choudhary", "given": "Shruti", "initials": "S", "orcid": "0000-0002-6146-7224", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6ebad9d4ddf40949a19776df31a00c7.json"}}, {"family": "Moss", "given": "Oliver", "initials": "O"}, {"family": "Su", "given": "Yi", "initials": "Y", "orcid": "0009-0001-4802-5210", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7f56487ba584ac5b08cfa6c06c6f7a6.json"}}, {"family": "Van Aken", "given": "Olivier", "initials": "O", "orcid": "0000-0003-4024-968X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f8174aa4d9e4031822ea281b6f0f9dd.json"}}, {"family": "Runemark", "given": "Anna", "initials": "A", "orcid": "0000-0002-8976-5530", "researcher": {"href": "https://publications.scilifelab.se/researcher/e914e2d1ccbd4d35ae574187762ae01f.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "34", "issue": "4", "pages": "e17653"}, "abstract": "How gene expression evolves to enable divergent ecological adaptation and how changes in gene expression relate to genomic architecture are pressing questions for understanding the mechanisms enabling adaptation and ecological speciation. Furthermore, how plasticity in gene expression can both contribute to and be affected by the process of ecological adaptation is crucial to understanding gene expression evolution, colonisation of novel niches and response to rapid environmental change. Here, we investigate the role of constitutive and plastic gene expression differences between host races, or host-specific ecotypes, of the peacock fly Tephritis conura, a thistle bud specialist. By cross-fostering larvae to new buds of their natal host plant or the alternative, novel host plant, we uncover extensive constitutive differences in gene expression between the host races, especially genes associated with processing of host plant chemicals. However, evidence for expression plasticity was minimal and limited to the ancestral host race. Genes with host race-specific expression are found more often than expected within a large inversion in the T. conura genome, adding to evidence that inversions are important for enabling diversification in the face of gene flow and underscores that altered gene expression may be key to understanding the evolutionary consequences of inversions.", "doi": "10.1111/mec.17653", "pmid": "39783891", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11789552"}], "notes": [], "created": "2025-01-30T10:48:38.552Z", "modified": "2025-11-28T10:51:21.794Z"}, {"entity": "publication", "iuid": "b5b5c7255f784a05bc6f42ac2af8a6a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5b5c7255f784a05bc6f42ac2af8a6a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5b5c7255f784a05bc6f42ac2af8a6a1"}}, "title": "The dynamics of touch-responsive gene expression in cereals.", "authors": [{"family": "Darwish", "given": "Essam", "initials": "E"}, {"family": "Ghosh", "given": "Ritesh", "initials": "R"}, {"family": "Bentzer", "given": "Johan", "initials": "J"}, {"family": "Tsardakas Renhuldt", "given": "Nikos", "initials": "N"}, {"family": "Proux-Wera", "given": "Estelle", "initials": "E"}, {"family": "Kamal", "given": "Nadia", "initials": "N"}, {"family": "Spannagl", "given": "Manuel", "initials": "M"}, {"family": "Hause", "given": "Bettina", "initials": "B"}, {"family": "Sirijovski", "given": "Nick", "initials": "N"}, {"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": "2023-10-00", "journal": {"title": "Plant J.", "issn": "1365-313X", "issn-l": "0960-7412", "volume": "116", "issue": "1", "pages": "282-302"}, "abstract": "Wind, rain, herbivores, obstacles, neighbouring plants, etc. provide important mechanical cues to steer plant growth and survival. Mechanostimulation to stimulate yield and stress resistance of crops is of significant research interest, yet a molecular understanding of transcriptional responses to touch is largely absent in cereals. To address this, we performed whole-genome transcriptomics following mechanostimulation of wheat, barley, and the recent genome-sequenced oat. The largest transcriptome changes occurred \u00b125 min after touching, with most of the genes being upregulated. While most genes returned to basal expression level by 1-2 h in oat, many genes retained high expression even 4 h post-treatment in barley and wheat. Functional categories such as transcription factors, kinases, phytohormones, and Ca2+ regulation were affected. In addition, cell wall-related genes involved in (hemi)cellulose, lignin, suberin, and callose biosynthesis were touch-responsive, providing molecular insight into mechanically induced changes in cell wall composition. Furthermore, several cereal-specific transcriptomic footprints were identified that were not observed in Arabidopsis. In oat and barley, we found evidence for systemic spreading of touch-induced signalling. Finally, we provide evidence that both the jasmonic acid-dependent and the jasmonic acid-independent pathways underlie touch-signalling in cereals, providing a detailed framework and marker genes for further study of (a)biotic stress responses in cereals.", "doi": "10.1111/tpj.16269", "pmid": "37159480", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-05-16T13:33:51.071Z", "modified": "2023-10-19T12:14:37.586Z"}, {"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": "05252c2ee2e24c1caba55097e6100408", "links": {"self": {"href": "https://publications.scilifelab.se/publication/05252c2ee2e24c1caba55097e6100408.json"}, "display": {"href": "https://publications.scilifelab.se/publication/05252c2ee2e24c1caba55097e6100408"}}, "title": "Touch signaling and thigmomorphogenesis are regulated by complementary CAMTA3- and JA-dependent pathways.", "authors": [{"family": "Darwish", "given": "Essam", "initials": "E", "orcid": "0000-0002-8204-0772", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a087f251f64ef3a0e21fe0909a8841.json"}}, {"family": "Ghosh", "given": "Ritesh", "initials": "R", "orcid": "0000-0002-2528-7277", "researcher": {"href": "https://publications.scilifelab.se/researcher/73d9fdc04f7e44b697cc669014c7bbd3.json"}}, {"family": "Ontiveros-Cisneros", "given": "Abraham", "initials": "A", "orcid": "0000-0003-3983-8380", "researcher": {"href": "https://publications.scilifelab.se/researcher/f47950d286194253814b41b1899440c6.json"}}, {"family": "Tran", "given": "Huy Cuong", "initials": "HC", "orcid": "0000-0002-7670-2215", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf057352ae445079a2e9dc51b6326a7.json"}}, {"family": "Petersson", "given": "Marcus", "initials": "M", "orcid": "0000-0002-2466-9038", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c80b9fcb01144528c230d9844da4dad.json"}}, {"family": "De Milde", "given": "Liesbeth", "initials": "L"}, {"family": "Broda", "given": "Martyna", "initials": "M", "orcid": "0000-0003-0591-7814", "researcher": {"href": "https://publications.scilifelab.se/researcher/115370b9582d4b079cda461027833ae3.json"}}, {"family": "Goossens", "given": "Alain", "initials": "A", "orcid": "0000-0002-1599-551X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fe20d16e62445b9b734a7c12da3b71d.json"}}, {"family": "Van Moerkercke", "given": "Alex", "initials": "A"}, {"family": "Khan", "given": "Kasim", "initials": "K", "orcid": "0000-0001-7336-2764", "researcher": {"href": "https://publications.scilifelab.se/researcher/76561aa1400a457aa3aff29a105097f8.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": "2022-05-20", "journal": {"title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "volume": "8", "issue": "20", "pages": "eabm2091"}, "abstract": "Plants respond to mechanical stimuli to direct their growth and counteract environmental threats. Mechanical stimulation triggers rapid gene expression changes and affects plant appearance (thigmomorphogenesis) and flowering. Previous studies reported the importance of jasmonic acid (JA) in touch signaling. Here, we used reverse genetics to further characterize the molecular mechanisms underlying touch signaling. We show that Piezo mechanosensitive ion channels have no major role in touch-induced gene expression and thigmomorphogenesis. In contrast, the receptor-like kinase Feronia acts as a strong negative regulator of the JA-dependent branch of touch signaling. Last, we show that calmodulin-binding transcriptional activators CAMTA1/2/3 are key regulators of JA-independent touch signaling. CAMTA1/2/3 cooperate to directly bind the promoters and activate gene expression of JA-independent touch marker genes like TCH2 and TCH4. In agreement, camta3 mutants show a near complete loss of thigmomorphogenesis and touch-induced delay of flowering. In conclusion, we have now identified key regulators of two independent touch-signaling pathways.", "doi": "10.1126/sciadv.abm2091", "pmid": "35594358", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9122320"}], "notes": [], "created": "2022-08-19T08:38:07.571Z", "modified": "2023-10-16T11:24:07.553Z"}, {"entity": "publication", "iuid": "0b7ee8925aaf4fefbf706851d670dd34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b7ee8925aaf4fefbf706851d670dd34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b7ee8925aaf4fefbf706851d670dd34"}}, "title": "A MYC2/MYC3/MYC4-dependent transcription factor network regulates water spray-responsive gene expression and jasmonate levels.", "authors": [{"family": "Van Moerkercke", "given": "Alex", "initials": "A"}, {"family": "Duncan", "given": "Owen", "initials": "O"}, {"family": "Zander", "given": "Mark", "initials": "M"}, {"family": "\u0160imura", "given": "Jan", "initials": "J"}, {"family": "Broda", "given": "Martyna", "initials": "M", "orcid": "0000-0003-0591-7814", "researcher": {"href": "https://publications.scilifelab.se/researcher/115370b9582d4b079cda461027833ae3.json"}}, {"family": "Vanden Bossche", "given": "Robin", "initials": "R"}, {"family": "Lewsey", "given": "Mathew G", "initials": "MG", "orcid": "0000-0002-2631-4337", "researcher": {"href": "https://publications.scilifelab.se/researcher/320b497b2b8b4a34b48fe6eb79bd9496.json"}}, {"family": "Lama", "given": "Sbatie", "initials": "S"}, {"family": "Singh", "given": "Karam B", "initials": "KB"}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Ecker", "given": "Joseph R", "initials": "JR"}, {"family": "Goossens", "given": "Alain", "initials": "A", "orcid": "0000-0002-1599-551X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fe20d16e62445b9b734a7c12da3b71d.json"}}, {"family": "Millar", "given": "A Harvey", "initials": "AH"}, {"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": "2019-11-12", "journal": {"volume": "116", "issn": "1091-6490", "issue": "46", "pages": "23345-23356", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Mechanical stimuli, such as wind, rain, and touch affect plant development, growth, pest resistance, and ultimately reproductive success. Using water spray to simulate rain, we demonstrate that jasmonic acid (JA) signaling plays a key role in early gene-expression changes, well before it leads to developmental changes in flowering and plant architecture. The JA-activated transcription factors MYC2/MYC3/MYC4 modulate transiently induced expression of 266 genes, most of which peak within 30 min, and control 52% of genes induced >100-fold. Chromatin immunoprecipitation-sequencing analysis indicates that MYC2 dynamically binds >1,300 promoters and trans-activation assays show that MYC2 activates these promoters. By mining our multiomic datasets, we identified a core MYC2/MYC3/MYC4-dependent \"regulon\" of 82 genes containing many previously unknown MYC2 targets, including transcription factors bHLH19 and ERF109 bHLH19 can in turn directly activate the ORA47 promoter, indicating that MYC2/MYC3/MYC4 initiate a hierarchical network of downstream transcription factors. Finally, we also reveal that rapid water spray-induced accumulation of JA and JA-isoleucine is directly controlled by MYC2/MYC3/MYC4 through a positive amplification loop that regulates JA-biosynthesis genes.", "doi": "10.1073/pnas.1911758116", "pmid": "31662474", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "1911758116"}, {"db": "pmc", "key": "PMC6859355"}], "notes": [], "created": "2020-01-07T15:50:58.987Z", "modified": "2025-10-17T13:03:17.215Z"}]}