[{"acknowledgement":"ISTA and the Werner Siemens Foundation financially supported this work. The Scientific Service Units (SSU) of ISTA supported this research through resources provided by the Electron Microscopy Facility (EMF), NMR Facility and the Lab Support Facility (LSF).","publication":"Proceedings of the MATSUS Spring 2025 Conference","status":"public","quality_controlled":"1","month":"03","date_created":"2025-07-21T08:33:20Z","title":"Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case","publisher":"Fundació de la comunitat valenciana SCITO","abstract":[{"text":"Supercrystals represent three-dimensional orderings of colloidal nanocrystals (NCs), showcasing collective properties in photonics, phononics, and electronics applications.1,2 Recent studies have shown that such assemblies are directly produced during nanocrystal reactions.3–6 However, a fundamental understanding of in situ formed supercrystals that withstand typical NC purification processes remains underexplored, which is important for further use. Herein, we report the reaction precursor-mediated formation of stable PbTe supercrystals. Rationalizing the formation of these assemblies through small-angle x-ray scattering (SAXS) measurements, we unveil their formation mechanism. Our findings reveal that the supercrystal formation occurs in the presence of an excess of lead oleates in the crude solution. It should be noted that the formed supercrystals can be stabilized under specific conditions determined by the lead oleate cluster concentration, content of trioctylphosphine telluride (TOP-Te), NC size and the need of an annealing step at mild conditions. Furthermore, this approach allows for the continuous growth of a secondary phase within the supercrystal; for example in the case of PbTe supercrystals, a PbS shell can be grown on each PbTe NC constituent, resulting in core-shell PbTe-PbS supercrystals. Our work elucidates that reaction precursors play an important role in in situ SC formation and stabilization, implying the possibility of applying this knowledge to other NC reactions.","lang":"eng"}],"article_processing_charge":"No","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NMR"},{"_id":"LifeSc"}],"date_published":"2025-03-15T00:00:00Z","day":"15","oa_version":"None","date_updated":"2026-02-19T09:25:57Z","publication_status":"published","doi":"10.29363/nanoge.matsusspring.2025.173","_id":"20055","conference":{"end_date":"2025-03-07","name":"MATSUS: Materials for Sustainable Development Conference","start_date":"2025-03-03","location":"Sevilla, Spain"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-6962-8598","first_name":"Seungho","full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","last_name":"Lee"},{"orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel","first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","last_name":"Balazs"},{"full_name":"Horta, Sharona","first_name":"Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","last_name":"Horta"},{"full_name":"Rayaroth Puthiyaveettil, Aiswarya","first_name":"Aiswarya","id":"8aceb01b-8972-11ed-ae7b-d5fe53775add","last_name":"Rayaroth Puthiyaveettil"},{"first_name":"Maria","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87"}],"citation":{"apa":"Lee, S., Balazs, D., Horta, S., Rayaroth Puthiyaveettil, A., &#38; Ibáñez, M. (2025). Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case. In <i>Proceedings of the MATSUS Spring 2025 Conference</i>. Sevilla, Spain: Fundació de la comunitat valenciana SCITO. <a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.173\">https://doi.org/10.29363/nanoge.matsusspring.2025.173</a>","chicago":"Lee, Seungho, Daniel Balazs, Sharona Horta, Aiswarya Rayaroth Puthiyaveettil, and Maria Ibáñez. “Reaction Precursor-Mediated Formation of Stable Supercrystals in Colloidal Nanocrystal Synthesis: PbTe Case.” In <i>Proceedings of the MATSUS Spring 2025 Conference</i>. Fundació de la comunitat valenciana SCITO, 2025. <a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.173\">https://doi.org/10.29363/nanoge.matsusspring.2025.173</a>.","mla":"Lee, Seungho, et al. “Reaction Precursor-Mediated Formation of Stable Supercrystals in Colloidal Nanocrystal Synthesis: PbTe Case.” <i>Proceedings of the MATSUS Spring 2025 Conference</i>, 173, Fundació de la comunitat valenciana SCITO, 2025, doi:<a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.173\">10.29363/nanoge.matsusspring.2025.173</a>.","ieee":"S. Lee, D. Balazs, S. Horta, A. Rayaroth Puthiyaveettil, and M. Ibáñez, “Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case,” in <i>Proceedings of the MATSUS Spring 2025 Conference</i>, Sevilla, Spain, 2025.","ama":"Lee S, Balazs D, Horta S, Rayaroth Puthiyaveettil A, Ibáñez M. Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case. In: <i>Proceedings of the MATSUS Spring 2025 Conference</i>. Fundació de la comunitat valenciana SCITO; 2025. doi:<a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.173\">10.29363/nanoge.matsusspring.2025.173</a>","short":"S. Lee, D. Balazs, S. Horta, A. Rayaroth Puthiyaveettil, M. Ibáñez, in:, Proceedings of the MATSUS Spring 2025 Conference, Fundació de la comunitat valenciana SCITO, 2025.","ista":"Lee S, Balazs D, Horta S, Rayaroth Puthiyaveettil A, Ibáñez M. 2025. Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case. Proceedings of the MATSUS Spring 2025 Conference. MATSUS: Materials for Sustainable Development Conference, 173."},"language":[{"iso":"eng"}],"article_number":"173","type":"conference","OA_type":"closed access","corr_author":"1","year":"2025"},{"language":[{"iso":"eng"}],"OA_type":"green","article_type":"original","author":[{"last_name":"Nabeel","full_name":"Nabeel, Arshed","first_name":"Arshed"},{"last_name":"Karichannavar","first_name":"Ashwin","full_name":"Karichannavar, Ashwin"},{"last_name":"Palathingal","full_name":"Palathingal, Shuaib","first_name":"Shuaib"},{"last_name":"Jhawar","full_name":"Jhawar, Jitesh","first_name":"Jitesh"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","orcid":"0000-0001-7205-2975","first_name":"David","full_name":"Brückner, David"},{"full_name":"Raj M, Danny","first_name":"Danny","last_name":"Raj M"},{"last_name":"Guttal","full_name":"Guttal, Vishwesha","first_name":"Vishwesha"}],"intvolume":"       205","_id":"20056","oa_version":"Preprint","publication_identifier":{"issn":["0003-0147"],"eissn":["1537-5323"]},"date_published":"2025-04-01T00:00:00Z","department":[{"_id":"EdHa"}],"publication_status":"published","date_updated":"2025-09-30T14:14:43Z","external_id":{"pmid":["40179429"],"arxiv":["2205.02645"],"isi":["001433250500001"]},"title":"Discovering stochastic dynamical equations from ecological time series data","publisher":"University of Chicago Press","article_processing_charge":"No","month":"04","volume":205,"acknowledgement":"V.G. acknowledges support from the Science and Engi-neering Research Board, Department of Biotechnology,and the Indo-French Centre for the Promotion of Ad-vanced Research (64T4-1). D.R.M. acknowledges supportfrom a Department of Science and Technology (DST) In-novation in Science Pursuit for Inspired Research (IN-SPIRE) Faculty Award. J.J. acknowledges support froma Humboldt postdoctoral fellowship and the Heidelber-ger Akademie der Wissenschaften, Heidelberg, Germany.D.B.B. acknowledges support from the NOMIS Founda-tion and an European Molecular Biology Organization(EMBO) postdoctoral fellowship (ALTF 343-2022). A.N.and S.P. acknowledge support from Ministry of Educa-tion (MoE) PhD fellowships. We thank Ashrit Mangal-wedhekar, Vivek Jadhav, Shikhara Bhat, Cassandre Aimon,and Harishankar Muppirala for comments on the manu-script and code. We thank Kollegala Sharma for his inputon the Kannada translation of the title and abstract.Data-Driven Model Discovery E115","quality_controlled":"1","status":"public","year":"2025","type":"journal_article","related_material":{"record":[{"relation":"software","status":"public","id":"20121"}]},"citation":{"apa":"Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D., Raj M, D., &#38; Guttal, V. (2025). Discovering stochastic dynamical equations from ecological time series data. <i>The American Naturalist</i>. University of Chicago Press. <a href=\"https://doi.org/10.1086/734083\">https://doi.org/10.1086/734083</a>","chicago":"Nabeel, Arshed, Ashwin Karichannavar, Shuaib Palathingal, Jitesh Jhawar, David Brückner, Danny Raj M, and Vishwesha Guttal. “Discovering Stochastic Dynamical Equations from Ecological Time Series Data.” <i>The American Naturalist</i>. University of Chicago Press, 2025. <a href=\"https://doi.org/10.1086/734083\">https://doi.org/10.1086/734083</a>.","mla":"Nabeel, Arshed, et al. “Discovering Stochastic Dynamical Equations from Ecological Time Series Data.” <i>The American Naturalist</i>, vol. 205, no. 4, University of Chicago Press, 2025, pp. E100–17, doi:<a href=\"https://doi.org/10.1086/734083\">10.1086/734083</a>.","ieee":"A. Nabeel <i>et al.</i>, “Discovering stochastic dynamical equations from ecological time series data,” <i>The American Naturalist</i>, vol. 205, no. 4. University of Chicago Press, pp. E100–E117, 2025.","ista":"Nabeel A, Karichannavar A, Palathingal S, Jhawar J, Brückner D, Raj M D, Guttal V. 2025. Discovering stochastic dynamical equations from ecological time series data. The American Naturalist. 205(4), E100–E117.","short":"A. Nabeel, A. Karichannavar, S. Palathingal, J. Jhawar, D. Brückner, D. Raj M, V. Guttal, The American Naturalist 205 (2025) E100–E117.","ama":"Nabeel A, Karichannavar A, Palathingal S, et al. Discovering stochastic dynamical equations from ecological time series data. <i>The American Naturalist</i>. 2025;205(4):E100-E117. doi:<a href=\"https://doi.org/10.1086/734083\">10.1086/734083</a>"},"OA_place":"repository","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"isi":1,"page":"E100-E117","day":"01","doi":"10.1086/734083","oa":1,"pmid":1,"project":[{"grant_number":"ALTF 343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2205.02645"}],"abstract":[{"text":"Theoretical studies have shown that stochasticity can affect the dynamics of ecosystems in counterintuitive ways. However, without knowing the equations governing the dynamics of populations or ecosystems, it is difficult to ascertain the role of stochasticity in real datasets. Therefore, the inverse problem of inferring the governing stochastic equations from datasets is important. Here, we present an equation discovery methodology that takes time series data of state variables as input and outputs a stochastic differential equation. We achieve this by combining traditional approaches from stochastic calculus with the equation discovery techniques. We demonstrate the generality of the method via several applications. First, we deliberately choose various stochastic models with fundamentally different governing equations, yet they produce nearly identical steady-state distributions. We show that we can recover the correct underlying equations, and thus infer the structure of their stability, accurately from the analysis of time series data alone. We demonstrate our method on two real-world datasets—fish schooling and single-cell migration—that have vastly different spatiotemporal scales and dynamics. We illustrate various limitations and potential pitfalls of the method and how to overcome them via diagnostic measures. Finally, we provide our open-source code via a package named PyDaDDy (Python Library for Data-Driven Dynamics).","lang":"eng"}],"issue":"4","date_created":"2025-07-21T08:37:27Z","publication":"The American Naturalist"},{"abstract":[{"lang":"eng","text":"Hyaluronic acid (HA) is a key extracellular matrix component of vertebrates, where it mediates cell adhesion, immune regulation, and tissue remodeling through its interaction with specific receptors. Although HA has been detected in a few invertebrate species, the lack of fundamental components of the molecular HA pathway poses relevant objections about its functional role in these species. Mining genomic and transcriptomic data, we considered the conservation of the gene locus encoding for the extracellular link protein (XLINK) in marine mussels as well as its expression patterns. Structural and phylogenetic analyses were undertaken to evaluate possible similarities with vertebrate orthologs and to infer the origin of this gene in invertebrates. Biochemical analysis was used to quantify HA in tissues of Mytilus galloprovincialis. As a result, we confirm that the mussel can produce HA (up to 1.02 ng/mg in mantle) and that its genome encodes two XLINK gene loci. These loci are conserved in Mytilidae species and show a complex evolutionary path. Mussel XLINK genes appeared to be expressed during developmental stages in three mussel species, ranking in the top 100 expressed genes in M. trossulus at 17 h post-fertilization. In conclusion, the presence of HA and an active gene with the potential to bind HA suggests that mussels have the potential to synthesize and use HA and are among the few invertebrates encoding this gene."}],"oa":1,"doi":"10.3390/biology14080930","day":"24","isi":1,"publication":"Biology","file":[{"creator":"dernst","relation":"main_file","access_level":"open_access","date_created":"2025-07-31T09:11:09Z","checksum":"f5e059e66803fa54249c1db029aef0f6","file_size":1885781,"file_id":"20097","content_type":"application/pdf","date_updated":"2025-07-31T09:11:09Z","file_name":"2025_Biology_Rosani.pdf","success":1}],"issue":"8","date_created":"2025-07-25T08:28:26Z","ddc":["570"],"citation":{"short":"U. Rosani, N. Altan, P. Venier, E. Bortoletto, N. Volpi, C. Bernecky, Biology 14 (2025).","ama":"Rosani U, Altan N, Venier P, Bortoletto E, Volpi N, Bernecky C. Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels. <i>Biology</i>. 2025;14(8). doi:<a href=\"https://doi.org/10.3390/biology14080930\">10.3390/biology14080930</a>","ista":"Rosani U, Altan N, Venier P, Bortoletto E, Volpi N, Bernecky C. 2025. Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels. Biology. 14(8), 930.","ieee":"U. Rosani, N. Altan, P. Venier, E. Bortoletto, N. Volpi, and C. Bernecky, “Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels,” <i>Biology</i>, vol. 14, no. 8. MDPI, 2025.","mla":"Rosani, Umberto, et al. “Ancestral Origin and Functional Expression of a Hyaluronic Acid Pathway Complement in Mussels.” <i>Biology</i>, vol. 14, no. 8, 930, MDPI, 2025, doi:<a href=\"https://doi.org/10.3390/biology14080930\">10.3390/biology14080930</a>.","apa":"Rosani, U., Altan, N., Venier, P., Bortoletto, E., Volpi, N., &#38; Bernecky, C. (2025). Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels. <i>Biology</i>. MDPI. <a href=\"https://doi.org/10.3390/biology14080930\">https://doi.org/10.3390/biology14080930</a>","chicago":"Rosani, Umberto, Nehir Altan, Paola Venier, Enrico Bortoletto, Nicola Volpi, and Carrie Bernecky. “Ancestral Origin and Functional Expression of a Hyaluronic Acid Pathway Complement in Mussels.” <i>Biology</i>. MDPI, 2025. <a href=\"https://doi.org/10.3390/biology14080930\">https://doi.org/10.3390/biology14080930</a>."},"type":"journal_article","year":"2025","article_number":"930","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","OA_place":"publisher","article_processing_charge":"Yes","publisher":"MDPI","title":"Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels","date_updated":"2025-09-30T14:10:07Z","external_id":{"isi":["001557922100001"]},"publication_status":"published","publication_identifier":{"issn":["2079-7737"]},"date_published":"2025-07-24T00:00:00Z","department":[{"_id":"CaBe"}],"oa_version":"Published Version","status":"public","quality_controlled":"1","acknowledgement":"This research was funded by the Italian Ministry of University and Research (MIUR), grant ID: P2022JEEMT (Developing a tool for the study of haplotype diversity in Mytilus galloprovincialis (HAMIGA)).","DOAJ_listed":"1","volume":14,"month":"07","PlanS_conform":"1","article_type":"original","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_type":"gold","language":[{"iso":"eng"}],"_id":"20077","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2025-07-31T09:11:09Z","intvolume":"        14","author":[{"last_name":"Rosani","first_name":"Umberto","full_name":"Rosani, Umberto"},{"first_name":"Nehir","full_name":"Altan, Nehir","last_name":"Altan"},{"last_name":"Venier","full_name":"Venier, Paola","first_name":"Paola"},{"last_name":"Bortoletto","full_name":"Bortoletto, Enrico","first_name":"Enrico"},{"full_name":"Volpi, Nicola","first_name":"Nicola","last_name":"Volpi"},{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","first_name":"Carrie A"}]},{"article_type":"original","OA_type":"closed access","language":[{"iso":"eng"}],"intvolume":"        51","author":[{"first_name":"Iveta","full_name":"Yotova, Iveta","last_name":"Yotova"},{"full_name":"Proestling, Katharina","first_name":"Katharina","last_name":"Proestling"},{"last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048"},{"last_name":"Rainer","full_name":"Rainer, Lisa","first_name":"Lisa"},{"full_name":"Kaup, Leonie","first_name":"Leonie","last_name":"Kaup"},{"last_name":"Heine","first_name":"Jana","full_name":"Heine, Jana"},{"last_name":"Sandrieser","full_name":"Sandrieser, Lejla","first_name":"Lejla"},{"last_name":"Wenzl","first_name":"René","full_name":"Wenzl, René"},{"full_name":"Hudson, Quanah J.","first_name":"Quanah J.","last_name":"Hudson"}],"_id":"20079","publication_status":"published","external_id":{"pmid":["40680553"],"isi":["001549819000002"]},"date_updated":"2025-09-30T14:10:46Z","oa_version":"None","publication_identifier":{"eissn":["1472-6491"],"issn":["1472-6483"]},"date_published":"2025-07-17T00:00:00Z","department":[{"_id":"SiHi"}],"article_processing_charge":"No","title":"LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression","publisher":"Elsevier","volume":51,"month":"07","quality_controlled":"1","status":"public","acknowledgement":"The authors wish to thank all the participants and health professionals involved in this study. In addition, the authors wish to thank technical assistants Barbara Widmar, Matthias Witzmann-Stern and Isabella Haslinger for their work assisting with this study; and Simon Hippenmeyer for access to bioinformatic infrastructure and resources.\r\nOpen access funding was provided by the Medical University of Vienna.","year":"2025","type":"journal_article","article_number":"104942","citation":{"ista":"Yotova I, Proestling K, Pauler F, Rainer L, Kaup L, Heine J, Sandrieser L, Wenzl R, Hudson QJ. 2025. LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression. Reproductive Biomedicine Online. 51(3), 104942.","ama":"Yotova I, Proestling K, Pauler F, et al. LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression. <i>Reproductive Biomedicine Online</i>. 2025;51(3). doi:<a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">10.1016/j.rbmo.2025.104942</a>","short":"I. Yotova, K. Proestling, F. Pauler, L. Rainer, L. Kaup, J. Heine, L. Sandrieser, R. Wenzl, Q.J. Hudson, Reproductive Biomedicine Online 51 (2025).","chicago":"Yotova, Iveta, Katharina Proestling, Florian Pauler, Lisa Rainer, Leonie Kaup, Jana Heine, Lejla Sandrieser, René Wenzl, and Quanah J. Hudson. “LINC01638 Promotes Epithelial-to-Mesenchymal Transition in Endometriosis Epithelial Cells by up-Regulating RHOB via HDAC1 Suppression.” <i>Reproductive Biomedicine Online</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">https://doi.org/10.1016/j.rbmo.2025.104942</a>.","apa":"Yotova, I., Proestling, K., Pauler, F., Rainer, L., Kaup, L., Heine, J., … Hudson, Q. J. (2025). LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression. <i>Reproductive Biomedicine Online</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">https://doi.org/10.1016/j.rbmo.2025.104942</a>","ieee":"I. Yotova <i>et al.</i>, “LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression,” <i>Reproductive Biomedicine Online</i>, vol. 51, no. 3. Elsevier, 2025.","mla":"Yotova, Iveta, et al. “LINC01638 Promotes Epithelial-to-Mesenchymal Transition in Endometriosis Epithelial Cells by up-Regulating RHOB via HDAC1 Suppression.” <i>Reproductive Biomedicine Online</i>, vol. 51, no. 3, 104942, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">10.1016/j.rbmo.2025.104942</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1016/j.rbmo.2025.104942","scopus_import":"1","isi":1,"day":"17","abstract":[{"lang":"eng","text":"Research question: Is LINC01638 involved in regulation of epithelial-to-mesenchymal transition (EMT) in endometriosis?\r\nDesign: A prospective patient cohort study was combined with functional experiments in the 12Z endometriosis epithelial cell line to investigate the role of LINC01638 in endometriosis. Eutopic endometrial samples were collected by curettage, and ectopic endometrial lesion samples were collected by laparoscopic surgery from 24 control patients and 41 patients with endometriosis. The phenotype of 12Z cells was assessed following LINC01638 knockdown using siRNA, performing proliferation, adhesion, migration and invasion assays, as well as assessing apoptosis and cell cycle changes with flow cytometry assays. In order to assess the relationship between LINC01638 and histone deacetylase class 1 enzyme (HDAC1), LINC01638 knockdown was combined with HDAC inhibition with the specific HDAC inhibitor romidepsin.\r\nResults: LINC01638 was up-regulated in the epithelial layer of endometriotic lesions, and LINC01638 knockdown in 12Z cells led to reduced proliferation, adhesion, migration and invasion. The reduction in proliferation was associated with increased p21 and p27 expression, and G1 phase arrest. Further analysis of LINC01638 control and knockdown cells revealed that a number of transcription factors associated with EMT are down-regulated in knockdown cells, along with the cytoskeleton regulatory gene RHOB, while HDAC1 was up-regulated. Chromatin immunoprecipitation analysis and HDAC1 inhibitory treatment combined with LINC01638 knockdown indicated that LINC01638 regulates RHOB expression via HDAC1-mediated promoter deacetylation. RHOB is up-regulated in the epithelial layer of endometriotic lesions compared with eutopic endometrium, supporting a role in the disease.\r\nConclusions: LINC01638 is an epigenetic regulator of the pathogenesis of endometriosis, promoting proliferation and EMT of endometriotic lesions."}],"pmid":1,"issue":"3","date_created":"2025-07-27T22:01:25Z","publication":"Reproductive Biomedicine Online"},{"title":"Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties","publisher":"Frontiers Media","article_processing_charge":"Yes","oa_version":"Published Version","department":[{"_id":"EdHa"},{"_id":"EvBe"},{"_id":"CaGu"}],"date_published":"2025-07-04T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"}],"ec_funded":1,"publication_identifier":{"eissn":["1664-462X"]},"publication_status":"published","external_id":{"pmid":["40688689"],"isi":["001530690900001"]},"date_updated":"2026-05-20T07:53:03Z","acknowledgement":"The author(s) declare that financial support was received for the research and/or publication of this article. This work was supported by grants from the European Research Council (Starting Independent Research Grant ERC-2007-Stg- 207362-HCPO to EB) and MG was recipient of an IST Interdisciplinary project (IC1022IPC03).\r\nWe acknowledge Jaume F. Martı́nez Garcı́a for phyAphyB mutant seeds. We acknowledge CF Nanobiotechnology of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127). We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and Library. We thank Stefan Riegler for the efforts to establish immunodetection method.","DOAJ_listed":"1","quality_controlled":"1","status":"public","month":"07","volume":16,"APC_amount":"3642,79 EUR","PlanS_conform":"1","language":[{"iso":"eng"}],"article_type":"original","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_type":"gold","_id":"20080","author":[{"last_name":"Gallemi","id":"460C6802-F248-11E8-B48F-1D18A9856A87","full_name":"Gallemi, Marçal","first_name":"Marçal","orcid":"0000-0003-4675-6893"},{"last_name":"Montesinos López","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","first_name":"Juan C","full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099"},{"first_name":"Nikola","full_name":"Zarevski, Nikola","id":"18e95355-e05a-11ea-a9c0-8fba1b89e83a","last_name":"Zarevski"},{"first_name":"Jan","full_name":"Pribyl, Jan","last_name":"Pribyl"},{"last_name":"Skládal","first_name":"Petr","full_name":"Skládal, Petr"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"}],"file_date_updated":"2025-07-31T07:28:54Z","intvolume":"        16","pmid":1,"project":[{"call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"abstract":[{"lang":"eng","text":"Introduction: Acid-growth theory has been postulated in the 70s to explain the rapid elongation of plant cells in response to the hormone auxin. More recently, it has been demonstrated that activation of the proton ATPs pump (H+-ATPs) promoting acidification of the apoplast is the principal mechanism by which auxin and other hormones such as brassinosteroids (BR) induce cell elongation. Despite these advances, the impact of this acidification on the mechanical properties of the cell wall remained largely unexplored.\r\n\r\nMethods: Here, we use elongation assays of Arabidopsis thaliana hypocotyls and Atomic Force Microscopy (AFM) to correlate hormone-induced tissue elongation and local changes in cell wall mechanical properties. Furthermore, employing transgenic lines over-expressing Pectin Methyl Esterase (PME), along with calcium chelators, we investigate the effect of pectin modification in hormone-driven cell elongation.\r\n\r\nResults: We demonstrate that acidification of apoplast is necessary and sufficient to induce cell elongation through promoting cell wall softening. Moreover, we show that enhanced PME activity can induce both cell wall softening or stiffening in extracellular calcium dependent-manner and that tight control of PME activity is required for proper hypocotyl elongation.\r\n\r\nDiscussion: Our results confirm a dual role of PME in plant cell elongation. However, further investigation is needed to assess the status of pectin following short- or long-term PME treatments in order to determine if pectin methyl-esterification might promote its degradation as well as the role of PME inhibitors upon PME induction."}],"isi":1,"day":"04","scopus_import":"1","doi":"10.3389/fpls.2025.1612366","oa":1,"file":[{"content_type":"application/pdf","file_id":"20093","date_updated":"2025-07-31T07:28:54Z","success":1,"file_name":"2025_FrontiersPlantSc_Gallemi.pdf","access_level":"open_access","relation":"main_file","creator":"dernst","date_created":"2025-07-31T07:28:54Z","file_size":3665187,"checksum":"9e6b8b53ba56d4a24a9bd91cf6d2dc58"}],"publication":"Frontiers in Plant Science","ddc":["580"],"date_created":"2025-07-27T22:01:26Z","citation":{"ama":"Gallemi M, Montesinos López JC, Zarevski N, et al. Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. <i>Frontiers in Plant Science</i>. 2025;16. doi:<a href=\"https://doi.org/10.3389/fpls.2025.1612366\">10.3389/fpls.2025.1612366</a>","short":"M. Gallemi, J.C. Montesinos López, N. Zarevski, J. Pribyl, P. Skládal, E.B. Hannezo, E. Benková, Frontiers in Plant Science 16 (2025).","ista":"Gallemi M, Montesinos López JC, Zarevski N, Pribyl J, Skládal P, Hannezo EB, Benková E. 2025. Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. Frontiers in Plant Science. 16, 1612366.","apa":"Gallemi, M., Montesinos López, J. C., Zarevski, N., Pribyl, J., Skládal, P., Hannezo, E. B., &#38; Benková, E. (2025). Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. <i>Frontiers in Plant Science</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fpls.2025.1612366\">https://doi.org/10.3389/fpls.2025.1612366</a>","chicago":"Gallemi, Marçal, Juan C Montesinos López, Nikola Zarevski, Jan Pribyl, Petr Skládal, Edouard B Hannezo, and Eva Benková. “Dual Role of Pectin Methyl Esterase Activity in the Regulation of Plant Cell Wall Biophysical Properties.” <i>Frontiers in Plant Science</i>. Frontiers Media, 2025. <a href=\"https://doi.org/10.3389/fpls.2025.1612366\">https://doi.org/10.3389/fpls.2025.1612366</a>.","ieee":"M. Gallemi <i>et al.</i>, “Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties,” <i>Frontiers in Plant Science</i>, vol. 16. Frontiers Media, 2025.","mla":"Gallemi, Marçal, et al. “Dual Role of Pectin Methyl Esterase Activity in the Regulation of Plant Cell Wall Biophysical Properties.” <i>Frontiers in Plant Science</i>, vol. 16, 1612366, Frontiers Media, 2025, doi:<a href=\"https://doi.org/10.3389/fpls.2025.1612366\">10.3389/fpls.2025.1612366</a>."},"article_number":"1612366","corr_author":"1","year":"2025","type":"journal_article","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher"},{"OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","type":"journal_article","corr_author":"1","year":"2025","citation":{"ama":"Dos Reis Rodrigues P, Avellaneda Sarrió M, Canigova N, et al. Migrating immune cells globally coordinate protrusive forces. <i>Nature Immunology</i>. 2025;26:1258–1266. doi:<a href=\"https://doi.org/10.1038/s41590-025-02211-w\">10.1038/s41590-025-02211-w</a>","short":"P. Dos Reis Rodrigues, M. Avellaneda Sarrió, N. Canigova, F.R. Gärtner, K. Vaahtomeri, M. Riedl, I. de Vries, J. Merrin, R. Hauschild, Y. Fukui, A. Juanes Garcia, M.K. Sixt, Nature Immunology 26 (2025) 1258–1266.","ista":"Dos Reis Rodrigues P, Avellaneda Sarrió M, Canigova N, Gärtner FR, Vaahtomeri K, Riedl M, de Vries I, Merrin J, Hauschild R, Fukui Y, Juanes Garcia A, Sixt MK. 2025. Migrating immune cells globally coordinate protrusive forces. Nature Immunology. 26, 1258–1266.","ieee":"P. Dos Reis Rodrigues <i>et al.</i>, “Migrating immune cells globally coordinate protrusive forces,” <i>Nature Immunology</i>, vol. 26. Springer Nature, pp. 1258–1266, 2025.","mla":"Dos Reis Rodrigues, Patricia, et al. “Migrating Immune Cells Globally Coordinate Protrusive Forces.” <i>Nature Immunology</i>, vol. 26, Springer Nature, 2025, pp. 1258–1266, doi:<a href=\"https://doi.org/10.1038/s41590-025-02211-w\">10.1038/s41590-025-02211-w</a>.","apa":"Dos Reis Rodrigues, P., Avellaneda Sarrió, M., Canigova, N., Gärtner, F. R., Vaahtomeri, K., Riedl, M., … Sixt, M. K. (2025). Migrating immune cells globally coordinate protrusive forces. <i>Nature Immunology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41590-025-02211-w\">https://doi.org/10.1038/s41590-025-02211-w</a>","chicago":"Dos Reis Rodrigues, Patricia, Mario Avellaneda Sarrió, Nikola Canigova, Florian R Gärtner, Kari Vaahtomeri, Michael Riedl, Ingrid de Vries, et al. “Migrating Immune Cells Globally Coordinate Protrusive Forces.” <i>Nature Immunology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41590-025-02211-w\">https://doi.org/10.1038/s41590-025-02211-w</a>."},"related_material":{"link":[{"url":"https://ista.ac.at/en/news/bench-pressing-cells/","description":"News on ISTA website","relation":"press_release"}],"record":[{"id":"20149","relation":"dissertation_contains","status":"public"}]},"date_created":"2025-07-27T22:01:26Z","ddc":["570"],"publication":"Nature Immunology","file":[{"checksum":"0c725123dca7797c682609bff2c4c5ac","file_size":13514646,"date_created":"2025-07-31T08:00:33Z","creator":"dernst","relation":"main_file","access_level":"open_access","file_name":"2025_NatureImmunology_ReisRodrigues.pdf","success":1,"date_updated":"2025-07-31T08:00:33Z","content_type":"application/pdf","file_id":"20096"}],"oa":1,"doi":"10.1038/s41590-025-02211-w","scopus_import":"1","day":"01","isi":1,"page":"1258–1266","abstract":[{"lang":"eng","text":"Efficient immune responses rely on the capacity of leukocytes to traverse diverse and complex tissues. To meet such changing environmental conditions, leukocytes usually adopt an ameboid configuration, using their forward-positioned nucleus as a probe to identify and follow the path of least resistance among pre-existing pores. We show that, in dense environments where even the largest pores preclude free passage, leukocytes position their nucleus behind the centrosome and organelles. The local compression imposed on the cell body by its surroundings triggers assembly of a central F-actin pool, located between cell front and nucleus. Central actin pushes outward to transiently dilate a path for organelles and nucleus. Pools of central and front actin are tightly coupled and experimental depletion of the central pool enhances actin accumulation and protrusion formation at the cell front. Although this shifted balance speeds up cells in permissive environments, migration in restrictive environments is impaired, as the unleashed leading edge dissociates from the trapped cell body. Our findings establish an actin regulatory loop that balances path dilation with advancement of the leading edge to maintain cellular coherence."}],"project":[{"_id":"bd91e723-d553-11ed-ba76-fe7eeb2185fd","name":"Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces","grant_number":"101071793"},{"_id":"c092d618-5a5b-11eb-8a69-f92e1e843fc8","grant_number":"944-2020","name":"Bioelectric patrolling: the role of the local membrane potential in immune cell migration"}],"pmid":1,"file_date_updated":"2025-07-31T08:00:33Z","intvolume":"        26","author":[{"id":"26E95904-5160-11E9-9C0B-C5B0DC97E90F","last_name":"Dos Reis Rodrigues","orcid":"0000-0003-1681-508X","full_name":"Dos Reis Rodrigues, Patricia","first_name":"Patricia"},{"id":"DC4BA84C-56E6-11EA-AD5D-348C3DDC885E","last_name":"Avellaneda Sarrió","orcid":"0000-0001-6406-524X","first_name":"Mario","full_name":"Avellaneda Sarrió, Mario"},{"full_name":"Canigova, Nikola","first_name":"Nikola","orcid":"0000-0002-8518-5926","last_name":"Canigova","id":"3795523E-F248-11E8-B48F-1D18A9856A87"},{"id":"397A88EE-F248-11E8-B48F-1D18A9856A87","last_name":"Gärtner","orcid":"0000-0001-6120-3723","full_name":"Gärtner, Florian R","first_name":"Florian R"},{"orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari","first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri"},{"full_name":"Riedl, Michael","first_name":"Michael","orcid":"0000-0003-4844-6311","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ingrid","full_name":"De Vries, Ingrid","last_name":"De Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","first_name":"Jack","orcid":"0000-0001-5145-4609"},{"first_name":"Robert","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yoshinori","full_name":"Fukui, Yoshinori","last_name":"Fukui"},{"orcid":"0000-0002-1009-9652","first_name":"Alba","full_name":"Juanes Garcia, Alba","id":"40F05888-F248-11E8-B48F-1D18A9856A87","last_name":"Juanes Garcia"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"}],"_id":"20082","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"letter_note","OA_type":"hybrid","language":[{"iso":"eng"}],"PlanS_conform":"1","volume":26,"month":"08","status":"public","quality_controlled":"1","acknowledgement":"This research was supported by the Scientific Service Units of ISTA through resources provided by the Imaging and Optics, Preclinical and Lab Support Facilities. In particular, we thank M. A. Symth and F. G. G. Leite, from the Virus Service Team, who helped generating the lentiviral particles used in this study. We thank all the members of the Sixt group for valuable discussions and feedback, in particular, I. Mayer, for helping with T cell isolation and Z. (P.) Li for providing the Actin–GFP DC line. We are also thankful to J. Mandl and C. Shen for their feedback during the writing of this manuscript. This work was supported by a European Research Council grant ERC-SyG 101071793 to M.S. M.J.A. was supported by an HFSP Postdoctoral Fellowship LTF 177 2021 and A.J.G. by a Lise Meitner Fellowship of the FWF (Austrian Science Fund). Y.F. was supported by the AMED-CREST (JP19gm1310005), the Medical Research Center Initiative for High Depth Omics and CURE:JPMXP1323015486 for MIB, Kyushu University. Open access funding provided by Institute of Science and Technology (IST Austria).","date_updated":"2026-04-28T13:26:50Z","external_id":{"pmid":["40664976"],"isi":["001529134300001"]},"publication_status":"published","publication_identifier":{"eissn":["1529-2916"],"issn":["1529-2908"]},"date_published":"2025-08-01T00:00:00Z","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","title":"Migrating immune cells globally coordinate protrusive forces","publisher":"Springer Nature"},{"quality_controlled":"1","status":"public","acknowledgement":"We thank Marina Andrijevic, Giacomo Falchetta, Samuel Lüthi, Caroline Muller, Carl Schleussner, and Adriano Vinca for providing useful ideas and feedback for this work. YLH is supported by funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska‐Curie Grant No. 101034413. EB, MW, and YQ are supported by the European Union’s Horizon Europe research and innovation programme under Grant Agreement No. 101081369 (SPARCCLE). We also thank the two anonymous reviewers for providing helpful feedback that greatly improved this manuscript.","DOAJ_listed":"1","volume":4,"month":"07","article_processing_charge":"Yes","publisher":"IOP Publishing","title":"Sustainable development key to limiting climate change-driven wildfire damages","publication_status":"published","date_updated":"2025-08-04T07:46:33Z","oa_version":"Published Version","department":[{"_id":"CaMu"}],"date_published":"2025-07-15T00:00:00Z","ec_funded":1,"publication_identifier":{"eissn":["2752-5295"]},"_id":"20098","intvolume":"         4","file_date_updated":"2025-08-04T07:38:14Z","author":[{"last_name":"Hwong","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22","full_name":"Hwong, Yi-Ling","first_name":"Yi-Ling","orcid":"0000-0001-9281-3479"},{"first_name":"Edward","full_name":"Byers, Edward","last_name":"Byers"},{"last_name":"Werning","first_name":"Michaela","full_name":"Werning, Michaela"},{"full_name":"Quilcaille, Yann","first_name":"Yann","last_name":"Quilcaille"}],"PlanS_conform":"1","OA_type":"gold","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"original","language":[{"iso":"eng"}],"file":[{"date_created":"2025-08-04T07:38:14Z","checksum":"ca679496767021e792b0378c48fdee8c","file_size":2807041,"creator":"dernst","access_level":"open_access","relation":"main_file","date_updated":"2025-08-04T07:38:14Z","file_name":"2025_EnvironResearchClimate_Hwong.pdf","success":1,"content_type":"application/pdf","file_id":"20108"}],"publication":"Environmental Research: Climate","issue":"3","date_created":"2025-07-31T14:03:16Z","ddc":["550"],"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"abstract":[{"lang":"eng","text":"Climate change is causing wildfires to become more frequent and intense. While predicting burned areas using bioclimatic and anthropogenic factors is an active research area, few studies have examined what drives the economic damages of wildfires. Our study aims to fill this gap by analyzing key factors influencing global economic wildfire damages and projecting future damages under three shared socioeconomic pathways (SSPs). We apply regression analyses to identify significant predictors of economic wildfire damages at country levels and use the fitted model to project future damages under SSP126, SSP245, and SSP370. Results show that the human vulnerability index (HVI), reflecting socioeconomic conditions, is the strongest predictor of historical wildfire damages, followed by water vapor pressure deficit during the fire season and population density around forested areas. We found high population density to be associated with lower damages. These findings contrast with studies of burned areas, where climate factors are more dominant. Our model projects that by 2070, average global economic wildfire damages will be three times higher under SSP370 than SSP126. Our model also shows that following SSP126 not only reduces wildfire damages but also lessens the inequalities in damage distribution across countries. This pathway’s dual focus on equitable socioeconomic progress and climate action potentially enhances a country’s resilience that helps mitigate wildfire damages. Our analyses also indicate that strong socioeconomic development can offset wildfire damages associated with climate hazards, although this is less certain under SSP370. SSP126’s integrated approach improves both socioeconomic conditions and limits global warming, providing substantial benefits to less developed countries while still reducing damages in developed nations, despite their already low HVI scores. Our work complements existing research on burned areas and underscores the importance of sustainable development and international collaboration in reducing the economic damages of wildfires."}],"scopus_import":"1","doi":"10.1088/2752-5295/adec11","oa":1,"day":"15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","OA_place":"publisher","related_material":{"record":[{"id":"20107","relation":"research_data","status":"public"}]},"citation":{"ieee":"Y.-L. Hwong, E. Byers, M. Werning, and Y. Quilcaille, “Sustainable development key to limiting climate change-driven wildfire damages,” <i>Environmental Research: Climate</i>, vol. 4, no. 3. IOP Publishing, 2025.","mla":"Hwong, Yi-Ling, et al. “Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages.” <i>Environmental Research: Climate</i>, vol. 4, no. 3, 035005, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/2752-5295/adec11\">10.1088/2752-5295/adec11</a>.","apa":"Hwong, Y.-L., Byers, E., Werning, M., &#38; Quilcaille, Y. (2025). Sustainable development key to limiting climate change-driven wildfire damages. <i>Environmental Research: Climate</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2752-5295/adec11\">https://doi.org/10.1088/2752-5295/adec11</a>","chicago":"Hwong, Yi-Ling, Edward Byers, Michaela Werning, and Yann Quilcaille. “Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages.” <i>Environmental Research: Climate</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/2752-5295/adec11\">https://doi.org/10.1088/2752-5295/adec11</a>.","short":"Y.-L. Hwong, E. Byers, M. Werning, Y. Quilcaille, Environmental Research: Climate 4 (2025).","ama":"Hwong Y-L, Byers E, Werning M, Quilcaille Y. Sustainable development key to limiting climate change-driven wildfire damages. <i>Environmental Research: Climate</i>. 2025;4(3). doi:<a href=\"https://doi.org/10.1088/2752-5295/adec11\">10.1088/2752-5295/adec11</a>","ista":"Hwong Y-L, Byers E, Werning M, Quilcaille Y. 2025. Sustainable development key to limiting climate change-driven wildfire damages. Environmental Research: Climate. 4(3), 035005."},"year":"2025","corr_author":"1","type":"journal_article","article_number":"035005"},{"isi":1,"day":"01","doi":"10.1016/j.celrep.2025.116080","scopus_import":"1","oa":1,"project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","grant_number":"P36232","name":"Mechanisms of GABA release in hippocampal circuits"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"abstract":[{"text":"The hippocampus, critical for learning and memory, is dogmatically described as a trisynaptic circuit where dentate gyrus granule cells (GCs), CA3 pyramidal neurons (PNs), and CA1 PNs are serially connected. However, CA3 also forms an autoassociative network, and its PNs have diverse morphologies, intrinsic properties, and GC input levels. How PN subtypes compose this recurrent network is unknown. To determine the synaptic arrangement of identified CA3 PNs, we combine multicellular patch-clamp recording and post hoc morphological analysis in mouse hippocampal slices. PNs can be divided into distinct “superficial” and “deep” subclasses, the latter including previously reported “athorny” cells. Subclasses have distinct input-output transformations and asymmetric connectivity, which is more abundant from superficial to deep PNs, splitting CA3 locally into two parallel recurrent networks. Coincident spontaneous inhibition occurs frequently within but not between subclasses, implying subclass-specific inhibitory innervation. Our results suggest two separately controlled sublayers for parallel information processing in hippocampal CA3.","lang":"eng"}],"ddc":["570"],"issue":"8","date_created":"2025-08-03T22:01:30Z","publication":"Cell Reports","file":[{"content_type":"application/pdf","file_id":"20106","date_updated":"2025-08-04T06:53:07Z","file_name":"2025_CellReports_Watson.pdf","success":1,"creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2025-08-04T06:53:07Z","checksum":"556ff9760661ecd23949d75031043b1f","file_size":27695214}],"article_number":"116080","corr_author":"1","year":"2025","type":"journal_article","citation":{"ama":"Watson J, Vargas Barroso VM, Jonas PM. Cell-specific wiring routes information flow through hippocampal CA3. <i>Cell Reports</i>. 2025;44(8). doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">10.1016/j.celrep.2025.116080</a>","short":"J. Watson, V.M. Vargas Barroso, P.M. Jonas, Cell Reports 44 (2025).","ista":"Watson J, Vargas Barroso VM, Jonas PM. 2025. Cell-specific wiring routes information flow through hippocampal CA3. Cell Reports. 44(8), 116080.","apa":"Watson, J., Vargas Barroso, V. M., &#38; Jonas, P. M. (2025). Cell-specific wiring routes information flow through hippocampal CA3. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">https://doi.org/10.1016/j.celrep.2025.116080</a>","chicago":"Watson, Jake, Victor M Vargas Barroso, and Peter M Jonas. “Cell-Specific Wiring Routes Information Flow through Hippocampal CA3.” <i>Cell Reports</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">https://doi.org/10.1016/j.celrep.2025.116080</a>.","ieee":"J. Watson, V. M. Vargas Barroso, and P. M. Jonas, “Cell-specific wiring routes information flow through hippocampal CA3,” <i>Cell Reports</i>, vol. 44, no. 8. Elsevier, 2025.","mla":"Watson, Jake, et al. “Cell-Specific Wiring Routes Information Flow through Hippocampal CA3.” <i>Cell Reports</i>, vol. 44, no. 8, 116080, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">10.1016/j.celrep.2025.116080</a>."},"OA_place":"publisher","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","ec_funded":1,"publication_identifier":{"issn":["2639-1856"],"eissn":["2211-1247"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"date_published":"2025-08-01T00:00:00Z","department":[{"_id":"PeJo"}],"publication_status":"published","date_updated":"2025-09-30T14:12:02Z","external_id":{"isi":["001544472300002"]},"title":"Cell-specific wiring routes information flow through hippocampal CA3","publisher":"Elsevier","article_processing_charge":"Yes","month":"08","volume":44,"DOAJ_listed":"1","acknowledgement":"We thank Andrea Navas-Olive and Rebecca J. Morse-Mora for critically reading an earlier version of the manuscript. We also thank Florian Marr and Christina Altmutter for excellent technical assistance, Alois Schlögl for programming and data-handling assistance, Todor Asenov for technical support, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA. We are particularly grateful for assistance from the Imaging and Optics Facility, Preclinical Facility, Lab Support Facility, and Miba Machine Shop. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692 to P.J., Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W., and an ISTplus Fellowship through Marie Skłodowska-Curie grant agreement no. 754411 to V.V.-B.), the Austrian Science Fund (P 36232-B, PAT 4178023, and Cluster of Excellence 10.55776/COE16 to P.J.), and a CONACyT fellowship (289638 to V.V.-B.) and was supported by a non-stipendiary EMBO fellowship (ALTF 756–2020 to J.F.W.).","quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"OA_type":"gold","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"original","PlanS_conform":"1","author":[{"first_name":"Jake","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"full_name":"Vargas Barroso, Victor M","first_name":"Victor M","last_name":"Vargas Barroso","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jonas, Peter M","first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"        44","file_date_updated":"2025-08-04T06:53:07Z","_id":"20099"},{"month":"06","volume":27,"DOAJ_listed":"1","acknowledgement":"AM acknowledges the financial support of the Helmsley Fellowships Program for Sustainability and Health. AMB is supported by the Schmidt Chair in Artificial Intelligence.","quality_controlled":"1","status":"public","oa_version":"Published Version","department":[{"_id":"AlBr"}],"publication_identifier":{"eissn":["2001-0370"]},"date_published":"2025-06-27T00:00:00Z","publication_status":"published","external_id":{"isi":["001583543100001"]},"date_updated":"2025-11-27T14:09:59Z","title":"Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment","publisher":"Elsevier","article_processing_charge":"Yes","author":[{"id":"94f2fe44-70fa-11f0-b76b-92922c09452b","last_name":"Vedula","first_name":"Sanketh","full_name":"Vedula, Sanketh"},{"full_name":"Bronstein, Alexander","first_name":"Alexander","orcid":"0000-0001-9699-8730","last_name":"Bronstein","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6"},{"full_name":"Marx, Ailie","first_name":"Ailie","last_name":"Marx"}],"intvolume":"        27","file_date_updated":"2025-08-04T06:25:23Z","_id":"20100","language":[{"iso":"eng"}],"OA_type":"gold","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"original","PlanS_conform":"1","ddc":["000","570"],"date_created":"2025-08-03T22:01:31Z","file":[{"file_size":6609770,"checksum":"78d01f30fc1dc11dd2bd1d7bb7ac8a62","date_created":"2025-08-04T06:25:23Z","access_level":"open_access","relation":"main_file","creator":"dernst","success":1,"file_name":"2025_CompStrucBiotechJour_Vedula.pdf","date_updated":"2025-08-04T06:25:23Z","file_id":"20104","content_type":"application/pdf"}],"publication":"Computational and Structural Biotechnology Journal","isi":1,"page":"3292-3298","day":"27","doi":"10.1016/j.csbj.2025.07.039","scopus_import":"1","oa":1,"abstract":[{"lang":"eng","text":"A key step in protein structure prediction involves the detection of co-evolving pairs of residues, a signal for spatial proximity. This information is gleaned from multiple sequence alignment and underscores Alphafold’s structure prediction for almost every known protein. A simple means to create proteins beyond those found in nature, is by unnaturally fusing together two known proteins or protein parts. Here we demonstrate that structured peptides are predicted with significantly reduced accuracy when added to the terminal ends of scaffold proteins. Appending the multiple sequence alignment for the individual peptide tags to that of the scaffold protein often restores prediction accuracy. This work suggests that this windowed multiple sequence alignment approach can be a useful tool for predicting the structure of fused, chimeric proteins."}],"OA_place":"publisher","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","type":"journal_article","related_material":{"link":[{"url":"https://github.com/sankethvedula/AFChimera","relation":"software"}],"record":[{"id":"20103","status":"public","relation":"software"}]},"citation":{"ama":"Vedula S, Bronstein AM, Marx A. Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment. <i>Computational and Structural Biotechnology Journal</i>. 2025;27:3292-3298. doi:<a href=\"https://doi.org/10.1016/j.csbj.2025.07.039\">10.1016/j.csbj.2025.07.039</a>","short":"S. Vedula, A.M. Bronstein, A. Marx, Computational and Structural Biotechnology Journal 27 (2025) 3292–3298.","ista":"Vedula S, Bronstein AM, Marx A. 2025. Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment. Computational and Structural Biotechnology Journal. 27, 3292–3298.","apa":"Vedula, S., Bronstein, A. M., &#38; Marx, A. (2025). Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment. <i>Computational and Structural Biotechnology Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.csbj.2025.07.039\">https://doi.org/10.1016/j.csbj.2025.07.039</a>","chicago":"Vedula, Sanketh, Alex M. Bronstein, and Ailie Marx. “Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.” <i>Computational and Structural Biotechnology Journal</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.csbj.2025.07.039\">https://doi.org/10.1016/j.csbj.2025.07.039</a>.","mla":"Vedula, Sanketh, et al. “Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.” <i>Computational and Structural Biotechnology Journal</i>, vol. 27, Elsevier, 2025, pp. 3292–98, doi:<a href=\"https://doi.org/10.1016/j.csbj.2025.07.039\">10.1016/j.csbj.2025.07.039</a>.","ieee":"S. Vedula, A. M. Bronstein, and A. Marx, “Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment,” <i>Computational and Structural Biotechnology Journal</i>, vol. 27. Elsevier, pp. 3292–3298, 2025."}},{"PlanS_conform":"1","language":[{"iso":"eng"}],"article_type":"original","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_type":"hybrid","_id":"20102","author":[{"last_name":"Raffini","first_name":"Francesca","full_name":"Raffini, Francesca"},{"last_name":"De Jode","full_name":"De Jode, Aurélien","first_name":"Aurélien"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Zagrodzka, Zuzanna B.","first_name":"Zuzanna B.","last_name":"Zagrodzka"},{"orcid":"0000-0003-1050-4969","first_name":"Anja M","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram"},{"first_name":"Juan","full_name":"Galindo, Juan","last_name":"Galindo"},{"last_name":"Rolán-Alvarez","full_name":"Rolán-Alvarez, Emilio","first_name":"Emilio"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"file_date_updated":"2025-12-30T09:25:17Z","intvolume":"        34","title":"Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail","publisher":"Wiley","article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"date_published":"2025-11-01T00:00:00Z","department":[{"_id":"NiBa"}],"oa_version":"Published Version","date_updated":"2025-12-30T09:25:45Z","external_id":{"isi":["001538172800001"]},"publication_status":"published","acknowledgement":"This study was supported by European Research Council grant 693030-BARRIERS to RKB; the Swedish Research Council (grant number 2021-04191) to KJ; the Portuguese Foundation for Science and Technology (FCT: 2020.00275.CEECIND and PTDC/BIA-EVL/1614/2021) to RF; grant PID2022-137935NB-I00 by MICIU/AEI/ 10.13039/501100011033/and ERDF/EU (ED431C 2020-05) to JG, grant PID2021-124930NB-I00 funded by MICIU/AEI/ 10.13039/501100011033/and ERDF/EU to ERA, Xunta de Galicia (ED431C 2024/22), Centro singular de Investigación de Galicia accreditation 2024-2027 (ED431G 2023/07), ‘ERDF A way of making Europe’ and Norwegian Research Council RCN, project 315287 to AMW.","status":"public","quality_controlled":"1","month":"11","volume":34,"citation":{"apa":"Raffini, F., De Jode, A., Johannesson, K., Faria, R., Zagrodzka, Z. B., Westram, A. M., … Butlin, R. K. (2025). Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.70025\">https://doi.org/10.1111/mec.70025</a>","chicago":"Raffini, Francesca, Aurélien De Jode, Kerstin Johannesson, Rui Faria, Zuzanna B. Zagrodzka, Anja M Westram, Juan Galindo, Emilio Rolán-Alvarez, and Roger K. Butlin. “Phenotypic Divergence and Genomic Architecture between Parallel Ecotypes at Two Different Points on the Speciation Continuum in a Marine Snail.” <i>Molecular Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/mec.70025\">https://doi.org/10.1111/mec.70025</a>.","mla":"Raffini, Francesca, et al. “Phenotypic Divergence and Genomic Architecture between Parallel Ecotypes at Two Different Points on the Speciation Continuum in a Marine Snail.” <i>Molecular Ecology</i>, vol. 34, no. 21, e70025, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/mec.70025\">10.1111/mec.70025</a>.","ieee":"F. Raffini <i>et al.</i>, “Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail,” <i>Molecular Ecology</i>, vol. 34, no. 21. Wiley, 2025.","short":"F. Raffini, A. De Jode, K. Johannesson, R. Faria, Z.B. Zagrodzka, A.M. Westram, J. Galindo, E. Rolán-Alvarez, R.K. Butlin, Molecular Ecology 34 (2025).","ama":"Raffini F, De Jode A, Johannesson K, et al. Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail. <i>Molecular Ecology</i>. 2025;34(21). doi:<a href=\"https://doi.org/10.1111/mec.70025\">10.1111/mec.70025</a>","ista":"Raffini F, De Jode A, Johannesson K, Faria R, Zagrodzka ZB, Westram AM, Galindo J, Rolán-Alvarez E, Butlin RK. 2025. Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail. Molecular Ecology. 34(21), e70025."},"article_number":"e70025","type":"journal_article","year":"2025","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","abstract":[{"text":"Speciation is rarely observable directly. A way forward is to compare pairs of ecotypes that evolved in parallel in similar contexts but have reached different degrees of reproductive isolation. Such comparisons are possible in the marine snail Littorina saxatilis by contrasting barriers to gene flow between parallel ecotypes in Spain and Sweden. In both countries, divergent ecotypes have evolved to withstand either crab predation or wave action. Here, we explore transects spanning contact zones between the Crab and the Wave ecotypes using low-coverage whole-genome sequencing, morphological and behavioural traits. Despite parallel phenotypic divergence, distinct patterns of differentiation between the ecotypes emerged: a continuous cline in Sweden indicating a weak barrier to gene flow, but two highly genetically and phenotypically divergent, and partly spatially overlapping clusters in Spain suggesting a much stronger barrier to gene flow. The absence of Spanish early-generation hybrids supported strong isolation, but a low level of gene flow is evident from molecular data. In both countries, highly differentiated loci were located in both shared and country-specific chromosomal inversions but were also present in collinear regions. Despite being considered the same species and showing similar levels of phenotypic divergence, the Spanish ecotypes are much closer to full reproductive isolation than the Swedish ones. Barriers to gene flow of very different strengths between ecotypes within the same species might be explained by dissimilarities in the spatial arrangement of habitats, the selection gradients or the ages of the systems.","lang":"eng"}],"isi":1,"day":"01","oa":1,"scopus_import":"1","doi":"10.1111/mec.70025","file":[{"relation":"main_file","access_level":"open_access","creator":"dernst","date_created":"2025-12-30T09:25:17Z","file_size":2767745,"checksum":"ec01edda64cfbc6cbc8adf300f719644","content_type":"application/pdf","file_id":"20906","date_updated":"2025-12-30T09:25:17Z","success":1,"file_name":"2025_MolecEcology_Raffini.pdf"}],"publication":"Molecular Ecology","ddc":["570"],"issue":"21","date_created":"2025-08-03T22:01:31Z"},{"OA_place":"repository","author":[{"full_name":"Vedula, Sanketh","first_name":"Sanketh","last_name":"Vedula","id":"94f2fe44-70fa-11f0-b76b-92922c09452b"},{"full_name":"Bronstein, Alexander","first_name":"Alexander","orcid":"0000-0001-9699-8730","last_name":"Bronstein","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6"},{"full_name":"Marx, Ailie","first_name":"Ailie","last_name":"Marx"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","has_accepted_license":"1","_id":"20103","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"year":"2025","type":"research_data_reference","related_material":{"record":[{"id":"20100","relation":"used_for_analysis_in","status":"public"}]},"citation":{"ista":"Vedula S, Bronstein AM, Marx A. 2025. Replication Data for: ‘Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment’, Harvard Dataverse, <a href=\"https://doi.org/10.7910/DVN/DYEBVM\">10.7910/DVN/DYEBVM</a>.","short":"S. Vedula, A.M. Bronstein, A. Marx, (2025).","ama":"Vedula S, Bronstein AM, Marx A. Replication Data for: “Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.” 2025. doi:<a href=\"https://doi.org/10.7910/DVN/DYEBVM\">10.7910/DVN/DYEBVM</a>","chicago":"Vedula, Sanketh, Alex M. Bronstein, and Ailie Marx. “Replication Data for: ‘Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.’” Harvard Dataverse, 2025. <a href=\"https://doi.org/10.7910/DVN/DYEBVM\">https://doi.org/10.7910/DVN/DYEBVM</a>.","apa":"Vedula, S., Bronstein, A. M., &#38; Marx, A. (2025). Replication Data for: “Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.” Harvard Dataverse. <a href=\"https://doi.org/10.7910/DVN/DYEBVM\">https://doi.org/10.7910/DVN/DYEBVM</a>","mla":"Vedula, Sanketh, et al. <i>Replication Data for: “Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.”</i> Harvard Dataverse, 2025, doi:<a href=\"https://doi.org/10.7910/DVN/DYEBVM\">10.7910/DVN/DYEBVM</a>.","ieee":"S. Vedula, A. M. Bronstein, and A. Marx, “Replication Data for: ‘Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.’” Harvard Dataverse, 2025."},"month":"06","ddc":["000"],"date_created":"2025-08-04T06:18:55Z","status":"public","oa_version":"Published Version","date_published":"2025-06-27T00:00:00Z","day":"27","department":[{"_id":"AlBr"}],"doi":"10.7910/DVN/DYEBVM","date_updated":"2025-11-27T14:09:58Z","oa":1,"publisher":"Harvard Dataverse","title":"Replication Data for: \"Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment\"","main_file_link":[{"open_access":"1","url":"https://doi.org/10.7910/DVN/DYEBVM"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Official implementation, windowed MSAs, and the predictions as reported in the manuscript titled \"Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment\". (2025-06-27)"}]},{"oa_version":"Published Version","ec_funded":1,"date_published":"2025-05-21T00:00:00Z","department":[{"_id":"CaMu"}],"day":"21","doi":"10.5281/ZENODO.13988679","oa":1,"date_updated":"2025-08-04T07:46:33Z","publisher":"Zenodo","title":"Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages","project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.15409324","open_access":"1"}],"article_processing_charge":"No","abstract":[{"text":"This repository contains the data and scripts required to reproduce the results of the manuscript \"Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages\" submitted to the Environmental Research Climate Journal (ERCL). ","lang":"eng"}],"month":"05","ddc":["550"],"date_created":"2025-08-04T07:34:39Z","status":"public","year":"2025","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_type":"green","corr_author":"1","type":"research_data_reference","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"20098"}]},"citation":{"chicago":"Hwong, Yi-Ling, Edward Byers, Michaela Werning, and Yann Quilcaille. “Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages.” Zenodo, 2025. <a href=\"https://doi.org/10.5281/ZENODO.13988679\">https://doi.org/10.5281/ZENODO.13988679</a>.","apa":"Hwong, Y.-L., Byers, E., Werning, M., &#38; Quilcaille, Y. (2025). Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.13988679\">https://doi.org/10.5281/ZENODO.13988679</a>","ieee":"Y.-L. Hwong, E. Byers, M. Werning, and Y. Quilcaille, “Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages.” Zenodo, 2025.","mla":"Hwong, Yi-Ling, et al. <i>Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages</i>. Zenodo, 2025, doi:<a href=\"https://doi.org/10.5281/ZENODO.13988679\">10.5281/ZENODO.13988679</a>.","ama":"Hwong Y-L, Byers E, Werning M, Quilcaille Y. Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages. 2025. doi:<a href=\"https://doi.org/10.5281/ZENODO.13988679\">10.5281/ZENODO.13988679</a>","short":"Y.-L. Hwong, E. Byers, M. Werning, Y. Quilcaille, (2025).","ista":"Hwong Y-L, Byers E, Werning M, Quilcaille Y. 2025. Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.13988679\">10.5281/ZENODO.13988679</a>."},"OA_place":"repository","author":[{"id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22","last_name":"Hwong","orcid":"0000-0001-9281-3479","full_name":"Hwong, Yi-Ling","first_name":"Yi-Ling"},{"full_name":"Byers, Edward","first_name":"Edward","last_name":"Byers"},{"first_name":"Michaela","full_name":"Werning, Michaela","last_name":"Werning"},{"last_name":"Quilcaille","full_name":"Quilcaille, Yann","first_name":"Yann"}],"has_accepted_license":"1","_id":"20107","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_number":"116056","type":"journal_article","year":"2025","citation":{"ista":"Xu F, Yu Y, Guan B, Xu T, Xu Z, Xue H. 2025. Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis. Cell Reports. 44(8), 116056.","ama":"Xu F, Yu Y, Guan B, Xu T, Xu Z, Xue H. Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis. <i>Cell Reports</i>. 2025;44(8). doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.116056\">10.1016/j.celrep.2025.116056</a>","short":"F. Xu, Y. Yu, B. Guan, T. Xu, Z. Xu, H. Xue, Cell Reports 44 (2025).","mla":"Xu, Faqing, et al. “Germin-like Protein 1 Interacts with Proteasome Regulator 1 to Regulate Auxin Signaling by Controlling Aux/IAA Homeostasis.” <i>Cell Reports</i>, vol. 44, no. 8, 116056, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.116056\">10.1016/j.celrep.2025.116056</a>.","ieee":"F. Xu, Y. Yu, B. Guan, T. Xu, Z. Xu, and H. Xue, “Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis,” <i>Cell Reports</i>, vol. 44, no. 8. Elsevier, 2025.","chicago":"Xu, Faqing, Yongqiang Yu, Bin Guan, Tongda Xu, Zhihong Xu, and Hongwei Xue. “Germin-like Protein 1 Interacts with Proteasome Regulator 1 to Regulate Auxin Signaling by Controlling Aux/IAA Homeostasis.” <i>Cell Reports</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.celrep.2025.116056\">https://doi.org/10.1016/j.celrep.2025.116056</a>.","apa":"Xu, F., Yu, Y., Guan, B., Xu, T., Xu, Z., &#38; Xue, H. (2025). Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2025.116056\">https://doi.org/10.1016/j.celrep.2025.116056</a>"},"OA_place":"publisher","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"24","isi":1,"oa":1,"doi":"10.1016/j.celrep.2025.116056","scopus_import":"1","pmid":1,"abstract":[{"text":"Auxin regulates various aspects of plant growth and development by modulating the transcription of target genes through the degradation of auxin/indole-3-acetic acid (Aux/IAA) repressors via the 26S proteasome. Proteasome regulator 1 (PTRE1), a positive regulator of proteasome activity, has been implicated in auxin-mediated proteasome suppression; however, the mechanism by which auxin modulates PTRE1 function remains unclear. Here, we demonstrate that auxin promotes the interaction between germin-like protein 1 (GLP1) and PTRE1, facilitating PTRE1 retention at the plasma membrane. The relocation of PTRE1 results in reduced nuclear 26S proteasome activity, and thus the attenuated Aux/IAA degradation and altered Aux/IAA homeostasis, ultimately resulting in suppressed auxin-mediated transcriptional regulation. Our findings uncover a previously uncharacterized regulatory axis in auxin signaling that controls Aux/IAA protein stability, functioning alongside the TIR1- and TRANSMEMBRANE KINASE 1 (TMK1)-mediated pathways, and highlight the coordination of auxin signaling from the cell surface to the nucleus via auxin-induced PTRE1 relocation, which fine-tunes Aux/IAA protein homeostasis and auxin responses.","lang":"eng"}],"ddc":["580"],"issue":"8","date_created":"2025-08-04T13:39:11Z","publication":"Cell Reports","file":[{"checksum":"3c43e040a4a7a65ec67ae1d2bb81261a","file_size":24178018,"date_created":"2025-08-05T06:15:09Z","creator":"dernst","relation":"main_file","access_level":"open_access","file_name":"2025_CellReports_Xu.pdf","success":1,"date_updated":"2025-08-05T06:15:09Z","file_id":"20120","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"OA_type":"gold","tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"article_type":"original","author":[{"last_name":"Xu","full_name":"Xu, Faqing","first_name":"Faqing"},{"first_name":"Yongqiang","full_name":"Yu, Yongqiang","last_name":"Yu"},{"id":"56aad729-cca2-11ed-a45a-9b4138991a48","last_name":"Guan","first_name":"Bin","full_name":"Guan, Bin"},{"first_name":"Tongda","full_name":"Xu, Tongda","last_name":"Xu"},{"first_name":"Zhihong","full_name":"Xu, Zhihong","last_name":"Xu"},{"first_name":"Hongwei","full_name":"Xue, Hongwei","last_name":"Xue"}],"file_date_updated":"2025-08-05T06:15:09Z","intvolume":"        44","_id":"20116","license":"https://creativecommons.org/licenses/by-nc/4.0/","date_published":"2025-07-24T00:00:00Z","publication_identifier":{"eissn":["2211-1247"]},"department":[{"_id":"JiFr"}],"oa_version":"Published Version","external_id":{"isi":["001542038500001"],"pmid":["40714631"]},"date_updated":"2025-09-30T14:13:45Z","publication_status":"published","title":"Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis","publisher":"Elsevier","article_processing_charge":"Yes","month":"07","volume":44,"DOAJ_listed":"1","acknowledgement":"The study was supported by the National Natural Science Foundation of China (NSFC; 32230011, 91954206, and 31721001). We thank Dr. Deli Lin (Shanghai Jiao Tong University) for kind help with the laser confocal microscope observation and the Arabidopsis Biological Resource Center (ABRC) for providing T-DNA insertional mutants.","status":"public","quality_controlled":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","OA_place":"publisher","citation":{"chicago":"Zhang, Zhiying, Thomas C. Todeschini, Yi Wu, Roman Kogay, Ameena Naji, Joaquin Cardenas Rodriguez, Rupavidhya Mondi, et al. “Kiwa Is a Membrane-Embedded Defense Supercomplex Activated at Phage Attachment Sites.” <i>Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">https://doi.org/10.1016/j.cell.2025.07.002</a>.","apa":"Zhang, Z., Todeschini, T. C., Wu, Y., Kogay, R., Naji, A., Cardenas Rodriguez, J., … Nobrega, F. L. (2025). Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">https://doi.org/10.1016/j.cell.2025.07.002</a>","ieee":"Z. Zhang <i>et al.</i>, “Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites,” <i>Cell</i>, vol. 188, no. 21. Elsevier, p. 5862–5877.e23, 2025.","mla":"Zhang, Zhiying, et al. “Kiwa Is a Membrane-Embedded Defense Supercomplex Activated at Phage Attachment Sites.” <i>Cell</i>, vol. 188, no. 21, Elsevier, 2025, p. 5862–5877.e23, doi:<a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">10.1016/j.cell.2025.07.002</a>.","ista":"Zhang Z, Todeschini TC, Wu Y, Kogay R, Naji A, Cardenas Rodriguez J, Mondi R, Kaganovich D, Taylor DW, Bravo JPK, Teplova M, Amen T, Koonin E, Patel DJ, Nobrega FL. 2025. Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites. Cell. 188(21), 5862–5877.e23.","ama":"Zhang Z, Todeschini TC, Wu Y, et al. Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites. <i>Cell</i>. 2025;188(21):5862-5877.e23. doi:<a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">10.1016/j.cell.2025.07.002</a>","short":"Z. Zhang, T.C. Todeschini, Y. Wu, R. Kogay, A. Naji, J. Cardenas Rodriguez, R. Mondi, D. Kaganovich, D.W. Taylor, J.P.K. Bravo, M. Teplova, T. Amen, E. Koonin, D.J. Patel, F.L. Nobrega, Cell 188 (2025) 5862–5877.e23."},"type":"journal_article","year":"2025","file":[{"file_size":32104588,"checksum":"b944de5fbd7455f58e1ff338ad352239","date_created":"2025-12-29T14:15:25Z","relation":"main_file","access_level":"open_access","creator":"dernst","success":1,"file_name":"2025_Cell_Zhang.pdf","date_updated":"2025-12-29T14:15:25Z","file_id":"20875","content_type":"application/pdf"}],"publication":"Cell","date_created":"2025-08-07T05:00:04Z","issue":"21","ddc":["570"],"abstract":[{"text":"Bacteria and archaea deploy diverse antiviral defense systems, many of which remain mechanistically uncharacterized. Here, we characterize Kiwa, a widespread two-component system composed of the transmembrane sensor KwaA and the DNA-binding effector KwaB. Cryogenic electron microscopy (cryo-EM) analysis reveals that KwaA and KwaB assemble into a large, membrane-associated supercomplex. Upon phage binding, KwaA senses infection at the membrane, leading to KwaB binding of ejected phage DNA and inhibition of replication and late transcription, without inducing host cell death. Although KwaB can bind DNA independently, its antiviral activity requires association with KwaA, suggesting spatial or conformational regulation. We show that the phage-encoded DNA-mimic protein Gam directly binds and inhibits KwaB but that co-expression with the Gam-targeted RecBCD system restores protection by Kiwa. Our findings support a model in which Kiwa coordinates membrane-associated detection of phage infection with downstream DNA binding by its effector, forming a spatially coordinated antiviral mechanism.","lang":"eng"}],"pmid":1,"oa":1,"doi":"10.1016/j.cell.2025.07.002","scopus_import":"1","day":"16","page":"5862-5877.e23","isi":1,"_id":"20143","file_date_updated":"2025-12-29T14:15:25Z","intvolume":"       188","author":[{"first_name":"Zhiying","full_name":"Zhang, Zhiying","last_name":"Zhang"},{"first_name":"Thomas C.","full_name":"Todeschini, Thomas C.","last_name":"Todeschini"},{"first_name":"Yi","full_name":"Wu, Yi","last_name":"Wu"},{"last_name":"Kogay","first_name":"Roman","full_name":"Kogay, Roman"},{"full_name":"Naji, Ameena","first_name":"Ameena","last_name":"Naji"},{"first_name":"Joaquin","full_name":"Cardenas Rodriguez, Joaquin","last_name":"Cardenas Rodriguez"},{"full_name":"Mondi, Rupavidhya","first_name":"Rupavidhya","last_name":"Mondi"},{"last_name":"Kaganovich","first_name":"Daniel","full_name":"Kaganovich, Daniel"},{"last_name":"Taylor","first_name":"David W.","full_name":"Taylor, David W."},{"id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","last_name":"Bravo","orcid":"0000-0003-0456-0753","first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly"},{"last_name":"Teplova","first_name":"Marianna","full_name":"Teplova, Marianna"},{"first_name":"Triana","full_name":"Amen, Triana","last_name":"Amen"},{"full_name":"Koonin, Eugene","first_name":"Eugene","last_name":"Koonin"},{"full_name":"Patel, Dinshaw J.","first_name":"Dinshaw J.","last_name":"Patel"},{"last_name":"Nobrega","full_name":"Nobrega, Franklin L.","first_name":"Franklin L."}],"PlanS_conform":"1","article_type":"original","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_type":"hybrid","language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","acknowledgement":"We thank Rotem Sorek (Weizmann Institute of Science) for the Lambda Gam mutant and Ian Molineux (University of Texas) for T4Δgp2. We thank You Yu (Zhejiang University-University of Edinburgh Institute) and J. De La Cruz (MSK) for assistance with cryo-EM data collection and Lyuqin Zheng (MSK) for discussions on structural analysis. We thank the Imaging and Microscopy Centre (IMC) at the University of Southampton. This work was supported by Royal Society grant RGS\\R2\\222312 to F.L.N.; Welch Foundation grant F-1938 and National Institutes of Health R35GM138348 to D.W.T.; Wessex Medical Research Innovation grant AE06 to T.A.; and NIH grant GM145888 and Maloris Foundation and Memorial Sloan-Kettering Core grant (P30-CA008748) to D.J.P. In addition to MSKCC cryo-EM resources, some of this work was performed at the National Center for CryoEM Access and Training (NCCAT) and the Simons Electron Microscopy Center located at the New York Structural Biology Center, supported by the NIH Common Fund Transformative High Resolution Cryo-Electron Microscopy program (U24 GM129539) and Simons Foundation (SF349247) and NY State Assembly grants. This research used NSLS-II MX X-ray User Resources (FMX) of the National Synchrotron Light Source II, operated for the DOE Office of Science by Brookhaven National Laboratory under contract no. DE-SC0012704. The Center for BioMolecular Structure (CBMS) is primarily supported by the NIH, the National Institute of General Medical Sciences (NIGMS) through a Center Core P30 Grant (P30GM133893), and by the DOE Office of Biological and Environmental Research (KP1605010). R.K. and E.V.K. are supported by the Intramural Research Program of the NIH (National Library of Medicine).","volume":188,"month":"10","article_processing_charge":"Yes (in subscription journal)","title":"Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites","publisher":"Elsevier","external_id":{"isi":["001603560700005"],"pmid":["40730155"]},"date_updated":"2025-12-29T14:15:58Z","publication_status":"published","date_published":"2025-10-16T00:00:00Z","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"department":[{"_id":"JaBr"}],"oa_version":"Published Version"},{"file":[{"success":1,"file_name":"2025_ReisRodrigues_Patricia_Thesis.pdf","date_updated":"2025-08-27T12:59:10Z","content_type":"application/pdf","file_id":"20232","file_size":63885565,"checksum":"fda8a1070667c3562263f4867609b41b","date_created":"2025-08-27T12:59:10Z","access_level":"open_access","relation":"main_file","creator":"prodrigu"},{"relation":"source_file","access_level":"closed","creator":"prodrigu","file_size":50483434,"checksum":"e8b65affcbce846a926454df4b2867b9","date_created":"2025-08-27T13:00:30Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"20233","file_name":"2025_ReisRodrigues_Patricia_Thesis.docx","date_updated":"2025-08-27T13:02:28Z"}],"date_created":"2025-08-08T09:18:02Z","ddc":["570"],"project":[{"grant_number":"101071793","name":"Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces","_id":"bd91e723-d553-11ed-ba76-fe7eeb2185fd"}],"abstract":[{"lang":"eng","text":"Immune responses depend on the coordinated and efficient migration of leukocytes. These\r\ncells, which are embedded and tightly confined within tissues, must navigate and traverse\r\ndiverse and complex three-dimensional environments. Leukocytes adapt their locomotory\r\nbehavior to the mechanical, geometrical, and biochemical characteristics of their\r\nsurroundings. In low-density environments, where the pore size of the interstitial matrix\r\nallows free passage, these cells position the nucleus directly behind the lamellipodium, the\r\nprotrusive actin structure that forms the leading front of the cell. In this configuration, they\r\nuse the nucleus as a gauge to identify the path of least resistance.\r\nHere, we show that in high-density environments, where the pore size precludes free passage\r\nof the cell body, leukocytes reposition the microtubule-organizing center (MTOC) and\r\nassociated organelles in front of the nucleus. In this configuration, they use actin structures\r\nprotruding orthogonally to the direction of migration in order to open a path for the cell body.\r\nWe identify two distinct actin populations that serve this purpose at different subcellular\r\nlocalizations. At the leading edge, local indentation of the plasma membrane leads to\r\nrecruitment of the Wiskott-Aldrich syndrome protein (WASp), which, via Arp2/3, results in\r\nthe formation of individual actin foci. At the cell body, actin polymerization is triggered by\r\nDOCK8, a Cdc42 exchange factor, resulting in the formation of a central actin pool.\r\nWe demonstrate that the central and peripheral actin pools are functionally communicating\r\nand that depletion of the central actin pool leads to increased actin accumulation at the cell\r\nfront, resulting in excessive extension of the leading edge."}],"doi":"10.15479/AT-ISTA-20149","oa":1,"day":"08","page":"114","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","has_accepted_license":"1","OA_place":"publisher","related_material":{"record":[{"id":"10703","status":"public","relation":"part_of_dissertation"},{"id":"20082","relation":"part_of_dissertation","status":"public"}]},"citation":{"apa":"Dos Reis Rodrigues, P. (2025). <i>Coordination of protrusive forces in immune cell migration </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20149\">https://doi.org/10.15479/AT-ISTA-20149</a>","chicago":"Dos Reis Rodrigues, Patricia. “Coordination of Protrusive Forces in Immune Cell Migration .” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20149\">https://doi.org/10.15479/AT-ISTA-20149</a>.","ieee":"P. Dos Reis Rodrigues, “Coordination of protrusive forces in immune cell migration ,” Institute of Science and Technology Austria, 2025.","mla":"Dos Reis Rodrigues, Patricia. <i>Coordination of Protrusive Forces in Immune Cell Migration </i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20149\">10.15479/AT-ISTA-20149</a>.","short":"P. Dos Reis Rodrigues, Coordination of Protrusive Forces in Immune Cell Migration , Institute of Science and Technology Austria, 2025.","ama":"Dos Reis Rodrigues P. Coordination of protrusive forces in immune cell migration . 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20149\">10.15479/AT-ISTA-20149</a>","ista":"Dos Reis Rodrigues P. 2025. Coordination of protrusive forces in immune cell migration . Institute of Science and Technology Austria."},"year":"2025","corr_author":"1","alternative_title":["ISTA Thesis"],"type":"dissertation","status":"public","acknowledgement":"I would like to acknowledge the\r\nfinancial support of the European Research Council through the ERC-SyG grant “Pushing from\r\nwithin: Control of cell shape, integrity and motility by cytoskeletal pushing forces”\r\n(01071793), which made this research possible. ","month":"08","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","title":"Coordination of protrusive forces in immune cell migration ","publication_status":"published","date_updated":"2026-04-28T13:26:50Z","oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"NanoFab"}],"department":[{"_id":"GradSch"},{"_id":"MiSi"}],"date_published":"2025-08-08T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","_id":"20149","file_date_updated":"2025-08-27T13:02:28Z","author":[{"orcid":"0000-0003-1681-508X","first_name":"Patricia","full_name":"Dos Reis Rodrigues, Patricia","id":"26E95904-5160-11E9-9C0B-C5B0DC97E90F","last_name":"Dos Reis Rodrigues"}],"supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"language":[{"iso":"eng"}]},{"page":"645-654","day":"01","isi":1,"scopus_import":"1","doi":"10.1016/j.tins.2025.07.004","oa":1,"pmid":1,"abstract":[{"lang":"eng","text":"In long-lived mammals, including humans, brain cell homeostasis is critical for maintaining brain function throughout life. Most neurons are generated during development and must maintain their cellular identity and plasticity to preserve brain function. Although extensive studies indicate the importance of recycling and regenerating cellular molecules to maintain cellular homeostasis, recent evidence has shown that some proteins and RNAs do not turn over for months and even years. We propose that these long-lived cellular molecules may be the basis for maintaining brain function in the long term, but also a potential convergent target of brain aging. We highlight key discoveries and challenges, and propose potential directions to unravel the mystery of brain cell longevity."}],"ddc":["570"],"issue":"9","date_created":"2025-08-10T22:01:29Z","publication":"Trends in Neurosciences","file":[{"content_type":"application/pdf","file_id":"20873","date_updated":"2025-12-29T13:47:27Z","success":1,"file_name":"2025_TrendsNeurosciences_Hetzer.pdf","access_level":"open_access","relation":"main_file","creator":"dernst","date_created":"2025-12-29T13:47:27Z","file_size":327847,"checksum":"90942491b499f70b0bf48b8aec2e7387"}],"year":"2025","corr_author":"1","type":"journal_article","citation":{"ieee":"M. Hetzer and T. Toda, “Long-lived cellular molecules in the brain,” <i>Trends in Neurosciences</i>, vol. 48, no. 9. Elsevier, pp. 645–654, 2025.","mla":"Hetzer, Martin, and Tomohisa Toda. “Long-Lived Cellular Molecules in the Brain.” <i>Trends in Neurosciences</i>, vol. 48, no. 9, Elsevier, 2025, pp. 645–54, doi:<a href=\"https://doi.org/10.1016/j.tins.2025.07.004\">10.1016/j.tins.2025.07.004</a>.","chicago":"Hetzer, Martin, and Tomohisa Toda. “Long-Lived Cellular Molecules in the Brain.” <i>Trends in Neurosciences</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.tins.2025.07.004\">https://doi.org/10.1016/j.tins.2025.07.004</a>.","apa":"Hetzer, M., &#38; Toda, T. (2025). Long-lived cellular molecules in the brain. <i>Trends in Neurosciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tins.2025.07.004\">https://doi.org/10.1016/j.tins.2025.07.004</a>","ama":"Hetzer M, Toda T. Long-lived cellular molecules in the brain. <i>Trends in Neurosciences</i>. 2025;48(9):645-654. doi:<a href=\"https://doi.org/10.1016/j.tins.2025.07.004\">10.1016/j.tins.2025.07.004</a>","short":"M. Hetzer, T. Toda, Trends in Neurosciences 48 (2025) 645–654.","ista":"Hetzer M, Toda T. 2025. Long-lived cellular molecules in the brain. Trends in Neurosciences. 48(9), 645–654."},"OA_place":"publisher","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","publication_identifier":{"eissn":["1878-108X"],"issn":["0166-2236"]},"date_published":"2025-09-01T00:00:00Z","department":[{"_id":"MaHe"}],"publication_status":"published","external_id":{"isi":["001568965400001"],"pmid":["40744775"]},"date_updated":"2025-12-29T13:47:58Z","title":"Long-lived cellular molecules in the brain","publisher":"Elsevier","article_processing_charge":"Yes (in subscription journal)","month":"09","volume":48,"acknowledgement":"The work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) (470322152 – T1347/3-1; 497658532 – T1347/4-1; 507965872 – T1347/5-1; and 460333672 – CRC1540 Exploring Brain Mechanics) to T.T., the Schram Foundation (T.T.), the European Research Council (ERC-2018-STG, 804468 EAGER; ERC-2023-COG, 101125034 NEUTIME) to T.T., the Hans-Georg Geis und Xue Hong Dong-Geis Foundation and Forschungsstiftung Medizin am Universitätsklinikum Erlangen to T.T., and the Interdisciplinary Centre for Clinical Research Erlangen (Interdisziplinäres Zentrum für Klinische Forschung, Universitätsklinikum Erlangen; P162 to T.T.). We thank Dr Laura J. Harrison for editing assistance.","quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"article_type":"original","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_type":"hybrid","PlanS_conform":"1","author":[{"first_name":"Martin W","full_name":"Hetzer, Martin W","orcid":"0000-0002-2111-992X","last_name":"Hetzer","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"},{"full_name":"Toda, Tomohisa","first_name":"Tomohisa","last_name":"Toda"}],"intvolume":"        48","file_date_updated":"2025-12-29T13:47:27Z","_id":"20154"},{"OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","corr_author":"1","year":"2025","citation":{"chicago":"Brigati, Giovanni, and Gabriel Stoltz. “How to Construct Explicit Decay Rates for Kinetic Fokker–Planck Equations?” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2025. <a href=\"https://doi.org/10.1137/24M1700351\">https://doi.org/10.1137/24M1700351</a>.","apa":"Brigati, G., &#38; Stoltz, G. (2025). How to construct explicit decay rates for kinetic Fokker–Planck equations? <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/24M1700351\">https://doi.org/10.1137/24M1700351</a>","mla":"Brigati, Giovanni, and Gabriel Stoltz. “How to Construct Explicit Decay Rates for Kinetic Fokker–Planck Equations?” <i>SIAM Journal on Mathematical Analysis</i>, vol. 57, no. 4, Society for Industrial and Applied Mathematics, 2025, pp. 3587–622, doi:<a href=\"https://doi.org/10.1137/24M1700351\">10.1137/24M1700351</a>.","ieee":"G. Brigati and G. Stoltz, “How to construct explicit decay rates for kinetic Fokker–Planck equations?,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 57, no. 4. Society for Industrial and Applied Mathematics, pp. 3587–3622, 2025.","ista":"Brigati G, Stoltz G. 2025. How to construct explicit decay rates for kinetic Fokker–Planck equations? SIAM Journal on Mathematical Analysis. 57(4), 3587–3622.","ama":"Brigati G, Stoltz G. How to construct explicit decay rates for kinetic Fokker–Planck equations? <i>SIAM Journal on Mathematical Analysis</i>. 2025;57(4):3587-3622. doi:<a href=\"https://doi.org/10.1137/24M1700351\">10.1137/24M1700351</a>","short":"G. Brigati, G. Stoltz, SIAM Journal on Mathematical Analysis 57 (2025) 3587–3622."},"date_created":"2025-08-10T22:01:29Z","issue":"4","publication":"SIAM Journal on Mathematical Analysis","page":"3587-3622","isi":1,"day":"01","arxiv":1,"oa":1,"doi":"10.1137/24M1700351","scopus_import":"1","abstract":[{"lang":"eng","text":"We study time averages for the norm of solutions to kinetic Fokker–Planck equations associated with general Hamiltonians. We provide fully explicit and constructive decay estimates for systems subject to a confining potential, allowing fat-tail, subexponential and (super-)exponential local equilibria, which also include the classic Maxwellian case. The key step in our estimates is a modified Poincaré inequality, obtained via a Lions–Poincaré inequality and an averaging lemma."}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2302.14506","open_access":"1"}],"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"author":[{"id":"63ff57e8-1fbb-11ee-88f2-f558ffc59cf1","last_name":"Brigati","full_name":"Brigati, Giovanni","first_name":"Giovanni"},{"first_name":"Gabriel","full_name":"Stoltz, Gabriel","last_name":"Stoltz"}],"intvolume":"        57","_id":"20155","language":[{"iso":"eng"}],"OA_type":"green","article_type":"original","month":"08","volume":57,"acknowledgement":"The first author was funded by the European Union's Horizon 2020 research andinnovation program under the Marie Sklodowska-Curie grant agreements 754362 and 101034413,and partially by Project EFI (ANR-17-CE40-0030) of the French National Research Agency (ANR).The work of the second author was partially funded by the European Research Council (ERC) underthe European Union's Horizon 2020 research and innovation programme (grant agreement 810367),and by the Agence Nationale de la Recherche under grants ANR-19-CE40-0010 (QuAMProcs) andANR-21-CE40-0006 (SINEQ).","status":"public","quality_controlled":"1","department":[{"_id":"JaMa"}],"date_published":"2025-08-01T00:00:00Z","ec_funded":1,"publication_identifier":{"eissn":["1095-7154"],"issn":["0036-1410"]},"oa_version":"Preprint","external_id":{"isi":["001550830900006"],"arxiv":["2302.14506"]},"date_updated":"2025-11-05T13:51:40Z","publication_status":"published","title":"How to construct explicit decay rates for kinetic Fokker–Planck equations?","publisher":"Society for Industrial and Applied Mathematics","article_processing_charge":"No"},{"date_published":"2025-12-01T00:00:00Z","publication_identifier":{"eissn":["2214-5753"],"issn":["2214-5745"]},"department":[{"_id":"BeVi"}],"oa_version":"Published Version","date_updated":"2025-12-30T13:14:38Z","external_id":{"isi":["001582424100001"]},"publication_status":"published","publisher":"Elsevier","title":"Insect sex chromosome evolution: Conservation, turnover, and mechanisms of dosage compensation","article_processing_charge":"Yes (via OA deal)","month":"12","volume":72,"acknowledgement":"This work was supported by an Austrian Research Fund (FWF) grant to B.V. (PAT 8748323) and by the Louisiana Board of Regents Research Competitiveness Subprogram (LEQSF(2025-28)-RD-A-20) to MAT.","status":"public","quality_controlled":"1","language":[{"iso":"eng"}],"OA_type":"hybrid","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"review","PlanS_conform":"1","author":[{"last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A","first_name":"Melissa A","orcid":"0000-0002-9752-7380"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"file_date_updated":"2025-12-30T13:14:20Z","intvolume":"        72","_id":"20182","isi":1,"day":"01","oa":1,"doi":"10.1016/j.cois.2025.101411","scopus_import":"1","abstract":[{"lang":"eng","text":"Sex chromosomes have evolved many times throughout the tree of life, and understanding what has shaped their unusual morphological, sequence, and regulatory features has been a long-standing goal. Most early insights into insect sex chromosome biology came from a few model species, such as the fruit fly Drosophila melanogaster, which limited broad-scale evolutionary inferences. More recently, extensive comparative genomics studies have uncovered several unexpected patterns, which we highlight in this review. First, we describe the conservation of the ancestral X chromosome over 450 million years but also its recurrent turnover (i.e. its reversal to an autosome when a new X chromosome arose) in at least one order. We then summarize classical and more recent findings on how insects modulate the expression of X-linked genes following the degradation of the Y chromosome and how the diverse mechanisms of dosage compensation identified may elucidate important principles of sex chromosome regulatory evolution."}],"project":[{"name":"Sex chromosomes in evolution and development","grant_number":"PAT 8748323","_id":"8ed82125-16d5-11f0-9cad-fbcae312235b"}],"ddc":["570"],"date_created":"2025-08-17T22:01:35Z","publication":"Current Opinion in Insect Science","file":[{"access_level":"open_access","relation":"main_file","creator":"dernst","date_created":"2025-12-30T13:14:20Z","file_size":897079,"checksum":"262640abc34277686b56eb60102976f6","content_type":"application/pdf","file_id":"20917","date_updated":"2025-12-30T13:14:20Z","success":1,"file_name":"2025_CurrOpinionInsectScience_Toups.pdf"}],"article_number":"101411","type":"journal_article","corr_author":"1","year":"2025","citation":{"ieee":"M. A. Toups and B. Vicoso, “Insect sex chromosome evolution: Conservation, turnover, and mechanisms of dosage compensation,” <i>Current Opinion in Insect Science</i>, vol. 72. Elsevier, 2025.","mla":"Toups, Melissa A., and Beatriz Vicoso. “Insect Sex Chromosome Evolution: Conservation, Turnover, and Mechanisms of Dosage Compensation.” <i>Current Opinion in Insect Science</i>, vol. 72, 101411, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.cois.2025.101411\">10.1016/j.cois.2025.101411</a>.","chicago":"Toups, Melissa A, and Beatriz Vicoso. “Insect Sex Chromosome Evolution: Conservation, Turnover, and Mechanisms of Dosage Compensation.” <i>Current Opinion in Insect Science</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.cois.2025.101411\">https://doi.org/10.1016/j.cois.2025.101411</a>.","apa":"Toups, M. A., &#38; Vicoso, B. (2025). Insect sex chromosome evolution: Conservation, turnover, and mechanisms of dosage compensation. <i>Current Opinion in Insect Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cois.2025.101411\">https://doi.org/10.1016/j.cois.2025.101411</a>","ista":"Toups MA, Vicoso B. 2025. Insect sex chromosome evolution: Conservation, turnover, and mechanisms of dosage compensation. Current Opinion in Insect Science. 72, 101411.","ama":"Toups MA, Vicoso B. Insect sex chromosome evolution: Conservation, turnover, and mechanisms of dosage compensation. <i>Current Opinion in Insect Science</i>. 2025;72. doi:<a href=\"https://doi.org/10.1016/j.cois.2025.101411\">10.1016/j.cois.2025.101411</a>","short":"M.A. Toups, B. Vicoso, Current Opinion in Insect Science 72 (2025)."},"OA_place":"publisher","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"DOAJ_listed":"1","acknowledgement":"We thank members of the Conradt lab, the Center for Cell and Molecular Dynamics (https://www.uclccmd.co.uk/) and T. Schedl for discussions and comments on the manuscript. We thank L. McGuinness for excellent technical support. Some strains were provided by the Caenorhabditis Genetics Center (CGC), which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). We thank Alex Hajnal (University of Zurich, Switzerland) and Andrew deMello (ETH Zurich, Switzerland) for their support of S.B. This work was supported by a predoctoral fellowship from the Studienstiftung des deutschen Volkes to NM, funds from UCL (Division of Biosciences, UCL LSM Capital Equipment Fund) to B.C., and a Wolfson Fellowship from the Royal Society (https://royalsociety.org/) to B.C. (RSWF\\R1\\180008), and the Biotechnology and Biological Sciences Research Council (https://bbsrc.ukri.org/) (BB/V007572/1 and BB/V015648/1to B.C.).","quality_controlled":"1","status":"public","month":"08","volume":16,"title":"Unequal segregation of mitochondria during asymmetric cell division contributes to cell fate divergence in sister cells in vivo","publisher":"Springer Nature","article_processing_charge":"Yes","oa_version":"Published Version","publication_identifier":{"eissn":["2041-1723"]},"date_published":"2025-08-04T00:00:00Z","department":[{"_id":"CaHe"}],"publication_status":"published","date_updated":"2025-09-01T09:47:29Z","external_id":{"pmid":["40759648"]},"_id":"20183","author":[{"last_name":"Segos","first_name":"Ioannis","full_name":"Segos, Ioannis"},{"last_name":"Van Eeckhoven","first_name":"Jens","full_name":"Van Eeckhoven, Jens"},{"last_name":"Berger","first_name":"Simon","full_name":"Berger, Simon"},{"last_name":"Mishra","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E","first_name":"Nikhil","full_name":"Mishra, Nikhil","orcid":"0000-0002-6425-5788"},{"last_name":"Lambie","full_name":"Lambie, Eric J.","first_name":"Eric J."},{"last_name":"Conradt","full_name":"Conradt, Barbara","first_name":"Barbara"}],"file_date_updated":"2025-09-01T09:46:44Z","intvolume":"        16","PlanS_conform":"1","language":[{"iso":"eng"}],"OA_type":"gold","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"original","publication":"Nature Communications","file":[{"access_level":"open_access","relation":"main_file","creator":"dernst","date_created":"2025-09-01T09:46:44Z","file_size":3775190,"checksum":"f28e73963ea1f55876d0d1afca0f706a","content_type":"application/pdf","file_id":"20261","date_updated":"2025-09-01T09:46:44Z","success":1,"file_name":"2025_NatureComm_Segos.pdf"}],"ddc":["570"],"date_created":"2025-08-17T22:01:35Z","pmid":1,"abstract":[{"text":"The unequal segregation of organelles has been proposed to be an intrinsic mechanism that contributes to cell fate divergence during asymmetric cell division; however, in vivo evidence is sparse. Using super-resolution microscopy, we analysed the segregation of organelles during the division of the neuroblast QL.p in C. elegans larvae. QL.p divides to generate a daughter that survives, QL.pa, and a daughter that dies, QL.pp. We found that mitochondria segregate unequally by density and morphology and that this is dependent on mitochondrial dynamics. Furthermore, we found that mitochondrial density in QL.pp correlates with the time it takes QL.pp to die. We propose that low mitochondrial density in QL.pp promotes the cell death fate and ensures that QL.pp dies in a highly reproducible and timely manner. Our results provide in vivo evidence that the unequal segregation of mitochondria can contribute to cell fate divergence during asymmetric cell division in a developing animal.","lang":"eng"}],"day":"04","doi":"10.1038/s41467-025-62484-5","scopus_import":"1","oa":1,"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","citation":{"apa":"Segos, I., Van Eeckhoven, J., Berger, S., Mishra, N., Lambie, E. J., &#38; Conradt, B. (2025). Unequal segregation of mitochondria during asymmetric cell division contributes to cell fate divergence in sister cells in vivo. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-62484-5\">https://doi.org/10.1038/s41467-025-62484-5</a>","chicago":"Segos, Ioannis, Jens Van Eeckhoven, Simon Berger, Nikhil Mishra, Eric J. Lambie, and Barbara Conradt. “Unequal Segregation of Mitochondria during Asymmetric Cell Division Contributes to Cell Fate Divergence in Sister Cells in Vivo.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-62484-5\">https://doi.org/10.1038/s41467-025-62484-5</a>.","mla":"Segos, Ioannis, et al. “Unequal Segregation of Mitochondria during Asymmetric Cell Division Contributes to Cell Fate Divergence in Sister Cells in Vivo.” <i>Nature Communications</i>, vol. 16, 7174, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-62484-5\">10.1038/s41467-025-62484-5</a>.","ieee":"I. Segos, J. Van Eeckhoven, S. Berger, N. Mishra, E. J. Lambie, and B. Conradt, “Unequal segregation of mitochondria during asymmetric cell division contributes to cell fate divergence in sister cells in vivo,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","short":"I. Segos, J. Van Eeckhoven, S. Berger, N. Mishra, E.J. Lambie, B. Conradt, Nature Communications 16 (2025).","ama":"Segos I, Van Eeckhoven J, Berger S, Mishra N, Lambie EJ, Conradt B. Unequal segregation of mitochondria during asymmetric cell division contributes to cell fate divergence in sister cells in vivo. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-62484-5\">10.1038/s41467-025-62484-5</a>","ista":"Segos I, Van Eeckhoven J, Berger S, Mishra N, Lambie EJ, Conradt B. 2025. Unequal segregation of mitochondria during asymmetric cell division contributes to cell fate divergence in sister cells in vivo. Nature Communications. 16, 7174."},"article_number":"7174","year":"2025","type":"journal_article"},{"date_created":"2025-08-17T22:01:35Z","ddc":["570"],"publication":"Communications Biology","oa":1,"scopus_import":"1","doi":"10.1038/s42003-025-08589-5","isi":1,"day":"02","abstract":[{"lang":"eng","text":"Specialized DNA polymerases facilitate various cellular processes. Despite extensive research, the mutagenic effects of these error-prone enzymes on genomes are not fully understood. Here we show that Pol IV promotes genomic instability in Pseudomonas aeruginosa by misincorporating oxidized guanine nucleotides. This activity led to a distinctive mutational signature, characterized by A-to-C transversions occurring preferentially at AT sites flanked by a 5’G and/or 3’C. Furthermore, Pol IV preferentially targeted pathogenicity genes located at specific chromosomal locations near the replication termination region and rRNA-encoding operons. Half of the mutation events catalyzed by Pol IV impaired gene function. This can be attributed to the bias of Pol IV for mutating codons with its preferred sequence contexts, leading to substitutions to unreactive alanine and glycine residues. Remarkably, mutation signatures identified for Pol IV were found in clinical isolate genomes of P. aeruginosa, providing compelling evidence for its role in genetic diversification during pathogen adaptation."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s42003-025-08589-5"}],"pmid":1,"OA_place":"publisher","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","type":"journal_article","year":"2025","article_number":"1148","citation":{"ista":"Castell SD, Fernandez CM, Tumas IN, Margara LM, Miserendino MC, Ceschin DG, Pezza RJ, Monti MR. 2025. The low-fidelity DNA Pol IV accelerates evolution of pathogenicity genes in Pseudomonas aeruginosa. Communications Biology. 8, 1148.","short":"S.D. Castell, C.M. Fernandez, I.N. Tumas, L.M. Margara, M.C. Miserendino, D.G. Ceschin, R.J. Pezza, M.R. Monti, Communications Biology 8 (2025).","ama":"Castell SD, Fernandez CM, Tumas IN, et al. The low-fidelity DNA Pol IV accelerates evolution of pathogenicity genes in Pseudomonas aeruginosa. <i>Communications Biology</i>. 2025;8. doi:<a href=\"https://doi.org/10.1038/s42003-025-08589-5\">10.1038/s42003-025-08589-5</a>","mla":"Castell, Sofía D., et al. “The Low-Fidelity DNA Pol IV Accelerates Evolution of Pathogenicity Genes in Pseudomonas Aeruginosa.” <i>Communications Biology</i>, vol. 8, 1148, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s42003-025-08589-5\">10.1038/s42003-025-08589-5</a>.","ieee":"S. D. Castell <i>et al.</i>, “The low-fidelity DNA Pol IV accelerates evolution of pathogenicity genes in Pseudomonas aeruginosa,” <i>Communications Biology</i>, vol. 8. Springer Nature, 2025.","apa":"Castell, S. D., Fernandez, C. M., Tumas, I. N., Margara, L. M., Miserendino, M. C., Ceschin, D. G., … Monti, M. R. (2025). The low-fidelity DNA Pol IV accelerates evolution of pathogenicity genes in Pseudomonas aeruginosa. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-025-08589-5\">https://doi.org/10.1038/s42003-025-08589-5</a>","chicago":"Castell, Sofía D., Consuelo M. Fernandez, Ignacio N. Tumas, Lucía M. Margara, Maria C Miserendino, Danilo G. Ceschin, Roberto J. Pezza, and Mariela R. Monti. “The Low-Fidelity DNA Pol IV Accelerates Evolution of Pathogenicity Genes in Pseudomonas Aeruginosa.” <i>Communications Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s42003-025-08589-5\">https://doi.org/10.1038/s42003-025-08589-5</a>."},"volume":8,"month":"08","status":"public","quality_controlled":"1","acknowledgement":"This work was supported by the Secretaría de Ciencia y Técnica (33620230100926CB), Universidad Nacional de Córdoba; and the Agencia Nacional de Promoción Científica y Técnica (PICT 2018-4527).\r\n\r\n","DOAJ_listed":"1","date_updated":"2025-09-30T14:18:46Z","external_id":{"isi":["001541878500001"],"pmid":["40753298"]},"publication_status":"published","publication_identifier":{"eissn":["2399-3642"]},"date_published":"2025-08-02T00:00:00Z","department":[{"_id":"PaSc"},{"_id":"GradSch"}],"oa_version":"Published Version","article_processing_charge":"Yes","title":"The low-fidelity DNA Pol IV accelerates evolution of pathogenicity genes in Pseudomonas aeruginosa","publisher":"Springer Nature","intvolume":"         8","author":[{"full_name":"Castell, Sofía D.","first_name":"Sofía D.","last_name":"Castell"},{"full_name":"Fernandez, Consuelo M.","first_name":"Consuelo M.","last_name":"Fernandez"},{"first_name":"Ignacio N.","full_name":"Tumas, Ignacio N.","last_name":"Tumas"},{"last_name":"Margara","first_name":"Lucía M.","full_name":"Margara, Lucía M."},{"first_name":"Maria C","full_name":"Miserendino, Maria C","last_name":"Miserendino","id":"273e0cbd-72f0-11ef-b75a-f9f932e292fa"},{"last_name":"Ceschin","first_name":"Danilo G.","full_name":"Ceschin, Danilo G."},{"first_name":"Roberto J.","full_name":"Pezza, Roberto J.","last_name":"Pezza"},{"full_name":"Monti, Mariela R.","first_name":"Mariela R.","last_name":"Monti"}],"_id":"20184","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"OA_type":"gold","article_type":"original","language":[{"iso":"eng"}],"PlanS_conform":"1"}]