[{"publication_status":"published","intvolume":"       220","language":[{"iso":"eng"}],"month":"04","day":"30","pmid":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"article_number":"e202009154","quality_controlled":"1","scopus_import":"1","keyword":["cell biology"],"doi":"10.1083/jcb.202009154","date_updated":"2021-11-25T15:33:08Z","article_processing_charge":"No","date_published":"2021-04-30T00:00:00Z","author":[{"last_name":"Zeng","first_name":"Longhui","full_name":"Zeng, Longhui"},{"full_name":"Palaia, Ivan","first_name":"Ivan","last_name":"Palaia"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela"},{"full_name":"Su, Xiaolei","last_name":"Su","first_name":"Xiaolei"}],"year":"2021","_id":"10337","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":220,"publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"citation":{"chicago":"Zeng, Longhui, Ivan Palaia, Anđela Šarić, and Xiaolei Su. “PLCγ1 Promotes Phase Separation of T Cell Signaling Components.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2021. <a href=\"https://doi.org/10.1083/jcb.202009154\">https://doi.org/10.1083/jcb.202009154</a>.","ieee":"L. Zeng, I. Palaia, A. Šarić, and X. Su, “PLCγ1 promotes phase separation of T cell signaling components,” <i>Journal of Cell Biology</i>, vol. 220, no. 6. Rockefeller University Press, 2021.","apa":"Zeng, L., Palaia, I., Šarić, A., &#38; Su, X. (2021). PLCγ1 promotes phase separation of T cell signaling components. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202009154\">https://doi.org/10.1083/jcb.202009154</a>","ama":"Zeng L, Palaia I, Šarić A, Su X. PLCγ1 promotes phase separation of T cell signaling components. <i>Journal of Cell Biology</i>. 2021;220(6). doi:<a href=\"https://doi.org/10.1083/jcb.202009154\">10.1083/jcb.202009154</a>","ista":"Zeng L, Palaia I, Šarić A, Su X. 2021. PLCγ1 promotes phase separation of T cell signaling components. Journal of Cell Biology. 220(6), e202009154.","mla":"Zeng, Longhui, et al. “PLCγ1 Promotes Phase Separation of T Cell Signaling Components.” <i>Journal of Cell Biology</i>, vol. 220, no. 6, e202009154, Rockefeller University Press, 2021, doi:<a href=\"https://doi.org/10.1083/jcb.202009154\">10.1083/jcb.202009154</a>.","short":"L. Zeng, I. Palaia, A. Šarić, X. Su, Journal of Cell Biology 220 (2021)."},"external_id":{"pmid":["33929486"]},"article_type":"original","issue":"6","acknowledgement":"Charles H. Hood Foundation (NO AWARD) ; Rally Foundation (NO AWARD)","status":"public","oa_version":"None","date_created":"2021-11-25T15:21:30Z","publisher":"Rockefeller University Press","title":"PLCγ1 promotes phase separation of T cell signaling components","publication":"Journal of Cell Biology","extern":"1","abstract":[{"lang":"eng","text":"The T cell receptor (TCR) pathway receives, processes, and amplifies the signal from pathogenic antigens to the activation of T cells. Although major components in this pathway have been identified, the knowledge on how individual components cooperate to effectively transduce signals remains limited. Phase separation emerges as a biophysical principle in organizing signaling molecules into liquid-like condensates. Here, we report that phospholipase Cγ1 (PLCγ1) promotes phase separation of LAT, a key adaptor protein in the TCR pathway. PLCγ1 directly cross-links LAT through its two SH2 domains. PLCγ1 also protects LAT from dephosphorylation by the phosphatase CD45 and promotes LAT-dependent ERK activation and SLP76 phosphorylation. Intriguingly, a nonmonotonic effect of PLCγ1 on LAT clustering was discovered. Computer simulations, based on patchy particles, revealed how the cluster size is regulated by protein compositions. Together, these results define a critical function of PLCγ1 in promoting phase separation of the LAT complex and TCR signal transduction."}]},{"intvolume":"        10","publication_status":"published","file":[{"date_created":"2022-05-16T10:42:22Z","success":1,"content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","checksum":"22ed4c55fb550f6da02ae55c359be651","file_name":"2021_eLife_Choi.pdf","file_size":2715200,"file_id":"11384","date_updated":"2022-05-16T10:42:22Z"}],"project":[{"_id":"62935a00-2b32-11ec-9570-eff30fa39068","grant_number":"725746","name":"Quantitative analysis of DNA methylation maintenance with chromatin","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"month":"12","isi":1,"pmid":1,"day":"01","ddc":["570"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2022-05-16T10:42:22Z","article_number":"e72676","scopus_import":"1","keyword":["genetics and molecular biology"],"quality_controlled":"1","date_published":"2021-12-01T00:00:00Z","author":[{"last_name":"Choi","first_name":"Jaemyung","full_name":"Choi, Jaemyung"},{"first_name":"David B","last_name":"Lyons","full_name":"Lyons, David B"},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman"}],"doi":"10.7554/elife.72676","date_updated":"2023-08-17T06:21:08Z","article_processing_charge":"No","_id":"10533","year":"2021","has_accepted_license":"1","volume":10,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Choi J, Lyons DB, Zilberman D. 2021. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 10, e72676.","short":"J. Choi, D.B. Lyons, D. Zilberman, ELife 10 (2021).","mla":"Choi, Jaemyung, et al. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” <i>ELife</i>, vol. 10, e72676, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.72676\">10.7554/elife.72676</a>.","ama":"Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.72676\">10.7554/elife.72676</a>","apa":"Choi, J., Lyons, D. B., &#38; Zilberman, D. (2021). Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.72676\">https://doi.org/10.7554/elife.72676</a>","ieee":"J. Choi, D. B. Lyons, and D. Zilberman, “Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","chicago":"Choi, Jaemyung, David B Lyons, and Daniel Zilberman. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.72676\">https://doi.org/10.7554/elife.72676</a>."},"publication_identifier":{"issn":["2050-084X"]},"status":"public","oa":1,"acknowledgement":"We thank X Feng for helpful comments on the manuscript. This work was supported by a European Research Council grant MaintainMeth (725746) to DZ.","external_id":{"isi":["000754832000001"],"pmid":["34850679"]},"article_type":"original","oa_version":"Published Version","ec_funded":1,"date_created":"2021-12-10T13:12:08Z","department":[{"_id":"DaZi"}],"title":"Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin","publication":"eLife","publisher":"eLife Sciences Publications","abstract":[{"text":"Flowering plants utilize small RNA molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically associated with small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin.","lang":"eng"}]},{"language":[{"iso":"eng"}],"month":"05","day":"17","publication_status":"published","intvolume":"        12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-021-23073-4"}],"quality_controlled":"1","scopus_import":"1","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"doi":"10.1038/s41467-021-23073-4","date_updated":"2023-02-28T13:21:51Z","article_processing_charge":"No","author":[{"first_name":"Evan","last_name":"Miles","full_name":"Miles, Evan"},{"first_name":"Michael","last_name":"McCarthy","full_name":"McCarthy, Michael"},{"full_name":"Dehecq, Amaury","last_name":"Dehecq","first_name":"Amaury"},{"full_name":"Kneib, Marin","first_name":"Marin","last_name":"Kneib"},{"full_name":"Fugger, Stefan","last_name":"Fugger","first_name":"Stefan"},{"first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"}],"date_published":"2021-05-17T00:00:00Z","article_number":"2868","publication_identifier":{"issn":["2041-1723"]},"citation":{"apa":"Miles, E., McCarthy, M., Dehecq, A., Kneib, M., Fugger, S., &#38; Pellicciotti, F. (2021). Health and sustainability of glaciers in High Mountain Asia. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23073-4\">https://doi.org/10.1038/s41467-021-23073-4</a>","ieee":"E. Miles, M. McCarthy, A. Dehecq, M. Kneib, S. Fugger, and F. Pellicciotti, “Health and sustainability of glaciers in High Mountain Asia,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021.","chicago":"Miles, Evan, Michael McCarthy, Amaury Dehecq, Marin Kneib, Stefan Fugger, and Francesca Pellicciotti. “Health and Sustainability of Glaciers in High Mountain Asia.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23073-4\">https://doi.org/10.1038/s41467-021-23073-4</a>.","short":"E. Miles, M. McCarthy, A. Dehecq, M. Kneib, S. Fugger, F. Pellicciotti, Nature Communications 12 (2021).","ista":"Miles E, McCarthy M, Dehecq A, Kneib M, Fugger S, Pellicciotti F. 2021. Health and sustainability of glaciers in High Mountain Asia. Nature Communications. 12, 2868.","mla":"Miles, Evan, et al. “Health and Sustainability of Glaciers in High Mountain Asia.” <i>Nature Communications</i>, vol. 12, 2868, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23073-4\">10.1038/s41467-021-23073-4</a>.","ama":"Miles E, McCarthy M, Dehecq A, Kneib M, Fugger S, Pellicciotti F. Health and sustainability of glaciers in High Mountain Asia. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-23073-4\">10.1038/s41467-021-23073-4</a>"},"article_type":"original","oa":1,"status":"public","year":"2021","_id":"12585","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":12,"extern":"1","abstract":[{"text":"Glaciers in High Mountain Asia generate meltwater that supports the water needs of 250 million people, but current knowledge of annual accumulation and ablation is limited to sparse field measurements biased in location and glacier size. Here, we present altitudinally-resolved specific mass balances (surface, internal, and basal combined) for 5527 glaciers in High Mountain Asia for 2000–2016, derived by correcting observed glacier thinning patterns for mass redistribution due to ice flow. We find that 41% of glaciers accumulated mass over less than 20% of their area, and only 60% ± 10% of regional annual ablation was compensated by accumulation. Even without 21st century warming, 21% ± 1% of ice volume will be lost by 2100 due to current climatic-geometric imbalance, representing a reduction in glacier ablation into rivers of 28% ± 1%. The ablation of glaciers in the Himalayas and Tien Shan was mostly unsustainable and ice volume in these regions will reduce by at least 30% by 2100. The most important and vulnerable glacier-fed river basins (Amu Darya, Indus, Syr Darya, Tarim Interior) were supplied with >50% sustainable glacier ablation but will see long-term reductions in ice mass and glacier meltwater supply regardless of the Karakoram Anomaly.","lang":"eng"}],"oa_version":"Published Version","date_created":"2023-02-20T08:11:29Z","publisher":"Springer Nature","title":"Health and sustainability of glaciers in High Mountain Asia","publication":"Nature Communications"},{"file_date_updated":"2021-12-17T11:34:50Z","article_number":"2912","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"SSU"}],"date_published":"2021-05-18T00:00:00Z","author":[{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","last_name":"Vandael","first_name":"David H"},{"last_name":"Okamoto","orcid":"0000-0003-0408-6094","first_name":"Yuji","id":"3337E116-F248-11E8-B48F-1D18A9856A87","full_name":"Okamoto, Yuji"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"date_updated":"2023-08-10T14:16:16Z","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/synaptic-transmission-not-a-one-way-street/"}]},"doi":"10.1038/s41467-021-23153-5","article_processing_charge":"No","scopus_import":"1","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"quality_controlled":"1","intvolume":"        12","publication_status":"published","file":[{"date_updated":"2021-12-17T11:34:50Z","file_id":"10563","checksum":"6036a8cdae95e1707c2a04d54e325ff4","file_name":"2021_NatureCommunications_Vandael.pdf","file_size":3108845,"access_level":"open_access","creator":"kschuh","relation":"main_file","date_created":"2021-12-17T11:34:50Z","success":1,"content_type":"application/pdf"}],"day":"18","ddc":["570"],"project":[{"call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize"}],"language":[{"iso":"eng"}],"isi":1,"month":"05","department":[{"_id":"PeJo"}],"title":"Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses","publication":"Nature Communications","publisher":"Springer","oa_version":"Published Version","date_created":"2021-08-06T07:22:55Z","ec_funded":1,"abstract":[{"text":"The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit. Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this synaptic connection. It is widely believed that mossy fiber PTP is an entirely presynaptic phenomenon, implying that PTP induction is input-specific, and requires neither activity of multiple inputs nor stimulation of postsynaptic neurons. To directly test cooperativity and associativity, we made paired recordings between single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain slices. By stimulating non-overlapping mossy fiber inputs converging onto single CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly, mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only minimal PTP after combined pre- and postsynaptic high-frequency stimulation with intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels, group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire of synaptic computations, implementing a brake on mossy fiber detonation and a “smart teacher” function of hippocampal mossy fiber synapses.","lang":"eng"}],"volume":12,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9778","has_accepted_license":"1","year":"2021","oa":1,"status":"public","acknowledgement":"We thank Drs. Carolina Borges-Merjane and Jose Guzman for critically reading the manuscript, and Pablo Castillo for discussions. We are grateful to Alois Schlögl for help with analysis, Florian Marr for excellent technical assistance and cell reconstruction, Christina Altmutter for technical help, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for support. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J.","external_id":{"isi":["000655481800014"]},"article_type":"original","issue":"1","citation":{"ama":"Vandael DH, Okamoto Y, Jonas PM. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23153-5\">10.1038/s41467-021-23153-5</a>","short":"D.H. Vandael, Y. Okamoto, P.M. Jonas, Nature Communications 12 (2021).","ista":"Vandael DH, Okamoto Y, Jonas PM. 2021. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. 12(1), 2912.","mla":"Vandael, David H., et al. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” <i>Nature Communications</i>, vol. 12, no. 1, 2912, Springer, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23153-5\">10.1038/s41467-021-23153-5</a>.","chicago":"Vandael, David H, Yuji Okamoto, and Peter M Jonas. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” <i>Nature Communications</i>. Springer, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23153-5\">https://doi.org/10.1038/s41467-021-23153-5</a>.","ieee":"D. H. Vandael, Y. Okamoto, and P. M. Jonas, “Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses,” <i>Nature Communications</i>, vol. 12, no. 1. Springer, 2021.","apa":"Vandael, D. H., Okamoto, Y., &#38; Jonas, P. M. (2021). Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. <i>Nature Communications</i>. Springer. <a href=\"https://doi.org/10.1038/s41467-021-23153-5\">https://doi.org/10.1038/s41467-021-23153-5</a>"},"publication_identifier":{"issn":["2041-1723"]}},{"article_number":"e54383","file_date_updated":"2022-04-08T06:53:10Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","date_updated":"2022-07-18T08:30:37Z","doi":"10.7554/elife.54383","date_published":"2020-09-08T00:00:00Z","author":[{"full_name":"Bersini, Simone","first_name":"Simone","last_name":"Bersini"},{"full_name":"Schulte, Roberta","first_name":"Roberta","last_name":"Schulte"},{"first_name":"Ling","last_name":"Huang","full_name":"Huang, Ling"},{"full_name":"Tsai, Hannah","last_name":"Tsai","first_name":"Hannah"},{"full_name":"HETZER, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER","orcid":"0000-0002-2111-992X"}],"quality_controlled":"1","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"scopus_import":"1","file":[{"date_created":"2022-04-08T06:53:10Z","success":1,"content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","checksum":"f8b3821349a194050be02570d8fe7d4b","file_name":"2020_eLife_Bersini.pdf","file_size":4399825,"file_id":"11132","date_updated":"2022-04-08T06:53:10Z"}],"publication_status":"published","intvolume":"         9","ddc":["570"],"day":"08","pmid":1,"month":"09","language":[{"iso":"eng"}],"publisher":"eLife Sciences Publications","publication":"eLife","title":"Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome","date_created":"2022-04-07T07:43:48Z","oa_version":"Published Version","extern":"1","abstract":[{"lang":"eng","text":"Vascular dysfunctions are a common feature of multiple age-related diseases. However, modeling healthy and pathological aging of the human vasculature represents an unresolved experimental challenge. Here, we generated induced vascular endothelial cells (iVECs) and smooth muscle cells (iSMCs) by direct reprogramming of healthy human fibroblasts from donors of different ages and Hutchinson-Gilford Progeria Syndrome (HGPS) patients. iVECs induced from old donors revealed upregulation of GSTM1 and PALD1, genes linked to oxidative stress, inflammation and endothelial junction stability, as vascular aging markers. A functional assay performed on PALD1 KD VECs demonstrated a recovery in vascular permeability. We found that iSMCs from HGPS donors overexpressed bone morphogenetic protein (BMP)−4, which plays a key role in both vascular calcification and endothelial barrier damage observed in HGPS. Strikingly, BMP4 concentrations are higher in serum from HGPS vs. age-matched mice. Furthermore, targeting BMP4 with blocking antibody recovered the functionality of the vascular barrier in vitro, hence representing a potential future therapeutic strategy to limit cardiovascular dysfunction in HGPS. These results show that iVECs and iSMCs retain disease-related signatures, allowing modeling of vascular aging and HGPS in vitro."}],"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","type":"journal_article","volume":9,"has_accepted_license":"1","year":"2020","_id":"11055","external_id":{"pmid":["32896271"]},"article_type":"original","oa":1,"status":"public","publication_identifier":{"issn":["2050-084X"]},"citation":{"ama":"Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.54383\">10.7554/elife.54383</a>","ista":"Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. 2020. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. eLife. 9, e54383.","mla":"Bersini, Simone, et al. “Direct Reprogramming of Human Smooth Muscle and Vascular Endothelial Cells Reveals Defects Associated with Aging and Hutchinson-Gilford Progeria Syndrome.” <i>ELife</i>, vol. 9, e54383, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.54383\">10.7554/elife.54383</a>.","short":"S. Bersini, R. Schulte, L. Huang, H. Tsai, M. Hetzer, ELife 9 (2020).","chicago":"Bersini, Simone, Roberta Schulte, Ling Huang, Hannah Tsai, and Martin Hetzer. “Direct Reprogramming of Human Smooth Muscle and Vascular Endothelial Cells Reveals Defects Associated with Aging and Hutchinson-Gilford Progeria Syndrome.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.54383\">https://doi.org/10.7554/elife.54383</a>.","ieee":"S. Bersini, R. Schulte, L. Huang, H. Tsai, and M. Hetzer, “Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","apa":"Bersini, S., Schulte, R., Huang, L., Tsai, H., &#38; Hetzer, M. (2020). Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.54383\">https://doi.org/10.7554/elife.54383</a>"}},{"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication_status":"published","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2022-04-08T07:06:05Z","file_id":"11134","date_updated":"2022-04-08T07:06:05Z","file_size":2490829,"file_name":"2020_AdvancedBiosystems_Bersini.pdf","checksum":"5584d9a1609812dc75c02ce1e35d2ec0"}],"intvolume":"         4","day":"01","ddc":["570"],"pmid":1,"language":[{"iso":"eng"}],"month":"05","article_number":"2000044","file_date_updated":"2022-04-08T07:06:05Z","tmp":{"short":"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","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_updated":"2022-07-18T08:30:48Z","doi":"10.1002/adbi.202000044","article_processing_charge":"No","date_published":"2020-05-01T00:00:00Z","author":[{"first_name":"Simone","last_name":"Bersini","full_name":"Bersini, Simone"},{"full_name":"Arrojo e Drigo, Rafael","last_name":"Arrojo e Drigo","first_name":"Rafael"},{"full_name":"Huang, Ling","last_name":"Huang","first_name":"Ling"},{"first_name":"Maxim N.","last_name":"Shokhirev","full_name":"Shokhirev, Maxim N."},{"full_name":"HETZER, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER","orcid":"0000-0002-2111-992X"}],"quality_controlled":"1","scopus_import":"1","keyword":["General Biochemistry","Genetics and Molecular Biology","Biomedical Engineering","Biomaterials"],"type":"journal_article","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","volume":4,"has_accepted_license":"1","year":"2020","_id":"11056","external_id":{"pmid":["32402127"]},"article_type":"original","issue":"5","status":"public","oa":1,"publication_identifier":{"issn":["2366-7478","2366-7478"]},"citation":{"ama":"Bersini S, Arrojo e Drigo R, Huang L, Shokhirev MN, Hetzer M. Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. <i>Advanced Biosystems</i>. 2020;4(5). doi:<a href=\"https://doi.org/10.1002/adbi.202000044\">10.1002/adbi.202000044</a>","short":"S. Bersini, R. Arrojo e Drigo, L. Huang, M.N. Shokhirev, M. Hetzer, Advanced Biosystems 4 (2020).","ista":"Bersini S, Arrojo e Drigo R, Huang L, Shokhirev MN, Hetzer M. 2020. Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. Advanced Biosystems. 4(5), 2000044.","mla":"Bersini, Simone, et al. “Transcriptional and Functional Changes of the Human Microvasculature during Physiological Aging and Alzheimer Disease.” <i>Advanced Biosystems</i>, vol. 4, no. 5, 2000044, Wiley, 2020, doi:<a href=\"https://doi.org/10.1002/adbi.202000044\">10.1002/adbi.202000044</a>.","ieee":"S. Bersini, R. Arrojo e Drigo, L. Huang, M. N. Shokhirev, and M. Hetzer, “Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease,” <i>Advanced Biosystems</i>, vol. 4, no. 5. Wiley, 2020.","chicago":"Bersini, Simone, Rafael Arrojo e Drigo, Ling Huang, Maxim N. Shokhirev, and Martin Hetzer. “Transcriptional and Functional Changes of the Human Microvasculature during Physiological Aging and Alzheimer Disease.” <i>Advanced Biosystems</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/adbi.202000044\">https://doi.org/10.1002/adbi.202000044</a>.","apa":"Bersini, S., Arrojo e Drigo, R., Huang, L., Shokhirev, M. N., &#38; Hetzer, M. (2020). Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. <i>Advanced Biosystems</i>. Wiley. <a href=\"https://doi.org/10.1002/adbi.202000044\">https://doi.org/10.1002/adbi.202000044</a>"},"publisher":"Wiley","title":"Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease","publication":"Advanced Biosystems","oa_version":"Published Version","date_created":"2022-04-07T07:43:57Z","extern":"1","abstract":[{"lang":"eng","text":"Aging of the circulatory system correlates with the pathogenesis of a large spectrum of diseases. However, it is largely unknown which factors drive the age-dependent or pathological decline of the vasculature and how vascular defects relate to tissue aging. The goal of the study is to design a multianalytical approach to identify how the cellular microenvironment (i.e., fibroblasts) and serum from healthy donors of different ages or Alzheimer disease (AD) patients can modulate the functionality of organ-specific vascular endothelial cells (VECs). Long-living human microvascular networks embedding VECs and fibroblasts from skin biopsies are generated. RNA-seq, secretome analyses, and microfluidic assays demonstrate that fibroblasts from young donors restore the functionality of aged endothelial cells, an effect also achieved by serum from young donors. New biomarkers of vascular aging are validated in human biopsies and it is shown that young serum induces angiopoietin-like-4, which can restore compromised vascular barriers. This strategy is then employed to characterize transcriptional/functional changes induced on the blood–brain barrier by AD serum, demonstrating the importance of PTP4A3 in the regulation of permeability. Features of vascular degeneration during aging and AD are recapitulated, and a tool to identify novel biomarkers that can be exploited to develop future therapeutics modulating vascular function is established."}]},{"keyword":["Developmental Biology","Genetics"],"scopus_import":"1","quality_controlled":"1","date_published":"2020-04-28T00:00:00Z","author":[{"first_name":"Hyeseon","last_name":"Kang","full_name":"Kang, Hyeseon"},{"full_name":"Shokhirev, Maxim N.","first_name":"Maxim N.","last_name":"Shokhirev"},{"full_name":"Xu, Zhichao","first_name":"Zhichao","last_name":"Xu"},{"full_name":"Chandran, Sahaana","first_name":"Sahaana","last_name":"Chandran"},{"full_name":"Dixon, Jesse R.","last_name":"Dixon","first_name":"Jesse R."},{"last_name":"HETZER","orcid":"0000-0002-2111-992X","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W"}],"article_processing_charge":"No","date_updated":"2022-07-18T08:31:08Z","doi":"10.1101/gad.335794.119","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2022-04-08T07:12:33Z","month":"04","language":[{"iso":"eng"}],"pmid":1,"ddc":["570"],"day":"28","intvolume":"        34","file":[{"date_created":"2022-04-08T07:12:33Z","success":1,"content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","checksum":"84e92d40e67936c739628315c238daf9","file_name":"2020_GenesDevelopment_Kang.pdf","file_size":4406772,"file_id":"11136","date_updated":"2022-04-08T07:12:33Z"}],"publication_status":"published","abstract":[{"lang":"eng","text":"During mitosis, transcription of genomic DNA is dramatically reduced, before it is reactivated during nuclear reformation in anaphase/telophase. Many aspects of the underlying principles that mediate transcriptional memory and reactivation in the daughter cells remain unclear. Here, we used ChIP-seq on synchronized cells at different stages after mitosis to generate genome-wide maps of histone modifications. Combined with EU-RNA-seq and Hi-C analyses, we found that during prometaphase, promoters, enhancers, and insulators retain H3K4me3 and H3K4me1, while losing H3K27ac. Enhancers globally retaining mitotic H3K4me1 or locally retaining mitotic H3K27ac are associated with cell type-specific genes and their transcription factors for rapid transcriptional activation. As cells exit mitosis, promoters regain H3K27ac, which correlates with transcriptional reactivation. Insulators also gain H3K27ac and CCCTC-binding factor (CTCF) in anaphase/telophase. This increase of H3K27ac in anaphase/telophase is required for posttranscriptional activation and may play a role in the establishment of topologically associating domains (TADs). Together, our results suggest that the genome is reorganized in a sequential order, in which histone methylations occur first in prometaphase, histone acetylation, and CTCF in anaphase/telophase, transcription in cytokinesis, and long-range chromatin interactions in early G1. We thus provide insights into the histone modification landscape that allows faithful reestablishment of the transcriptional program and TADs during cell division."}],"extern":"1","date_created":"2022-04-07T07:44:09Z","oa_version":"Published Version","publication":"Genes & Development","title":"Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation","publisher":"Cold Spring Harbor Laboratory Press","citation":{"mla":"Kang, Hyeseon, et al. “Dynamic Regulation of Histone Modifications and Long-Range Chromosomal Interactions during Postmitotic Transcriptional Reactivation.” <i>Genes &#38; Development</i>, vol. 34, no. 13–14, Cold Spring Harbor Laboratory Press, 2020, pp. 913–30, doi:<a href=\"https://doi.org/10.1101/gad.335794.119\">10.1101/gad.335794.119</a>.","short":"H. Kang, M.N. Shokhirev, Z. Xu, S. Chandran, J.R. Dixon, M. Hetzer, Genes &#38; Development 34 (2020) 913–930.","ista":"Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer M. 2020. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. Genes &#38; Development. 34(13–14), 913–930.","ama":"Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer M. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. <i>Genes &#38; Development</i>. 2020;34(13-14):913-930. doi:<a href=\"https://doi.org/10.1101/gad.335794.119\">10.1101/gad.335794.119</a>","apa":"Kang, H., Shokhirev, M. N., Xu, Z., Chandran, S., Dixon, J. R., &#38; Hetzer, M. (2020). Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.335794.119\">https://doi.org/10.1101/gad.335794.119</a>","ieee":"H. Kang, M. N. Shokhirev, Z. Xu, S. Chandran, J. R. Dixon, and M. Hetzer, “Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation,” <i>Genes &#38; Development</i>, vol. 34, no. 13–14. Cold Spring Harbor Laboratory Press, pp. 913–930, 2020.","chicago":"Kang, Hyeseon, Maxim N. Shokhirev, Zhichao Xu, Sahaana Chandran, Jesse R. Dixon, and Martin Hetzer. “Dynamic Regulation of Histone Modifications and Long-Range Chromosomal Interactions during Postmitotic Transcriptional Reactivation.” <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory Press, 2020. <a href=\"https://doi.org/10.1101/gad.335794.119\">https://doi.org/10.1101/gad.335794.119</a>."},"publication_identifier":{"issn":["0890-9369","1549-5477"]},"oa":1,"status":"public","issue":"13-14","external_id":{"pmid":["32499403"]},"article_type":"original","_id":"11057","has_accepted_license":"1","year":"2020","volume":34,"page":"913-930","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","type":"journal_article"},{"author":[{"last_name":"Bersini","first_name":"Simone","full_name":"Bersini, Simone"},{"full_name":"Lytle, Nikki K","last_name":"Lytle","first_name":"Nikki K"},{"full_name":"Schulte, Roberta","last_name":"Schulte","first_name":"Roberta"},{"last_name":"Huang","first_name":"Ling","full_name":"Huang, Ling"},{"first_name":"Geoffrey M","last_name":"Wahl","full_name":"Wahl, Geoffrey M"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W"}],"date_published":"2020-01-01T00:00:00Z","article_processing_charge":"No","doi":"10.26508/lsa.201900623","date_updated":"2022-07-18T08:31:20Z","keyword":["Health","Toxicology and Mutagenesis","Plant Science","Biochemistry","Genetics and Molecular Biology (miscellaneous)","Ecology"],"scopus_import":"1","quality_controlled":"1","file_date_updated":"2022-04-08T07:33:01Z","article_number":"e201900623","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pmid":1,"ddc":["570"],"day":"01","month":"01","language":[{"iso":"eng"}],"intvolume":"         3","file":[{"file_size":2653960,"checksum":"3bf33e7e93bef7823287807206b69b38","file_name":"2020_LifeScienceAlliance_Bersini.pdf","file_id":"11137","date_updated":"2022-04-08T07:33:01Z","content_type":"application/pdf","date_created":"2022-04-08T07:33:01Z","success":1,"relation":"main_file","creator":"dernst","access_level":"open_access"}],"publication_status":"published","abstract":[{"text":"Nucleoporin 93 (Nup93) expression inversely correlates with the survival of triple-negative breast cancer patients. However, our knowledge of Nup93 function in breast cancer besides its role as structural component of the nuclear pore complex is not understood. Combination of functional assays and genetic analyses suggested that chromatin interaction of Nup93 partially modulates the expression of genes associated with actin cytoskeleton remodeling and epithelial to mesenchymal transition, resulting in impaired invasion of triple-negative, claudin-low breast cancer cells. Nup93 depletion induced stress fiber formation associated with reduced cell migration/proliferation and impaired expression of mesenchymal-like genes. Silencing LIMCH1, a gene responsible for actin cytoskeleton remodeling and up-regulated upon Nup93 depletion, partially restored the invasive phenotype of cancer cells. Loss of Nup93 led to significant defects in tumor establishment/propagation in vivo, whereas patient samples revealed that high Nup93 and low LIMCH1 expression correlate with late tumor stage. Our approach identified Nup93 as contributor of triple-negative, claudin-low breast cancer cell invasion and paves the way to study the role of nuclear envelope proteins during breast cancer tumorigenesis.","lang":"eng"}],"extern":"1","publication":"Life Science Alliance","title":"Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling","publisher":"Life Science Alliance","date_created":"2022-04-07T07:44:18Z","oa_version":"Published Version","status":"public","oa":1,"issue":"1","article_type":"original","external_id":{"pmid":["31959624"]},"citation":{"ista":"Bersini S, Lytle NK, Schulte R, Huang L, Wahl GM, Hetzer M. 2020. Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. Life Science Alliance. 3(1), e201900623.","mla":"Bersini, Simone, et al. “Nup93 Regulates Breast Tumor Growth by Modulating Cell Proliferation and Actin Cytoskeleton Remodeling.” <i>Life Science Alliance</i>, vol. 3, no. 1, e201900623, Life Science Alliance, 2020, doi:<a href=\"https://doi.org/10.26508/lsa.201900623\">10.26508/lsa.201900623</a>.","short":"S. Bersini, N.K. Lytle, R. Schulte, L. Huang, G.M. Wahl, M. Hetzer, Life Science Alliance 3 (2020).","ama":"Bersini S, Lytle NK, Schulte R, Huang L, Wahl GM, Hetzer M. Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. <i>Life Science Alliance</i>. 2020;3(1). doi:<a href=\"https://doi.org/10.26508/lsa.201900623\">10.26508/lsa.201900623</a>","apa":"Bersini, S., Lytle, N. K., Schulte, R., Huang, L., Wahl, G. M., &#38; Hetzer, M. (2020). Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. <i>Life Science Alliance</i>. Life Science Alliance. <a href=\"https://doi.org/10.26508/lsa.201900623\">https://doi.org/10.26508/lsa.201900623</a>","chicago":"Bersini, Simone, Nikki K Lytle, Roberta Schulte, Ling Huang, Geoffrey M Wahl, and Martin Hetzer. “Nup93 Regulates Breast Tumor Growth by Modulating Cell Proliferation and Actin Cytoskeleton Remodeling.” <i>Life Science Alliance</i>. Life Science Alliance, 2020. <a href=\"https://doi.org/10.26508/lsa.201900623\">https://doi.org/10.26508/lsa.201900623</a>.","ieee":"S. Bersini, N. K. Lytle, R. Schulte, L. Huang, G. M. Wahl, and M. Hetzer, “Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling,” <i>Life Science Alliance</i>, vol. 3, no. 1. Life Science Alliance, 2020."},"publication_identifier":{"issn":["2575-1077"]},"volume":3,"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","type":"journal_article","_id":"11058","year":"2020","has_accepted_license":"1"},{"_id":"8402","year":"2020","volume":18,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","citation":{"ieee":"H. Rampelt <i>et al.</i>, “The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments,” <i>BMC Biology</i>, vol. 18. Springer Nature, 2020.","chicago":"Rampelt, Heike, Iva Sucec, Beate Bersch, Patrick Horten, Inge Perschil, Jean-Claude Martinou, Martin van der Laan, Nils Wiedemann, Paul Schanda, and Nikolaus Pfanner. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates with an Odd Number of Transmembrane Segments.” <i>BMC Biology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1186/s12915-019-0733-6\">https://doi.org/10.1186/s12915-019-0733-6</a>.","apa":"Rampelt, H., Sucec, I., Bersch, B., Horten, P., Perschil, I., Martinou, J.-C., … Pfanner, N. (2020). The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. <i>BMC Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12915-019-0733-6\">https://doi.org/10.1186/s12915-019-0733-6</a>","ama":"Rampelt H, Sucec I, Bersch B, et al. The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. <i>BMC Biology</i>. 2020;18. doi:<a href=\"https://doi.org/10.1186/s12915-019-0733-6\">10.1186/s12915-019-0733-6</a>","short":"H. Rampelt, I. Sucec, B. Bersch, P. Horten, I. Perschil, J.-C. Martinou, M. van der Laan, N. Wiedemann, P. Schanda, N. Pfanner, BMC Biology 18 (2020).","mla":"Rampelt, Heike, et al. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates with an Odd Number of Transmembrane Segments.” <i>BMC Biology</i>, vol. 18, 2, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1186/s12915-019-0733-6\">10.1186/s12915-019-0733-6</a>.","ista":"Rampelt H, Sucec I, Bersch B, Horten P, Perschil I, Martinou J-C, van der Laan M, Wiedemann N, Schanda P, Pfanner N. 2020. The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. BMC Biology. 18, 2."},"publication_identifier":{"issn":["1741-7007"]},"status":"public","oa":1,"external_id":{"pmid":["31907035"]},"article_type":"original","date_created":"2020-09-17T10:26:53Z","oa_version":"Published Version","publication":"BMC Biology","title":"The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments","publisher":"Springer Nature","abstract":[{"lang":"eng","text":"Background: The mitochondrial pyruvate carrier (MPC) plays a central role in energy metabolism by transporting pyruvate across the inner mitochondrial membrane. Its heterodimeric composition and homology to SWEET and semiSWEET transporters set the MPC apart from the canonical mitochondrial carrier family (named MCF or SLC25). The import of the canonical carriers is mediated by the carrier translocase of the inner membrane (TIM22) pathway and is dependent on their structure, which features an even number of transmembrane segments and both termini in the intermembrane space. The import pathway of MPC proteins has not been elucidated. The odd number of transmembrane segments and positioning of the N-terminus in the matrix argues against an import via the TIM22 carrier pathway but favors an import via the flexible presequence pathway.\r\nResults: Here, we systematically analyzed the import pathways of Mpc2 and Mpc3 and report that, contrary to an expected import via the flexible presequence pathway, yeast MPC proteins with an odd number of transmembrane segments and matrix-exposed N-terminus are imported by the carrier pathway, using the receptor Tom70, small TIM chaperones, and the TIM22 complex. The TIM9·10 complex chaperones MPC proteins through the mitochondrial intermembrane space using conserved hydrophobic motifs that are also required for the interaction with canonical carrier proteins.\r\nConclusions: The carrier pathway can import paired and non-paired transmembrane helices and translocate N-termini to either side of the mitochondrial inner membrane, revealing an unexpected versatility of the mitochondrial import pathway for non-cleavable inner membrane proteins."}],"extern":"1","intvolume":"        18","main_file_link":[{"url":"https://doi.org/10.1186/s12915-019-0733-6","open_access":"1"}],"publication_status":"published","month":"01","language":[{"iso":"eng"}],"pmid":1,"day":"06","article_number":"2","keyword":["Biotechnology","Plant Science","General Biochemistry","Genetics and Molecular Biology","Developmental Biology","Cell Biology","Physiology","Ecology","Evolution","Behavior and Systematics","Structural Biology","General Agricultural and Biological Sciences"],"quality_controlled":"1","date_published":"2020-01-06T00:00:00Z","author":[{"first_name":"Heike","last_name":"Rampelt","full_name":"Rampelt, Heike"},{"full_name":"Sucec, Iva","last_name":"Sucec","first_name":"Iva"},{"first_name":"Beate","last_name":"Bersch","full_name":"Bersch, Beate"},{"last_name":"Horten","first_name":"Patrick","full_name":"Horten, Patrick"},{"full_name":"Perschil, Inge","last_name":"Perschil","first_name":"Inge"},{"first_name":"Jean-Claude","last_name":"Martinou","full_name":"Martinou, Jean-Claude"},{"last_name":"van der Laan","first_name":"Martin","full_name":"van der Laan, Martin"},{"first_name":"Nils","last_name":"Wiedemann","full_name":"Wiedemann, Nils"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul"},{"full_name":"Pfanner, Nikolaus","first_name":"Nikolaus","last_name":"Pfanner"}],"article_processing_charge":"No","date_updated":"2021-01-12T08:19:02Z","doi":"10.1186/s12915-019-0733-6"},{"language":[{"iso":"eng"}],"project":[{"_id":"2674F658-B435-11E9-9278-68D0E5697425","name":"Protein structure and function in filopodia across scales","grant_number":"M02495","call_identifier":"FWF"}],"month":"04","isi":1,"day":"09","ddc":["570"],"pmid":1,"publication_status":"published","file":[{"access_level":"open_access","creator":"dernst","relation":"main_file","date_created":"2020-09-17T14:07:51Z","content_type":"application/pdf","file_id":"8435","date_updated":"2020-10-11T22:30:02Z","embargo":"2020-10-10","file_name":"2020_JournalCellScience_Dimchev.pdf","checksum":"ba917e551acc4ece2884b751434df9ae","file_size":13493302}],"intvolume":"       133","quality_controlled":"1","keyword":["Cell Biology"],"date_updated":"2023-09-05T15:41:48Z","doi":"10.1242/jcs.239020","article_processing_charge":"No","author":[{"last_name":"Dimchev","orcid":"0000-0001-8370-6161","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Dimchev, Georgi A"},{"full_name":"Amiri, Behnam","last_name":"Amiri","first_name":"Behnam"},{"full_name":"Humphries, Ashley C.","first_name":"Ashley C.","last_name":"Humphries"},{"first_name":"Matthias","last_name":"Schaks","full_name":"Schaks, Matthias"},{"first_name":"Vanessa","last_name":"Dimchev","full_name":"Dimchev, Vanessa"},{"first_name":"Theresia E. B.","last_name":"Stradal","full_name":"Stradal, Theresia E. B."},{"full_name":"Faix, Jan","last_name":"Faix","first_name":"Jan"},{"first_name":"Matthias","last_name":"Krause","full_name":"Krause, Matthias"},{"full_name":"Way, Michael","first_name":"Michael","last_name":"Way"},{"last_name":"Falcke","first_name":"Martin","full_name":"Falcke, Martin"},{"last_name":"Rottner","first_name":"Klemens","full_name":"Rottner, Klemens"}],"date_published":"2020-04-09T00:00:00Z","article_number":"jcs239020","file_date_updated":"2020-10-11T22:30:02Z","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"citation":{"ista":"Dimchev GA, Amiri B, Humphries AC, Schaks M, Dimchev V, Stradal TEB, Faix J, Krause M, Way M, Falcke M, Rottner K. 2020. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 133(7), jcs239020.","short":"G.A. Dimchev, B. Amiri, A.C. Humphries, M. Schaks, V. Dimchev, T.E.B. Stradal, J. Faix, M. Krause, M. Way, M. Falcke, K. Rottner, Journal of Cell Science 133 (2020).","mla":"Dimchev, Georgi A., et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” <i>Journal of Cell Science</i>, vol. 133, no. 7, jcs239020, The Company of Biologists, 2020, doi:<a href=\"https://doi.org/10.1242/jcs.239020\">10.1242/jcs.239020</a>.","ama":"Dimchev GA, Amiri B, Humphries AC, et al. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. <i>Journal of Cell Science</i>. 2020;133(7). doi:<a href=\"https://doi.org/10.1242/jcs.239020\">10.1242/jcs.239020</a>","apa":"Dimchev, G. A., Amiri, B., Humphries, A. C., Schaks, M., Dimchev, V., Stradal, T. E. B., … Rottner, K. (2020). Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.239020\">https://doi.org/10.1242/jcs.239020</a>","chicago":"Dimchev, Georgi A, Behnam Amiri, Ashley C. Humphries, Matthias Schaks, Vanessa Dimchev, Theresia E. B. Stradal, Jan Faix, et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” <i>Journal of Cell Science</i>. The Company of Biologists, 2020. <a href=\"https://doi.org/10.1242/jcs.239020\">https://doi.org/10.1242/jcs.239020</a>.","ieee":"G. A. Dimchev <i>et al.</i>, “Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation,” <i>Journal of Cell Science</i>, vol. 133, no. 7. The Company of Biologists, 2020."},"external_id":{"isi":["000534387800005"],"pmid":[" 32094266"]},"article_type":"original","issue":"7","acknowledgement":"This work was supported in part by Deutsche Forschungsgemeinschaft (DFG)[GRK2223/1, RO2414/5-1 (to K.R.), FA350/11-1 (to M.F.) and FA330/11-1 (to J.F.)],as well as by intramural funding from the Helmholtz Association (to T.E.B.S. andK.R.). G.D. was additionally funded by the Austrian Science Fund (FWF) LiseMeitner Program [M-2495]. A.C.H. and M.W. are supported by the Francis CrickInstitute, which receives its core funding from Cancer Research UK [FC001209], theMedical Research Council [FC001209] and the Wellcome Trust [FC001209]. M.K. issupported by the Biotechnology and Biological Sciences Research Council [BB/F011431/1, BB/J000590/1, BB/N000226/1]. Deposited in PMC for release after 6months.","oa":1,"status":"public","has_accepted_license":"1","year":"2020","_id":"8434","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":133,"abstract":[{"text":"Efficient migration on adhesive surfaces involves the protrusion of lamellipodial actin networks and their subsequent stabilization by nascent adhesions. The actin-binding protein lamellipodin (Lpd) is thought to play a critical role in lamellipodium protrusion, by delivering Ena/VASP proteins onto the growing plus ends of actin filaments and by interacting with the WAVE regulatory complex, an activator of the Arp2/3 complex, at the leading edge. Using B16-F1 melanoma cell lines, we demonstrate that genetic ablation of Lpd compromises protrusion efficiency and coincident cell migration without altering essential parameters of lamellipodia, including their maximal rate of forward advancement and actin polymerization. We also confirmed lamellipodia and migration phenotypes with CRISPR/Cas9-mediated Lpd knockout Rat2 fibroblasts, excluding cell type-specific effects. Moreover, computer-aided analysis of cell-edge morphodynamics on B16-F1 cell lamellipodia revealed that loss of Lpd correlates with reduced temporal protrusion maintenance as a prerequisite of nascent adhesion formation. We conclude that Lpd optimizes protrusion and nascent adhesion formation by counteracting frequent, chaotic retraction and membrane ruffling.This article has an associated First Person interview with the first author of the paper. ","lang":"eng"}],"oa_version":"Published Version","date_created":"2020-09-17T14:00:33Z","publisher":"The Company of Biologists","title":"Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation","department":[{"_id":"FlSc"}],"publication":"Journal of Cell Science"},{"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"quality_controlled":"1","author":[{"last_name":"Arnold","orcid":"0000-0003-1397-7876","first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M"},{"orcid":"0000-0001-6613-1378","last_name":"Wulf","first_name":"Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","full_name":"Wulf, Matthias"},{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","first_name":"Shabir"},{"full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Redchenko"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez","first_name":"Alfredo R"},{"full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","first_name":"William J","orcid":"0000-0001-9868-2166","last_name":"Hease"},{"first_name":"Farid","last_name":"Hassani","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M"}],"date_published":"2020-09-08T00:00:00Z","article_processing_charge":"No","doi":"10.1038/s41467-020-18269-z","date_updated":"2024-08-07T07:11:51Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"13056"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-020-18912-9"},{"url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/","relation":"press_release","description":"News on IST Homepage"}]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"NanoFab"}],"file_date_updated":"2020-09-18T13:02:37Z","article_number":"4460","isi":1,"month":"09","project":[{"name":"Hybrid Optomechanical Technologies","grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","name":"Quantum readout techniques and technologies","grant_number":"862644"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"ddc":["530"],"day":"08","intvolume":"        11","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2020-09-18T13:02:37Z","success":1,"date_updated":"2020-09-18T13:02:37Z","file_id":"8530","file_size":1002818,"checksum":"88f92544889eb18bb38e25629a422a86","file_name":"2020_NatureComm_Arnold.pdf"}],"publication_status":"published","abstract":[{"text":"Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a <jats:italic>V</jats:italic><jats:sub><jats:italic>π</jats:italic></jats:sub> as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform.","lang":"eng"}],"date_created":"2020-09-18T10:56:20Z","ec_funded":1,"oa_version":"Published Version","publication":"Nature Communications","title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","department":[{"_id":"JoFi"}],"publisher":"Springer Nature","citation":{"ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-18269-z\">10.1038/s41467-020-18269-z</a>","mla":"Arnold, Georg M., et al. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” <i>Nature Communications</i>, vol. 11, 4460, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-18269-z\">10.1038/s41467-020-18269-z</a>.","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, Nature Communications 11 (2020).","ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 11, 4460.","ieee":"G. M. Arnold <i>et al.</i>, “Converting microwave and telecom photons with a silicon photonic nanomechanical interface,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-18269-z\">https://doi.org/10.1038/s41467-020-18269-z</a>.","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-18269-z\">https://doi.org/10.1038/s41467-020-18269-z</a>"},"publication_identifier":{"issn":["2041-1723"]},"oa":1,"status":"public","acknowledgement":"We thank Yuan Chen for performing supplementary FEM simulations and Andrew Higginbotham, Ralf Riedinger, Sungkun Hong, and Lorenzo Magrini for valuable discussions. This work was supported by IST Austria, the IST nanofabrication facility (NFF), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 732894 (FET Proactive HOT) and the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 754411. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and innovation program under grant agreement no. 862644 (FET Open QUARTET).","article_type":"original","external_id":{"isi":["000577280200001"]},"_id":"8529","has_accepted_license":"1","year":"2020","volume":11,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article"},{"publication_status":"published","file":[{"checksum":"eada7bc8dd16a49390137cff882ef328","file_name":"2020_NatureComm_Prehal.pdf","file_size":1822469,"date_updated":"2020-09-28T13:16:15Z","file_id":"8585","date_created":"2020-09-28T13:16:15Z","success":1,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file"}],"intvolume":"        11","day":"24","ddc":["530"],"language":[{"iso":"eng"}],"month":"09","isi":1,"article_number":"4838","file_date_updated":"2020-09-28T13:16:15Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-22T09:37:24Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-020-19720-x"}]},"doi":"10.1038/s41467-020-18610-6","article_processing_charge":"No","date_published":"2020-09-24T00:00:00Z","author":[{"first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"full_name":"Fitzek, Harald","last_name":"Fitzek","first_name":"Harald"},{"first_name":"Gerald","last_name":"Kothleitner","full_name":"Kothleitner, Gerald"},{"last_name":"Presser","first_name":"Volker","full_name":"Presser, Volker"},{"first_name":"Bernhard","last_name":"Gollas","full_name":"Gollas, Bernhard"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger","first_name":"Stefan Alexander"},{"full_name":"Abbas, Qamar","first_name":"Qamar","last_name":"Abbas"}],"quality_controlled":"1","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":11,"has_accepted_license":"1","year":"2020","_id":"8568","external_id":{"isi":["000573756600004"]},"article_type":"original","oa":1,"status":"public","publication_identifier":{"issn":["2041-1723"]},"citation":{"ieee":"C. Prehal <i>et al.</i>, “Persistent and reversible solid iodine electrodeposition in nanoporous carbons,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","chicago":"Prehal, Christian, Harald Fitzek, Gerald Kothleitner, Volker Presser, Bernhard Gollas, Stefan Alexander Freunberger, and Qamar Abbas. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-18610-6\">https://doi.org/10.1038/s41467-020-18610-6</a>.","apa":"Prehal, C., Fitzek, H., Kothleitner, G., Presser, V., Gollas, B., Freunberger, S. A., &#38; Abbas, Q. (2020). Persistent and reversible solid iodine electrodeposition in nanoporous carbons. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-18610-6\">https://doi.org/10.1038/s41467-020-18610-6</a>","ama":"Prehal C, Fitzek H, Kothleitner G, et al. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-18610-6\">10.1038/s41467-020-18610-6</a>","short":"C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger, Q. Abbas, Nature Communications 11 (2020).","mla":"Prehal, Christian, et al. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” <i>Nature Communications</i>, vol. 11, 4838, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-18610-6\">10.1038/s41467-020-18610-6</a>.","ista":"Prehal C, Fitzek H, Kothleitner G, Presser V, Gollas B, Freunberger SA, Abbas Q. 2020. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 11, 4838."},"publisher":"Springer Nature","department":[{"_id":"StFr"}],"title":"Persistent and reversible solid iodine electrodeposition in nanoporous carbons","publication":"Nature Communications","oa_version":"Published Version","date_created":"2020-09-25T07:23:13Z","abstract":[{"text":"Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries.","lang":"eng"}]},{"issue":"21","external_id":{"isi":["000573860700001"]},"article_type":"original","status":"public","acknowledgement":"The authors thank Drs. J. Eisen, QR. Lu, S. Duan, Z‐H. Li, W. Mo, and Q. Wu for their critical comments on the manuscript. They also thank Dr. H. Zong for providing the CKO_NG2‐CreER model. This work is supported by the National Key Research and Development Program of China, Stem Cell and Translational Research (2016YFA0101201 to C.L., 2016YFA0100303 to Y.J.W.), the National Natural Science Foundation of China (81673035 and 81972915 to C.L., 81472722 to Y.J.W.), the Science Foundation for Distinguished Young Scientists of Zhejiang Province (LR17H160001 to C.L.), Fundamental Research Funds for the Central Universities (2016QNA7023 and 2017QNA7028 to C.L.) and the Thousand Talent Program for Young Outstanding Scientists, China (to C.L.), IST Austria institutional funds (to S.H.), European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (725780 LinPro to S.H.). C.L. is a scholar of K. C. Wong Education Foundation.","oa":1,"publication_identifier":{"issn":["2198-3844"]},"citation":{"ama":"Tian A, Kang B, Li B, et al. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. <i>Advanced Science</i>. 2020;7(21). doi:<a href=\"https://doi.org/10.1002/advs.202001724\">10.1002/advs.202001724</a>","short":"A. Tian, B. Kang, B. Li, B. Qiu, W. Jiang, F. Shao, Q. Gao, R. Liu, C. Cai, R. Jing, W. Wang, P. Chen, Q. Liang, L. Bao, J. Man, Y. Wang, Y. Shi, J. Li, M. Yang, L. Wang, J. Zhang, S. Hippenmeyer, J. Zhu, X. Bian, Y. Wang, C. Liu, Advanced Science 7 (2020).","ista":"Tian A, Kang B, Li B, Qiu B, Jiang W, Shao F, Gao Q, Liu R, Cai C, Jing R, Wang W, Chen P, Liang Q, Bao L, Man J, Wang Y, Shi Y, Li J, Yang M, Wang L, Zhang J, Hippenmeyer S, Zhu J, Bian X, Wang Y, Liu C. 2020. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. 7(21), 2001724.","mla":"Tian, Anhao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” <i>Advanced Science</i>, vol. 7, no. 21, 2001724, Wiley, 2020, doi:<a href=\"https://doi.org/10.1002/advs.202001724\">10.1002/advs.202001724</a>.","chicago":"Tian, Anhao, Bo Kang, Baizhou Li, Biying Qiu, Wenhong Jiang, Fangjie Shao, Qingqing Gao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” <i>Advanced Science</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/advs.202001724\">https://doi.org/10.1002/advs.202001724</a>.","ieee":"A. Tian <i>et al.</i>, “Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting,” <i>Advanced Science</i>, vol. 7, no. 21. Wiley, 2020.","apa":"Tian, A., Kang, B., Li, B., Qiu, B., Jiang, W., Shao, F., … Liu, C. (2020). Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. <i>Advanced Science</i>. Wiley. <a href=\"https://doi.org/10.1002/advs.202001724\">https://doi.org/10.1002/advs.202001724</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":7,"year":"2020","has_accepted_license":"1","_id":"8592","abstract":[{"text":"Glioblastoma is the most malignant cancer in the brain and currently incurable. It is urgent to identify effective targets for this lethal disease. Inhibition of such targets should suppress the growth of cancer cells and, ideally also precancerous cells for early prevention, but minimally affect their normal counterparts. Using genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility of cells within the development hierarchy of glioma to the knockout of insulin‐like growth factor I receptor (IGF1R) is determined not only by their oncogenic states, but also by their cell identities/states. Knockout of IGF1R selectively disrupts the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable outcome of IGF1R knockout on cell growth requires the mutant cells to commit to the OPC identity regardless of its development hierarchical status. At the molecular level, oncogenic mutations reprogram the cellular network of OPCs and force them to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed. The findings reveal the cellular window of IGF1R targeting and establish IGF1R as an effective target for the prevention and treatment of glioblastoma.","lang":"eng"}],"publisher":"Wiley","publication":"Advanced Science","title":"Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting","department":[{"_id":"SiHi"}],"date_created":"2020-10-01T09:44:13Z","ec_funded":1,"oa_version":"Published Version","ddc":["570"],"day":"04","isi":1,"month":"11","language":[{"iso":"eng"}],"project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020"}],"file":[{"creator":"dernst","access_level":"open_access","relation":"main_file","success":1,"date_created":"2020-12-10T14:07:24Z","content_type":"application/pdf","file_id":"8938","date_updated":"2020-12-10T14:07:24Z","file_name":"2020_AdvScience_Tian.pdf","checksum":"92818c23ecc70e35acfa671f3cfb9909","file_size":7835833}],"publication_status":"published","intvolume":"         7","article_processing_charge":"No","date_updated":"2023-08-22T09:53:01Z","doi":"10.1002/advs.202001724","date_published":"2020-11-04T00:00:00Z","author":[{"last_name":"Tian","first_name":"Anhao","full_name":"Tian, Anhao"},{"full_name":"Kang, Bo","first_name":"Bo","last_name":"Kang"},{"full_name":"Li, Baizhou","last_name":"Li","first_name":"Baizhou"},{"first_name":"Biying","last_name":"Qiu","full_name":"Qiu, Biying"},{"last_name":"Jiang","first_name":"Wenhong","full_name":"Jiang, Wenhong"},{"full_name":"Shao, Fangjie","last_name":"Shao","first_name":"Fangjie"},{"full_name":"Gao, Qingqing","last_name":"Gao","first_name":"Qingqing"},{"full_name":"Liu, Rui","last_name":"Liu","first_name":"Rui"},{"full_name":"Cai, Chengwei","first_name":"Chengwei","last_name":"Cai"},{"full_name":"Jing, Rui","last_name":"Jing","first_name":"Rui"},{"last_name":"Wang","first_name":"Wei","full_name":"Wang, Wei"},{"last_name":"Chen","first_name":"Pengxiang","full_name":"Chen, Pengxiang"},{"full_name":"Liang, Qinghui","first_name":"Qinghui","last_name":"Liang"},{"last_name":"Bao","first_name":"Lili","full_name":"Bao, Lili"},{"full_name":"Man, Jianghong","last_name":"Man","first_name":"Jianghong"},{"full_name":"Wang, Yan","first_name":"Yan","last_name":"Wang"},{"first_name":"Yu","last_name":"Shi","full_name":"Shi, Yu"},{"first_name":"Jin","last_name":"Li","full_name":"Li, Jin"},{"full_name":"Yang, Minmin","last_name":"Yang","first_name":"Minmin"},{"last_name":"Wang","first_name":"Lisha","full_name":"Wang, Lisha"},{"first_name":"Jianmin","last_name":"Zhang","full_name":"Zhang, Jianmin"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"},{"last_name":"Zhu","first_name":"Junming","full_name":"Zhu, Junming"},{"full_name":"Bian, Xiuwu","last_name":"Bian","first_name":"Xiuwu"},{"first_name":"Ying‐Jie","last_name":"Wang","full_name":"Wang, Ying‐Jie"},{"last_name":"Liu","first_name":"Chong","full_name":"Liu, Chong"}],"quality_controlled":"1","keyword":["General Engineering","General Physics and Astronomy","General Materials Science","Medicine (miscellaneous)","General Chemical Engineering","Biochemistry","Genetics and Molecular Biology (miscellaneous)"],"article_number":"2001724","file_date_updated":"2020-12-10T14:07:24Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"abstract":[{"text":"Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.","lang":"eng"}],"title":"Cysteine oxidation and disulfide formation in the ribosomal exit tunnel","department":[{"_id":"EM-Fac"}],"publication":"Nature Communications","publisher":"Springer Nature","oa_version":"Published Version","date_created":"2020-11-09T07:49:36Z","acknowledgement":"We acknowledge help from Anja Seybert, Margot Frangakis, Diana Grewe, Mikhail Eltsov, Utz Ermel, and Shintaro Aibara. The work was supported by Deutsche Forschungsgemeinschaft in the CLiC graduate school. Work at the Center for Biomolecular Magnetic Resonance (BMRZ) is supported by the German state of Hesse. The work at BMRZ has been supported by the state of Hesse. L.S. has been supported by the DFG graduate college: CLiC.","status":"public","oa":1,"article_type":"original","external_id":{"isi":["000592028600001"]},"citation":{"apa":"Schulte, L., Mao, J., Reitz, J., Sreeramulu, S., Kudlinzki, D., Hodirnau, V.-V., … Schwalbe, H. (2020). Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-19372-x\">https://doi.org/10.1038/s41467-020-19372-x</a>","ieee":"L. Schulte <i>et al.</i>, “Cysteine oxidation and disulfide formation in the ribosomal exit tunnel,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","chicago":"Schulte, Linda, Jiafei Mao, Julian Reitz, Sridhar Sreeramulu, Denis Kudlinzki, Victor-Valentin Hodirnau, Jakob Meier-Credo, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-19372-x\">https://doi.org/10.1038/s41467-020-19372-x</a>.","short":"L. Schulte, J. Mao, J. Reitz, S. Sreeramulu, D. Kudlinzki, V.-V. Hodirnau, J. Meier-Credo, K. Saxena, F. Buhr, J.D. Langer, M. Blackledge, A.S. Frangakis, C. Glaubitz, H. Schwalbe, Nature Communications 11 (2020).","mla":"Schulte, Linda, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” <i>Nature Communications</i>, vol. 11, 5569, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-19372-x\">10.1038/s41467-020-19372-x</a>.","ista":"Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau V-V, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H. 2020. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 11, 5569.","ama":"Schulte L, Mao J, Reitz J, et al. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-19372-x\">10.1038/s41467-020-19372-x</a>"},"publication_identifier":{"issn":["2041-1723"]},"volume":11,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8744","year":"2020","has_accepted_license":"1","author":[{"last_name":"Schulte","first_name":"Linda","full_name":"Schulte, Linda"},{"last_name":"Mao","first_name":"Jiafei","full_name":"Mao, Jiafei"},{"full_name":"Reitz, Julian","first_name":"Julian","last_name":"Reitz"},{"last_name":"Sreeramulu","first_name":"Sridhar","full_name":"Sreeramulu, Sridhar"},{"full_name":"Kudlinzki, Denis","first_name":"Denis","last_name":"Kudlinzki"},{"first_name":"Victor-Valentin","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jakob","last_name":"Meier-Credo","full_name":"Meier-Credo, Jakob"},{"first_name":"Krishna","last_name":"Saxena","full_name":"Saxena, Krishna"},{"last_name":"Buhr","first_name":"Florian","full_name":"Buhr, Florian"},{"full_name":"Langer, Julian D.","last_name":"Langer","first_name":"Julian D."},{"full_name":"Blackledge, Martin","first_name":"Martin","last_name":"Blackledge"},{"full_name":"Frangakis, Achilleas S.","first_name":"Achilleas S.","last_name":"Frangakis"},{"first_name":"Clemens","last_name":"Glaubitz","full_name":"Glaubitz, Clemens"},{"full_name":"Schwalbe, Harald","last_name":"Schwalbe","first_name":"Harald"}],"date_published":"2020-11-04T00:00:00Z","date_updated":"2023-08-22T12:36:07Z","doi":"10.1038/s41467-020-19372-x","article_processing_charge":"No","scopus_import":"1","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"quality_controlled":"1","file_date_updated":"2020-11-09T07:56:24Z","article_number":"5569","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"04","ddc":["570"],"language":[{"iso":"eng"}],"isi":1,"month":"11","intvolume":"        11","publication_status":"published","file":[{"file_id":"8745","date_updated":"2020-11-09T07:56:24Z","file_size":1670898,"checksum":"b2688f0347e69e6629bba582077278c5","file_name":"2020_NatureComm_Schulte.pdf","relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2020-11-09T07:56:24Z","success":1}]},{"publisher":"Public Library of Science","publication":"PLOS Computational Biology","title":"The Moran process on 2-chromatic graphs","department":[{"_id":"KrCh"}],"date_created":"2020-11-18T07:20:23Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":16,"has_accepted_license":"1","year":"2020","_id":"8767","issue":"11","external_id":{"isi":["000591317200004"]},"article_type":"original","status":"public","oa":1,"acknowledgement":"We thank Igor Erovenko for many helpful comments on an earlier version of this paper. : Army Research Laboratory (grant W911NF-18-2-0265) (M.A.N.); the Bill & Melinda Gates Foundation (grant OPP1148627) (M.A.N.); the NVIDIA Corporation (A.M.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"citation":{"chicago":"Kaveh, Kamran, Alex McAvoy, Krishnendu Chatterjee, and Martin A. Nowak. “The Moran Process on 2-Chromatic Graphs.” <i>PLOS Computational Biology</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">https://doi.org/10.1371/journal.pcbi.1008402</a>.","ieee":"K. Kaveh, A. McAvoy, K. Chatterjee, and M. A. Nowak, “The Moran process on 2-chromatic graphs,” <i>PLOS Computational Biology</i>, vol. 16, no. 11. Public Library of Science, 2020.","apa":"Kaveh, K., McAvoy, A., Chatterjee, K., &#38; Nowak, M. A. (2020). The Moran process on 2-chromatic graphs. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">https://doi.org/10.1371/journal.pcbi.1008402</a>","ama":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. The Moran process on 2-chromatic graphs. <i>PLOS Computational Biology</i>. 2020;16(11). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">10.1371/journal.pcbi.1008402</a>","mla":"Kaveh, Kamran, et al. “The Moran Process on 2-Chromatic Graphs.” <i>PLOS Computational Biology</i>, vol. 16, no. 11, e1008402, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">10.1371/journal.pcbi.1008402</a>.","short":"K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology 16 (2020).","ista":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. 2020. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 16(11), e1008402."},"article_number":"e1008402","file_date_updated":"2020-11-18T07:26:10Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","date_updated":"2023-08-22T12:49:18Z","doi":"10.1371/journal.pcbi.1008402","author":[{"last_name":"Kaveh","first_name":"Kamran","full_name":"Kaveh, Kamran"},{"full_name":"McAvoy, Alex","first_name":"Alex","last_name":"McAvoy"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"last_name":"Nowak","first_name":"Martin A.","full_name":"Nowak, Martin A."}],"date_published":"2020-11-05T00:00:00Z","quality_controlled":"1","keyword":["Ecology","Modelling and Simulation","Computational Theory and Mathematics","Genetics","Ecology","Evolution","Behavior and Systematics","Molecular Biology","Cellular and Molecular Neuroscience"],"scopus_import":"1","file":[{"file_size":2498594,"file_name":"2020_PlosCompBio_Kaveh.pdf","checksum":"555456dd0e47bcf9e0994bcb95577e88","file_id":"8768","date_updated":"2020-11-18T07:26:10Z","content_type":"application/pdf","success":1,"date_created":"2020-11-18T07:26:10Z","relation":"main_file","access_level":"open_access","creator":"dernst"}],"publication_status":"published","intvolume":"        16","ddc":["000"],"day":"05","isi":1,"month":"11","language":[{"iso":"eng"}]},{"_id":"8951","has_accepted_license":"1","file":[{"relation":"main_file","creator":"bkavcic","access_level":"open_access","content_type":"text/plain","date_created":"2020-12-20T09:52:52Z","success":1,"file_id":"8952","date_updated":"2020-12-20T09:52:52Z","file_size":523,"checksum":"f57862aeee1690c7effd2b1117d40ed1","file_name":"readme.txt"},{"success":1,"date_created":"2020-12-20T22:01:44Z","content_type":"application/octet-stream","access_level":"open_access","creator":"bkavcic","relation":"main_file","file_name":"GRNs Research depository.gb","checksum":"f2c6d5232ec6d551b6993991e8689e9f","file_size":379228,"file_id":"8954","date_updated":"2020-12-20T22:01:44Z"}],"year":"2020","contributor":[{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Anna A","last_name":"Nagy-Staron"},{"contributor_type":"project_member","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","first_name":"Kathrin"},{"last_name":"Caruso Carter","first_name":"Caroline","contributor_type":"project_member"},{"last_name":"Sonnleitner","first_name":"Elisabeth","contributor_type":"project_member"},{"contributor_type":"project_member","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","last_name":"Kavcic","first_name":"Bor"},{"contributor_type":"project_member","first_name":"Tiago","last_name":"Paixão"},{"orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C","contributor_type":"project_manager","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"A.A. Nagy-Staron, (2020).","ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>.","mla":"Nagy-Staron, Anna A. <i>Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>.","ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>","apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">https://doi.org/10.15479/AT:ISTA:8951</a>","chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">https://doi.org/10.15479/AT:ISTA:8951</a>.","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020."},"month":"12","status":"public","oa":1,"day":"21","ddc":["570"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","date_created":"2020-12-20T10:00:26Z","title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","file_date_updated":"2020-12-20T22:01:44Z","department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks."}],"keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"date_published":"2020-12-21T00:00:00Z","author":[{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","full_name":"Nagy-Staron, Anna A","orcid":"0000-0002-1391-8377","last_name":"Nagy-Staron","first_name":"Anna A"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"9283"}]},"date_updated":"2024-02-21T12:41:57Z","doi":"10.15479/AT:ISTA:8951","article_processing_charge":"No"},{"status":"public","acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical reading of the manuscript. We also thank Gregory Voth (University of Chicago) for providing us the MD-derived branch junction model for comparison. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S. ","oa":1,"external_id":{"isi":["000603078000003"]},"article_type":"original","citation":{"apa":"Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., &#38; Schur, F. K. (2020). Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>","ieee":"F. Fäßler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","chicago":"Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan, and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>.","short":"F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (2020).","ista":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 11, 6437.","mla":"Fäßler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>, vol. 11, 6437, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>.","ama":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>"},"publication_identifier":{"issn":["2041-1723"]},"volume":11,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","_id":"8971","year":"2020","has_accepted_license":"1","abstract":[{"text":"The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation.","lang":"eng"}],"publication":"Nature Communications","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction","publisher":"Springer Nature","date_created":"2020-12-23T08:25:45Z","oa_version":"Published Version","ddc":["570"],"day":"22","isi":1,"month":"12","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"},{"call_identifier":"FWF","_id":"2674F658-B435-11E9-9278-68D0E5697425","grant_number":"M02495","name":"Protein structure and function in filopodia across scales"}],"language":[{"iso":"eng"}],"intvolume":"        11","file":[{"content_type":"application/pdf","date_created":"2020-12-28T08:16:10Z","success":1,"relation":"main_file","creator":"dernst","access_level":"open_access","file_size":3958727,"checksum":"55d43ea0061cc4027ba45e966e1db8cc","file_name":"2020_NatureComm_Faessler.pdf","file_id":"8975","date_updated":"2020-12-28T08:16:10Z"}],"publication_status":"published","date_published":"2020-12-22T00:00:00Z","author":[{"first_name":"Florian","last_name":"Fäßler","orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Georgi A","last_name":"Dimchev","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","first_name":"Victor-Valentin"},{"first_name":"William","last_name":"Wan","full_name":"Wan, William"},{"first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","date_updated":"2023-08-24T11:01:50Z","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/"}]},"doi":"10.1038/s41467-020-20286-x","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"scopus_import":"1","quality_controlled":"1","file_date_updated":"2020-12-28T08:16:10Z","article_number":"6437","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}]},{"article_processing_charge":"No","date_updated":"2024-02-28T12:37:54Z","doi":"10.1016/j.jmb.2020.09.001","date_published":"2020-10-02T00:00:00Z","author":[{"last_name":"Rosa","first_name":"Higor Vinícius Dias","full_name":"Rosa, Higor Vinícius Dias"},{"full_name":"Leonardo, Diego Antonio","first_name":"Diego Antonio","last_name":"Leonardo"},{"full_name":"Brognara, Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425","first_name":"Gabriel","last_name":"Brognara"},{"full_name":"Brandão-Neto, José","first_name":"José","last_name":"Brandão-Neto"},{"last_name":"D'Muniz Pereira","first_name":"Humberto","full_name":"D'Muniz Pereira, Humberto"},{"last_name":"Araújo","first_name":"Ana Paula Ulian","full_name":"Araújo, Ana Paula Ulian"},{"first_name":"Richard Charles","last_name":"Garratt","full_name":"Garratt, Richard Charles"}],"quality_controlled":"1","keyword":["Molecular Biology","Structural Biology"],"publication_status":"published","intvolume":"       432","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jmb.2020.09.001"}],"day":"02","pmid":1,"month":"10","language":[{"iso":"eng"}],"publisher":"Elsevier","publication":"Journal of Molecular Biology","department":[{"_id":"MaLo"}],"title":"Molecular recognition at septin interfaces: The switches hold the key","date_created":"2024-02-28T08:50:34Z","oa_version":"Published Version","abstract":[{"text":"The assembly of a septin filament requires that homologous monomers must distinguish between one another in establishing appropriate interfaces with their neighbors. To understand this phenomenon at the molecular level, we present the first four crystal structures of heterodimeric septin complexes. We describe in detail the two distinct types of G-interface present within the octameric particles, which must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and between SEPT7 and SEPT3, and their description permits an understanding of the structural basis for the selectivity necessary for correct filament assembly. By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita's postulate, which predicts the exchangeability of septins from within a subgroup. Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent conformational change, have been repurposed in septins to play a fundamental role in molecular recognition. Specifically, it is switch I which holds the key to discriminating between the two different G-interfaces. Moreover, residues which are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing that the correct interfaces are formed.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":432,"page":"5784-5801","year":"2020","_id":"15036","issue":"21","external_id":{"pmid":["32910969"]},"article_type":"original","status":"public","oa":1,"publication_identifier":{"issn":["0022-2836"]},"citation":{"chicago":"Rosa, Higor Vinícius Dias, Diego Antonio Leonardo, Gabriel Brognara, José Brandão-Neto, Humberto D’Muniz Pereira, Ana Paula Ulian Araújo, and Richard Charles Garratt. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” <i>Journal of Molecular Biology</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">https://doi.org/10.1016/j.jmb.2020.09.001</a>.","ieee":"H. V. D. Rosa <i>et al.</i>, “Molecular recognition at septin interfaces: The switches hold the key,” <i>Journal of Molecular Biology</i>, vol. 432, no. 21. Elsevier, pp. 5784–5801, 2020.","apa":"Rosa, H. V. D., Leonardo, D. A., Brognara, G., Brandão-Neto, J., D’Muniz Pereira, H., Araújo, A. P. U., &#38; Garratt, R. C. (2020). Molecular recognition at septin interfaces: The switches hold the key. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">https://doi.org/10.1016/j.jmb.2020.09.001</a>","ama":"Rosa HVD, Leonardo DA, Brognara G, et al. Molecular recognition at septin interfaces: The switches hold the key. <i>Journal of Molecular Biology</i>. 2020;432(21):5784-5801. doi:<a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">10.1016/j.jmb.2020.09.001</a>","mla":"Rosa, Higor Vinícius Dias, et al. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” <i>Journal of Molecular Biology</i>, vol. 432, no. 21, Elsevier, 2020, pp. 5784–801, doi:<a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">10.1016/j.jmb.2020.09.001</a>.","short":"H.V.D. Rosa, D.A. Leonardo, G. Brognara, J. Brandão-Neto, H. D’Muniz Pereira, A.P.U. Araújo, R.C. Garratt, Journal of Molecular Biology 432 (2020) 5784–5801.","ista":"Rosa HVD, Leonardo DA, Brognara G, Brandão-Neto J, D’Muniz Pereira H, Araújo APU, Garratt RC. 2020. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 432(21), 5784–5801."}},{"quality_controlled":"1","keyword":["Plant Science","Molecular Biology"],"article_processing_charge":"No","date_updated":"2024-02-28T12:41:52Z","doi":"10.1016/j.molp.2020.02.012","date_published":"2020-05-04T00:00:00Z","author":[{"last_name":"Moulinier-Anzola","first_name":"Jeanette","full_name":"Moulinier-Anzola, Jeanette"},{"last_name":"Schwihla","first_name":"Maximilian","full_name":"Schwihla, Maximilian"},{"full_name":"De-Araújo, Lucinda","first_name":"Lucinda","last_name":"De-Araújo"},{"full_name":"Artner, Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","first_name":"Christina","last_name":"Artner"},{"full_name":"Jörg, Lisa","first_name":"Lisa","last_name":"Jörg"},{"full_name":"Konstantinova, Nataliia","last_name":"Konstantinova","first_name":"Nataliia"},{"first_name":"Christian","last_name":"Luschnig","full_name":"Luschnig, Christian"},{"last_name":"Korbei","first_name":"Barbara","full_name":"Korbei, Barbara"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2024-02-28T12:39:56Z","month":"05","language":[{"iso":"eng"}],"ddc":["580"],"day":"04","pmid":1,"file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2024-02-28T12:39:56Z","success":1,"file_id":"15038","date_updated":"2024-02-28T12:39:56Z","file_size":3089212,"checksum":"c538a5008f7827f62d17d40a3bfabe65","file_name":"2020_MolecularPlant_MoulinierAnzola.pdf"}],"publication_status":"published","intvolume":"        13","abstract":[{"text":"Protein abundance and localization at the plasma membrane (PM) shapes plant development and mediates adaptation to changing environmental conditions. It is regulated by ubiquitination, a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation. To understand the significance and the variety of roles played by this reversible modification, the function of ubiquitin receptors, which translate the ubiquitin signature into a cellular response, needs to be elucidated. In this study, we show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6 interact with components of the ESCRT machinery and bind to K63-linked ubiquitin via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these domains results not only in a loss of ubiquitin binding but also altered localization, abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6 is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially modulates degradation of PM-localized cargoes, assisting in the fine-tuning of the delicate interplay between protein recycling and downregulation. Taken together, our findings demonstrate the function and regulation of a ubiquitin receptor that mediates vacuolar degradation of PM proteins in higher plants.","lang":"eng"}],"date_created":"2024-02-28T08:55:56Z","oa_version":"Published Version","publisher":"Elsevier","publication":"Molecular Plant","title":"TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants","department":[{"_id":"EvBe"}],"publication_identifier":{"issn":["1674-2052"]},"citation":{"mla":"Moulinier-Anzola, Jeanette, et al. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” <i>Molecular Plant</i>, vol. 13, no. 5, Elsevier, 2020, pp. 717–31, doi:<a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">10.1016/j.molp.2020.02.012</a>.","ista":"Moulinier-Anzola J, Schwihla M, De-Araújo L, Artner C, Jörg L, Konstantinova N, Luschnig C, Korbei B. 2020. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 13(5), 717–731.","short":"J. Moulinier-Anzola, M. Schwihla, L. De-Araújo, C. Artner, L. Jörg, N. Konstantinova, C. Luschnig, B. Korbei, Molecular Plant 13 (2020) 717–731.","ama":"Moulinier-Anzola J, Schwihla M, De-Araújo L, et al. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. <i>Molecular Plant</i>. 2020;13(5):717-731. doi:<a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">10.1016/j.molp.2020.02.012</a>","apa":"Moulinier-Anzola, J., Schwihla, M., De-Araújo, L., Artner, C., Jörg, L., Konstantinova, N., … Korbei, B. (2020). TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">https://doi.org/10.1016/j.molp.2020.02.012</a>","ieee":"J. Moulinier-Anzola <i>et al.</i>, “TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants,” <i>Molecular Plant</i>, vol. 13, no. 5. Elsevier, pp. 717–731, 2020.","chicago":"Moulinier-Anzola, Jeanette, Maximilian Schwihla, Lucinda De-Araújo, Christina Artner, Lisa Jörg, Nataliia Konstantinova, Christian Luschnig, and Barbara Korbei. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” <i>Molecular Plant</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">https://doi.org/10.1016/j.molp.2020.02.012</a>."},"issue":"5","article_type":"original","external_id":{"pmid":["32087370"]},"status":"public","oa":1,"year":"2020","has_accepted_license":"1","_id":"15037","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":13,"page":"717-731"},{"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/bioinformatics/btaa843"}],"intvolume":"        36","day":"01","pmid":1,"language":[{"iso":"eng"}],"month":"12","related_material":{"link":[{"relation":"software","url":"https://github.com/ratschlab/scim"}]},"doi":"10.1093/bioinformatics/btaa843","date_updated":"2023-09-11T10:21:00Z","article_processing_charge":"No","author":[{"last_name":"Stark","first_name":"Stefan G","full_name":"Stark, Stefan G"},{"last_name":"Ficek","first_name":"Joanna","full_name":"Ficek, Joanna"},{"full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello"},{"full_name":"Bonilla, Ximena","first_name":"Ximena","last_name":"Bonilla"},{"last_name":"Chevrier","first_name":"Stéphane","full_name":"Chevrier, Stéphane"},{"full_name":"Singer, Franziska","last_name":"Singer","first_name":"Franziska"},{"first_name":"Rudolf","last_name":"Aebersold","full_name":"Aebersold, Rudolf"},{"full_name":"Al-Quaddoomi, Faisal S","first_name":"Faisal S","last_name":"Al-Quaddoomi"},{"first_name":"Jonas","last_name":"Albinus","full_name":"Albinus, Jonas"},{"last_name":"Alborelli","first_name":"Ilaria","full_name":"Alborelli, Ilaria"},{"last_name":"Andani","first_name":"Sonali","full_name":"Andani, Sonali"},{"full_name":"Attinger, Per-Olof","first_name":"Per-Olof","last_name":"Attinger"},{"full_name":"Bacac, Marina","first_name":"Marina","last_name":"Bacac"},{"full_name":"Baumhoer, Daniel","last_name":"Baumhoer","first_name":"Daniel"},{"full_name":"Beck-Schimmer, Beatrice","first_name":"Beatrice","last_name":"Beck-Schimmer"},{"first_name":"Niko","last_name":"Beerenwinkel","full_name":"Beerenwinkel, Niko"},{"first_name":"Christian","last_name":"Beisel","full_name":"Beisel, Christian"},{"full_name":"Bernasconi, Lara","first_name":"Lara","last_name":"Bernasconi"},{"last_name":"Bertolini","first_name":"Anne","full_name":"Bertolini, Anne"},{"full_name":"Bodenmiller, Bernd","first_name":"Bernd","last_name":"Bodenmiller"},{"full_name":"Bonilla, Ximena","last_name":"Bonilla","first_name":"Ximena"},{"full_name":"Casanova, Ruben","first_name":"Ruben","last_name":"Casanova"},{"full_name":"Chevrier, Stéphane","last_name":"Chevrier","first_name":"Stéphane"},{"full_name":"Chicherova, Natalia","last_name":"Chicherova","first_name":"Natalia"},{"full_name":"D'Costa, Maya","first_name":"Maya","last_name":"D'Costa"},{"full_name":"Danenberg, Esther","first_name":"Esther","last_name":"Danenberg"},{"full_name":"Davidson, Natalie","last_name":"Davidson","first_name":"Natalie"},{"full_name":"gan, Monica-Andreea Dră","last_name":"gan","first_name":"Monica-Andreea Dră"},{"first_name":"Reinhard","last_name":"Dummer","full_name":"Dummer, Reinhard"},{"last_name":"Engler","first_name":"Stefanie","full_name":"Engler, Stefanie"},{"first_name":"Martin","last_name":"Erkens","full_name":"Erkens, Martin"},{"full_name":"Eschbach, Katja","first_name":"Katja","last_name":"Eschbach"},{"last_name":"Esposito","first_name":"Cinzia","full_name":"Esposito, Cinzia"},{"first_name":"André","last_name":"Fedier","full_name":"Fedier, André"},{"last_name":"Ferreira","first_name":"Pedro","full_name":"Ferreira, Pedro"},{"full_name":"Ficek, Joanna","first_name":"Joanna","last_name":"Ficek"},{"full_name":"Frei, Anja L","last_name":"Frei","first_name":"Anja L"},{"full_name":"Frey, Bruno","first_name":"Bruno","last_name":"Frey"},{"full_name":"Goetze, Sandra","first_name":"Sandra","last_name":"Goetze"},{"first_name":"Linda","last_name":"Grob","full_name":"Grob, Linda"},{"full_name":"Gut, Gabriele","last_name":"Gut","first_name":"Gabriele"},{"full_name":"Günther, Detlef","first_name":"Detlef","last_name":"Günther"},{"full_name":"Haberecker, Martina","first_name":"Martina","last_name":"Haberecker"},{"last_name":"Haeuptle","first_name":"Pirmin","full_name":"Haeuptle, Pirmin"},{"first_name":"Viola","last_name":"Heinzelmann-Schwarz","full_name":"Heinzelmann-Schwarz, Viola"},{"first_name":"Sylvia","last_name":"Herter","full_name":"Herter, Sylvia"},{"full_name":"Holtackers, Rene","first_name":"Rene","last_name":"Holtackers"},{"full_name":"Huesser, Tamara","first_name":"Tamara","last_name":"Huesser"},{"last_name":"Irmisch","first_name":"Anja","full_name":"Irmisch, Anja"},{"full_name":"Jacob, Francis","first_name":"Francis","last_name":"Jacob"},{"first_name":"Andrea","last_name":"Jacobs","full_name":"Jacobs, Andrea"},{"first_name":"Tim M","last_name":"Jaeger","full_name":"Jaeger, Tim M"},{"last_name":"Jahn","first_name":"Katharina","full_name":"Jahn, Katharina"},{"full_name":"James, Alva R","first_name":"Alva R","last_name":"James"},{"last_name":"Jermann","first_name":"Philip M","full_name":"Jermann, Philip M"},{"full_name":"Kahles, André","last_name":"Kahles","first_name":"André"},{"first_name":"Abdullah","last_name":"Kahraman","full_name":"Kahraman, Abdullah"},{"full_name":"Koelzer, Viktor H","last_name":"Koelzer","first_name":"Viktor H"},{"full_name":"Kuebler, Werner","first_name":"Werner","last_name":"Kuebler"},{"first_name":"Jack","last_name":"Kuipers","full_name":"Kuipers, Jack"},{"first_name":"Christian P","last_name":"Kunze","full_name":"Kunze, Christian P"},{"full_name":"Kurzeder, Christian","first_name":"Christian","last_name":"Kurzeder"},{"full_name":"Lehmann, Kjong-Van","last_name":"Lehmann","first_name":"Kjong-Van"},{"full_name":"Levesque, Mitchell","last_name":"Levesque","first_name":"Mitchell"},{"last_name":"Lugert","first_name":"Sebastian","full_name":"Lugert, Sebastian"},{"last_name":"Maass","first_name":"Gerd","full_name":"Maass, Gerd"},{"last_name":"Manz","first_name":"Markus","full_name":"Manz, Markus"},{"full_name":"Markolin, Philipp","last_name":"Markolin","first_name":"Philipp"},{"full_name":"Mena, Julien","last_name":"Mena","first_name":"Julien"},{"full_name":"Menzel, Ulrike","first_name":"Ulrike","last_name":"Menzel"},{"last_name":"Metzler","first_name":"Julian M","full_name":"Metzler, Julian M"},{"full_name":"Miglino, Nicola","first_name":"Nicola","last_name":"Miglino"},{"last_name":"Milani","first_name":"Emanuela S","full_name":"Milani, Emanuela S"},{"full_name":"Moch, Holger","first_name":"Holger","last_name":"Moch"},{"first_name":"Simone","last_name":"Muenst","full_name":"Muenst, Simone"},{"full_name":"Murri, Riccardo","first_name":"Riccardo","last_name":"Murri"},{"last_name":"Ng","first_name":"Charlotte 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Rebekka","last_name":"Wegmann","first_name":"Rebekka"},{"full_name":"Weller, Michael","first_name":"Michael","last_name":"Weller"},{"full_name":"Wendt, Fabian","last_name":"Wendt","first_name":"Fabian"},{"full_name":"Wey, Norbert","last_name":"Wey","first_name":"Norbert"},{"full_name":"Wicki, Andreas","last_name":"Wicki","first_name":"Andreas"},{"last_name":"Wollscheid","first_name":"Bernd","full_name":"Wollscheid, Bernd"},{"full_name":"Yu, Shuqing","last_name":"Yu","first_name":"Shuqing"},{"last_name":"Ziegler","first_name":"Johanna","full_name":"Ziegler, Johanna"},{"first_name":"Marc","last_name":"Zimmermann","full_name":"Zimmermann, Marc"},{"first_name":"Martin","last_name":"Zoche","full_name":"Zoche, Martin"},{"full_name":"Zuend, Gregor","first_name":"Gregor","last_name":"Zuend"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"},{"last_name":"Lehmann","first_name":"Kjong-Van","full_name":"Lehmann, Kjong-Van"}],"date_published":"2020-12-01T00:00:00Z","quality_controlled":"1","scopus_import":"1","keyword":["Computational Mathematics","Computational Theory and Mathematics","Computer Science Applications","Molecular Biology","Biochemistry","Statistics and Probability"],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"i919-i927","volume":36,"year":"2020","_id":"14125","external_id":{"pmid":["33381818"]},"article_type":"original","issue":"Supplement_2","status":"public","oa":1,"publication_identifier":{"eissn":["1367-4811"]},"citation":{"apa":"Stark, S. G., Ficek, J., Locatello, F., Bonilla, X., Chevrier, S., Singer, F., … Lehmann, K.-V. (2020). SCIM: Universal single-cell matching with unpaired feature sets. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">https://doi.org/10.1093/bioinformatics/btaa843</a>","ieee":"S. G. Stark <i>et al.</i>, “SCIM: Universal single-cell matching with unpaired feature sets,” <i>Bioinformatics</i>, vol. 36, no. Supplement_2. Oxford University Press, pp. i919–i927, 2020.","chicago":"Stark, Stefan G, Joanna Ficek, Francesco Locatello, Ximena Bonilla, Stéphane Chevrier, Franziska Singer, Rudolf Aebersold, et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” <i>Bioinformatics</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">https://doi.org/10.1093/bioinformatics/btaa843</a>.","short":"S.G. Stark, J. Ficek, F. Locatello, X. Bonilla, S. Chevrier, F. Singer, R. Aebersold, F.S. Al-Quaddoomi, J. Albinus, I. Alborelli, S. Andani, P.-O. Attinger, M. Bacac, D. Baumhoer, B. Beck-Schimmer, N. Beerenwinkel, C. Beisel, L. Bernasconi, A. Bertolini, B. Bodenmiller, X. Bonilla, R. Casanova, S. Chevrier, N. Chicherova, M. D’Costa, E. Danenberg, N. Davidson, M.-A.D. gan, R. Dummer, S. Engler, M. Erkens, K. Eschbach, C. Esposito, A. Fedier, P. Ferreira, J. Ficek, A.L. Frei, B. Frey, S. Goetze, L. Grob, G. Gut, D. Günther, M. Haberecker, P. Haeuptle, V. Heinzelmann-Schwarz, S. Herter, R. Holtackers, T. Huesser, A. Irmisch, F. Jacob, A. Jacobs, T.M. Jaeger, K. Jahn, A.R. James, P.M. Jermann, A. Kahles, A. Kahraman, V.H. Koelzer, W. Kuebler, J. Kuipers, C.P. Kunze, C. Kurzeder, K.-V. Lehmann, M. Levesque, S. Lugert, G. Maass, M. Manz, P. Markolin, J. Mena, U. Menzel, J.M. Metzler, N. Miglino, E.S. Milani, H. Moch, S. Muenst, R. Murri, C.K. Ng, S. Nicolet, M. Nowak, P.G. Pedrioli, L. Pelkmans, S. Piscuoglio, M. Prummer, M. Ritter, C. Rommel, M.L. Rosano-González, G. Rätsch, N. Santacroce, J.S. del Castillo, R. Schlenker, P.C. Schwalie, S. Schwan, T. Schär, G. Senti, F. Singer, S. Sivapatham, B. Snijder, B. Sobottka, V.T. Sreedharan, S. Stark, D.J. Stekhoven, A.P. Theocharides, T.M. Thomas, M. Tolnay, V. Tosevski, N.C. Toussaint, M.A. Tuncel, M. Tusup, A.V. Drogen, M. Vetter, T. Vlajnic, S. Weber, W.P. Weber, R. Wegmann, M. Weller, F. Wendt, N. Wey, A. Wicki, B. Wollscheid, S. Yu, J. Ziegler, M. Zimmermann, M. Zoche, G. Zuend, G. Rätsch, K.-V. Lehmann, Bioinformatics 36 (2020) i919–i927.","mla":"Stark, Stefan G., et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” <i>Bioinformatics</i>, vol. 36, no. Supplement_2, Oxford University Press, 2020, pp. i919–27, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">10.1093/bioinformatics/btaa843</a>.","ista":"Stark SG et al. 2020. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 36(Supplement_2), i919–i927.","ama":"Stark SG, Ficek J, Locatello F, et al. SCIM: Universal single-cell matching with unpaired feature sets. <i>Bioinformatics</i>. 2020;36(Supplement_2):i919-i927. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">10.1093/bioinformatics/btaa843</a>"},"publisher":"Oxford University Press","department":[{"_id":"FrLo"}],"title":"SCIM: Universal single-cell matching with unpaired feature sets","publication":"Bioinformatics","oa_version":"Published Version","date_created":"2023-08-21T12:28:20Z","extern":"1","abstract":[{"text":"Motivation: Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed.\r\nResults: We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively.","lang":"eng"}]}]