[{"doi":"10.7554/eLife.68238","date_updated":"2023-08-14T07:23:39Z","article_processing_charge":"No","author":[{"full_name":"Vuong-Brender, Thanh","id":"D389312E-10C4-11EA-ABF4-A4B43DDC885E","first_name":"Thanh","last_name":"Vuong-Brender"},{"first_name":"Sean","last_name":"Flynn","full_name":"Flynn, Sean"},{"full_name":"Vallis, Yvonne","id":"05A2795C-31B5-11EA-83A7-7DA23DDC885E","first_name":"Yvonne","last_name":"Vallis"},{"first_name":"Mario","last_name":"De Bono","orcid":"0000-0001-8347-0443","full_name":"De Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2021-09-17T00:00:00Z","quality_controlled":"1","scopus_import":"1","article_number":"e68238","file_date_updated":"2021-10-11T14:15:07Z","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":"17","ddc":["610"],"pmid":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"isi":1,"month":"09","publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","date_created":"2021-10-11T14:15:07Z","success":1,"file_id":"10122","date_updated":"2021-10-11T14:15:07Z","file_size":1774624,"checksum":"b465e172d2b1f57aa26a2571a085d052","file_name":"2021_eLife_VuongBrender.pdf"}],"intvolume":"        10","abstract":[{"lang":"eng","text":"The ubiquitous Ca2+ sensor calmodulin (CaM) binds and regulates many proteins, including ion channels, CaM kinases, and calcineurin, according to Ca2+-CaM levels. What regulates neuronal CaM levels, is, however, unclear. CaM-binding transcription activators (CAMTAs) are ancient proteins expressed broadly in nervous systems and whose loss confers pleiotropic behavioral defects in flies, mice, and humans. Using Caenorhabditis elegans and Drosophila, we show that CAMTAs control neuronal CaM levels. The behavioral and neuronal Ca2+ signaling defects in mutants lacking camt-1, the sole C. elegans CAMTA, can be rescued by supplementing neuronal CaM. CAMT-1 binds multiple sites in the CaM promoter and deleting these sites phenocopies camt-1. Our data suggest CAMTAs mediate a conserved and general mechanism that controls neuronal CaM levels, thereby regulating Ca2+ signaling, physiology, and behavior."}],"publisher":"eLife Sciences Publications","title":"Neuronal calmodulin levels are controlled by CAMTA transcription factors","department":[{"_id":"MaDe"}],"publication":"eLife","oa_version":"Published Version","date_created":"2021-10-10T22:01:22Z","ec_funded":1,"article_type":"original","external_id":{"pmid":["34499028"],"isi":["000695716100001"]},"oa":1,"acknowledgement":"The authors thank the MRC-LMB Flow Cytometry facility and Imaging Service for support, the Cancer Research UK Cambridge Institute Genomics Core for Next Generation Sequencing, Julie Ahringer and Alex Appert for advice and technical help for ChIP-seq experiments, Paula Freire-Pritchett, Tim Stevens, and Gurpreet Ghattaoraya for RNA-seq and ChIP-seq analyses, Nikos Chronis for the TN-XL plasmid, Hong-Sheng Li and Daisuke Yamamoto for generously sending the tes2 and cro mutants, Daria Siekhaus for hosting the fly work, Michaela Misova for technical assistance. The authors are very grateful to Salihah Ece Sönmez for teaching us how to dissect, mount and stain Drosophila retinae. This work was supported by an Advanced ERC grant (269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z) to MdB, and an IST Plus Fellowship to TV-B (Marie Sklodowska-Curie Agreement no 754411).","status":"public","publication_identifier":{"eissn":["2050-084X"]},"citation":{"apa":"Vuong-Brender, T., Flynn, S., Vallis, Y., &#38; de Bono, M. (2021). Neuronal calmodulin levels are controlled by CAMTA transcription factors. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.68238\">https://doi.org/10.7554/eLife.68238</a>","ieee":"T. Vuong-Brender, S. Flynn, Y. Vallis, and M. de Bono, “Neuronal calmodulin levels are controlled by CAMTA transcription factors,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","chicago":"Vuong-Brender, Thanh, Sean Flynn, Yvonne Vallis, and Mario de Bono. “Neuronal Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.68238\">https://doi.org/10.7554/eLife.68238</a>.","ista":"Vuong-Brender T, Flynn S, Vallis Y, de Bono M. 2021. Neuronal calmodulin levels are controlled by CAMTA transcription factors. eLife. 10, e68238.","short":"T. Vuong-Brender, S. Flynn, Y. Vallis, M. de Bono, ELife 10 (2021).","mla":"Vuong-Brender, Thanh, et al. “Neuronal Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” <i>ELife</i>, vol. 10, e68238, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.68238\">10.7554/eLife.68238</a>.","ama":"Vuong-Brender T, Flynn S, Vallis Y, de Bono M. Neuronal calmodulin levels are controlled by CAMTA transcription factors. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.68238\">10.7554/eLife.68238</a>"},"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":10,"has_accepted_license":"1","year":"2021","_id":"10116"},{"acknowledgement":"We thank de Bono lab members for helpful comments on the manuscript, IST Austria and University of Vienna Mass Spec Facilities for invaluable discussions and comments for the optimization of mass spec analyses of worm samples. The biotin auxotropic E. coli strain MG1655bioB:kan was gift from John Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3′UTR entry vector were kindly shared by Dr Dominique Glauser (University of Fribourg). Codon-optimized mScarlet vector was a generous gift from Dr Manuel Zimmer (University of Vienna).","oa":1,"status":"public","issue":"3","external_id":{"isi":["000706409200006"]},"article_type":"original","citation":{"apa":"Artan, M., Barratt, S., Flynn, S. M., Begum, F., Skehel, M., Nicolas, A., &#38; de Bono, M. (2021). Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. <i>Journal of Biological Chemistry</i>. Elsevier. <a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">https://doi.org/10.1016/J.JBC.2021.101094</a>","ieee":"M. Artan <i>et al.</i>, “Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling,” <i>Journal of Biological Chemistry</i>, vol. 297, no. 3. Elsevier, 2021.","chicago":"Artan, Murat, Stephen Barratt, Sean M. Flynn, Farida Begum, Mark Skehel, Armel Nicolas, and Mario de Bono. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” <i>Journal of Biological Chemistry</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">https://doi.org/10.1016/J.JBC.2021.101094</a>.","short":"M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de Bono, Journal of Biological Chemistry 297 (2021).","mla":"Artan, Murat, et al. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” <i>Journal of Biological Chemistry</i>, vol. 297, no. 3, 101094, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">10.1016/J.JBC.2021.101094</a>.","ista":"Artan M, Barratt S, Flynn SM, Begum F, Skehel M, Nicolas A, de Bono M. 2021. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. 297(3), 101094.","ama":"Artan M, Barratt S, Flynn SM, et al. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. <i>Journal of Biological Chemistry</i>. 2021;297(3). doi:<a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">10.1016/J.JBC.2021.101094</a>"},"publication_identifier":{"eissn":["1083-351X"],"issn":["0021-9258"]},"volume":297,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","_id":"10117","has_accepted_license":"1","year":"2021","abstract":[{"text":"Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins. The nematode Caenorhabditis elegans is one of the most intensely studied organisms in biology, offering many advantages for biochemistry. Using the highly active biotin ligase TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage of TurboID is that biotin's high affinity for streptavidin means biotin-labeled proteins can be affinity-purified under harsh denaturing conditions. By combining extensive sonication with aggressive denaturation using SDS and urea, we achieved near-complete solubilization of worm proteins. We then used this protocol to characterize the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among the smallest C. elegans cells. To probe the method's sensitivity, we expressed TurboID exclusively in the two AFD neurons and showed that the protocol could identify known and previously unknown proteins expressed selectively in AFD. The active zones of synapses are composed of a protein matrix that is difficult to solubilize and purify. To test if our protocol could solubilize active zone proteins, we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic active zone protein. We identified many known ELKS-1-interacting active zone proteins, as well as previously uncharacterized synaptic proteins. Versatile vectors and the inherent advantages of using C. elegans, including fast growth and the ability to rapidly make and functionally test knock-ins, make proximity labeling a valuable addition to the armory of this model organism.","lang":"eng"}],"publication":"Journal of Biological Chemistry","title":"Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling","department":[{"_id":"MaDe"},{"_id":"LifeSc"}],"publisher":"Elsevier","ec_funded":1,"date_created":"2021-10-10T22:01:23Z","oa_version":"Published Version","ddc":["612"],"day":"01","isi":1,"month":"09","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"intvolume":"       297","file":[{"file_id":"10121","date_updated":"2021-10-11T12:20:58Z","checksum":"19e39d36c5b9387c6dc0e89c9ae856ab","file_name":"2021_JBC_Artan.pdf","file_size":1680010,"access_level":"open_access","creator":"cchlebak","relation":"main_file","date_created":"2021-10-11T12:20:58Z","success":1,"content_type":"application/pdf"}],"publication_status":"published","author":[{"full_name":"Artan, Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425","first_name":"Murat","orcid":"0000-0001-8945-6992","last_name":"Artan"},{"last_name":"Barratt","first_name":"Stephen","id":"57740d2b-2a88-11ec-97cf-d9e6d1b39677","full_name":"Barratt, Stephen"},{"full_name":"Flynn, Sean M.","first_name":"Sean M.","last_name":"Flynn"},{"last_name":"Begum","first_name":"Farida","full_name":"Begum, Farida"},{"full_name":"Skehel, Mark","first_name":"Mark","last_name":"Skehel"},{"first_name":"Armel","last_name":"Nicolas","full_name":"Nicolas, Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mario","orcid":"0000-0001-8347-0443","last_name":"De Bono","full_name":"De Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2021-09-01T00:00:00Z","article_processing_charge":"Yes","date_updated":"2023-08-14T07:24:09Z","doi":"10.1016/J.JBC.2021.101094","scopus_import":"1","quality_controlled":"1","file_date_updated":"2021-10-11T12:20:58Z","article_number":"101094","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":[{"lang":"eng","text":"Solution synthesis of particles emerged as an alternative to prepare thermoelectric materials with less demanding processing conditions than conventional solid-state synthetic methods. However, solution synthesis generally involves the presence of additional molecules or ions belonging to the precursors or added to enable solubility and/or regulate nucleation and growth. These molecules or ions can end up in the particles as surface adsorbates and interfere in the material properties. This work demonstrates that ionic adsorbates, in particular Na⁺ ions, are electrostatically adsorbed in SnSe particles synthesized in water and play a crucial role not only in directing the material nano/microstructure but also in determining the transport properties of the consolidated material. In dense pellets prepared by sintering SnSe particles, Na remains within the crystal lattice as dopant, in dislocations, precipitates, and forming grain boundary complexions. These results highlight the importance of considering all the possible unintentional impurities to establish proper structure-property relationships and control material properties in solution-processed thermoelectric materials."}],"ec_funded":1,"date_created":"2021-10-11T20:07:24Z","oa_version":"Published Version","publisher":"Wiley","publication":"Advanced Materials","department":[{"_id":"EM-Fac"},{"_id":"MaIb"}],"title":"The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe","publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"citation":{"ama":"Liu Y, Calcabrini M, Yu Y, et al. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. <i>Advanced Materials</i>. 2021;33(52). doi:<a href=\"https://doi.org/10.1002/adma.202106858\">10.1002/adma.202106858</a>","short":"Y. Liu, M. Calcabrini, Y. Yu, A. Genç, C. Chang, T. Costanzo, T. Kleinhanns, S. Lee, J. Llorca, O. Cojocaru‐Mirédin, M. Ibáñez, Advanced Materials 33 (2021).","ista":"Liu Y, Calcabrini M, Yu Y, Genç A, Chang C, Costanzo T, Kleinhanns T, Lee S, Llorca J, Cojocaru‐Mirédin O, Ibáñez M. 2021. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. 33(52), 2106858.","mla":"Liu, Yu, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” <i>Advanced Materials</i>, vol. 33, no. 52, 2106858, Wiley, 2021, doi:<a href=\"https://doi.org/10.1002/adma.202106858\">10.1002/adma.202106858</a>.","ieee":"Y. Liu <i>et al.</i>, “The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe,” <i>Advanced Materials</i>, vol. 33, no. 52. Wiley, 2021.","chicago":"Liu, Yu, Mariano Calcabrini, Yuan Yu, Aziz Genç, Cheng Chang, Tommaso Costanzo, Tobias Kleinhanns, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” <i>Advanced Materials</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/adma.202106858\">https://doi.org/10.1002/adma.202106858</a>.","apa":"Liu, Y., Calcabrini, M., Yu, Y., Genç, A., Chang, C., Costanzo, T., … Ibáñez, M. (2021). The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.202106858\">https://doi.org/10.1002/adma.202106858</a>"},"issue":"52","external_id":{"pmid":["34626034"],"isi":["000709899300001"]},"article_type":"original","acknowledgement":"Y.L. and M.C. contributed equally to this work. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). This work was financially supported by IST Austria and the Werner Siemens Foundation. Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. M.C. has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385. Y.Y. and O.C.-M. acknowledge the financial support from DFG within the project SFB 917: Nanoswitches. J.L. is a Serra Húnter Fellow and is grateful to ICREA Academia program. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N.","status":"public","oa":1,"year":"2021","has_accepted_license":"1","_id":"10123","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":33,"quality_controlled":"1","keyword":["mechanical engineering","mechanics of materials","general materials science"],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","related_material":{"record":[{"id":"12885","relation":"dissertation_contains","status":"public"}]},"doi":"10.1002/adma.202106858","date_updated":"2023-08-14T07:25:27Z","date_published":"2021-12-29T00:00:00Z","author":[{"first_name":"Yu","last_name":"Liu","orcid":"0000-0001-7313-6740","full_name":"Liu, Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Calcabrini, Mariano","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","first_name":"Mariano","last_name":"Calcabrini","orcid":"0000-0003-4566-5877"},{"full_name":"Yu, Yuan","first_name":"Yuan","last_name":"Yu"},{"first_name":"Aziz","last_name":"Genç","full_name":"Genç, Aziz"},{"full_name":"Chang, Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","first_name":"Cheng","orcid":"0000-0002-9515-4277","last_name":"Chang"},{"full_name":"Costanzo, Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso","orcid":"0000-0001-9732-3815","last_name":"Costanzo"},{"first_name":"Tobias","last_name":"Kleinhanns","full_name":"Kleinhanns, Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425"},{"first_name":"Seungho","last_name":"Lee","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"first_name":"Oana","last_name":"Cojocaru‐Mirédin","full_name":"Cojocaru‐Mirédin, Oana"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","first_name":"Maria"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"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_number":"2106858","file_date_updated":"2022-02-03T13:16:14Z","isi":1,"month":"12","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"},{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"language":[{"iso":"eng"}],"ddc":["620"],"day":"29","pmid":1,"file":[{"file_id":"10720","date_updated":"2022-02-03T13:16:14Z","checksum":"990bccc527c64d85cf1c97885110b5f4","file_name":"2021_AdvancedMaterials_Liu.pdf","file_size":5595666,"creator":"cchlebak","access_level":"open_access","relation":"main_file","date_created":"2022-02-03T13:16:14Z","success":1,"content_type":"application/pdf"}],"publication_status":"published","intvolume":"        33"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.04.01.438065","open_access":"1"}],"_id":"10124","year":"2021","publication_status":"published","status":"public","acknowledgement":"We acknowledge support from the Engineering and Physical Sciences Research Council (A.P. and A.Š.), the Royal Society (A.Š.) and the European Research Council (I.P. and A.Š.).","oa":1,"pmid":1,"external_id":{"pmid":["34550677 "]},"day":"22","article_type":"original","citation":{"ista":"Palaia I, Paraschiv A, Debets V, Storm C, Šarić A. 2021. Durotaxis of passive nanoparticles on elastic membranes. ACS Nano.","mla":"Palaia, Ivan, et al. “Durotaxis of Passive Nanoparticles on Elastic Membranes.” <i>ACS Nano</i>, American Chemical Society, 2021, doi:<a href=\"https://doi.org/10.1021/acsnano.1c02777 \">10.1021/acsnano.1c02777 </a>.","short":"I. Palaia, A. Paraschiv, V. Debets, C. Storm, A. Šarić, ACS Nano (2021).","ama":"Palaia I, Paraschiv A, Debets V, Storm C, Šarić A. Durotaxis of passive nanoparticles on elastic membranes. <i>ACS Nano</i>. 2021. doi:<a href=\"https://doi.org/10.1021/acsnano.1c02777 \">10.1021/acsnano.1c02777 </a>","apa":"Palaia, I., Paraschiv, A., Debets, V., Storm, C., &#38; Šarić, A. (2021). Durotaxis of passive nanoparticles on elastic membranes. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.1c02777 \">https://doi.org/10.1021/acsnano.1c02777 </a>","chicago":"Palaia, Ivan, Alexandru Paraschiv, Vincent Debets, Cornelis Storm, and Anđela Šarić. “Durotaxis of Passive Nanoparticles on Elastic Membranes.” <i>ACS Nano</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acsnano.1c02777 \">https://doi.org/10.1021/acsnano.1c02777 </a>.","ieee":"I. Palaia, A. Paraschiv, V. Debets, C. Storm, and A. Šarić, “Durotaxis of passive nanoparticles on elastic membranes,” <i>ACS Nano</i>. American Chemical Society, 2021."},"month":"09","language":[{"iso":"eng"}],"publication":"ACS Nano","title":"Durotaxis of passive nanoparticles on elastic membranes","publisher":"American Chemical Society","date_created":"2021-10-12T07:31:21Z","oa_version":"Preprint","author":[{"last_name":"Palaia","first_name":"Ivan","full_name":"Palaia, Ivan"},{"full_name":"Paraschiv, Alexandru","first_name":"Alexandru","last_name":"Paraschiv"},{"full_name":"Debets, Vincent","first_name":"Vincent","last_name":"Debets"},{"full_name":"Storm, Cornelis","last_name":"Storm","first_name":"Cornelis"},{"first_name":"Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"date_published":"2021-09-22T00:00:00Z","article_processing_charge":"No","date_updated":"2021-10-12T09:50:19Z","doi":"10.1021/acsnano.1c02777 ","abstract":[{"text":"The transport of macromolecules and nanoscopic particles to a target cellular site is a crucial aspect in many physiological processes. This directional motion is generally controlled via active mechanical and chemical processes. Here we show, by means of molecular dynamics simulations and an analytical theory, that completely passive nanoparticles can exhibit directional motion when embedded in non-uniform mechanical environments. Specifically, we study the motion of a passive nanoparticle adhering to a mechanically non-uniform elastic membrane. We observe a non-monotonic affinity of the particle to the membrane as a function of the membrane’s rigidity, which results in the particle transport. This transport can be both up or down the rigidity gradient, depending on the absolute values of the rigidities that the gradient spans across. We conclude that rigidity gradients can be used to direct average motion of passive macromolecules and nanoparticles on deformable membranes, resulting in the preferential accumulation of the macromolecules in regions of certain mechanical properties.","lang":"eng"}],"extern":"1","quality_controlled":"1"},{"oa":1,"acknowledgement":"We acknowledge support from the Biotechnology and Biological Sciences Research Council (L.H.K.), EPSRC (A.E.H), UCL IPLS (T.Y and D. H.), Wellcome Trust (203276/Z/16/Z, A.P., S.C., R. H., B.B.), Volkswagen Foundation (Az 96727, A.P., B.B., A.Š.), MRC (MC CF1226, R.H., B.B., A.Š.), the ERC grant (”NEPA” 802960, A.Š.), the Royal Society (C.V.-H., A.Š.), the UK Materials and Molecular Modelling Hub for computational resources (EP/P020194/1).","status":"public","day":"23","citation":{"apa":"Harker-Kirschneck, L., Hafner, A. E., Yao, T., Pulschen, A., Hurtig, F., Vanhille-Campos, C., … Šarić, A. (n.d.). Physical mechanisms of ESCRT-III-driven cell division in archaea. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2021.03.23.436559\">https://doi.org/10.1101/2021.03.23.436559</a>","chicago":"Harker-Kirschneck, L., A. E. Hafner, T. Yao, A. Pulschen, F. Hurtig, C. Vanhille-Campos, D. Hryniuk, et al. “Physical Mechanisms of ESCRT-III-Driven Cell Division in Archaea.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2021.03.23.436559\">https://doi.org/10.1101/2021.03.23.436559</a>.","ieee":"L. Harker-Kirschneck <i>et al.</i>, “Physical mechanisms of ESCRT-III-driven cell division in archaea,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","mla":"Harker-Kirschneck, L., et al. “Physical Mechanisms of ESCRT-III-Driven Cell Division in Archaea.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2021.03.23.436559\">10.1101/2021.03.23.436559</a>.","ista":"Harker-Kirschneck L, Hafner AE, Yao T, Pulschen A, Hurtig F, Vanhille-Campos C, Hryniuk D, Culley S, Henriques R, Baum B, Šarić A. Physical mechanisms of ESCRT-III-driven cell division in archaea. bioRxiv, <a href=\"https://doi.org/10.1101/2021.03.23.436559\">10.1101/2021.03.23.436559</a>.","short":"L. Harker-Kirschneck, A.E. Hafner, T. Yao, A. Pulschen, F. Hurtig, C. Vanhille-Campos, D. Hryniuk, S. Culley, R. Henriques, B. Baum, A. Šarić, BioRxiv (n.d.).","ama":"Harker-Kirschneck L, Hafner AE, Yao T, et al. Physical mechanisms of ESCRT-III-driven cell division in archaea. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.03.23.436559\">10.1101/2021.03.23.436559</a>"},"month":"03","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"preprint","_id":"10125","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.03.23.436559","open_access":"1"}],"year":"2021","publication_status":"submitted","author":[{"full_name":"Harker-Kirschneck, L.","first_name":"L.","last_name":"Harker-Kirschneck"},{"full_name":"Hafner, A. E.","last_name":"Hafner","first_name":"A. E."},{"last_name":"Yao","first_name":"T.","full_name":"Yao, T."},{"first_name":"A.","last_name":"Pulschen","full_name":"Pulschen, A."},{"last_name":"Hurtig","first_name":"F.","full_name":"Hurtig, F."},{"first_name":"C.","last_name":"Vanhille-Campos","full_name":"Vanhille-Campos, C."},{"first_name":"D.","last_name":"Hryniuk","full_name":"Hryniuk, D."},{"last_name":"Culley","first_name":"S.","full_name":"Culley, S."},{"full_name":"Henriques, R.","last_name":"Henriques","first_name":"R."},{"full_name":"Baum, B.","last_name":"Baum","first_name":"B."},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139"}],"date_published":"2021-03-23T00:00:00Z","article_processing_charge":"No","date_updated":"2021-10-12T09:50:26Z","doi":"10.1101/2021.03.23.436559","abstract":[{"lang":"eng","text":"Living systems propagate by undergoing rounds of cell growth and division. Cell division is at heart a physical process that requires mechanical forces, usually exerted by protein assemblies. Here we developed the first physical model for the division of archaeal cells, which despite their structural simplicity share machinery and evolutionary origins with eukaryotes. We show how active geometry changes of elastic ESCRT-III filaments, coupled to filament disassembly, are sufficient to efficiently split the cell. We explore how the non-equilibrium processes that govern the filament behaviour impact the resulting cell division. We show how a quantitative comparison between our simulations and dynamic data for ESCRTIII-mediated division in Sulfolobus acidocaldarius, the closest archaeal relative to eukaryotic cells that can currently be cultured in the lab, and reveal the most likely physical mechanism behind its division."}],"extern":"1","publication":"bioRxiv","title":"Physical mechanisms of ESCRT-III-driven cell division in archaea","publisher":"Cold Spring Harbor Laboratory","date_created":"2021-10-12T07:45:07Z","oa_version":"Preprint"},{"oa_version":"Preprint","ec_funded":1,"date_created":"2021-10-13T09:21:33Z","publisher":"American Physical Society ","department":[{"_id":"MiLe"}],"title":"Anderson localization of composite particles","publication":"Physical Review Letters","abstract":[{"lang":"eng","text":"We investigate the effect of coupling between translational and internal degrees of freedom of composite quantum particles on their localization in a random potential. We show that entanglement between the two degrees of freedom weakens localization due to the upper bound imposed on the inverse participation ratio by purity of a quantum state. We perform numerical calculations for a two-particle system bound by a harmonic force in a 1D disordered lattice and a rigid rotor in a 2D disordered lattice. We illustrate that the coupling has a dramatic effect on localization properties, even with a small number of internal states participating in quantum dynamics."}],"arxiv":1,"year":"2021","_id":"10134","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":127,"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"citation":{"short":"F. Suzuki, M. Lemeshko, W.H. Zurek, R.V. Krems, Physical Review Letters 127 (2021).","ista":"Suzuki F, Lemeshko M, Zurek WH, Krems RV. 2021. Anderson localization of composite particles. Physical Review Letters. 127(16), 160602.","mla":"Suzuki, Fumika, et al. “Anderson Localization of Composite Particles.” <i>Physical Review Letters</i>, vol. 127, no. 16, 160602, American Physical Society , 2021, doi:<a href=\"https://doi.org/10.1103/physrevlett.127.160602\">10.1103/physrevlett.127.160602</a>.","ama":"Suzuki F, Lemeshko M, Zurek WH, Krems RV. Anderson localization of composite particles. <i>Physical Review Letters</i>. 2021;127(16). doi:<a href=\"https://doi.org/10.1103/physrevlett.127.160602\">10.1103/physrevlett.127.160602</a>","apa":"Suzuki, F., Lemeshko, M., Zurek, W. H., &#38; Krems, R. V. (2021). Anderson localization of composite particles. <i>Physical Review Letters</i>. American Physical Society . <a href=\"https://doi.org/10.1103/physrevlett.127.160602\">https://doi.org/10.1103/physrevlett.127.160602</a>","chicago":"Suzuki, Fumika, Mikhail Lemeshko, Wojciech H. Zurek, and Roman V. Krems. “Anderson Localization of Composite Particles.” <i>Physical Review Letters</i>. American Physical Society , 2021. <a href=\"https://doi.org/10.1103/physrevlett.127.160602\">https://doi.org/10.1103/physrevlett.127.160602</a>.","ieee":"F. Suzuki, M. Lemeshko, W. H. Zurek, and R. V. Krems, “Anderson localization of composite particles,” <i>Physical Review Letters</i>, vol. 127, no. 16. American Physical Society , 2021."},"external_id":{"arxiv":["2011.06279"],"isi":["000707495700001"]},"article_type":"original","issue":"16","acknowledgement":"We acknowledge helpful discussions with W. G. Unruh and A. Rodriguez. F. S. is supported by European Union’s\r\nHorizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant No. 754411. M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). W. H. Z. is\r\nsupported by Department of Energy under the Los\r\nAlamos National Laboratory LDRD Program as well as by the U.S. Department of Energy, Office of Science, Basic\r\nEnergy Sciences, Materials Sciences and Engineering Division, Condensed Matter Theory Program. R. V. K. is supported by NSERC of Canada.\r\n","status":"public","oa":1,"article_number":"160602","quality_controlled":"1","scopus_import":"1","keyword":["General Physics and Astronomy"],"doi":"10.1103/physrevlett.127.160602","date_updated":"2024-02-29T12:34:10Z","article_processing_charge":"No","date_published":"2021-10-12T00:00:00Z","author":[{"first_name":"Fumika","last_name":"Suzuki","orcid":"0000-0003-4982-5970","full_name":"Suzuki, Fumika","id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E"},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zurek, Wojciech H.","last_name":"Zurek","first_name":"Wojciech H."},{"full_name":"Krems, Roman V.","last_name":"Krems","first_name":"Roman V."}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.06279"}],"intvolume":"       127","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"month":"10","isi":1,"day":"12"},{"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-014-5"]},"citation":{"ama":"Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10135\">10.15479/at:ista:10135</a>","mla":"Semerádová, Hana. <i>Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10135\">10.15479/at:ista:10135</a>.","ista":"Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria.","short":"H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021.","chicago":"Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10135\">https://doi.org/10.15479/at:ista:10135</a>.","ieee":"H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021.","apa":"Semerádová, H. (2021). <i>Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10135\">https://doi.org/10.15479/at:ista:10135</a>"},"status":"public","oa":1,"year":"2021","has_accepted_license":"1","supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva"}],"_id":"10135","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically throughout their whole life and thereby flexibly adapt to ever-changing environmental conditions. Plant hormones auxin and cytokinin are the main regulators of the lateral root organogenesis. Additionally to their solo activities, the interaction between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root development and growth. In particular, cytokinin modulates auxin distribution within the developing lateral root by affecting the endomembrane trafficking of auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al., 2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore, it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational level. Impact of cytokinin and other plant hormones on auxin transporters (including PIN1) on the posttranslational level is described in detail in the introduction part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights into the molecular machinery underlying cytokinin effect on the endomembrane trafficking in the plant cell, in particular on the PIN1 degradation, we conducted two large proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A). We found that DRP2A plays a role in cytokinin regulated processes during the plant growth and that cytokinin treatment promotes destabilization of DRP2A protein. However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation. Altogether, we identified proteins, which bind to cytokinin and proteins that in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation pattern. By combining information from these two screens, we can pave our way towards understanding of noncanonical cytokinin effects.","lang":"eng"}],"oa_version":"Published Version","date_created":"2021-10-13T13:42:48Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"title":"Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis","project":[{"_id":"261821BC-B435-11E9-9278-68D0E5697425","grant_number":"24746","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis."}],"language":[{"iso":"eng"}],"month":"10","day":"13","ddc":["570"],"publication_status":"published","file":[{"file_size":28508629,"checksum":"ce7108853e6cec6224f17cd6429b51fe","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx","file_id":"10186","date_updated":"2022-12-20T23:30:05Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2021-10-27T07:45:37Z","relation":"source_file","creator":"cziletti","access_level":"closed"},{"file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf","checksum":"0d7afb846e8e31ec794de47bf44e12ef","file_size":10623525,"file_id":"10187","embargo":"2022-10-28","date_updated":"2022-12-20T23:30:05Z","date_created":"2021-10-27T07:45:57Z","content_type":"application/pdf","creator":"cziletti","access_level":"open_access","relation":"main_file"}],"degree_awarded":"PhD","date_updated":"2024-01-25T10:53:29Z","related_material":{"record":[{"id":"9160","status":"public","relation":"part_of_dissertation"}]},"doi":"10.15479/at:ista:10135","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","date_published":"2021-10-13T00:00:00Z","author":[{"id":"42FE702E-F248-11E8-B48F-1D18A9856A87","full_name":"Semerádová, Hana","last_name":"Semerádová","first_name":"Hana"}],"file_date_updated":"2022-12-20T23:30:05Z"},{"file":[{"file_size":2055981,"checksum":"89fb95b211dbe8678809e7cca4626952","file_name":"2021_LifeScAlliance_Rauschendorfer.pdf","file_id":"10152","date_updated":"2021-10-18T14:48:06Z","content_type":"application/pdf","date_created":"2021-10-18T14:48:06Z","success":1,"relation":"main_file","access_level":"open_access","creator":"cchlebak"}],"publication_status":"published","intvolume":"         4","month":"09","language":[{"iso":"eng"}],"ddc":["576"],"day":"21","pmid":1,"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_number":"e202101100","file_date_updated":"2021-10-18T14:48:06Z","quality_controlled":"1","scopus_import":"1","article_processing_charge":"Yes","doi":"10.26508/lsa.202101100","date_updated":"2022-08-31T14:01:56Z","date_published":"2021-09-21T00:00:00Z","author":[{"full_name":"Rauschendorfer, Theresa","first_name":"Theresa","last_name":"Rauschendorfer"},{"last_name":"Gurri","first_name":"Selina","full_name":"Gurri, Selina"},{"full_name":"Heggli, Irina","first_name":"Irina","last_name":"Heggli"},{"full_name":"Maddaluno, Luigi","last_name":"Maddaluno","first_name":"Luigi"},{"first_name":"Michael","last_name":"Meyer","full_name":"Meyer, Michael"},{"id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571","last_name":"Inglés Prieto","first_name":"Álvaro"},{"first_name":"Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Werner, Sabine","last_name":"Werner","first_name":"Sabine"}],"year":"2021","has_accepted_license":"1","_id":"10144","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":4,"publication_identifier":{"eissn":["2575-1077"]},"citation":{"chicago":"Rauschendorfer, Theresa, Selina Gurri, Irina Heggli, Luigi Maddaluno, Michael Meyer, Álvaro Inglés Prieto, Harald L Janovjak, and Sabine Werner. “Acute and Chronic Effects of a Light-Activated FGF Receptor in Keratinocytes in Vitro and in Mice.” <i>Life Science Alliance</i>. Life Science Alliance, 2021. <a href=\"https://doi.org/10.26508/lsa.202101100\">https://doi.org/10.26508/lsa.202101100</a>.","ieee":"T. Rauschendorfer <i>et al.</i>, “Acute and chronic effects of a light-activated FGF receptor in keratinocytes in vitro and in mice,” <i>Life Science Alliance</i>, vol. 4, no. 11. Life Science Alliance, 2021.","apa":"Rauschendorfer, T., Gurri, S., Heggli, I., Maddaluno, L., Meyer, M., Inglés Prieto, Á., … Werner, S. (2021). Acute and chronic effects of a light-activated FGF receptor in keratinocytes in vitro and in mice. <i>Life Science Alliance</i>. Life Science Alliance. <a href=\"https://doi.org/10.26508/lsa.202101100\">https://doi.org/10.26508/lsa.202101100</a>","ama":"Rauschendorfer T, Gurri S, Heggli I, et al. Acute and chronic effects of a light-activated FGF receptor in keratinocytes in vitro and in mice. <i>Life Science Alliance</i>. 2021;4(11). doi:<a href=\"https://doi.org/10.26508/lsa.202101100\">10.26508/lsa.202101100</a>","short":"T. Rauschendorfer, S. Gurri, I. Heggli, L. Maddaluno, M. Meyer, Á. Inglés Prieto, H.L. Janovjak, S. Werner, Life Science Alliance 4 (2021).","ista":"Rauschendorfer T, Gurri S, Heggli I, Maddaluno L, Meyer M, Inglés Prieto Á, Janovjak HL, Werner S. 2021. Acute and chronic effects of a light-activated FGF receptor in keratinocytes in vitro and in mice. Life Science Alliance. 4(11), e202101100.","mla":"Rauschendorfer, Theresa, et al. “Acute and Chronic Effects of a Light-Activated FGF Receptor in Keratinocytes in Vitro and in Mice.” <i>Life Science Alliance</i>, vol. 4, no. 11, e202101100, Life Science Alliance, 2021, doi:<a href=\"https://doi.org/10.26508/lsa.202101100\">10.26508/lsa.202101100</a>."},"issue":"11","article_type":"original","external_id":{"pmid":["34548382"]},"oa":1,"acknowledgement":"We thank Connor Richterich and Patricia Reinert, ETH Zurich, for invaluable experimental help; Manuela Pérez Berlanga, University Zurich, for help with the confocal imaging; Lukas Fischer for help with electrical engineering; Thomas Hennek, Sol Taguinod, and Dr. Stephan Sonntag, EPIC Phenomics Center, ETH Zürich, for the generation and maintenance of K14-OptoR2 mice; and Dr. Petra Boukamp, Leibniz Institute, Düsseldorf, Germany, for early-passage HaCaT keratinocytes. This work was supported by the ETH Zurich (grant ETH-06 15-1 to S Werner and L Maddaluno), the Swiss National Science Foundation (grant 31003B-189364 to S Werner), and a Marie Curie postdoctoral fellowship from the European Union (to L Maddaluno).","status":"public","date_created":"2021-10-17T22:01:16Z","oa_version":"Published Version","publisher":"Life Science Alliance","publication":"Life Science Alliance","title":"Acute and chronic effects of a light-activated FGF receptor in keratinocytes in vitro and in mice","extern":"1","abstract":[{"text":"FGFs and their high-affinity receptors (FGFRs) play key roles in development, tissue repair, and disease. Because FGFRs bind overlapping sets of ligands, their individual functions cannot be determined using ligand stimulation. Here, we generated a light-activated FGFR2 variant (OptoR2) to selectively activate signaling by the major FGFR in keratinocytes. Illumination of OptoR2-expressing HEK 293T cells activated FGFR signaling with remarkable temporal precision and promoted cell migration and proliferation. In murine and human keratinocytes, OptoR2 activation rapidly induced the classical FGFR signaling pathways and expression of FGF target genes. Surprisingly, multi-level counter-regulation occurred in keratinocytes in vitro and in transgenic mice in vivo, including OptoR2 down-regulation and loss of responsiveness to light activation. These results demonstrate unexpected cell type-specific limitations of optogenetic FGFRs in long-term in vitro and in vivo settings and highlight the complex consequences of transferring optogenetic cell signaling tools into their relevant cellular contexts.","lang":"eng"}]},{"citation":{"short":"I. Vercellino, L.A. Sazanov, Nature 598 (2021) 364–367.","mla":"Vercellino, Irene, and Leonid A. Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII<sub>2</sub>CIV.” <i>Nature</i>, vol. 598, no. 7880, Springer Nature, 2021, pp. 364–67, doi:<a href=\"https://doi.org/10.1038/s41586-021-03927-z\">10.1038/s41586-021-03927-z</a>.","ista":"Vercellino I, Sazanov LA. 2021. Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV. Nature. 598(7880), 364–367.","ama":"Vercellino I, Sazanov LA. Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV. <i>Nature</i>. 2021;598(7880):364-367. doi:<a href=\"https://doi.org/10.1038/s41586-021-03927-z\">10.1038/s41586-021-03927-z</a>","apa":"Vercellino, I., &#38; Sazanov, L. A. (2021). Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-021-03927-z\">https://doi.org/10.1038/s41586-021-03927-z</a>","chicago":"Vercellino, Irene, and Leonid A Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII<sub>2</sub>CIV.” <i>Nature</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41586-021-03927-z\">https://doi.org/10.1038/s41586-021-03927-z</a>.","ieee":"I. Vercellino and L. A. Sazanov, “Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV,” <i>Nature</i>, vol. 598, no. 7880. Springer Nature, pp. 364–367, 2021."},"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"acknowledgement":"We thank the pre-clinical facility of the IST Austria and A. Venturino for assistance with the animals; and V.-V. Hodirnau for assistance during the Titan Krios data collection, performed at the IST Austria. The data processing was performed at the IST high-performance computing cluster. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411.","status":"public","external_id":{"isi":["000704581600001"],"pmid":["34616041"]},"article_type":"original","issue":"7880","_id":"10146","year":"2021","page":"364-367","volume":598,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes1, whose precise role is debated. Supercomplexes CIII2CIV1-2 (refs. 2,3), CICIII2 (ref. 4) and CICIII2CIV (respirasome)5,6,7,8,9,10 exist in mammals, but in contrast to CICIII2 and the respirasome, to date the only known eukaryotic structures of CIII2CIV1-2 come from Saccharomyces cerevisiae11,12 and plants13, which have different organization. Here we present the first, to our knowledge, structures of mammalian (mouse and ovine) CIII2CIV and its assembly intermediates, in different conformations. We describe the assembly of CIII2CIV from the CIII2 precursor to the final CIII2CIV conformation, driven by the insertion of the N terminus of the assembly factor SCAF1 (ref. 14) deep into CIII2, while its C terminus is integrated into CIV. Our structures (which include CICIII2 and the respirasome) also confirm that SCAF1 is exclusively required for the assembly of CIII2CIV and has no role in the assembly of the respirasome. We show that CIII2 is asymmetric due to the presence of only one copy of subunit 9, which straddles both monomers and prevents the attachment of a second copy of SCAF1 to CIII2, explaining the presence of one copy of CIV in CIII2CIV in mammals. Finally, we show that CIII2 and CIV gain catalytic advantage when assembled into the supercomplex and propose a role for CIII2CIV in fine tuning the efficiency of electron transfer in the electron transport chain."}],"oa_version":"None","ec_funded":1,"date_created":"2021-10-17T22:01:17Z","department":[{"_id":"LeSa"}],"title":"Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV","publication":"Nature","publisher":"Springer Nature","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"isi":1,"month":"10","pmid":1,"day":"14","intvolume":"       598","publication_status":"published","scopus_import":"1","quality_controlled":"1","author":[{"first_name":"Irene","orcid":"0000-0001-5618-3449","last_name":"Vercellino","full_name":"Vercellino, Irene","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sazanov","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"date_published":"2021-10-14T00:00:00Z","date_updated":"2023-08-14T08:01:21Z","doi":"10.1038/s41586-021-03927-z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/boosting-the-cells-power-house/","description":"News on IST Webpage","relation":"press_release"}]},"article_processing_charge":"No","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"ScienComp"}]},{"abstract":[{"lang":"eng","text":"Tactile feedback of an object’s surface enables us to discern its material properties and affordances. This understanding is used in digital fabrication processes by creating objects with high-resolution surface variations to influence a user’s tactile perception. As the design of such surface haptics commonly relies on knowledge from real-life experiences, it is unclear how to adapt this information for digital design methods. In this work, we investigate replicating the haptics of real materials. Using an existing process for capturing an object’s microgeometry, we digitize and reproduce the stable surface information of a set of 15 fabric samples. In a psychophysical experiment, we evaluate the tactile qualities of our set of original samples and their replicas. From our results, we see that direct reproduction of surface variations is able to influence different psychophysical dimensions of the tactile perception of surface textures. While the fabrication process did not preserve all properties, our approach underlines that replication of surface microgeometries benefits fabrication methods in terms of haptic perception by covering a large range of tactile variations. Moreover, by changing the surface structure of a single fabricated material, its material perception can be influenced. We conclude by proposing strategies for capturing and reproducing digitized textures to better resemble the perceived haptics of the originals."}],"publication":"34th Annual ACM Symposium","department":[{"_id":"BeBi"}],"title":"Capturing tactile properties of real surfaces for haptic reproduction","publisher":"Association for Computing Machinery","ec_funded":1,"date_created":"2021-10-18T07:36:11Z","oa_version":"Preprint","status":"public","oa":1,"acknowledgement":"Our gratitude goes out to Kamila Mushkina, Akhmajon Makhsadov, Jordan Espenshade, Bruno Fruchard, Roland Bennewitz, and Robert Drumm. This project has received funding from the EU’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO).","citation":{"ista":"Degraen D, Piovarci M, Bickel B, Kruger A. 2021. Capturing tactile properties of real surfaces for haptic reproduction. 34th Annual ACM Symposium. UIST: User Interface Software and Technology, 954–971.","short":"D. Degraen, M. Piovarci, B. Bickel, A. Kruger, in:, 34th Annual ACM Symposium, Association for Computing Machinery, 2021, pp. 954–971.","mla":"Degraen, Donald, et al. “Capturing Tactile Properties of Real Surfaces for Haptic Reproduction.” <i>34th Annual ACM Symposium</i>, Association for Computing Machinery, 2021, pp. 954–71, doi:<a href=\"https://doi.org/10.1145/3472749.3474798\">10.1145/3472749.3474798</a>.","ama":"Degraen D, Piovarci M, Bickel B, Kruger A. Capturing tactile properties of real surfaces for haptic reproduction. In: <i>34th Annual ACM Symposium</i>. Association for Computing Machinery; 2021:954-971. doi:<a href=\"https://doi.org/10.1145/3472749.3474798\">10.1145/3472749.3474798</a>","apa":"Degraen, D., Piovarci, M., Bickel, B., &#38; Kruger, A. (2021). Capturing tactile properties of real surfaces for haptic reproduction. In <i>34th Annual ACM Symposium</i> (pp. 954–971). Virtual: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3472749.3474798\">https://doi.org/10.1145/3472749.3474798</a>","chicago":"Degraen, Donald, Michael Piovarci, Bernd Bickel, and Antonio Kruger. “Capturing Tactile Properties of Real Surfaces for Haptic Reproduction.” In <i>34th Annual ACM Symposium</i>, 954–71. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3472749.3474798\">https://doi.org/10.1145/3472749.3474798</a>.","ieee":"D. Degraen, M. Piovarci, B. Bickel, and A. Kruger, “Capturing tactile properties of real surfaces for haptic reproduction,” in <i>34th Annual ACM Symposium</i>, Virtual, 2021, pp. 954–971."},"publication_identifier":{"isbn":["978-1-4503-8635-7"]},"page":"954-971","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"conference","_id":"10148","year":"2021","has_accepted_license":"1","author":[{"first_name":"Donald","last_name":"Degraen","full_name":"Degraen, Donald"},{"full_name":"Piovarci, Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","first_name":"Michael","last_name":"Piovarci"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel"},{"full_name":"Kruger, Antonio","first_name":"Antonio","last_name":"Kruger"}],"date_published":"2021-10-10T00:00:00Z","article_processing_charge":"No","doi":"10.1145/3472749.3474798","date_updated":"2021-10-19T19:29:06Z","quality_controlled":"1","file_date_updated":"2021-10-18T07:36:03Z","conference":{"location":"Virtual","start_date":"2021-10-10","name":"UIST: User Interface Software and Technology","end_date":"2021-10-14"},"ddc":["000"],"day":"10","month":"10","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","name":"Distributed 3D Object Design","grant_number":"642841","_id":"2508E324-B435-11E9-9278-68D0E5697425"}],"file":[{"relation":"main_file","access_level":"open_access","creator":"bbickel","content_type":"application/pdf","date_created":"2021-10-18T07:36:03Z","date_updated":"2021-10-18T07:36:03Z","file_id":"10149","file_size":29796364,"file_name":"degraen-UIST2021_Texture_Appropriation_CR_preprint.pdf","checksum":"b0b26464df79b3a59e8ed82e4e19ab15"}],"publication_status":"published"},{"volume":5,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","_id":"10153","has_accepted_license":"1","year":"2021","status":"public","acknowledgement":"We thank the reviewers for their valuable suggestions towards improving the paper. We also \r\nthank Mae Milano and Adrian Sampson, as well as the members of the Programming Languages Discussion Group at Cornell University and of the Programming Research Laboratory at Northeastern University, for their helpful feedback on preliminary findings of this work.\r\n\r\nThis material is based upon work supported in part by the National Science Foundation (NSF) through grant CCF-1350182 and the Austrian Science Fund (FWF) through grant Z211-N23 (Wittgenstein~Award).\r\nAny opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the NSF or the FWF.","oa":1,"article_type":"original","citation":{"ieee":"F. Mühlböck and R. Tate, “Transitioning from structural to nominal code with efficient gradual typing,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 5. Association for Computing Machinery, 2021.","chicago":"Mühlböck, Fabian, and Ross Tate. “Transitioning from Structural to Nominal Code with Efficient Gradual Typing.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3485504\">https://doi.org/10.1145/3485504</a>.","apa":"Mühlböck, F., &#38; Tate, R. (2021). Transitioning from structural to nominal code with efficient gradual typing. <i>Proceedings of the ACM on Programming Languages</i>. Chicago, IL, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3485504\">https://doi.org/10.1145/3485504</a>","ama":"Mühlböck F, Tate R. Transitioning from structural to nominal code with efficient gradual typing. <i>Proceedings of the ACM on Programming Languages</i>. 2021;5. doi:<a href=\"https://doi.org/10.1145/3485504\">10.1145/3485504</a>","short":"F. Mühlböck, R. Tate, Proceedings of the ACM on Programming Languages 5 (2021).","mla":"Mühlböck, Fabian, and Ross Tate. “Transitioning from Structural to Nominal Code with Efficient Gradual Typing.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 5, 127, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3485504\">10.1145/3485504</a>.","ista":"Mühlböck F, Tate R. 2021. Transitioning from structural to nominal code with efficient gradual typing. Proceedings of the ACM on Programming Languages. 5, 127."},"publication_identifier":{"eissn":["2475-1421"]},"publication":"Proceedings of the ACM on Programming Languages","department":[{"_id":"ToHe"}],"title":"Transitioning from structural to nominal code with efficient gradual typing","publisher":"Association for Computing Machinery","date_created":"2021-10-19T12:48:44Z","oa_version":"Published Version","abstract":[{"text":"Gradual typing is a principled means for mixing typed and untyped code. But typed and untyped code often exhibit different programming patterns. There is already substantial research investigating gradually giving types to code exhibiting typical untyped patterns, and some research investigating gradually removing types from code exhibiting typical typed patterns. This paper investigates how to extend these established gradual-typing concepts to give formal guarantees not only about how to change types as code evolves but also about how to change such programming patterns as well.\r\n\r\nIn particular, we explore mixing untyped \"structural\" code with typed \"nominal\" code in an object-oriented language. But whereas previous work only allowed \"nominal\" objects to be treated as \"structural\" objects, we also allow \"structural\" objects to dynamically acquire certain nominal types, namely interfaces. We present a calculus that supports such \"cross-paradigm\" code migration and interoperation in a manner satisfying both the static and dynamic gradual guarantees, and demonstrate that the calculus can be implemented efficiently.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-nd/4.0/","intvolume":"         5","file":[{"file_id":"10154","date_updated":"2021-10-19T12:52:23Z","file_name":"monnom-oopsla21.pdf","checksum":"71011efd2da771cafdec7f0d9693f8c1","file_size":770269,"access_level":"open_access","creator":"fmuehlbo","relation":"main_file","success":1,"date_created":"2021-10-19T12:52:23Z","content_type":"application/pdf"}],"publication_status":"published","ddc":["005"],"day":"15","month":"10","project":[{"call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"file_date_updated":"2021-10-19T12:52:23Z","article_number":"127","conference":{"start_date":"2021-10-17","location":"Chicago, IL, United States","end_date":"2021-10-23","name":"OOPSLA: Object-Oriented Programming, Systems, Languages, and Applications"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png"},"author":[{"last_name":"Mühlböck","orcid":"0000-0003-1548-0177","first_name":"Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","full_name":"Mühlböck, Fabian"},{"full_name":"Tate, Ross","first_name":"Ross","last_name":"Tate"}],"date_published":"2021-10-15T00:00:00Z","article_processing_charge":"No","doi":"10.1145/3485504","date_updated":"2021-11-12T11:30:07Z","keyword":["gradual typing","gradual guarantee","nominal","structural","call tags"],"quality_controlled":"1"},{"has_accepted_license":"1","year":"2021","_id":"10163","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":12,"publication_identifier":{"eissn":["2041-1723"]},"citation":{"apa":"Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-26360-2\">https://doi.org/10.1038/s41467-021-26360-2</a>","ieee":"L.-M. Appel <i>et al.</i>, “PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","chicago":"Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-26360-2\">https://doi.org/10.1038/s41467-021-26360-2</a>.","mla":"Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” <i>Nature Communications</i>, vol. 12, no. 1, 6078, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-26360-2\">10.1038/s41467-021-26360-2</a>.","short":"L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T. Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta, E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A. Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications 12 (2021).","ista":"Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078.","ama":"Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-26360-2\">10.1038/s41467-021-26360-2</a>"},"issue":"1","external_id":{"isi":["000709050300001"]},"article_type":"original","oa":1,"acknowledgement":"D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase; Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for design of the arrest assay sequences; Petra van der Lelij for help with generating mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing; Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis; staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support; Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for critical comments on the manuscript; Life Science Editors for editing assistance. M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K. is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S. is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic (CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement no. 649030); this publication reflects only the author’s view and the Research Executive Agency is not responsible for any use that may be made of the information it contains. M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276, P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative ‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action BM1405 Non-globular proteins - from sequence to structure, function and application in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF LS17-008), and by the University of Vienna. This project was funded by the MFPL start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”) to D.S.","status":"public","date_created":"2021-10-20T14:40:32Z","oa_version":"Published Version","publisher":"Springer Nature","publication":"Nature Communications","title":"PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC","department":[{"_id":"CaBe"}],"abstract":[{"lang":"eng","text":"The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay."}],"file":[{"access_level":"open_access","creator":"cchlebak","relation":"main_file","date_created":"2021-10-21T13:51:49Z","success":1,"content_type":"application/pdf","file_id":"10169","date_updated":"2021-10-21T13:51:49Z","checksum":"d99fcd51aebde19c21314e3de0148007","file_name":"2021_NatComm_Appel.pdf","file_size":5111706}],"publication_status":"published","intvolume":"        12","month":"10","isi":1,"language":[{"iso":"eng"}],"ddc":["610"],"day":"19","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_number":"6078","file_date_updated":"2021-10-21T13:51:49Z","quality_controlled":"1","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"article_processing_charge":"No","related_material":{"link":[{"description":"Preprint ","relation":"earlier_version","url":"https://www.biorxiv.org/content/10.1101/2020.02.11.943159"}]},"date_updated":"2023-08-14T08:02:31Z","doi":"10.1038/s41467-021-26360-2","date_published":"2021-10-19T00:00:00Z","author":[{"first_name":"Lisa-Marie","last_name":"Appel","full_name":"Appel, Lisa-Marie"},{"first_name":"Vedran","last_name":"Franke","full_name":"Franke, Vedran"},{"full_name":"Bruno, Melania","last_name":"Bruno","first_name":"Melania"},{"first_name":"Irina","last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina"},{"full_name":"Kasiliauskaite, Aiste","first_name":"Aiste","last_name":"Kasiliauskaite"},{"first_name":"Tanja","last_name":"Kaufmann","full_name":"Kaufmann, Tanja"},{"first_name":"Ursula E.","last_name":"Schoeberl","full_name":"Schoeberl, Ursula E."},{"first_name":"Martin G.","last_name":"Puchinger","full_name":"Puchinger, Martin G."},{"full_name":"Kostrhon, Sebastian","last_name":"Kostrhon","first_name":"Sebastian"},{"full_name":"Ebenwaldner, Carmen","last_name":"Ebenwaldner","first_name":"Carmen"},{"first_name":"Marek","last_name":"Sebesta","full_name":"Sebesta, Marek"},{"last_name":"Beltzung","first_name":"Etienne","full_name":"Beltzung, Etienne"},{"last_name":"Mechtler","first_name":"Karl","full_name":"Mechtler, Karl"},{"full_name":"Lin, Gen","first_name":"Gen","last_name":"Lin"},{"full_name":"Vlasova, Anna","last_name":"Vlasova","first_name":"Anna"},{"full_name":"Leeb, Martin","first_name":"Martin","last_name":"Leeb"},{"full_name":"Pavri, Rushad","first_name":"Rushad","last_name":"Pavri"},{"full_name":"Stark, Alexander","last_name":"Stark","first_name":"Alexander"},{"full_name":"Akalin, Altuna","last_name":"Akalin","first_name":"Altuna"},{"last_name":"Stefl","first_name":"Richard","full_name":"Stefl, Richard"},{"full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky"},{"full_name":"Djinovic-Carugo, Kristina","last_name":"Djinovic-Carugo","first_name":"Kristina"},{"full_name":"Slade, Dea","last_name":"Slade","first_name":"Dea"}]},{"abstract":[{"text":"While sexual reproduction is widespread among many taxa, asexual lineages have repeatedly evolved from sexual ancestors. Despite extensive research on the evolution of sex, it is still unclear whether this switch represents a major transition requiring major molecular reorganization, and how convergent the changes involved are. In this study, we investigated the phylogenetic relationship and patterns of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp, to assess how gene expression patterns are affected by the transition to asexuality. We find only a few genes that are consistently associated with the evolution of asexuality, suggesting that this shift may not require an extensive overhauling of the meiotic machinery. While genes with sex-biased expression have high rates of expression divergence within Eurasian Artemia, neither female- nor male-biased genes appear to show unusual evolutionary patterns after sexuality is lost, contrary to theoretical expectations.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"date_created":"2021-10-21T07:46:06Z","publisher":"The Royal Society","title":"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp","department":[{"_id":"BeVi"}],"publication":"Proceedings of the Royal Society B: Biological Sciences","publication_identifier":{"issn":["0962-8452"],"eissn":["1471-2954"]},"citation":{"chicago":"Huylmans, Ann K, Ariana Macon, Francisco Hontoria, and Beatriz Vicoso. “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society, 2021. <a href=\"https://doi.org/10.1098/rspb.2021.1720\">https://doi.org/10.1098/rspb.2021.1720</a>.","ieee":"A. K. Huylmans, A. Macon, F. Hontoria, and B. Vicoso, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp,” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 288, no. 1959. The Royal Society, 2021.","apa":"Huylmans, A. K., Macon, A., Hontoria, F., &#38; Vicoso, B. (2021). Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2021.1720\">https://doi.org/10.1098/rspb.2021.1720</a>","ama":"Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. <i>Proceedings of the Royal Society B: Biological Sciences</i>. 2021;288(1959). doi:<a href=\"https://doi.org/10.1098/rspb.2021.1720\">10.1098/rspb.2021.1720</a>","short":"A.K. Huylmans, A. Macon, F. Hontoria, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 288 (2021).","ista":"Huylmans AK, Macon A, Hontoria F, Vicoso B. 2021. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal Society B: Biological Sciences. 288(1959), 20211720.","mla":"Huylmans, Ann K., et al. “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 288, no. 1959, 20211720, The Royal Society, 2021, doi:<a href=\"https://doi.org/10.1098/rspb.2021.1720\">10.1098/rspb.2021.1720</a>."},"external_id":{"isi":["000697643700001"],"pmid":["34547909"]},"article_type":"original","issue":"1959","oa":1,"acknowledgement":"We thank the Vicoso laboratory, Thomas Lenormand and Tanja Schwander for helpful discussions, the group of Gonzalo Gajardo, especially Cristian Gallardo-Escárate and Margarita Parraguez Donoso, for sequencing data and advice, and the IST Scientific Computing Group for their support. This work was supported by the European Research Council under the European Union's Horizon 2020 research and innovation program (grant agreement no. 715257).","status":"public","has_accepted_license":"1","year":"2021","_id":"10166","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":288,"quality_controlled":"1","scopus_import":"1","keyword":["asexual reproduction","parthenogenesis","sex-biased genes","sexual conflict","automixis","crustaceans"],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9949"}],"link":[{"relation":"supplementary_material","url":"https://doi.org/10.6084/m9.figshare.c.5615488.v1"}]},"date_updated":"2024-02-21T12:40:29Z","doi":"10.1098/rspb.2021.1720","article_processing_charge":"Yes (via OA deal)","date_published":"2021-09-22T00:00:00Z","author":[{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","last_name":"Huylmans","first_name":"Ann K"},{"first_name":"Ariana","last_name":"Macon","full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hontoria","first_name":"Francisco","full_name":"Hontoria, Francisco"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"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_number":"20211720","file_date_updated":"2021-10-22T11:48:02Z","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"month":"09","isi":1,"day":"22","ddc":["595"],"pmid":1,"publication_status":"published","file":[{"date_updated":"2021-10-22T11:48:02Z","file_id":"10172","checksum":"76e7f253b7040bca2ad76f82bd7c45c0","file_name":"2021_ProRoSocBBioSci_Huylmans.pdf","file_size":995806,"creator":"cchlebak","access_level":"open_access","relation":"main_file","date_created":"2021-10-22T11:48:02Z","success":1,"content_type":"application/pdf"}],"intvolume":"       288"},{"publication_status":"published","file":[{"date_updated":"2022-05-06T09:47:18Z","file_id":"11352","file_size":1008594,"checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_created":"2022-05-06T09:47:18Z","success":1}],"pmid":1,"day":"19","ddc":["610"],"project":[{"grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"language":[{"iso":"eng"}],"month":"06","isi":1,"file_date_updated":"2022-05-06T09:47:18Z","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"}],"author":[{"first_name":"Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"first_name":"Mikhail A.","last_name":"Moldovan","orcid":"0000-0002-8876-6494","full_name":"Moldovan, Mikhail A.","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0"},{"full_name":"Picard, Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A L","last_name":"Picard","orcid":"0000-0002-8101-2518"},{"first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2021-06-19T00:00:00Z","doi":"10.1093/molbev/msab178","date_updated":"2023-08-14T08:03:06Z","article_processing_charge":"No","scopus_import":"1","keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"quality_controlled":"1","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10167","year":"2021","has_accepted_license":"1","acknowledgement":"The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V.","oa":1,"status":"public","article_type":"original","external_id":{"pmid":["34146097"],"isi":["000741368600009"]},"citation":{"ama":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. 2021. doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>","mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>, Oxford University Press , 2021, doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>.","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution (2021).","ista":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution.","ieee":"M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” <i>Molecular Biology and Evolution</i>. Oxford University Press , 2021.","chicago":"Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>. Oxford University Press , 2021. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>.","apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., &#38; Vicoso, B. (2021). Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. Oxford University Press . <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>"},"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"title":"Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","department":[{"_id":"BeVi"}],"publication":"Molecular Biology and Evolution","publisher":"Oxford University Press ","oa_version":"Published Version","date_created":"2021-10-21T07:49:12Z","abstract":[{"lang":"eng","text":"Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group."}]},{"date_updated":"2021-10-28T15:44:05Z","article_processing_charge":"No","arxiv":1,"author":[{"id":"fea1b376-906f-11eb-847d-b2c0cf46455b","full_name":"Clozeau, Nicolas","last_name":"Clozeau","first_name":"Nicolas"},{"full_name":"Gloria, Antoine","first_name":"Antoine","last_name":"Gloria"}],"date_published":"2021-04-09T00:00:00Z","abstract":[{"lang":"eng","text":"Quantitative stochastic homogenization of linear elliptic operators is by now well-understood. In this contribution we move forward to the nonlinear setting of monotone operators with p-growth. This first work is dedicated to a quantitative two-scale expansion result. Fluctuations will be addressed in companion articles. By treating the range of exponents 2≤p<∞ in dimensions d≤3, we are able to consider genuinely nonlinear elliptic equations and systems such as −∇⋅A(x)(1+|∇u|p−2)∇u=f (with A random, non-necessarily symmetric) for the first time. When going from p=2 to p>2, the main difficulty is to analyze the associated linearized operator, whose coefficients are degenerate, unbounded, and depend on the random input A via the solution of a nonlinear equation. One of our main achievements is the control of this intricate nonlinear dependence, leading to annealed Meyers' estimates for the linearized operator, which are key to the quantitative two-scale expansion result."}],"article_number":"2104.04263","department":[{"_id":"JuFi"}],"title":"Quantitative nonlinear homogenization: control of oscillations","publication":"arXiv","oa_version":"Preprint","date_created":"2021-10-23T10:50:55Z","external_id":{"arxiv":["2104.04263"]},"day":"09","oa":1,"acknowledgement":"The authors warmly thank Mitia Duerinckx for discussions on annealed estimates, and Mathias Schäffner for pointing out that the conditions of [14] apply to  ̄a in the setting of Theorem 2.2 and for discussions on regularity theory for operators with non-standard growth conditions. The authors received financial support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement n◦ 864066).","status":"public","language":[{"iso":"eng"}],"month":"04","citation":{"mla":"Clozeau, Nicolas, and Antoine Gloria. “Quantitative Nonlinear Homogenization: Control of Oscillations.” <i>ArXiv</i>, 2104.04263.","ista":"Clozeau N, Gloria A. Quantitative nonlinear homogenization: control of oscillations. arXiv, 2104.04263.","short":"N. Clozeau, A. Gloria, ArXiv (n.d.).","ama":"Clozeau N, Gloria A. Quantitative nonlinear homogenization: control of oscillations. <i>arXiv</i>.","apa":"Clozeau, N., &#38; Gloria, A. (n.d.). Quantitative nonlinear homogenization: control of oscillations. <i>arXiv</i>.","ieee":"N. Clozeau and A. Gloria, “Quantitative nonlinear homogenization: control of oscillations,” <i>arXiv</i>. .","chicago":"Clozeau, Nicolas, and Antoine Gloria. “Quantitative Nonlinear Homogenization: Control of Oscillations.” <i>ArXiv</i>, n.d."},"type":"preprint","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publication_status":"submitted","year":"2021","_id":"10174","main_file_link":[{"url":"https://arxiv.org/abs/2104.04263","open_access":"1"}]},{"publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1802.09978","open_access":"1"}],"intvolume":"        62","isi":1,"month":"10","language":[{"iso":"eng"}],"day":"01","article_number":"102302","quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","doi":"10.1063/5.0037826","date_updated":"2023-08-14T08:04:12Z","author":[{"full_name":"Runkel, Ingo","last_name":"Runkel","first_name":"Ingo"},{"first_name":"Lorant","orcid":"0000-0003-2834-5054","last_name":"Szegedy","full_name":"Szegedy, Lorant","id":"7943226E-220E-11EA-94C7-D59F3DDC885E"}],"date_published":"2021-10-01T00:00:00Z","year":"2021","_id":"10176","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":62,"publication_identifier":{"issn":["00222488"]},"citation":{"chicago":"Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2021. <a href=\"https://doi.org/10.1063/5.0037826\">https://doi.org/10.1063/5.0037826</a>.","ieee":"I. Runkel and L. Szegedy, “Topological field theory on r-spin surfaces and the Arf-invariant,” <i>Journal of Mathematical Physics</i>, vol. 62, no. 10. AIP Publishing, 2021.","apa":"Runkel, I., &#38; Szegedy, L. (2021). Topological field theory on r-spin surfaces and the Arf-invariant. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0037826\">https://doi.org/10.1063/5.0037826</a>","ama":"Runkel I, Szegedy L. Topological field theory on r-spin surfaces and the Arf-invariant. <i>Journal of Mathematical Physics</i>. 2021;62(10). doi:<a href=\"https://doi.org/10.1063/5.0037826\">10.1063/5.0037826</a>","mla":"Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” <i>Journal of Mathematical Physics</i>, vol. 62, no. 10, 102302, AIP Publishing, 2021, doi:<a href=\"https://doi.org/10.1063/5.0037826\">10.1063/5.0037826</a>.","ista":"Runkel I, Szegedy L. 2021. Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. 62(10), 102302.","short":"I. Runkel, L. Szegedy, Journal of Mathematical Physics 62 (2021)."},"issue":"10","external_id":{"arxiv":["1802.09978"],"isi":["000755638500010"]},"article_type":"original","status":"public","acknowledgement":"We would like to thank Nils Carqueville, Tobias Dyckerhoff, Jan Hesse, Ehud Meir, Sebastian Novak, Louis-Hadrien Robert, Nick Salter, Walker Stern, and Lukas Woike for helpful discussions and comments. L.S. was supported by the DFG Research Training Group 1670 “Mathematics Inspired by String Theory and Quantum Field Theory.”","oa":1,"date_created":"2021-10-24T22:01:32Z","oa_version":"Preprint","publisher":"AIP Publishing","publication":"Journal of Mathematical Physics","title":"Topological field theory on r-spin surfaces and the Arf-invariant","department":[{"_id":"MiLe"}],"abstract":[{"lang":"eng","text":"We give a combinatorial model for r-spin surfaces with parameterized boundary based on Novak (“Lattice topological field theories in two dimensions,” Ph.D. thesis, Universität Hamburg, 2015). The r-spin structure is encoded in terms of ℤ𝑟-valued indices assigned to the edges of a polygonal decomposition. This combinatorial model is designed for our state-sum construction of two-dimensional topological field theories on r-spin surfaces. We show that an example of such a topological field theory computes the Arf-invariant of an r-spin surface as introduced by Randal-Williams [J. Topol. 7, 155 (2014)] and Geiges et al. [Osaka J. Math. 49, 449 (2012)]. This implies, in particular, that the r-spin Arf-invariant is constant on orbits of the mapping class group, providing an alternative proof of that fact."}],"arxiv":1},{"abstract":[{"lang":"eng","text":"Phonon polaritons (PhPs)—light coupled to lattice vibrations—with in-plane hyperbolic dispersion exhibit ray-like propagation with large wave vectors and enhanced density of optical states along certain directions on a surface. As such, they have raised a surge of interest, promising unprecedented manipulation of infrared light at the nanoscale in a planar circuitry. Here, we demonstrate focusing of in-plane hyperbolic PhPs propagating along thin slabs of α-MoO3. To that end, we developed metallic nanoantennas of convex geometries for both efficient launching and focusing of the polaritons. The foci obtained exhibit enhanced near-field confinement and absorption compared to foci produced by in-plane isotropic PhPs. Foci sizes as small as λp/4.5 = λ0/50 were achieved (λp is the polariton wavelength and λ0 is the photon wavelength). Focusing of in-plane hyperbolic polaritons introduces a first and most basic building block developing planar polariton optics using in-plane anisotropic van der Waals materials."}],"arxiv":1,"oa_version":"Published Version","date_created":"2021-10-24T22:01:33Z","department":[{"_id":"NanoFab"}],"title":"Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas","publication":"Science Advances","publisher":"American Association for the Advancement of Science","citation":{"ista":"Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Ma W, Bao Q, Volkov VS, Hillenbrand R, Nikitin AY, Alonso-González P. 2021. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. 7(41), abj0127.","short":"J. Martín-Sánchez, J. Duan, J. Taboada-Gutiérrez, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, W. Ma, Q. Bao, V.S. Volkov, R. Hillenbrand, A.Y. Nikitin, P. Alonso-González, Science Advances 7 (2021).","mla":"Martín-Sánchez, Javier, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” <i>Science Advances</i>, vol. 7, no. 41, abj0127, American Association for the Advancement of Science, 2021, doi:<a href=\"https://doi.org/10.1126/sciadv.abj0127\">10.1126/sciadv.abj0127</a>.","ama":"Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, et al. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. <i>Science Advances</i>. 2021;7(41). doi:<a href=\"https://doi.org/10.1126/sciadv.abj0127\">10.1126/sciadv.abj0127</a>","apa":"Martín-Sánchez, J., Duan, J., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., … Alonso-González, P. (2021). Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.abj0127\">https://doi.org/10.1126/sciadv.abj0127</a>","ieee":"J. Martín-Sánchez <i>et al.</i>, “Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas,” <i>Science Advances</i>, vol. 7, no. 41. American Association for the Advancement of Science, 2021.","chicago":"Martín-Sánchez, Javier, Jiahua Duan, Javier Taboada-Gutiérrez, Gonzalo Álvarez-Pérez, Kirill V. Voronin, Ivan Prieto Gonzalez, Weiliang Ma, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” <i>Science Advances</i>. American Association for the Advancement of Science, 2021. <a href=\"https://doi.org/10.1126/sciadv.abj0127\">https://doi.org/10.1126/sciadv.abj0127</a>."},"publication_identifier":{"eissn":["23752548"]},"status":"public","acknowledgement":"J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain and FSE (RYC2018-026196-I) and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA, and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00). J.T.-G. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-18-PF-BP17-126). G.A.-P. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-20-PF-BP19-053). K.V.V. and V.S.V. acknowledge the financial support from the Ministry of Science and Higher Education of the Russian Federation (agreement no. 075-15-2021-606). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation, and Universities (national projects MAT2017-88358-C3-3-R and PID2020-115221GB-C42) and the Basque Department of Education (PIBA-2020-1-0014). R.H. acknowledges financial support from the Spanish Ministry of Science, Innovation, and Universities (national project number RTI2018-094830-B-100 and project number MDM-2016-0618 of the Marie de Maeztu Units of Excellence Program) and the Basque Government (grant number IT1164-19).","oa":1,"external_id":{"arxiv":["2103.10852"],"isi":["000704912700024"]},"article_type":"original","issue":"41","_id":"10177","has_accepted_license":"1","year":"2021","volume":7,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","quality_controlled":"1","date_published":"2021-10-08T00:00:00Z","author":[{"first_name":"Javier","last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, Javier"},{"full_name":"Duan, Jiahua","first_name":"Jiahua","last_name":"Duan"},{"first_name":"Javier","last_name":"Taboada-Gutiérrez","full_name":"Taboada-Gutiérrez, Javier"},{"first_name":"Gonzalo","last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, Gonzalo"},{"full_name":"Voronin, Kirill V.","first_name":"Kirill V.","last_name":"Voronin"},{"orcid":"0000-0002-7370-5357","last_name":"Prieto Gonzalez","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Prieto Gonzalez, Ivan"},{"first_name":"Weiliang","last_name":"Ma","full_name":"Ma, Weiliang"},{"full_name":"Bao, Qiaoliang","first_name":"Qiaoliang","last_name":"Bao"},{"last_name":"Volkov","first_name":"Valentyn S.","full_name":"Volkov, Valentyn S."},{"full_name":"Hillenbrand, Rainer","last_name":"Hillenbrand","first_name":"Rainer"},{"full_name":"Nikitin, Alexey Y.","last_name":"Nikitin","first_name":"Alexey Y."},{"last_name":"Alonso-González","first_name":"Pablo","full_name":"Alonso-González, Pablo"}],"doi":"10.1126/sciadv.abj0127","date_updated":"2023-08-14T08:04:42Z","article_processing_charge":"Yes","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"file_date_updated":"2021-10-27T14:16:06Z","article_number":"abj0127","language":[{"iso":"eng"}],"month":"10","isi":1,"day":"08","ddc":["530"],"intvolume":"         7","publication_status":"published","file":[{"file_size":2441163,"checksum":"0a470ef6a47d2b8a96ede4c4d28cfacd","file_name":"2021_ScienceAdv_Martin-Sanchez.pdf","file_id":"10189","date_updated":"2021-10-27T14:16:06Z","content_type":"application/pdf","date_created":"2021-10-27T14:16:06Z","success":1,"relation":"main_file","creator":"cziletti","access_level":"open_access"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/"},{"arxiv":1,"abstract":[{"text":"In dense biological tissues, cell types performing different roles remain segregated by maintaining sharp interfaces. To better understand the mechanisms for such sharp compartmentalization, we study the effect of an imposed heterotypic tension at the interface between two distinct cell types in a fully 3D Voronoi model for confluent tissues. We find that cells rapidly sort and self-organize to generate a tissue-scale interface between cell types, and cells adjacent to this interface exhibit signature geometric features including nematic-like ordering, bimodal facet areas, and registration, or alignment, of cell centers on either side of the two-tissue interface. The magnitude of these features scales directly with the magnitude of the imposed tension, suggesting that biologists can estimate the magnitude of tissue surface tension between two tissue types simply by segmenting a 3D tissue. To uncover the underlying physical mechanisms driving these geometric features, we develop two minimal, ordered models using two different underlying lattices that identify an energetic competition between bulk cell shapes and tissue interface area. When the interface area dominates, changes to neighbor topology are costly and occur less frequently, which generates the observed geometric features.","lang":"eng"}],"publisher":"IOP Publishing","publication":"New Journal of Physics","department":[{"_id":"EdHa"}],"title":"Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue","date_created":"2021-10-24T22:01:34Z","oa_version":"Published Version","issue":"9","article_type":"original","external_id":{"isi":["000702042400001"],"arxiv":["2102.05397"]},"status":"public","acknowledgement":"We thank Paula Sanematsu, Matthias Merkel, Daniel Sussman, Cristina Marchetti and Edouard Hannezo for helpful discussions, and M Merkel for developing and sharing the original version of the 3D Voronoi code. This work was primarily funded by NSF-PHY-1607416, NSF-PHY-2014192 , and are in the division of physics at the National Science Foundation. PS and MLM acknowledge additional support from Simons Grant No. 454947.\r\n","oa":1,"publication_identifier":{"eissn":["13672630"]},"citation":{"ama":"Sahu P, Schwarz JM, Manning ML. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. <i>New Journal of Physics</i>. 2021;23(9). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">10.1088/1367-2630/ac23f1</a>","mla":"Sahu, Preeti, et al. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” <i>New Journal of Physics</i>, vol. 23, no. 9, 093043, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">10.1088/1367-2630/ac23f1</a>.","ista":"Sahu P, Schwarz JM, Manning ML. 2021. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. 23(9), 093043.","short":"P. Sahu, J.M. Schwarz, M.L. Manning, New Journal of Physics 23 (2021).","ieee":"P. Sahu, J. M. Schwarz, and M. L. Manning, “Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue,” <i>New Journal of Physics</i>, vol. 23, no. 9. IOP Publishing, 2021.","chicago":"Sahu, Preeti, J. M. Schwarz, and M. Lisa Manning. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” <i>New Journal of Physics</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">https://doi.org/10.1088/1367-2630/ac23f1</a>.","apa":"Sahu, P., Schwarz, J. M., &#38; Manning, M. L. (2021). Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">https://doi.org/10.1088/1367-2630/ac23f1</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":23,"has_accepted_license":"1","year":"2021","_id":"10178","article_processing_charge":"Yes","date_updated":"2023-08-14T08:10:31Z","doi":"10.1088/1367-2630/ac23f1","author":[{"full_name":"Sahu, Preeti","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E","first_name":"Preeti","last_name":"Sahu"},{"first_name":"J. M.","last_name":"Schwarz","full_name":"Schwarz, J. M."},{"last_name":"Manning","first_name":"M. Lisa","full_name":"Manning, M. Lisa"}],"date_published":"2021-09-29T00:00:00Z","quality_controlled":"1","scopus_import":"1","article_number":"093043","file_date_updated":"2021-10-28T12:06:01Z","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"},"ddc":["570"],"day":"29","month":"09","isi":1,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","creator":"cziletti","access_level":"open_access","content_type":"application/pdf","date_created":"2021-10-28T12:06:01Z","success":1,"file_id":"10193","date_updated":"2021-10-28T12:06:01Z","file_size":2215016,"checksum":"ace603e8f0962b3ba55f23fa34f57764","file_name":"2021_NewJPhys_Sahu.pdf"}],"publication_status":"published","intvolume":"        23"},{"doi":"10.15252/embj.2021108714","date_updated":"2023-08-14T08:05:23Z","article_processing_charge":"Yes (in subscription journal)","author":[{"full_name":"Bajaj, Sunanjay","first_name":"Sunanjay","last_name":"Bajaj"},{"first_name":"Joshua A.","last_name":"Bagley","full_name":"Bagley, Joshua A."},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer","first_name":"Christoph M"},{"full_name":"Vertesy, Abel","last_name":"Vertesy","first_name":"Abel"},{"last_name":"Nagumo Wong","first_name":"Sakurako","full_name":"Nagumo Wong, Sakurako"},{"first_name":"Veronica","last_name":"Krenn","full_name":"Krenn, Veronica"},{"last_name":"Lévi-Strauss","first_name":"Julie","full_name":"Lévi-Strauss, Julie"},{"last_name":"Knoblich","first_name":"Juergen A.","full_name":"Knoblich, Juergen A."}],"date_published":"2021-10-18T00:00:00Z","quality_controlled":"1","scopus_import":"1","article_number":"e108714","file_date_updated":"2021-12-13T14:54:14Z","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":"18","ddc":["610"],"pmid":1,"language":[{"iso":"eng"}],"isi":1,"month":"10","publication_status":"published","file":[{"file_size":7819881,"checksum":"78d2d02e775322297e774f72810a41a4","file_name":"2021_EMBO_Bajaj.pdf","date_updated":"2021-12-13T14:54:14Z","file_id":"10541","content_type":"application/pdf","date_created":"2021-12-13T14:54:14Z","success":1,"relation":"main_file","creator":"alisjak","access_level":"open_access"}],"intvolume":"        40","abstract":[{"text":"Inhibitory GABAergic interneurons migrate over long distances from their extracortical origin into the developing cortex. In humans, this process is uniquely slow and prolonged, and it is unclear whether guidance cues unique to humans govern the various phases of this complex developmental process. Here, we use fused cerebral organoids to identify key roles of neurotransmitter signaling pathways in guiding the migratory behavior of human cortical interneurons. We use scRNAseq to reveal expression of GABA, glutamate, glycine, and serotonin receptors along distinct maturation trajectories across interneuron migration. We develop an image analysis software package, TrackPal, to simultaneously assess 48 parameters for entire migration tracks of individual cells. By chemical screening, we show that different modes of interneuron migration depend on distinct neurotransmitter signaling pathways, linking transcriptional maturation of interneurons with their migratory behavior. Altogether, our study provides a comprehensive quantitative analysis of human interneuron migration and its functional modulation by neurotransmitter signaling.","lang":"eng"}],"publisher":"Embo Press","department":[{"_id":"Bio"}],"title":"Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration","publication":"EMBO Journal","oa_version":"Published Version","date_created":"2021-10-24T22:01:34Z","external_id":{"pmid":["34661293"],"isi":["000708012800001"]},"article_type":"original","issue":"23","acknowledgement":"We thank all Knoblich laboratory members for continued support and discussions. We thank the IMP/IMBA BioOptics facility, particularly Pawel Pasierbek, Alberto Moreno Cencerrado and Gerald Schmauss, the IMP/IMBA Molecular Biology Service, in particular Robert Heinen, the IMP Bioinformatics facility, in particular Thomas Burkard, the Vienna Biocenter Core Facilities (VBCF) Histopathology facility, in particular Tamara Engelmaier, and the VBCF Next Generation Sequencing Facility, notably Volodymyr Shubchynskyy and Carmen Czepe. We would also like to thank Simon Haendeler for advice on statistical analyses, Jose Guzman for discussions and assistance with slice culture setups, Oliver L. Eichmueller for discussions and assistance with microscopy, and E.H. Gustafson, S. Wolfinger, and D. Reumann for technical assistance regarding generation of cerebral organoids. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie fellowship agreement Nr.707109 awarded to J.A.B. Work in J.A.K.'s laboratory is supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, the City of Vienna, a Research Program of the Austrian Science Fund FWF (SFBF78 Stem Cell, F 7803-B) and a European Research Council (ERC) Advanced Grant under the European 20 Union’s Horizon 2020 program (grant agreement no. 695642).","oa":1,"status":"public","publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"citation":{"ieee":"S. Bajaj <i>et al.</i>, “Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration,” <i>EMBO Journal</i>, vol. 40, no. 23. Embo Press, 2021.","chicago":"Bajaj, Sunanjay, Joshua A. Bagley, Christoph M Sommer, Abel Vertesy, Sakurako Nagumo Wong, Veronica Krenn, Julie Lévi-Strauss, and Juergen A. Knoblich. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” <i>EMBO Journal</i>. Embo Press, 2021. <a href=\"https://doi.org/10.15252/embj.2021108714\">https://doi.org/10.15252/embj.2021108714</a>.","apa":"Bajaj, S., Bagley, J. A., Sommer, C. M., Vertesy, A., Nagumo Wong, S., Krenn, V., … Knoblich, J. A. (2021). Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2021108714\">https://doi.org/10.15252/embj.2021108714</a>","ama":"Bajaj S, Bagley JA, Sommer CM, et al. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. <i>EMBO Journal</i>. 2021;40(23). doi:<a href=\"https://doi.org/10.15252/embj.2021108714\">10.15252/embj.2021108714</a>","mla":"Bajaj, Sunanjay, et al. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” <i>EMBO Journal</i>, vol. 40, no. 23, e108714, Embo Press, 2021, doi:<a href=\"https://doi.org/10.15252/embj.2021108714\">10.15252/embj.2021108714</a>.","short":"S. Bajaj, J.A. Bagley, C.M. Sommer, A. Vertesy, S. Nagumo Wong, V. Krenn, J. Lévi-Strauss, J.A. Knoblich, EMBO Journal 40 (2021).","ista":"Bajaj S, Bagley JA, Sommer CM, Vertesy A, Nagumo Wong S, Krenn V, Lévi-Strauss J, Knoblich JA. 2021. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. 40(23), e108714."},"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":40,"has_accepted_license":"1","year":"2021","_id":"10179"},{"month":"09","language":[{"iso":"eng"}],"ddc":["000"],"day":"01","main_file_link":[{"url":"https://www.jmlr.org/papers/v22/21-0366.html","open_access":"1"}],"intvolume":"        22","file":[{"file_id":"10192","date_updated":"2021-10-27T15:34:18Z","file_size":3527521,"file_name":"2021_JMachLearnRes_Hoefler.pdf","checksum":"3389d9d01fc58f8fb4c1a53e14a8abbf","relation":"main_file","access_level":"open_access","creator":"cziletti","content_type":"application/pdf","success":1,"date_created":"2021-10-27T15:34:18Z"}],"publication_status":"published","scopus_import":"1","quality_controlled":"1","author":[{"first_name":"Torsten","last_name":"Hoefler","full_name":"Hoefler, Torsten"},{"first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ben-Nun","first_name":"Tal","full_name":"Ben-Nun, Tal"},{"last_name":"Dryden","first_name":"Nikoli","full_name":"Dryden, Nikoli"},{"full_name":"Peste, Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87","first_name":"Elena-Alexandra","last_name":"Peste"}],"date_published":"2021-09-01T00:00:00Z","article_processing_charge":"No","date_updated":"2022-05-13T09:36:08Z","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":"2021-10-27T15:34:18Z","citation":{"apa":"Hoefler, T., Alistarh, D.-A., Ben-Nun, T., Dryden, N., &#38; Peste, E.-A. (2021). Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks. <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research.","ieee":"T. Hoefler, D.-A. Alistarh, T. Ben-Nun, N. Dryden, and E.-A. Peste, “Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks,” <i>Journal of Machine Learning Research</i>, vol. 22, no. 241. Journal of Machine Learning Research, pp. 1–124, 2021.","chicago":"Hoefler, Torsten, Dan-Adrian Alistarh, Tal Ben-Nun, Nikoli Dryden, and Elena-Alexandra Peste. “Sparsity in Deep Learning: Pruning and Growth for Efficient Inference and Training in Neural Networks.” <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research, 2021.","short":"T. Hoefler, D.-A. Alistarh, T. Ben-Nun, N. Dryden, E.-A. Peste, Journal of Machine Learning Research 22 (2021) 1–124.","mla":"Hoefler, Torsten, et al. “Sparsity in Deep Learning: Pruning and Growth for Efficient Inference and Training in Neural Networks.” <i>Journal of Machine Learning Research</i>, vol. 22, no. 241, Journal of Machine Learning Research, 2021, pp. 1–124.","ista":"Hoefler T, Alistarh D-A, Ben-Nun T, Dryden N, Peste E-A. 2021. Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks. Journal of Machine Learning Research. 22(241), 1–124.","ama":"Hoefler T, Alistarh D-A, Ben-Nun T, Dryden N, Peste E-A. Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks. <i>Journal of Machine Learning Research</i>. 2021;22(241):1-124."},"publication_identifier":{"issn":["1532-4435"],"eissn":["1533-7928"]},"oa":1,"acknowledgement":"We thank Doug Burger, Steve Scott, Marco Heddes, and the respective teams at Microsoft for inspiring discussions on the topic. We thank Angelika Steger for uplifting debates about the connections to biological brains, Sidak Pal Singh for his support regarding experimental results, and Utku Evci as well as Xin Wang for comments on previous versions of this\r\nwork. Special thanks go to Bernhard Schölkopf, our JMLR editor Samy Bengio, and the three anonymous reviewers who provided excellent comprehensive, pointed, and deep review comments that improved the quality of our manuscript significantly.","status":"public","issue":"241","article_type":"original","external_id":{"arxiv":["2102.00554"]},"_id":"10180","year":"2021","has_accepted_license":"1","volume":22,"page":"1-124","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","abstract":[{"lang":"eng","text":"The growing energy and performance costs of deep learning have driven the community to reduce the size of neural networks by selectively pruning components. Similarly to their biological counterparts, sparse networks generalize just as well, sometimes even better than, the original dense networks. Sparsity promises to reduce the memory footprint of regular networks to fit mobile devices, as well as shorten training time for ever growing networks. In this paper, we survey prior work on sparsity in deep learning and provide an extensive tutorial of sparsification for both inference and training. We describe approaches to remove and add elements of neural networks, different training strategies to achieve model sparsity, and mechanisms to exploit sparsity in practice. Our work distills ideas from more than 300 research papers and provides guidance to practitioners who wish to utilize sparsity today, as well as to researchers whose goal is to push the frontier forward. We include the necessary background on mathematical methods in sparsification, describe phenomena such as early structure adaptation, the intricate relations between sparsity and the training process, and show techniques for achieving acceleration on real hardware. We also define a metric of pruned parameter efficiency that could serve as a baseline for comparison of different sparse networks. We close by speculating on how sparsity can improve future workloads and outline major open problems in the field."}],"arxiv":1,"date_created":"2021-10-24T22:01:34Z","oa_version":"Published Version","publication":"Journal of Machine Learning Research","department":[{"_id":"DaAl"}],"title":"Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks","publisher":"Journal of Machine Learning Research"}]