[{"article_processing_charge":"No","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11932"}]},"date_created":"2021-10-04T06:23:34Z","language":[{"iso":"eng"}],"ec_funded":1,"_id":"10077","oa_version":"Preprint","status":"public","acknowledgement":"We thank Peter Baracskay, Karola Kaefer and Hugo Malagon-Vina for the acquisition of the data. We thank Federico Stella for comments on an earlier version of the manuscript. MN was supported by European Union Horizon 2020 grant 665385, JC was supported by European Research Council consolidator grant 281511, GT was supported by the Austrian Science Fund (FWF) grant P34015, CS was supported by an IST fellow grant, National Institute of Mental Health Award 1R01MH125571-01, by the National Science Foundation under NSF Award No. 1922658 and a Google faculty award.","oa":1,"publication_status":"submitted","year":"2021","date_updated":"2024-03-25T23:30:09Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_published":"2021-09-29T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publisher":"Cold Spring Harbor Laboratory","author":[{"orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele","last_name":"Nardin","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele"},{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari"},{"last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","first_name":"Cristina","full_name":"Savin, Cristina"}],"month":"09","department":[{"_id":"GradSch"},{"_id":"JoCs"},{"_id":"GaTk"}],"title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","day":"29","type":"preprint","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.09.28.460602","open_access":"1"}],"citation":{"ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2021.09.28.460602\">https://doi.org/10.1101/2021.09.28.460602</a>.","ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv, <a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>.","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>.","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., &#38; Savin, C. (n.d.). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2021.09.28.460602\">https://doi.org/10.1101/2021.09.28.460602</a>","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.)."},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"},{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"281511"},{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","name":"Efficient coding with biophysical realism","grant_number":"P34015"}],"doi":"10.1101/2021.09.28.460602","abstract":[{"lang":"eng","text":"Although much is known about how single neurons in the hippocampus represent an animal’s position, how cell-cell interactions contribute to spatial coding remains poorly understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured cell-to-cell interactions whose statistics depend on familiar vs. novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the signal-to-noise ratio of their spatial inputs. Moreover, the topology of the interactions facilitates linear decodability, making the information easy to read out by downstream circuits. These findings suggest that the efficient coding hypothesis is not applicable only to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain."}],"publication":"bioRxiv"},{"publisher":"Cold Spring Harbor Laboratory","author":[{"orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele","first_name":"Michele","last_name":"Nardin","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","last_name":"Käfer","full_name":"Käfer, Karola"},{"orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2021-10-02T00:00:00Z","publication_status":"submitted","year":"2021","date_updated":"2021-10-05T12:34:26Z","acknowledgement":"We thank Federico Stella for invaluable suggestions and discussions. We thank Yosman BapatDhar and Andrea Cumpelik for comments, help and suggestions on the exposure of the text. We thank Predrag Živadinović and Juliana Couras for comments on the text and the figures. This work was supported by the EU-FP7 MC-ITN IN-SENS (grant 607616).","oa":1,"oa_version":"Preprint","status":"public","date_created":"2021-10-04T06:28:32Z","language":[{"iso":"eng"}],"ec_funded":1,"_id":"10080","article_processing_charge":"No","publication":"bioRxiv","abstract":[{"text":"Hippocampal and neocortical neural activity is modulated by the position of the individual in space. While hippocampal neurons provide the basis for a spatial map, prefrontal cortical neurons generalize over environmental features. Whether these generalized representations result from a bidirectional interaction with, or are mainly derived from hippocampal spatial representations is not known. By examining simultaneously recorded hippocampal and medial prefrontal neurons, we observed that prefrontal spatial representations show a delayed coherence with hippocampal ones. We also identified subpopulations of cells in the hippocampus and medial prefrontal cortex that formed functional cross-area couplings; these resembled the optimal connections predicted by a probabilistic model of spatial information transfer and generalization. Moreover, cross-area couplings were strongest and had the shortest delay preceding spatial decision-making. Our results suggest that generalized spatial coding in the medial prefrontal cortex is inherited from spatial representations in the hippocampus, and that the routing of information can change dynamically with behavioral demands.","lang":"eng"}],"project":[{"_id":"257BBB4C-B435-11E9-9278-68D0E5697425","name":"Inter-and intracellular signalling in schizophrenia","call_identifier":"FP7","grant_number":"607616"}],"doi":"10.1101/2021.09.30.462269","citation":{"ista":"Nardin M, Käfer K, Csicsvari JL. The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus. bioRxiv, <a href=\"https://doi.org/10.1101/2021.09.30.462269\">10.1101/2021.09.30.462269</a>.","ama":"Nardin M, Käfer K, Csicsvari JL. The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.09.30.462269\">10.1101/2021.09.30.462269</a>","chicago":"Nardin, Michele, Karola Käfer, and Jozsef L Csicsvari. “The Generalized Spatial Representation in the Prefrontal Cortex Is Inherited from the Hippocampus.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2021.09.30.462269\">https://doi.org/10.1101/2021.09.30.462269</a>.","apa":"Nardin, M., Käfer, K., &#38; Csicsvari, J. L. (n.d.). The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2021.09.30.462269\">https://doi.org/10.1101/2021.09.30.462269</a>","mla":"Nardin, Michele, et al. “The Generalized Spatial Representation in the Prefrontal Cortex Is Inherited from the Hippocampus.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2021.09.30.462269\">10.1101/2021.09.30.462269</a>.","short":"M. Nardin, K. Käfer, J.L. Csicsvari, BioRxiv (n.d.).","ieee":"M. Nardin, K. Käfer, and J. L. Csicsvari, “The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory."},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.09.30.462269"}],"title":"The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"02","type":"preprint","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"month":"10"},{"date_created":"2021-10-04T13:33:10Z","_id":"10083","file_date_updated":"2022-12-20T23:30:03Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_updated":"2025-05-07T11:12:33Z","author":[{"full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin"}],"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"month":"10","day":"06","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"citation":{"apa":"Li, L. (2021). <i>Rapid cell growth regulation in Arabidopsis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10083\">https://doi.org/10.15479/at:ista:10083</a>","short":"L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science and Technology Austria, 2021.","mla":"Li, Lanxin. <i>Rapid Cell Growth Regulation in Arabidopsis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10083\">10.15479/at:ista:10083</a>.","ama":"Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10083\">10.15479/at:ista:10083</a>","chicago":"Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10083\">https://doi.org/10.15479/at:ista:10083</a>.","ista":"Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria.","ieee":"L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science and Technology Austria, 2021."},"related_material":{"record":[{"relation":"part_of_dissertation","id":"442","status":"public"},{"id":"8931","status":"public","relation":"part_of_dissertation"},{"id":"9287","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8283","status":"public"},{"relation":"part_of_dissertation","id":"8986","status":"public"},{"status":"public","id":"10015","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10095","status":"public"},{"status":"public","id":"6627","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"ec_funded":1,"supervisor":[{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"article_processing_charge":"No","has_accepted_license":"1","oa":1,"oa_version":"Published Version","status":"public","date_published":"2021-10-06T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"year":"2021","publication_status":"published","publisher":"Institute of Science and Technology Austria","file":[{"embargo":"2022-10-14","file_size":8616142,"file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf","date_updated":"2022-12-20T23:30:03Z","file_id":"10138","checksum":"3b2f55b3b8ae05337a0dcc1cd8595b10","access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","relation":"main_file","date_created":"2021-10-14T08:00:07Z"},{"access_level":"closed","creator":"cchlebak","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"f23ed258ca894f6aabf58b0c128bf242","relation":"source_file","date_created":"2021-10-14T08:00:13Z","embargo_to":"open_access","file_size":15058499,"file_id":"10139","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014.docx","date_updated":"2022-12-20T23:30:03Z"}],"ddc":["575"],"title":"Rapid cell growth regulation in Arabidopsis","degree_awarded":"PhD","type":"dissertation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.15479/at:ista:10083","abstract":[{"lang":"eng","text":"Plant motions occur across a wide spectrum of timescales, ranging from seed dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term adaptation of gross architecture. Relatively fast motions include water-driven growth as exemplified by root cell expansion under abiotic/biotic stresses or during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered by the phytohormone auxin. However, the cellular and molecular mechanisms are still largely unknown. This thesis covers the studies about this topic as follows. By taking advantage of microfluidics combined with live imaging, pharmaceutical tools, and transgenic lines, we examined the kinetics of and causal relationship among various auxininduced rapid cellular changes in root growth, apoplastic pH, cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology. We revealed that CMT reorientation and vacuolar constriction are the consequence of growth itself instead of responding directly to auxin. In contrast, auxin induces apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+ inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling. To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore the relation of two signaling pathways. Assisted with biochemistry and fluorescent imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with each other. The ability of TIR1/AFB binding to membrane lipid provides a basis for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides, transgenic analysis combined with genetic engineering and biochemistry showed that  vi\r\nthey do function in the same pathway. Particularly, auxin-induced TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely, TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling. To follow the study of rapid growth regulation, we analyzed another rapid growth regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid and reversible growth inhibition caused by H + influx, highly resembling but not dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1 hour, contributing to the sustained RALF1-triggered growth inhibition. These studies collectively contribute to understanding rapid regulation on plant cell\r\ngrowth, novel auxin signaling pathway as well as auxin-peptide crosstalk. "}]},{"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"doi":"10.21203/rs.3.rs-266395/v3","abstract":[{"lang":"eng","text":"Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment."}],"publication":"Research Square","article_processing_charge":"No","related_material":{"record":[{"status":"public","id":"10083","relation":"dissertation_contains"},{"relation":"later_version","status":"public","id":"10223"}]},"language":[{"iso":"eng"}],"ec_funded":1,"article_number":"266395","oa_version":"Preprint","status":"public","oa":1,"year":"2021","publication_status":"accepted","publication_identifier":{"issn":["2693-5015"]},"date_published":"2021-09-09T00:00:00Z","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"month":"09","day":"09","citation":{"mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <i>Research Square</i>, 266395, doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>.","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (n.d.). Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Research Square (n.d.).","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>","chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <i>Research Square</i>, n.d. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>.","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square, 266395.","ieee":"L. Li <i>et al.</i>, “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” <i>Research Square</i>. ."},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"},{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351"}],"date_created":"2021-10-06T08:56:22Z","_id":"10095","acknowledgement":"We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001.), the Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910),  the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship Council to J.C.","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2024-10-29T10:22:44Z","license":"https://creativecommons.org/licenses/by/4.0/","author":[{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X"},{"last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"last_name":"Roosjen","first_name":"Mark","full_name":"Roosjen, Mark"},{"full_name":"Takahashi, Koji","first_name":"Koji","last_name":"Takahashi"},{"orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia"},{"orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jian","last_name":"Chen","full_name":"Chen, Jian"},{"last_name":"Shabala","first_name":"Lana","full_name":"Shabala, Lana"},{"full_name":"Smet, Wouter","last_name":"Smet","first_name":"Wouter"},{"first_name":"Hong","last_name":"Ren","full_name":"Ren, Hong"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"full_name":"Shabala, Sergey","last_name":"Shabala","first_name":"Sergey"},{"last_name":"De Rybel","first_name":"Bert","full_name":"De Rybel, Bert"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"},{"last_name":"Kinoshita","first_name":"Toshinori","full_name":"Kinoshita, Toshinori"},{"full_name":"Gray, William M.","last_name":"Gray","first_name":"William M."},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}]},{"date_updated":"2023-08-14T07:21:51Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"keyword":["virology","infectious diseases"],"author":[{"orcid":"0000-0003-1756-6564","full_name":"Obr, Martin","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078"},{"full_name":"Dick, Robert A.","last_name":"Dick","first_name":"Robert A."}],"article_type":"original","date_created":"2021-10-07T09:13:29Z","_id":"10103","volume":13,"acknowledgement":"We thank Volker M. Vogt for his critical comments in preparation of the review.","file_date_updated":"2021-10-08T10:38:15Z","issue":"9","citation":{"ieee":"M. Obr, F. K. Schur, and R. A. Dick, “A structural perspective of the role of IP6 in immature and mature retroviral assembly,” <i>Viruses</i>, vol. 13, no. 9. MDPI, 2021.","chicago":"Obr, Martin, Florian KM Schur, and Robert A. Dick. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” <i>Viruses</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/v13091853\">https://doi.org/10.3390/v13091853</a>.","ista":"Obr M, Schur FK, Dick RA. 2021. A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. 13(9), 1853.","ama":"Obr M, Schur FK, Dick RA. A structural perspective of the role of IP6 in immature and mature retroviral assembly. <i>Viruses</i>. 2021;13(9). doi:<a href=\"https://doi.org/10.3390/v13091853\">10.3390/v13091853</a>","mla":"Obr, Martin, et al. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” <i>Viruses</i>, vol. 13, no. 9, 1853, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/v13091853\">10.3390/v13091853</a>.","short":"M. Obr, F.K. Schur, R.A. Dick, Viruses 13 (2021).","apa":"Obr, M., Schur, F. K., &#38; Dick, R. A. (2021). A structural perspective of the role of IP6 in immature and mature retroviral assembly. <i>Viruses</i>. MDPI. <a href=\"https://doi.org/10.3390/v13091853\">https://doi.org/10.3390/v13091853</a>"},"project":[{"name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31445"}],"external_id":{"pmid":["34578434"],"isi":["000699841100001"]},"isi":1,"pmid":1,"month":"09","department":[{"_id":"FlSc"}],"intvolume":"        13","day":"17","publication_identifier":{"issn":["1999-4915"]},"publication_status":"published","year":"2021","date_published":"2021-09-17T00:00:00Z","quality_controlled":"1","publisher":"MDPI","article_processing_charge":"Yes","language":[{"iso":"eng"}],"article_number":"1853","oa_version":"Published Version","status":"public","has_accepted_license":"1","oa":1,"doi":"10.3390/v13091853","abstract":[{"lang":"eng","text":"The small cellular molecule inositol hexakisphosphate (IP6) has been known for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like particles. However, the molecular details underlying this effect have been determined only recently, with the identification of the IP6 binding site in the immature Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice via a second IP6 binding site, and enhances core stability, creating a favorable environment for reverse transcription. IP6 also enhances assembly of other retroviruses, from both the Lentivirus and the Alpharetrovirus genera. These findings suggest that IP6 may have a conserved function throughout the family Retroviridae. Here, we discuss the different steps in the viral life cycle that are influenced by IP6, and describe in detail how IP6 interacts with the immature and mature lattices of different retroviruses."}],"publication":"Viruses","ddc":["616"],"file":[{"date_created":"2021-10-08T10:38:15Z","relation":"main_file","creator":"cchlebak","content_type":"application/pdf","access_level":"open_access","checksum":"bcfd72a12977d48e22df3d0cc55aacf1","file_id":"10115","date_updated":"2021-10-08T10:38:15Z","success":1,"file_name":"2021_Viruses_Obr.pdf","file_size":4146796}],"title":"A structural perspective of the role of IP6 in immature and mature retroviral assembly","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article"},{"doi":"10.1007/978-3-030-88494-9_12","abstract":[{"text":"We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs.","lang":"eng"}],"publication":"International Conference on Runtime Verification","file":[{"creator":"fmuehlbo","access_level":"open_access","content_type":"application/pdf","checksum":"554c7fdb259eda703a8b6328a6dad55a","date_created":"2021-10-07T23:32:18Z","relation":"main_file","file_size":350632,"file_id":"10109","date_updated":"2021-10-07T23:32:18Z","file_name":"differentialmonitoring-cameraready-openaccess.pdf","success":1}],"ddc":["005"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"conference","title":"Differential monitoring","publication_status":"published","publication_identifier":{"eisbn":["978-3-030-88494-9"],"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["978-3-030-88493-2"]},"year":"2021","date_published":"2021-10-06T00:00:00Z","publisher":"Springer Nature","quality_controlled":"1","page":"231-243","article_processing_charge":"No","related_material":{"record":[{"relation":"extended_version","status":"public","id":"9946"}]},"language":[{"iso":"eng"}],"alternative_title":["LNCS"],"status":"public","oa_version":"Preprint","oa":1,"has_accepted_license":"1","citation":{"apa":"Mühlböck, F., &#38; Henzinger, T. A. (2021). Differential monitoring. In <i>International Conference on Runtime Verification</i> (Vol. 12974, pp. 231–243). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">https://doi.org/10.1007/978-3-030-88494-9_12</a>","mla":"Mühlböck, Fabian, and Thomas A. Henzinger. “Differential Monitoring.” <i>International Conference on Runtime Verification</i>, vol. 12974, Springer Nature, 2021, pp. 231–43, doi:<a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">10.1007/978-3-030-88494-9_12</a>.","short":"F. Mühlböck, T.A. Henzinger, in:, International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 231–243.","ista":"Mühlböck F, Henzinger TA. 2021. Differential monitoring. International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 231–243.","chicago":"Mühlböck, Fabian, and Thomas A Henzinger. “Differential Monitoring.” In <i>International Conference on Runtime Verification</i>, 12974:231–43. Cham: Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">https://doi.org/10.1007/978-3-030-88494-9_12</a>.","ama":"Mühlböck F, Henzinger TA. Differential monitoring. In: <i>International Conference on Runtime Verification</i>. Vol 12974. Cham: Springer Nature; 2021:231-243. doi:<a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">10.1007/978-3-030-88494-9_12</a>","ieee":"F. Mühlböck and T. A. Henzinger, “Differential monitoring,” in <i>International Conference on Runtime Verification</i>, Virtual, 2021, vol. 12974, pp. 231–243."},"conference":{"end_date":"2021-10-14","start_date":"2021-10-11","name":"RV: Runtime Verification","location":"Virtual"},"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211"}],"scopus_import":"1","external_id":{"isi":["000719383800012"]},"month":"10","department":[{"_id":"ToHe"}],"isi":1,"day":"06","intvolume":"     12974","place":"Cham","date_updated":"2023-08-14T07:20:30Z","author":[{"first_name":"Fabian","last_name":"Mühlböck","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","orcid":"0000-0003-1548-0177","full_name":"Mühlböck, Fabian"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"}],"keyword":["run-time verification","software engineering","implicit specification"],"_id":"10108","date_created":"2021-10-07T23:30:10Z","file_date_updated":"2021-10-07T23:32:18Z","acknowledgement":"The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Mae Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper.","volume":12974},{"tmp":{"short":"GPL 3.0","legal_code_url":"https://www.gnu.org/licenses/gpl-3.0.en.html","name":"GNU General Public License 3.0"},"date_updated":"2024-03-25T23:30:07Z","year":"2021","date_published":"2021-12-16T00:00:00Z","publisher":"IST Austria","license":"https://opensource.org/licenses/GPL-3.0","author":[{"first_name":"José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","last_name":"Guzmán","full_name":"Guzmán, José","orcid":"0000-0003-2209-5242"},{"orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4710-2082","full_name":"Espinoza Martinez, Claudia ","first_name":"Claudia ","last_name":"Espinoza Martinez","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","full_name":"Zhang, Xiaomin"},{"last_name":"Suter","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","first_name":"Benjamin","orcid":"0000-0002-9885-6936","full_name":"Suter, Benjamin"},{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"_id":"10110","date_created":"2021-10-08T06:44:22Z","related_material":{"link":[{"description":"News on IST Webpage","relation":"press_release","url":"https://ist.ac.at/en/news/spot-the-difference/"}],"record":[{"id":"10816","status":"public","relation":"used_for_analysis_in"}]},"status":"public","oa":1,"file_date_updated":"2021-10-08T08:46:04Z","has_accepted_license":"1","citation":{"mla":"Guzmán, José, et al. <i>How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network</i>. IST Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>.","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, (2021).","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &#38; Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">https://doi.org/10.15479/AT:ISTA:10110</a>","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>.","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>","chicago":"Guzmán, José, Alois Schlögl, Claudia  Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” IST Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">https://doi.org/10.15479/AT:ISTA:10110</a>.","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021."},"doi":"10.15479/AT:ISTA:10110","abstract":[{"text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks.","lang":"eng"}],"department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"month":"12","file":[{"file_size":332990101,"date_updated":"2021-10-08T08:46:04Z","success":1,"file_name":"patternseparation-main (1).zip","file_id":"10114","checksum":"f92f8931cad0aa7e411c1715337bf408","creator":"cchlebak","content_type":"application/x-zip-compressed","access_level":"open_access","relation":"main_file","date_created":"2021-10-08T08:46:04Z"}],"ddc":["005"],"day":"16","type":"software","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network"},{"article_processing_charge":"No","language":[{"iso":"eng"}],"ec_funded":1,"article_number":"e68238","oa_version":"Published Version","status":"public","has_accepted_license":"1","oa":1,"year":"2021","publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"date_published":"2021-09-17T00:00:00Z","quality_controlled":"1","publisher":"eLife Sciences Publications","ddc":["610"],"file":[{"date_updated":"2021-10-11T14:15:07Z","success":1,"file_name":"2021_eLife_VuongBrender.pdf","file_id":"10122","file_size":1774624,"relation":"main_file","date_created":"2021-10-11T14:15:07Z","checksum":"b465e172d2b1f57aa26a2571a085d052","creator":"cchlebak","access_level":"open_access","content_type":"application/pdf"}],"title":"Neuronal calmodulin levels are controlled by CAMTA transcription factors","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","doi":"10.7554/eLife.68238","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."}],"publication":"eLife","date_created":"2021-10-10T22:01:22Z","_id":"10116","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).","volume":10,"file_date_updated":"2021-10-11T14:15:07Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-14T07:23:39Z","author":[{"first_name":"Thanh","last_name":"Vuong-Brender","id":"D389312E-10C4-11EA-ABF4-A4B43DDC885E","full_name":"Vuong-Brender, Thanh"},{"full_name":"Flynn, Sean","last_name":"Flynn","first_name":"Sean"},{"full_name":"Vallis, Yvonne","first_name":"Yvonne","id":"05A2795C-31B5-11EA-83A7-7DA23DDC885E","last_name":"Vallis"},{"first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"De Bono","full_name":"De Bono, Mario","orcid":"0000-0001-8347-0443"}],"article_type":"original","isi":1,"pmid":1,"department":[{"_id":"MaDe"}],"month":"09","intvolume":"        10","day":"17","citation":{"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.","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>","ista":"Vuong-Brender T, Flynn S, Vallis Y, de Bono M. 2021. Neuronal calmodulin levels are controlled by CAMTA transcription factors. eLife. 10, e68238.","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>.","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>.","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>"},"project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","external_id":{"isi":["000695716100001"],"pmid":["34499028"]}},{"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).","volume":297,"issue":"3","file_date_updated":"2021-10-11T12:20:58Z","date_created":"2021-10-10T22:01:23Z","_id":"10117","author":[{"last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425","first_name":"Murat","orcid":"0000-0001-8945-6992","full_name":"Artan, Murat"},{"full_name":"Barratt, Stephen","first_name":"Stephen","last_name":"Barratt","id":"57740d2b-2a88-11ec-97cf-d9e6d1b39677"},{"full_name":"Flynn, Sean M.","first_name":"Sean M.","last_name":"Flynn"},{"last_name":"Begum","first_name":"Farida","full_name":"Begum, Farida"},{"last_name":"Skehel","first_name":"Mark","full_name":"Skehel, Mark"},{"id":"2A103192-F248-11E8-B48F-1D18A9856A87","last_name":"Nicolas","first_name":"Armel","full_name":"Nicolas, Armel"},{"orcid":"0000-0001-8347-0443","full_name":"De Bono, Mario","first_name":"Mario","last_name":"De Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-14T07:24:09Z","intvolume":"       297","day":"01","isi":1,"department":[{"_id":"MaDe"},{"_id":"LifeSc"}],"month":"09","external_id":{"isi":["000706409200006"]},"citation":{"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.","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.","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>.","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>","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>.","short":"M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de Bono, Journal of Biological Chemistry 297 (2021).","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>"},"project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"scopus_import":"1","oa_version":"Published Version","status":"public","has_accepted_license":"1","oa":1,"article_processing_charge":"Yes","language":[{"iso":"eng"}],"ec_funded":1,"article_number":"101094","quality_controlled":"1","publisher":"Elsevier","publication_identifier":{"issn":["0021-9258"],"eissn":["1083-351X"]},"year":"2021","publication_status":"published","date_published":"2021-09-01T00:00:00Z","title":"Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_updated":"2021-10-11T12:20:58Z","file_name":"2021_JBC_Artan.pdf","success":1,"file_id":"10121","file_size":1680010,"date_created":"2021-10-11T12:20:58Z","relation":"main_file","checksum":"19e39d36c5b9387c6dc0e89c9ae856ab","creator":"cchlebak","content_type":"application/pdf","access_level":"open_access"}],"ddc":["612"],"abstract":[{"lang":"eng","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."}],"publication":"Journal of Biological Chemistry","doi":"10.1016/J.JBC.2021.101094"},{"file_date_updated":"2022-02-03T13:16:14Z","issue":"52","volume":33,"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.","_id":"10123","date_created":"2021-10-11T20:07:24Z","author":[{"full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu"},{"orcid":"0000-0003-4566-5877","full_name":"Calcabrini, Mariano","last_name":"Calcabrini","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","first_name":"Mariano"},{"first_name":"Yuan","last_name":"Yu","full_name":"Yu, Yuan"},{"first_name":"Aziz","last_name":"Genç","full_name":"Genç, Aziz"},{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","last_name":"Chang","first_name":"Cheng","full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277"},{"orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso"},{"last_name":"Kleinhanns","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias","full_name":"Kleinhanns, Tobias"},{"full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425","last_name":"Lee","first_name":"Seungho"},{"last_name":"Llorca","first_name":"Jordi","full_name":"Llorca, Jordi"},{"last_name":"Cojocaru‐Mirédin","first_name":"Oana","full_name":"Cojocaru‐Mirédin, Oana"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843"}],"keyword":["mechanical engineering","mechanics of materials","general materials science"],"article_type":"original","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-14T07:25:27Z","day":"29","intvolume":"        33","department":[{"_id":"EM-Fac"},{"_id":"MaIb"}],"month":"12","isi":1,"pmid":1,"external_id":{"isi":["000709899300001"],"pmid":["34626034"]},"project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"},{"name":"Bottom-up Engineering for Thermoelectric Applications","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889"},{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"scopus_import":"1","citation":{"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.","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>","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>.","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.","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>","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>.","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)."},"oa":1,"has_accepted_license":"1","status":"public","oa_version":"Published Version","article_number":"2106858","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12885"}]},"language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","publisher":"Wiley","quality_controlled":"1","date_published":"2021-12-29T00:00:00Z","publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"publication_status":"published","year":"2021","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe","ddc":["620"],"file":[{"file_size":5595666,"date_updated":"2022-02-03T13:16:14Z","success":1,"file_name":"2021_AdvancedMaterials_Liu.pdf","file_id":"10720","checksum":"990bccc527c64d85cf1c97885110b5f4","access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","date_created":"2022-02-03T13:16:14Z","relation":"main_file"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"publication":"Advanced Materials","abstract":[{"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.","lang":"eng"}],"doi":"10.1002/adma.202106858"},{"author":[{"full_name":"Palaia, Ivan","first_name":"Ivan","last_name":"Palaia"},{"full_name":"Paraschiv, Alexandru","last_name":"Paraschiv","first_name":"Alexandru"},{"full_name":"Debets, Vincent","last_name":"Debets","first_name":"Vincent"},{"full_name":"Storm, Cornelis","first_name":"Cornelis","last_name":"Storm"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"article_type":"original","publisher":"American Chemical Society","quality_controlled":"1","date_published":"2021-09-22T00:00:00Z","date_updated":"2021-10-12T09:50:19Z","publication_status":"published","year":"2021","oa":1,"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.).","status":"public","extern":"1","oa_version":"Preprint","_id":"10124","date_created":"2021-10-12T07:31:21Z","language":[{"iso":"eng"}],"article_processing_charge":"No","publication":"ACS Nano","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"}],"external_id":{"pmid":["34550677 "]},"doi":"10.1021/acsnano.1c02777 ","citation":{"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.","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>","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>.","ista":"Palaia I, Paraschiv A, Debets V, Storm C, Šarić A. 2021. Durotaxis of passive nanoparticles on elastic membranes. ACS Nano.","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>","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)."},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.04.01.438065"}],"type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"22","title":"Durotaxis of passive nanoparticles on elastic membranes","month":"09","pmid":1},{"_id":"10125","language":[{"iso":"eng"}],"date_created":"2021-10-12T07:45:07Z","article_processing_charge":"No","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","extern":"1","oa_version":"Preprint","date_published":"2021-03-23T00:00:00Z","date_updated":"2021-10-12T09:50:26Z","publication_status":"submitted","year":"2021","author":[{"full_name":"Harker-Kirschneck, L.","first_name":"L.","last_name":"Harker-Kirschneck"},{"full_name":"Hafner, A. E.","first_name":"A. E.","last_name":"Hafner"},{"first_name":"T.","last_name":"Yao","full_name":"Yao, T."},{"last_name":"Pulschen","first_name":"A.","full_name":"Pulschen, A."},{"first_name":"F.","last_name":"Hurtig","full_name":"Hurtig, F."},{"full_name":"Vanhille-Campos, C.","last_name":"Vanhille-Campos","first_name":"C."},{"first_name":"D.","last_name":"Hryniuk","full_name":"Hryniuk, D."},{"full_name":"Culley, S.","first_name":"S.","last_name":"Culley"},{"last_name":"Henriques","first_name":"R.","full_name":"Henriques, R."},{"first_name":"B.","last_name":"Baum","full_name":"Baum, B."},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"publisher":"Cold Spring Harbor Laboratory","month":"03","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.03.23.436559","open_access":"1"}],"day":"23","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"preprint","title":"Physical mechanisms of ESCRT-III-driven cell division in archaea","doi":"10.1101/2021.03.23.436559","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>","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.).","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>.","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>","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."},"publication":"bioRxiv","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."}]},{"type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Anderson localization of composite particles","main_file_link":[{"url":"https://arxiv.org/abs/2011.06279","open_access":"1"}],"doi":"10.1103/physrevlett.127.160602","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."}],"publication":"Physical Review Letters","article_processing_charge":"No","article_number":"160602","ec_funded":1,"language":[{"iso":"eng"}],"status":"public","oa_version":"Preprint","oa":1,"year":"2021","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"publication_status":"published","date_published":"2021-10-12T00:00:00Z","publisher":"American Physical Society ","quality_controlled":"1","month":"10","department":[{"_id":"MiLe"}],"isi":1,"day":"12","intvolume":"       127","arxiv":1,"citation":{"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>","ista":"Suzuki F, Lemeshko M, Zurek WH, Krems RV. 2021. Anderson localization of composite particles. Physical Review Letters. 127(16), 160602.","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>.","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>","short":"F. Suzuki, M. Lemeshko, W.H. Zurek, R.V. Krems, Physical Review Letters 127 (2021).","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>.","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."},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"},{"name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"801770"}],"scopus_import":"1","external_id":{"arxiv":["2011.06279"],"isi":["000707495700001"]},"_id":"10134","date_created":"2021-10-13T09:21:33Z","issue":"16","volume":127,"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","date_updated":"2024-02-29T12:34:10Z","keyword":["General Physics and Astronomy"],"author":[{"id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E","last_name":"Suzuki","first_name":"Fumika","full_name":"Suzuki, Fumika","orcid":"0000-0003-4982-5970"},{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"last_name":"Zurek","first_name":"Wojciech H.","full_name":"Zurek, Wojciech H."},{"last_name":"Krems","first_name":"Roman V.","full_name":"Krems, Roman V."}],"article_type":"original"},{"file_date_updated":"2022-12-20T23:30:05Z","_id":"10135","date_created":"2021-10-13T13:42:48Z","author":[{"first_name":"Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","last_name":"Semerádová","full_name":"Semerádová, Hana"}],"date_updated":"2024-01-25T10:53:29Z","day":"13","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"month":"10","project":[{"grant_number":"24746","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis.","_id":"261821BC-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"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>","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>.","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>","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>.","ista":"Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria.","ieee":"H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021."},"oa":1,"has_accepted_license":"1","status":"public","oa_version":"Published Version","related_material":{"record":[{"id":"9160","status":"public","relation":"part_of_dissertation"}]},"alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"article_processing_charge":"No","supervisor":[{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"publisher":"Institute of Science and Technology Austria","date_published":"2021-10-13T00:00:00Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-014-5"]},"year":"2021","publication_status":"published","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","degree_awarded":"PhD","title":"Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis","ddc":["570"],"file":[{"checksum":"ce7108853e6cec6224f17cd6429b51fe","creator":"cziletti","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_created":"2021-10-27T07:45:37Z","relation":"source_file","file_size":28508629,"embargo_to":"open_access","date_updated":"2022-12-20T23:30:05Z","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx","file_id":"10186"},{"date_created":"2021-10-27T07:45:57Z","relation":"main_file","creator":"cziletti","access_level":"open_access","content_type":"application/pdf","checksum":"0d7afb846e8e31ec794de47bf44e12ef","file_id":"10187","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf","date_updated":"2022-12-20T23:30:05Z","file_size":10623525,"embargo":"2022-10-28"}],"abstract":[{"lang":"eng","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."}],"doi":"10.15479/at:ista:10135"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","title":"Acute and chronic effects of a light-activated FGF receptor in keratinocytes in vitro and in mice","file":[{"file_size":2055981,"file_id":"10152","file_name":"2021_LifeScAlliance_Rauschendorfer.pdf","success":1,"date_updated":"2021-10-18T14:48:06Z","content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","checksum":"89fb95b211dbe8678809e7cca4626952","date_created":"2021-10-18T14:48:06Z","relation":"main_file"}],"ddc":["576"],"publication":"Life Science Alliance","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"}],"doi":"10.26508/lsa.202101100","oa":1,"has_accepted_license":"1","extern":"1","status":"public","oa_version":"Published Version","article_number":"e202101100","language":[{"iso":"eng"}],"article_processing_charge":"Yes","publisher":"Life Science Alliance","quality_controlled":"1","date_published":"2021-09-21T00:00:00Z","publication_identifier":{"eissn":["2575-1077"]},"year":"2021","publication_status":"published","day":"21","intvolume":"         4","month":"09","pmid":1,"external_id":{"pmid":["34548382"]},"scopus_import":"1","citation":{"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>.","short":"T. Rauschendorfer, S. Gurri, I. Heggli, L. Maddaluno, M. Meyer, Á. Inglés Prieto, H.L. Janovjak, S. Werner, Life Science Alliance 4 (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>","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.","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."},"issue":"11","file_date_updated":"2021-10-18T14:48:06Z","volume":4,"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).","_id":"10144","date_created":"2021-10-17T22:01:16Z","article_type":"original","author":[{"first_name":"Theresa","last_name":"Rauschendorfer","full_name":"Rauschendorfer, Theresa"},{"last_name":"Gurri","first_name":"Selina","full_name":"Gurri, Selina"},{"last_name":"Heggli","first_name":"Irina","full_name":"Heggli, Irina"},{"full_name":"Maddaluno, Luigi","last_name":"Maddaluno","first_name":"Luigi"},{"full_name":"Meyer, Michael","last_name":"Meyer","first_name":"Michael"},{"full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","last_name":"Inglés Prieto","first_name":"Álvaro"},{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sabine","last_name":"Werner","full_name":"Werner, Sabine"}],"date_updated":"2022-08-31T14:01:56Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"citation":{"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.","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>.","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>","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>.","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>"},"scopus_import":"1","project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000704581600001"],"pmid":["34616041"]},"isi":1,"pmid":1,"department":[{"_id":"LeSa"}],"month":"10","intvolume":"       598","day":"14","date_updated":"2023-08-14T08:01:21Z","article_type":"original","author":[{"orcid":"0000-0001-5618-3449","full_name":"Vercellino, Irene","last_name":"Vercellino","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","first_name":"Irene"},{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov"}],"date_created":"2021-10-17T22:01:17Z","_id":"10146","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.","volume":598,"issue":"7880","doi":"10.1038/s41586-021-03927-z","abstract":[{"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.","lang":"eng"}],"publication":"Nature","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"title":"Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2021","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication_status":"published","date_published":"2021-10-14T00:00:00Z","quality_controlled":"1","publisher":"Springer Nature","page":"364-367","article_processing_charge":"No","language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/boosting-the-cells-power-house/","description":"News on IST Webpage","relation":"press_release"}]},"ec_funded":1,"oa_version":"None","status":"public"},{"ddc":["000"],"file":[{"content_type":"application/pdf","creator":"bbickel","access_level":"open_access","checksum":"b0b26464df79b3a59e8ed82e4e19ab15","date_created":"2021-10-18T07:36:03Z","relation":"main_file","file_size":29796364,"file_id":"10149","date_updated":"2021-10-18T07:36:03Z","file_name":"degraen-UIST2021_Texture_Appropriation_CR_preprint.pdf"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"conference","title":"Capturing tactile properties of real surfaces for haptic reproduction","doi":"10.1145/3472749.3474798","abstract":[{"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.","lang":"eng"}],"publication":"34th Annual ACM Symposium","article_processing_charge":"No","ec_funded":1,"language":[{"iso":"eng"}],"status":"public","oa_version":"Preprint","oa":1,"has_accepted_license":"1","year":"2021","publication_status":"published","publication_identifier":{"isbn":["978-1-4503-8635-7"]},"date_published":"2021-10-10T00:00:00Z","publisher":"Association for Computing Machinery","quality_controlled":"1","page":"954-971","department":[{"_id":"BeBi"}],"month":"10","day":"10","citation":{"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.","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>","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>.","short":"D. Degraen, M. Piovarci, B. Bickel, A. Kruger, in:, 34th Annual ACM Symposium, Association for Computing Machinery, 2021, pp. 954–971.","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.","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>.","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>"},"conference":{"end_date":"2021-10-14","location":"Virtual","name":"UIST: User Interface Software and Technology","start_date":"2021-10-10"},"project":[{"_id":"2508E324-B435-11E9-9278-68D0E5697425","name":"Distributed 3D Object Design","call_identifier":"H2020","grant_number":"642841"}],"_id":"10148","date_created":"2021-10-18T07:36:11Z","file_date_updated":"2021-10-18T07:36:03Z","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).","date_updated":"2021-10-19T19:29:06Z","author":[{"full_name":"Degraen, Donald","first_name":"Donald","last_name":"Degraen"},{"first_name":"Michael","last_name":"Piovarci","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","full_name":"Piovarci, Michael"},{"first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"first_name":"Antonio","last_name":"Kruger","full_name":"Kruger, Antonio"}]},{"tmp":{"name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)"},"date_updated":"2021-11-12T11:30:07Z","author":[{"first_name":"Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","last_name":"Mühlböck","full_name":"Mühlböck, Fabian","orcid":"0000-0003-1548-0177"},{"last_name":"Tate","first_name":"Ross","full_name":"Tate, Ross"}],"license":"https://creativecommons.org/licenses/by-nd/4.0/","article_type":"original","keyword":["gradual typing","gradual guarantee","nominal","structural","call tags"],"date_created":"2021-10-19T12:48:44Z","_id":"10153","volume":5,"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.","file_date_updated":"2021-10-19T12:52:23Z","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF"}],"conference":{"location":"Chicago, IL, United States","start_date":"2021-10-17","name":"OOPSLA: Object-Oriented Programming, Systems, Languages, and Applications","end_date":"2021-10-23"},"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.","short":"F. Mühlböck, R. Tate, Proceedings of the ACM on Programming Languages 5 (2021).","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>","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>.","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>.","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.","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>"},"month":"10","department":[{"_id":"ToHe"}],"intvolume":"         5","day":"15","date_published":"2021-10-15T00:00:00Z","publication_status":"published","year":"2021","publication_identifier":{"eissn":["2475-1421"]},"quality_controlled":"1","publisher":"Association for Computing Machinery","language":[{"iso":"eng"}],"article_number":"127","article_processing_charge":"No","has_accepted_license":"1","oa":1,"oa_version":"Published Version","status":"public","doi":"10.1145/3485504","publication":"Proceedings of the ACM on Programming Languages","abstract":[{"lang":"eng","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."}],"ddc":["005"],"file":[{"file_size":770269,"file_id":"10154","file_name":"monnom-oopsla21.pdf","success":1,"date_updated":"2021-10-19T12:52:23Z","access_level":"open_access","creator":"fmuehlbo","content_type":"application/pdf","checksum":"71011efd2da771cafdec7f0d9693f8c1","date_created":"2021-10-19T12:52:23Z","relation":"main_file"}],"title":"Transitioning from structural to nominal code with efficient gradual typing","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article"},{"keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"author":[{"first_name":"Lisa-Marie","last_name":"Appel","full_name":"Appel, Lisa-Marie"},{"full_name":"Franke, Vedran","first_name":"Vedran","last_name":"Franke"},{"first_name":"Melania","last_name":"Bruno","full_name":"Bruno, Melania"},{"full_name":"Grishkovskaya, Irina","last_name":"Grishkovskaya","first_name":"Irina"},{"first_name":"Aiste","last_name":"Kasiliauskaite","full_name":"Kasiliauskaite, Aiste"},{"last_name":"Kaufmann","first_name":"Tanja","full_name":"Kaufmann, Tanja"},{"full_name":"Schoeberl, Ursula E.","last_name":"Schoeberl","first_name":"Ursula E."},{"first_name":"Martin G.","last_name":"Puchinger","full_name":"Puchinger, Martin G."},{"full_name":"Kostrhon, Sebastian","last_name":"Kostrhon","first_name":"Sebastian"},{"first_name":"Carmen","last_name":"Ebenwaldner","full_name":"Ebenwaldner, Carmen"},{"full_name":"Sebesta, Marek","last_name":"Sebesta","first_name":"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","first_name":"Anna","last_name":"Vlasova"},{"first_name":"Martin","last_name":"Leeb","full_name":"Leeb, Martin"},{"last_name":"Pavri","first_name":"Rushad","full_name":"Pavri, Rushad"},{"full_name":"Stark, Alexander","first_name":"Alexander","last_name":"Stark"},{"full_name":"Akalin, Altuna","last_name":"Akalin","first_name":"Altuna"},{"full_name":"Stefl, Richard","first_name":"Richard","last_name":"Stefl"},{"full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky"},{"first_name":"Kristina","last_name":"Djinovic-Carugo","full_name":"Djinovic-Carugo, Kristina"},{"last_name":"Slade","first_name":"Dea","full_name":"Slade, Dea"}],"article_type":"original","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-14T08:02:31Z","volume":12,"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.","file_date_updated":"2021-10-21T13:51:49Z","issue":"1","date_created":"2021-10-20T14:40:32Z","_id":"10163","external_id":{"isi":["000709050300001"]},"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>","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).","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>.","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>.","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>","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.","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."},"intvolume":"        12","day":"19","isi":1,"department":[{"_id":"CaBe"}],"month":"10","quality_controlled":"1","publisher":"Springer Nature","date_published":"2021-10-19T00:00:00Z","publication_status":"published","year":"2021","publication_identifier":{"eissn":["2041-1723"]},"has_accepted_license":"1","oa":1,"oa_version":"Published Version","status":"public","related_material":{"link":[{"description":"Preprint ","relation":"earlier_version","url":"https://www.biorxiv.org/content/10.1101/2020.02.11.943159"}]},"language":[{"iso":"eng"}],"article_number":"6078","article_processing_charge":"No","publication":"Nature Communications","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."}],"doi":"10.1038/s41467-021-26360-2","title":"PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":5111706,"file_name":"2021_NatComm_Appel.pdf","success":1,"date_updated":"2021-10-21T13:51:49Z","file_id":"10169","checksum":"d99fcd51aebde19c21314e3de0148007","access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","date_created":"2021-10-21T13:51:49Z","relation":"main_file"}],"ddc":["610"]},{"publication_status":"published","year":"2021","publication_identifier":{"issn":["0962-8452"],"eissn":["1471-2954"]},"date_published":"2021-09-22T00:00:00Z","quality_controlled":"1","publisher":"The Royal Society","article_processing_charge":"Yes (via OA deal)","related_material":{"link":[{"url":"https://doi.org/10.6084/m9.figshare.c.5615488.v1","relation":"supplementary_material"}],"record":[{"status":"public","id":"9949","relation":"research_data"}]},"language":[{"iso":"eng"}],"ec_funded":1,"article_number":"20211720","oa_version":"Published Version","status":"public","has_accepted_license":"1","oa":1,"doi":"10.1098/rspb.2021.1720","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"}],"publication":"Proceedings of the Royal Society B: Biological Sciences","acknowledged_ssus":[{"_id":"ScienComp"}],"ddc":["595"],"file":[{"file_size":995806,"file_id":"10172","success":1,"file_name":"2021_ProRoSocBBioSci_Huylmans.pdf","date_updated":"2021-10-22T11:48:02Z","creator":"cchlebak","content_type":"application/pdf","access_level":"open_access","checksum":"76e7f253b7040bca2ad76f82bd7c45c0","relation":"main_file","date_created":"2021-10-22T11:48:02Z"}],"title":"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2024-02-21T12:40:29Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"keyword":["asexual reproduction","parthenogenesis","sex-biased genes","sexual conflict","automixis","crustaceans"],"article_type":"original","author":[{"last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K"},{"full_name":"Macon, Ariana","first_name":"Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hontoria","first_name":"Francisco","full_name":"Hontoria, Francisco"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"date_created":"2021-10-21T07:46:06Z","_id":"10166","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).","volume":288,"file_date_updated":"2021-10-22T11:48:02Z","issue":"1959","citation":{"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>","short":"A.K. Huylmans, A. Macon, F. Hontoria, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 288 (2021).","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>.","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>","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.","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>."},"project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715257"}],"scopus_import":"1","external_id":{"pmid":["34547909"],"isi":["000697643700001"]},"isi":1,"pmid":1,"month":"09","department":[{"_id":"BeVi"}],"intvolume":"       288","day":"22"}]