[{"_id":"14794","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers","intvolume":" 5","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) technology enables the sparse labeling of genetically defined neurons. We present a protocol for time-lapse imaging of cortical projection neuron migration in mice using MADM. We describe steps for the isolation, culturing, and 4D imaging of neuronal dynamics in MADM-labeled brain tissue. While this protocol is compatible with other single-cell labeling methods, the MADM approach provides a genetic platform for the functional assessment of cell-autonomous candidate gene function and the relative contribution of non-cell-autonomous effects.\r\n\r\nFor complete details on the use and execution of this protocol, please refer to Hansen et al. (2022),1 Contreras et al. (2021),2 and Amberg and Hippenmeyer (2021).3"}],"issue":"1","publication":"STAR Protocols","citation":{"apa":"Hansen, A. H., & Hippenmeyer, S. (2024). Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2023.102795","ieee":"A. H. Hansen and S. Hippenmeyer, “Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers,” STAR Protocols, vol. 5, no. 1. Elsevier, 2024.","ista":"Hansen AH, Hippenmeyer S. 2024. Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. STAR Protocols. 5(1), 102795.","ama":"Hansen AH, Hippenmeyer S. Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. STAR Protocols. 2024;5(1). doi:10.1016/j.xpro.2023.102795","chicago":"Hansen, Andi H, and Simon Hippenmeyer. “Time-Lapse Imaging of Cortical Projection Neuron Migration in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2023.102795.","short":"A.H. Hansen, S. Hippenmeyer, STAR Protocols 5 (2024).","mla":"Hansen, Andi H., and Simon Hippenmeyer. “Time-Lapse Imaging of Cortical Projection Neuron Migration in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols, vol. 5, no. 1, 102795, Elsevier, 2024, doi:10.1016/j.xpro.2023.102795."},"article_type":"review","date_published":"2024-01-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes","year":"2024","acknowledgement":"We thank Florian Pauler for discussion and his expert technical support. This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging and Optics Facility (IOF) and Preclinical Facility (PCF). A.H.H. was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences.","pmid":1,"publication_status":"epub_ahead","department":[{"_id":"SiHi"}],"publisher":"Elsevier","author":[{"full_name":"Hansen, Andi H","last_name":"Hansen","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"}],"related_material":{"link":[{"url":"http://github.com/hippenmeyerlab","relation":"software"}]},"date_created":"2024-01-14T23:00:56Z","date_updated":"2024-01-17T10:32:31Z","volume":5,"article_number":"102795","oa":1,"external_id":{"pmid":["38165800"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.xpro.2023.102795","open_access":"1"}],"quality_controlled":"1","project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration"}],"doi":"10.1016/j.xpro.2023.102795","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"month":"01","publication_identifier":{"eissn":["2666-1667"]}},{"citation":{"chicago":"Kuhn, Andre, Mark Roosjen, Sumanth Mutte, Shiv Mani Dubey, Vanessa Polet Carrillo Carrasco, Sjef Boeren, Aline Monzer, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” Cell. Elsevier, 2024. https://doi.org/10.1016/j.cell.2023.11.021.","mla":"Kuhn, Andre, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” Cell, vol. 187, no. 1, Elsevier, 2024, p. 130–148.e17, doi:10.1016/j.cell.2023.11.021.","short":"A. Kuhn, M. Roosjen, S. Mutte, S.M. Dubey, V.P. Carrillo Carrasco, S. Boeren, A. Monzer, J. Koehorst, T. Kohchi, R. Nishihama, M. Fendrych, J. Sprakel, J. Friml, D. Weijers, Cell 187 (2024) 130–148.e17.","ista":"Kuhn A, Roosjen M, Mutte S, Dubey SM, Carrillo Carrasco VP, Boeren S, Monzer A, Koehorst J, Kohchi T, Nishihama R, Fendrych M, Sprakel J, Friml J, Weijers D. 2024. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. 187(1), 130–148.e17.","apa":"Kuhn, A., Roosjen, M., Mutte, S., Dubey, S. M., Carrillo Carrasco, V. P., Boeren, S., … Weijers, D. (2024). RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. Elsevier. https://doi.org/10.1016/j.cell.2023.11.021","ieee":"A. Kuhn et al., “RAF-like protein kinases mediate a deeply conserved, rapid auxin response,” Cell, vol. 187, no. 1. Elsevier, p. 130–148.e17, 2024.","ama":"Kuhn A, Roosjen M, Mutte S, et al. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. 2024;187(1):130-148.e17. doi:10.1016/j.cell.2023.11.021"},"publication":"Cell","page":"130-148.e17","article_type":"original","date_published":"2024-01-04T00:00:00Z","scopus_import":"1","keyword":["General Biochemistry","Genetics and Molecular Biology"],"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14826","intvolume":" 187","ddc":["580"],"status":"public","title":"RAF-like protein kinases mediate a deeply conserved, rapid auxin response","oa_version":"Published Version","file":[{"success":1,"checksum":"06fd236a9ee0b46ccb05f44695bfc34b","date_created":"2024-01-22T13:41:41Z","date_updated":"2024-01-22T13:41:41Z","file_id":"14874","relation":"main_file","creator":"dernst","file_size":13194060,"content_type":"application/pdf","access_level":"open_access","file_name":"2024_Cell_Kuhn.pdf"}],"type":"journal_article","issue":"1","abstract":[{"text":"The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage.","lang":"eng"}],"external_id":{"pmid":["38128538"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1016/j.cell.2023.11.021","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"month":"01","pmid":1,"year":"2024","acknowledgement":"We are grateful to Asuka Shitaku and Eri Koide for generating and sharing the Marchantia PRAF-mCitrine line and Peng-Cheng Wang for sharing the Arabidopsis raf mutant. We are grateful to our team members for discussions and helpful advice. This work was supported by funding from the Netherlands Organization for Scientific Research (NWO): VICI grant 865.14.001 and ENW-KLEIN OCENW.KLEIN.027 grants to D.W.; VENI grant VI.VENI.212.003 to A.K.; the European Research Council AdG DIRNDL (contract number 833867) to D.W.; CoG CATCH to J.S.; StG CELLONGATE (contract 803048) to M.F.; and AdG ETAP (contract 742985) to J.F.; MEXT KAKENHI grant number JP19H05675 to T.K.; JSPS KAKENHI grant number JP20H03275 to R.N.; Takeda Science Foundation to R.N.; and the Austrian Science Fund (FWF, P29988) to J.F.","department":[{"_id":"JiFr"}],"publisher":"Elsevier","publication_status":"published","author":[{"last_name":"Kuhn","first_name":"Andre","full_name":"Kuhn, Andre"},{"first_name":"Mark","last_name":"Roosjen","full_name":"Roosjen, Mark"},{"full_name":"Mutte, Sumanth","last_name":"Mutte","first_name":"Sumanth"},{"first_name":"Shiv Mani","last_name":"Dubey","full_name":"Dubey, Shiv Mani"},{"first_name":"Vanessa Polet","last_name":"Carrillo Carrasco","full_name":"Carrillo Carrasco, Vanessa Polet"},{"last_name":"Boeren","first_name":"Sjef","full_name":"Boeren, Sjef"},{"first_name":"Aline","last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline"},{"first_name":"Jasper","last_name":"Koehorst","full_name":"Koehorst, Jasper"},{"full_name":"Kohchi, Takayuki","first_name":"Takayuki","last_name":"Kohchi"},{"full_name":"Nishihama, Ryuichi","first_name":"Ryuichi","last_name":"Nishihama"},{"full_name":"Fendrych, Matyas","first_name":"Matyas","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699"},{"full_name":"Sprakel, Joris","first_name":"Joris","last_name":"Sprakel"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"}],"volume":187,"date_created":"2024-01-17T12:45:40Z","date_updated":"2024-01-22T13:43:40Z","ec_funded":1,"file_date_updated":"2024-01-22T13:41:41Z","license":"https://creativecommons.org/licenses/by-nc/4.0/"},{"day":"08","article_processing_charge":"No","scopus_import":"1","keyword":["Electrical and Electronic Engineering","Materials Chemistry","Electrochemistry","Energy Engineering and Power Technology","Chemical Engineering (miscellaneous)"],"date_published":"2024-01-08T00:00:00Z","publication":"ACS Applied Energy Materials","citation":{"ista":"Kiran GK, Singh S, Mahato N, Sreekanth TVM, Dillip GR, Yoo K, Kim J. 2024. Interface engineering modulation combined with electronic structure modification of Zn-doped NiO heterostructure for efficient water-splitting activity. ACS Applied Energy Materials. 7(1), 214–229.","ieee":"G. K. Kiran et al., “Interface engineering modulation combined with electronic structure modification of Zn-doped NiO heterostructure for efficient water-splitting activity,” ACS Applied Energy Materials, vol. 7, no. 1. American Chemical Society, pp. 214–229, 2024.","apa":"Kiran, G. K., Singh, S., Mahato, N., Sreekanth, T. V. M., Dillip, G. R., Yoo, K., & Kim, J. (2024). Interface engineering modulation combined with electronic structure modification of Zn-doped NiO heterostructure for efficient water-splitting activity. ACS Applied Energy Materials. American Chemical Society. https://doi.org/10.1021/acsaem.3c02519","ama":"Kiran GK, Singh S, Mahato N, et al. Interface engineering modulation combined with electronic structure modification of Zn-doped NiO heterostructure for efficient water-splitting activity. ACS Applied Energy Materials. 2024;7(1):214-229. doi:10.1021/acsaem.3c02519","chicago":"Kiran, Gundegowda Kalligowdanadoddi, Saurabh Singh, Neelima Mahato, Thupakula Venkata Madhukar Sreekanth, Gowra Raghupathy Dillip, Kisoo Yoo, and Jonghoon Kim. “Interface Engineering Modulation Combined with Electronic Structure Modification of Zn-Doped NiO Heterostructure for Efficient Water-Splitting Activity.” ACS Applied Energy Materials. American Chemical Society, 2024. https://doi.org/10.1021/acsaem.3c02519.","mla":"Kiran, Gundegowda Kalligowdanadoddi, et al. “Interface Engineering Modulation Combined with Electronic Structure Modification of Zn-Doped NiO Heterostructure for Efficient Water-Splitting Activity.” ACS Applied Energy Materials, vol. 7, no. 1, American Chemical Society, 2024, pp. 214–29, doi:10.1021/acsaem.3c02519.","short":"G.K. Kiran, S. Singh, N. Mahato, T.V.M. Sreekanth, G.R. Dillip, K. Yoo, J. Kim, ACS Applied Energy Materials 7 (2024) 214–229."},"article_type":"original","page":"214-229","abstract":[{"text":"Production of hydrogen at large scale requires development of non-noble, inexpensive, and high-performing catalysts for constructing water-splitting devices. Herein, we report the synthesis of Zn-doped NiO heterostructure (ZnNiO) catalysts at room temperature via a coprecipitation method followed by drying (at 80 °C, 6 h) and calcination at an elevated temperature of 400 °C for 5 h under three distinct conditions, namely, air, N2, and vacuum. The vacuum-synthesized catalyst demonstrates a low overpotential of 88 mV at −10 mA cm–2 and a small Tafel slope of 73 mV dec–1 suggesting relatively higher charge transfer kinetics for hydrogen evolution reactions (HER) compared with the specimens synthesized under N2 or O2 atmosphere. It also demonstrates an oxygen evolution (OER) overpotential of 260 mV at 10 mA cm–2 with a low Tafel slope of 63 mV dec–1. In a full-cell water-splitting device, the vacuum-synthesized ZnNiO heterostructure demonstrates a cell voltage of 1.94 V at 50 mA cm–2 and shows remarkable stability over 24 h at a high current density of 100 mA cm–2. It is also demonstrated in this study that Zn-doping, surface, and interface engineering in transition-metal oxides play a crucial role in efficient electrocatalytic water splitting. Also, the results obtained from density functional theory (DFT + U = 0–8 eV), where U is the on-site Coulomb repulsion parameter also known as Hubbard U, based electronic structure calculations confirm that Zn doping constructively modifies the electronic structure, in both the valence band and the conduction band, and found to be suitable in tailoring the carrier’s effective masses of electrons and holes. The decrease in electron’s effective masses together with large differences between the effective masses of electrons and holes is noticed, which is found to be mainly responsible for achieving the best water-splitting performance from a 9% Zn-doped NiO sample prepared under vacuum.","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"None","_id":"14828","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Interface engineering modulation combined with electronic structure modification of Zn-doped NiO heterostructure for efficient water-splitting activity","status":"public","intvolume":" 7","month":"01","publication_identifier":{"issn":["2574-0962"]},"doi":"10.1021/acsaem.3c02519","language":[{"iso":"eng"}],"external_id":{"isi":["001138342900001"]},"quality_controlled":"1","isi":1,"author":[{"first_name":"Gundegowda Kalligowdanadoddi","last_name":"Kiran","full_name":"Kiran, Gundegowda Kalligowdanadoddi"},{"full_name":"Singh, Saurabh","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","orcid":"0000-0003-2209-5269","first_name":"Saurabh","last_name":"Singh"},{"first_name":"Neelima","last_name":"Mahato","full_name":"Mahato, Neelima"},{"last_name":"Sreekanth","first_name":"Thupakula Venkata Madhukar","full_name":"Sreekanth, Thupakula Venkata Madhukar"},{"first_name":"Gowra Raghupathy","last_name":"Dillip","full_name":"Dillip, Gowra Raghupathy"},{"full_name":"Yoo, Kisoo","last_name":"Yoo","first_name":"Kisoo"},{"last_name":"Kim","first_name":"Jonghoon","full_name":"Kim, Jonghoon"}],"date_updated":"2024-01-22T13:47:39Z","date_created":"2024-01-17T12:48:35Z","volume":7,"year":"2024","acknowledgement":"This work was supported by the Technology Innovation Program (20011622, Development of Battery System Applied High-Efficiency Heat Control Polymer and Part Component) funded by the Ministry of Trade, Industry & Energy (MOTIE, Korea). Author acknowledge to Prof. Tsunehiro Takeuchi from Toyota Technological Institute, Nagoya, Japan for the support of computational resources.","publication_status":"published","department":[{"_id":"MaIb"}],"publisher":"American Chemical Society"},{"project":[{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.ejcb.2023.151380"}],"external_id":{"pmid":["38218128"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.ejcb.2023.151380","publication_identifier":{"issn":["0171-9335"]},"month":"01","publisher":"Elsevier","department":[{"_id":"MaLo"}],"publication_status":"epub_ahead","pmid":1,"acknowledgement":"We acknowledge members of the Loose laboratory at ISTA for helpful discussions—in particular M. Kojic for his insightful comments. This work was supported by the Austrian Science Fund (FWF P34607) to M.L.","year":"2024","volume":103,"date_updated":"2024-01-23T08:37:13Z","date_created":"2024-01-18T08:16:43Z","author":[{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","first_name":"Philipp","last_name":"Radler","full_name":"Radler, Philipp"},{"full_name":"Loose, Martin","first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724"}],"article_number":"151380","license":"https://creativecommons.org/licenses/by/4.0/","article_type":"review","citation":{"mla":"Radler, Philipp, and Martin Loose. “A Dynamic Duo: Understanding the Roles of FtsZ and FtsA for Escherichia Coli Cell Division through in Vitro Approaches.” European Journal of Cell Biology, vol. 103, no. 1, 151380, Elsevier, 2024, doi:10.1016/j.ejcb.2023.151380.","short":"P. Radler, M. Loose, European Journal of Cell Biology 103 (2024).","chicago":"Radler, Philipp, and Martin Loose. “A Dynamic Duo: Understanding the Roles of FtsZ and FtsA for Escherichia Coli Cell Division through in Vitro Approaches.” European Journal of Cell Biology. Elsevier, 2024. https://doi.org/10.1016/j.ejcb.2023.151380.","ama":"Radler P, Loose M. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. European Journal of Cell Biology. 2024;103(1). doi:10.1016/j.ejcb.2023.151380","ista":"Radler P, Loose M. 2024. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. European Journal of Cell Biology. 103(1), 151380.","ieee":"P. Radler and M. Loose, “A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches,” European Journal of Cell Biology, vol. 103, no. 1. Elsevier, 2024.","apa":"Radler, P., & Loose, M. (2024). A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. European Journal of Cell Biology. Elsevier. https://doi.org/10.1016/j.ejcb.2023.151380"},"publication":"European Journal of Cell Biology","date_published":"2024-01-12T00:00:00Z","keyword":["Cell Biology","General Medicine","Histology","Pathology and Forensic Medicine"],"scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"12","intvolume":" 103","title":"A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches","ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14834","oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"text":"Bacteria divide by binary fission. The protein machine responsible for this process is the divisome, a transient assembly of more than 30 proteins in and on the surface of the cytoplasmic membrane. Together, they constrict the cell envelope and remodel the peptidoglycan layer to eventually split the cell into two. For Escherichia coli, most molecular players involved in this process have probably been identified, but obtaining the quantitative information needed for a mechanistic understanding can often not be achieved from experiments in vivo alone. Since the discovery of the Z-ring more than 30 years ago, in vitro reconstitution experiments have been crucial to shed light on molecular processes normally hidden in the complex environment of the living cell. In this review, we summarize how rebuilding the divisome from purified components – or at least parts of it - have been instrumental to obtain the detailed mechanistic understanding of the bacterial cell division machinery that we have today.","lang":"eng"}]},{"publication_identifier":{"eissn":["1091-6490"]},"month":"01","external_id":{"pmid":["38194456"]},"project":[{"call_identifier":"H2020","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","grant_number":"819603"}],"quality_controlled":"1","doi":"10.1073/pnas.2307776121","language":[{"iso":"eng"}],"article_number":"e2307776121","ec_funded":1,"pmid":1,"acknowledgement":"This work was supported by an ERC Consolidator Grant (SYNAPSEEK) to T.P.V., the NOMIS Foundation through the NOMIS Fellowships program at IST Austria to C.B.C., a Jefferson Synaptic Biology Center Pilot Project Grant to M.C., NIH NINDS U54 NS108874 (PI, Alfred L. George), and NIH NINDS R01 NS122887 to E.M.G. The computations were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at the PDC Center for High-Performance Computing, KTH Royal Institute of Technology, partially funded by the Swedish Research Council through grant agreement no. 2018-05973. We thank Akshay Sridhar for the fruitful discussion of the project.","year":"2024","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"TiVo"}],"publication_status":"published","related_material":{"link":[{"url":"https://github.com/ChrisCurrin/pv-kcnc2 ","relation":"software"}]},"author":[{"last_name":"Clatot","first_name":"Jerome","full_name":"Clatot, Jerome"},{"full_name":"Currin, Christopher","first_name":"Christopher","last_name":"Currin","id":"e8321fc5-3091-11eb-8a53-83f309a11ac9","orcid":"0000-0002-4809-5059"},{"full_name":"Liang, Qiansheng","last_name":"Liang","first_name":"Qiansheng"},{"last_name":"Pipatpolkai","first_name":"Tanadet","full_name":"Pipatpolkai, Tanadet"},{"full_name":"Massey, Shavonne L.","first_name":"Shavonne L.","last_name":"Massey"},{"full_name":"Helbig, Ingo","first_name":"Ingo","last_name":"Helbig"},{"full_name":"Delemotte, Lucie","last_name":"Delemotte","first_name":"Lucie"},{"full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","first_name":"Tim P"},{"full_name":"Covarrubias, Manuel","last_name":"Covarrubias","first_name":"Manuel"},{"last_name":"Goldberg","first_name":"Ethan M.","full_name":"Goldberg, Ethan M."}],"volume":121,"date_updated":"2024-01-23T10:20:40Z","date_created":"2024-01-21T23:00:56Z","scopus_import":"1","article_processing_charge":"No","day":"16","citation":{"ama":"Clatot J, Currin C, Liang Q, et al. A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(3). doi:10.1073/pnas.2307776121","ieee":"J. Clatot et al., “A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 3. Proceedings of the National Academy of Sciences, 2024.","apa":"Clatot, J., Currin, C., Liang, Q., Pipatpolkai, T., Massey, S. L., Helbig, I., … Goldberg, E. M. (2024). A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2307776121","ista":"Clatot J, Currin C, Liang Q, Pipatpolkai T, Massey SL, Helbig I, Delemotte L, Vogels TP, Covarrubias M, Goldberg EM. 2024. A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction. Proceedings of the National Academy of Sciences of the United States of America. 121(3), e2307776121.","short":"J. Clatot, C. Currin, Q. Liang, T. Pipatpolkai, S.L. Massey, I. Helbig, L. Delemotte, T.P. Vogels, M. Covarrubias, E.M. Goldberg, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","mla":"Clatot, Jerome, et al. “A Structurally Precise Mechanism Links an Epilepsy-Associated KCNC2 Potassium Channel Mutation to Interneuron Dysfunction.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 3, e2307776121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2307776121.","chicago":"Clatot, Jerome, Christopher Currin, Qiansheng Liang, Tanadet Pipatpolkai, Shavonne L. Massey, Ingo Helbig, Lucie Delemotte, Tim P Vogels, Manuel Covarrubias, and Ethan M. Goldberg. “A Structurally Precise Mechanism Links an Epilepsy-Associated KCNC2 Potassium Channel Mutation to Interneuron Dysfunction.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2307776121."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","article_type":"original","date_published":"2024-01-16T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"De novo heterozygous variants in KCNC2 encoding the voltage-gated potassium (K+) channel subunit Kv3.2 are a recently described cause of developmental and epileptic encephalopathy (DEE). A de novo variant in KCNC2 c.374G > A (p.Cys125Tyr) was identified via exome sequencing in a patient with DEE. Relative to wild-type Kv3.2, Kv3.2-p.Cys125Tyr induces K+ currents exhibiting a large hyperpolarizing shift in the voltage dependence of activation, accelerated activation, and delayed deactivation consistent with a relative stabilization of the open conformation, along with increased current density. Leveraging the cryogenic electron microscopy (cryo-EM) structure of Kv3.1, molecular dynamic simulations suggest that a strong π-π stacking interaction between the variant Tyr125 and Tyr156 in the α-6 helix of the T1 domain promotes a relative stabilization of the open conformation of the channel, which underlies the observed gain of function. A multicompartment computational model of a Kv3-expressing parvalbumin-positive cerebral cortex fast-spiking γ-aminobutyric acidergic (GABAergic) interneuron (PV-IN) demonstrates how the Kv3.2-Cys125Tyr variant impairs neuronal excitability and dysregulates inhibition in cerebral cortex circuits to explain the resulting epilepsy."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14841","intvolume":" 121","status":"public","title":"A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction","oa_version":"None"},{"year":"2024","acknowledgement":"We would like to thank G. Bighin, I. Cherepanov, E. Paerschke, and E. Yakaboylu for insightful discussions on a wide range of topics. This work has been supported by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A.G. and A.G.V. acknowledge support from the European Union’s Horizon 2020 research and innovation\r\nprogram under the Marie Skłodowska-Curie Grant Agreement No. 754411. Numerical calculations were performed on the Euler cluster managed by the HPC team at ETH Zurich.\r\nR.S. acknowledges support by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy Grant No. EXC 2181/1-390900948 (the Heidelberg STRUCTURES Excellence Cluster). T.D. acknowledges support from the Isaac Newton Studentship and the Science and Technology Facilities Council under Grant No. ST/V50659X/1.","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","author":[{"last_name":"Dome","first_name":"Tibor","orcid":"0000-0003-2586-3702","id":"7e3293e2-b9dc-11ee-97a9-cd73400f6994","full_name":"Dome, Tibor"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev","full_name":"Volosniev, Artem"},{"full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","first_name":"Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","last_name":"Safari","first_name":"Laleh","full_name":"Safari, Laleh"},{"full_name":"Schmidt, Richard","last_name":"Schmidt","first_name":"Richard"},{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"}],"volume":109,"date_updated":"2024-01-23T10:51:09Z","date_created":"2024-01-21T23:00:57Z","article_number":"014102","ec_funded":1,"project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","doi":"10.1103/PhysRevB.109.014102","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"01","_id":"14845","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 109","status":"public","title":"Linear rotor in an ideal Bose gas near the threshold for binding","oa_version":"None","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"We study a linear rotor in a bosonic bath within the angulon formalism. Our focus is on systems where isotropic or anisotropic impurity-boson interactions support a shallow bound state. To study the fate of the angulon in the vicinity of bound-state formation, we formulate a beyond-linear-coupling angulon Hamiltonian. First, we use it to study attractive, spherically symmetric impurity-boson interactions for which the linear rotor can be mapped onto a static impurity. The well-known polaron formalism provides an adequate description in this limit. Second, we consider anisotropic potentials, and show that the presence of a shallow bound state with pronounced anisotropic character leads to a many-body instability that washes out the angulon dynamics."}],"citation":{"ista":"Dome T, Volosniev A, Ghazaryan A, Safari L, Schmidt R, Lemeshko M. 2024. Linear rotor in an ideal Bose gas near the threshold for binding. Physical Review B. 109(1), 014102.","ieee":"T. Dome, A. Volosniev, A. Ghazaryan, L. Safari, R. Schmidt, and M. Lemeshko, “Linear rotor in an ideal Bose gas near the threshold for binding,” Physical Review B, vol. 109, no. 1. American Physical Society, 2024.","apa":"Dome, T., Volosniev, A., Ghazaryan, A., Safari, L., Schmidt, R., & Lemeshko, M. (2024). Linear rotor in an ideal Bose gas near the threshold for binding. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.109.014102","ama":"Dome T, Volosniev A, Ghazaryan A, Safari L, Schmidt R, Lemeshko M. Linear rotor in an ideal Bose gas near the threshold for binding. Physical Review B. 2024;109(1). doi:10.1103/PhysRevB.109.014102","chicago":"Dome, Tibor, Artem Volosniev, Areg Ghazaryan, Laleh Safari, Richard Schmidt, and Mikhail Lemeshko. “Linear Rotor in an Ideal Bose Gas near the Threshold for Binding.” Physical Review B. American Physical Society, 2024. https://doi.org/10.1103/PhysRevB.109.014102.","mla":"Dome, Tibor, et al. “Linear Rotor in an Ideal Bose Gas near the Threshold for Binding.” Physical Review B, vol. 109, no. 1, 014102, American Physical Society, 2024, doi:10.1103/PhysRevB.109.014102.","short":"T. Dome, A. Volosniev, A. Ghazaryan, L. Safari, R. Schmidt, M. Lemeshko, Physical Review B 109 (2024)."},"publication":"Physical Review B","article_type":"original","date_published":"2024-01-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"file":[{"creator":"dernst","file_size":4521738,"content_type":"application/pdf","file_name":"2024_MNAstronomSoc_Kramarenko.pdf","access_level":"open_access","date_created":"2024-01-23T12:30:45Z","date_updated":"2024-01-23T12:30:45Z","success":1,"checksum":"9d02df4035c4951cf63dee0db1e462e9","file_id":"14879","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 527","status":"public","ddc":["520"],"title":"Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape","_id":"14852","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"4","abstract":[{"text":"The physical conditions giving rise to high escape fractions of ionizing radiation (LyC fesc) in star-forming galaxies – most likely protagonists of cosmic reionization – are not yet fully understood. Using the VLT/MUSE observations of ∼1400 Ly α emitters at 2.9 < z < 6.7, we compare stacked rest-frame UV spectra of candidates for LyC leakers and non-leakers selected based on their Ly α profiles. We find that the stacks of potential LyC leakers, i.e. galaxies with narrow, symmetric Ly α profiles with small peak separation, generally show (i) strong nebular O iii]λ1666, [Si iii]λ1883, and [C iii]λ1907 +C iii]λ1909 emission, indicating a high-ionization state of the interstellar medium (ISM); (ii) high equivalent widths of He iiλ1640 (∼1 − 3 Å), suggesting the presence of hard ionizing radiation fields; (iii) Si ii*λ1533 emission, revealing substantial amounts of neutral hydrogen off the line of sight; (iv) high C ivλλ1548,1550 to [C iii]λ1907 +C iii]λ1909 ratios (C iv/C iii] ≳0.75) , signalling the presence of low column density channels in the ISM. In contrast, the stacks with broad, asymmetric Ly α profiles with large peak separation show weak nebular emission lines, low He iiλ1640 equivalent widths (≲1 Å), and low C iv/C iii] (≲0.25), implying low-ionization states and high-neutral hydrogen column densities. Our results suggest that C iv/C iii] might be sensitive to the physical conditions that govern LyC photon escape, providing a promising tool for identification of ionizing sources among star-forming galaxies in the epoch of reionization.","lang":"eng"}],"type":"journal_article","date_published":"2024-02-01T00:00:00Z","page":"9853-9871","article_type":"original","citation":{"apa":"Kramarenko, I., Kerutt, J., Verhamme, A., Oesch, P. A., Barrufet, L., Matthee, J. J., … Thai, T. T. (2024). Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stad3853","ieee":"I. Kramarenko et al., “Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape,” Monthly Notices of the Royal Astronomical Society, vol. 527, no. 4. Oxford University Press, pp. 9853–9871, 2024.","ista":"Kramarenko I, Kerutt J, Verhamme A, Oesch PA, Barrufet L, Matthee JJ, Kusakabe H, Goovaerts I, Thai TT. 2024. Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape. Monthly Notices of the Royal Astronomical Society. 527(4), 9853–9871.","ama":"Kramarenko I, Kerutt J, Verhamme A, et al. Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape. Monthly Notices of the Royal Astronomical Society. 2024;527(4):9853-9871. doi:10.1093/mnras/stad3853","chicago":"Kramarenko, Ivan, J Kerutt, A Verhamme, P A Oesch, L Barrufet, Jorryt J Matthee, H Kusakabe, I Goovaerts, and T T Thai. “Linking UV Spectral Properties of MUSE Ly α Emitters at z ≳ 3 to Lyman Continuum Escape.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2024. https://doi.org/10.1093/mnras/stad3853.","short":"I. Kramarenko, J. Kerutt, A. Verhamme, P.A. Oesch, L. Barrufet, J.J. Matthee, H. Kusakabe, I. Goovaerts, T.T. Thai, Monthly Notices of the Royal Astronomical Society 527 (2024) 9853–9871.","mla":"Kramarenko, Ivan, et al. “Linking UV Spectral Properties of MUSE Ly α Emitters at z ≳ 3 to Lyman Continuum Escape.” Monthly Notices of the Royal Astronomical Society, vol. 527, no. 4, Oxford University Press, 2024, pp. 9853–71, doi:10.1093/mnras/stad3853."},"publication":"Monthly Notices of the Royal Astronomical Society","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"01","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"volume":527,"date_created":"2024-01-22T08:22:17Z","date_updated":"2024-01-23T12:33:50Z","author":[{"full_name":"Kramarenko, Ivan","id":"9a9394cb-3200-11ee-973b-f5ba2a8b16e4","last_name":"Kramarenko","first_name":"Ivan"},{"last_name":"Kerutt","first_name":"J","full_name":"Kerutt, J"},{"full_name":"Verhamme, A","first_name":"A","last_name":"Verhamme"},{"first_name":"P A","last_name":"Oesch","full_name":"Oesch, P A"},{"full_name":"Barrufet, L","first_name":"L","last_name":"Barrufet"},{"full_name":"Matthee, Jorryt J","first_name":"Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X"},{"full_name":"Kusakabe, H","first_name":"H","last_name":"Kusakabe"},{"full_name":"Goovaerts, I","first_name":"I","last_name":"Goovaerts"},{"first_name":"T T","last_name":"Thai","full_name":"Thai, T T"}],"publisher":"Oxford University Press","department":[{"_id":"GradSch"},{"_id":"JoMa"}],"publication_status":"published","year":"2024","acknowledgement":"We thank the anonymous referee for the constructive feedback that helped to improve the manuscript. We thank Michael Maseda, Daniel Schaerer, Charlotte Simmonds, and Rashmi Gottumukkala for useful comments and productive discussions. We also thank the organizers and participants of the 24th MUSE Science Busy Week in Leiden. IGK acknowledges an Excellence Master Fellowship granted by the Faculty of Science of the University of Geneva. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant number 200020_207349 and SNSF Professorship grant number 190079. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant number 140. This paper is based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programmes 094.A-0289(B), 095.A-0010(A), 096.A-0045(A), 096.A-0045(B), 094.A-0205, 095.A-0240, 096.A-0090, 097.A-0160, and 098.A-0017. We made extensive use of several open-source software packages and we are thankful to the respective authors for sharing their work: NUMPY (Harris et al. 2020), ASTROPY (Astropy Collaboration 2022), MATPLOTLIB (Hunter 2007), IPYTHON (Perez & Granger 2007), and TOPCAT (Taylor 2005).","file_date_updated":"2024-01-23T12:30:45Z","language":[{"iso":"eng"}],"doi":"10.1093/mnras/stad3853","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2305.07044"]},"publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"month":"02"},{"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Elaborate sexual signals are thought to have evolved and be maintained to serve as honest indicators of signaller quality. One measure of quality is health, which can be affected by parasite infection. Cnemaspis mysoriensis is a diurnal gecko that is often infested with ectoparasites in the wild, and males of this species express visual (coloured gular patches) and chemical (femoral gland secretions) traits that receivers could assess during social interactions. In this paper, we tested whether ectoparasites affect individual health, and whether signal quality is an indicator of ectoparasite levels. In wild lizards, we found that ectoparasite level was negatively correlated with body condition in both sexes. Moreover, some characteristics of both visual and chemical traits in males were strongly associated with ectoparasite levels. Specifically, males with higher ectoparasite levels had yellow gular patches with lower brightness and chroma, and chemical secretions with a lower proportion of aromatic compounds. We then determined whether ectoparasite levels in males influence female behaviour. Using sequential choice trials, wherein females were provided with either the visual or the chemical signals of wild-caught males that varied in ectoparasite level, we found that only chemical secretions evoked an elevated female response towards less parasitised males. Simultaneous choice trials in which females were exposed to the chemical secretions from males that varied in parasite level further confirmed a preference for males with lower parasites loads. Overall, we find that although health (body condition) or ectoparasite load can be honestly advertised through multiple modalities, the parasite-mediated female response is exclusively driven by chemical signals."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14850","intvolume":" 227","ddc":["570"],"title":"Too much information? Males convey parasite levels using more signal modalities than females utilise","status":"public","oa_version":"Published Version","file":[{"file_id":"14877","relation":"main_file","date_created":"2024-01-23T12:08:24Z","date_updated":"2024-01-23T12:08:24Z","success":1,"checksum":"136325372f6f45abaa62a71e2d23bfb6","file_name":"2024_JourExperimBiology_Pal.pdf","access_level":"open_access","creator":"dernst","file_size":594128,"content_type":"application/pdf"}],"keyword":["Insect Science","Molecular Biology","Animal Science and Zoology","Aquatic Science","Physiology","Ecology","Evolution","Behavior and Systematics"],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"10","citation":{"ama":"Pal A, Joshi M, Thaker M. Too much information? Males convey parasite levels using more signal modalities than females utilise. Journal of Experimental Biology. 2024;227(1). doi:10.1242/jeb.246217","ieee":"A. Pal, M. Joshi, and M. Thaker, “Too much information? Males convey parasite levels using more signal modalities than females utilise,” Journal of Experimental Biology, vol. 227, no. 1. The Company of Biologists, 2024.","apa":"Pal, A., Joshi, M., & Thaker, M. (2024). Too much information? Males convey parasite levels using more signal modalities than females utilise. Journal of Experimental Biology. The Company of Biologists. https://doi.org/10.1242/jeb.246217","ista":"Pal A, Joshi M, Thaker M. 2024. Too much information? Males convey parasite levels using more signal modalities than females utilise. Journal of Experimental Biology. 227(1), jeb246217.","short":"A. Pal, M. Joshi, M. Thaker, Journal of Experimental Biology 227 (2024).","mla":"Pal, Arka, et al. “Too Much Information? Males Convey Parasite Levels Using More Signal Modalities than Females Utilise.” Journal of Experimental Biology, vol. 227, no. 1, jeb246217, The Company of Biologists, 2024, doi:10.1242/jeb.246217.","chicago":"Pal, Arka, Mihir Joshi, and Maria Thaker. “Too Much Information? Males Convey Parasite Levels Using More Signal Modalities than Females Utilise.” Journal of Experimental Biology. The Company of Biologists, 2024. https://doi.org/10.1242/jeb.246217."},"publication":"Journal of Experimental Biology","article_type":"original","date_published":"2024-01-10T00:00:00Z","article_number":"jeb246217","file_date_updated":"2024-01-23T12:08:24Z","pmid":1,"acknowledgement":"We thank Anuradha Batabyal and Shakilur Kabir for scientific discussions, and help with sampling and colour analyses. We thank Muralidhar and the central LCMS facility of the IISc for their technical support with the GCMS.\r\nResearch funding was provided by the Department of Science and Technology Fund for Improvement of S&T Infrastructure (DST-FIST), the Department of Biotechnology-Indian Institute of Science (DBT-IISc) partnership program and a Science and Engineering Research Board (SERB) grant to M.T. (EMR/2017/002228). Open Access funding provided by Indian Institute of Science. Deposited in PMC for immediate release.","year":"2024","department":[{"_id":"NiBa"}],"publisher":"The Company of Biologists","publication_status":"published","related_material":{"link":[{"url":"https://github.com/arka-pal/Cnemaspis-SexualSignaling","relation":"software"}]},"author":[{"full_name":"Pal, Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","orcid":"0000-0002-4530-8469","first_name":"Arka","last_name":"Pal"},{"full_name":"Joshi, Mihir","last_name":"Joshi","first_name":"Mihir"},{"first_name":"Maria","last_name":"Thaker","full_name":"Thaker, Maria"}],"volume":227,"date_updated":"2024-01-23T12:13:08Z","date_created":"2024-01-22T08:14:49Z","publication_identifier":{"eissn":["0022-0949"],"issn":["1477-9145"]},"month":"01","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["38054353"]},"quality_controlled":"1","doi":"10.1242/jeb.246217","language":[{"iso":"eng"}]},{"month":"01","publication_identifier":{"issn":["2663 - 337X"]},"doi":"10.15479/at:ista:14711","supervisor":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"last_name":"Polechova","first_name":"Jitka","full_name":"Polechova, Jitka"},{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Causes and consequences of population fragmentation","grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"},{"_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6","grant_number":"26380","name":"Polygenic Adaptation in a Metapopulation"}],"file_date_updated":"2024-01-03T18:31:34Z","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","author":[{"orcid":"0000-0003-1971-8314","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","last_name":"Olusanya","first_name":"Oluwafunmilola O","full_name":"Olusanya, Oluwafunmilola O"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10658"},{"relation":"part_of_dissertation","status":"public","id":"10787"},{"id":"14732","relation":"part_of_dissertation","status":"public"}]},"date_created":"2023-12-26T22:49:53Z","date_updated":"2024-01-26T12:00:54Z","year":"2024","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"day":"19","article_processing_charge":"No","has_accepted_license":"1","date_published":"2024-01-19T00:00:00Z","citation":{"ieee":"O. O. Olusanya, “Local adaptation, genetic load and extinction in metapopulations,” Institute of Science and Technology Austria, 2024.","apa":"Olusanya, O. O. (2024). Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14711","ista":"Olusanya OO. 2024. Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria.","ama":"Olusanya OO. Local adaptation, genetic load and extinction in metapopulations. 2024. doi:10.15479/at:ista:14711","chicago":"Olusanya, Oluwafunmilola O. “Local Adaptation, Genetic Load and Extinction in Metapopulations.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:14711.","short":"O.O. Olusanya, Local Adaptation, Genetic Load and Extinction in Metapopulations, Institute of Science and Technology Austria, 2024.","mla":"Olusanya, Oluwafunmilola O. Local Adaptation, Genetic Load and Extinction in Metapopulations. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:14711."},"page":"183","abstract":[{"lang":"eng","text":"In nature, different species find their niche in a range of environments, each with its unique characteristics. While some thrive in uniform (homogeneous) landscapes where environmental conditions stay relatively consistent across space, others traverse the complexities of spatially heterogeneous terrains. Comprehending how species are distributed and how they interact within these landscapes holds the key to gaining insights into their evolutionary dynamics while also informing conservation and management strategies.\r\n\r\nFor species inhabiting heterogeneous landscapes, when the rate of dispersal is low compared to spatial fluctuations in selection pressure, localized adaptations may emerge. Such adaptation in response to varying selection strengths plays an important role in the persistence of populations in our rapidly changing world. Hence, species in nature are continuously in a struggle to adapt to local environmental conditions, to ensure their continued survival. Natural populations can often adapt in time scales short enough for evolutionary changes to influence ecological dynamics and vice versa, thereby creating a feedback between evolution and demography. The analysis of this feedback and the relative contributions of gene flow, demography, drift, and natural selection to genetic variation and differentiation has remained a recurring theme in evolutionary biology. Nevertheless, the effective role of these forces in maintaining variation and shaping patterns of diversity is not fully understood. Even in homogeneous environments devoid of local adaptations, such understanding remains elusive. Understanding this feedback is crucial, for example in determining the conditions under which extinction risk can be mitigated in peripheral populations subject to deleterious mutation accumulation at the edges of species’ ranges\r\nas well as in highly fragmented populations.\r\n\r\nIn this thesis we explore both uniform and spatially heterogeneous metapopulations, investigating and providing theoretical insights into the dynamics of local adaptation in the latter and examining the dynamics of load and extinction as well as the impact of joint ecological and evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided into 5 chapters.\r\n\r\nChapter 1 provides a general introduction into the subject matter, clarifying concepts and ideas used throughout the thesis. In chapter 2, we explore how fast a species distributed across a heterogeneous landscape adapts to changing conditions marked by alterations in carrying capacity, selection pressure, and migration rate.\r\n\r\nIn chapter 3, we investigate how migration selection and drift influences adaptation and the maintenance of variation in a metapopulation with three habitats, an extension of previous models of adaptation in two habitats. We further develop analytical approximations for the critical threshold required for polymorphism to persist.\r\n\r\nThe focus of chapter 4 of the thesis is on understanding the interplay between ecology and evolution as coupled processes. We investigate how eco-evolutionary feedback between migration, selection, drift, and demography influences eco-evolutionary outcomes in marginal populations subject to deleterious mutation accumulation. Using simulations as well as theoretical approximations of the coupled dynamics of population size and allele frequency, we analyze how gene flow from a large mainland source influences genetic load and population size on an island (i.e., in a marginal population) under genetically realistic assumptions. Analyses of this sort are important because small isolated populations, are repeatedly affected by complex interactions between ecological and evolutionary processes, which can lead to their death. Understanding these interactions can therefore provide an insight into the conditions under which extinction risk can be mitigated in peripheral populations thus, contributing to conservation and restoration efforts.\r\n\r\nChapter 5 extends the analysis in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation) and extinction risk in a metapopulation. We explore the role of gene flow, selection, and dominance on load and extinction risk and further pinpoint critical thresholds required for metapopulation persistence.\r\n\r\nOverall this research contributes to our understanding of ecological and evolutionary mechanisms that shape species’ persistence in fragmented landscapes, a crucial foundation for successful conservation efforts and biodiversity management."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"date_created":"2024-01-03T18:30:13Z","date_updated":"2024-01-03T18:30:13Z","checksum":"de179b1c6758f182ff0c70d8b38c1501","relation":"source_file","file_id":"14730","content_type":"application/zip","file_size":16986244,"creator":"oolusany","file_name":"FinalSubmission_Thesis_OLUSANYA.zip","access_level":"closed"},{"creator":"oolusany","content_type":"application/pdf","file_size":6460403,"access_level":"open_access","file_name":"FinalSubmission2_Thesis_OLUSANYA.pdf","success":1,"checksum":"0e331585e3cd4823320aab4e69e64ccf","date_created":"2024-01-03T18:31:34Z","date_updated":"2024-01-03T18:31:34Z","file_id":"14731","relation":"main_file"}],"oa_version":"Published Version","_id":"14711","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","ddc":["576"],"title":"Local adaptation, genetic load and extinction in metapopulations"},{"language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-49275-4_2","conference":{"name":"GD: Graph Drawing and Network Visualization","start_date":"2023-09-20","location":"Isola delle Femmine, Palermo, Italy","end_date":"2023-09-22"},"quality_controlled":"1","external_id":{"arxiv":["2202.12175"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2202.12175","open_access":"1"}],"oa":1,"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031492747"],"issn":["0302-9743"]},"month":"01","volume":14466,"date_updated":"2024-01-29T09:45:06Z","date_created":"2024-01-28T23:01:43Z","author":[{"full_name":"De Nooijer, Phoebe","last_name":"De Nooijer","first_name":"Phoebe"},{"last_name":"Terziadis","first_name":"Soeren","full_name":"Terziadis, Soeren"},{"full_name":"Weinberger, Alexandra","first_name":"Alexandra","last_name":"Weinberger"},{"first_name":"Zuzana","last_name":"Masárová","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6660-1322","full_name":"Masárová, Zuzana"},{"last_name":"Mchedlidze","first_name":"Tamara","full_name":"Mchedlidze, Tamara"},{"full_name":"Löffler, Maarten","last_name":"Löffler","first_name":"Maarten"},{"first_name":"Günter","last_name":"Rote","full_name":"Rote, Günter"}],"department":[{"_id":"UlWa"},{"_id":"HeEd"}],"publisher":"Springer Nature","publication_status":"published","year":"2024","acknowledgement":"This work was initiated at the 16th European Research Week on Geometric Graphs in Strobl in 2019. A.W. is supported by the Austrian Science Fund (FWF): W1230. S.T. has been funded by the Vienna Science and Technology Fund (WWTF) [10.47379/ICT19035]. A preliminary version of this work has been presented at the 38th European Workshop on Computational Geometry (EuroCG 2022) in Perugia [9]. A full version of this paper, which includes appendices but is otherwise identical, is available as a technical report [10].","date_published":"2024-01-06T00:00:00Z","page":"18-33","citation":{"ista":"De Nooijer P, Terziadis S, Weinberger A, Masárová Z, Mchedlidze T, Löffler M, Rote G. 2024. Removing popular faces in curve arrangements. 31st International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 14466, 18–33.","ieee":"P. De Nooijer et al., “Removing popular faces in curve arrangements,” in 31st International Symposium on Graph Drawing and Network Visualization, Isola delle Femmine, Palermo, Italy, 2024, vol. 14466, pp. 18–33.","apa":"De Nooijer, P., Terziadis, S., Weinberger, A., Masárová, Z., Mchedlidze, T., Löffler, M., & Rote, G. (2024). Removing popular faces in curve arrangements. In 31st International Symposium on Graph Drawing and Network Visualization (Vol. 14466, pp. 18–33). Isola delle Femmine, Palermo, Italy: Springer Nature. https://doi.org/10.1007/978-3-031-49275-4_2","ama":"De Nooijer P, Terziadis S, Weinberger A, et al. Removing popular faces in curve arrangements. In: 31st International Symposium on Graph Drawing and Network Visualization. Vol 14466. Springer Nature; 2024:18-33. doi:10.1007/978-3-031-49275-4_2","chicago":"De Nooijer, Phoebe, Soeren Terziadis, Alexandra Weinberger, Zuzana Masárová, Tamara Mchedlidze, Maarten Löffler, and Günter Rote. “Removing Popular Faces in Curve Arrangements.” In 31st International Symposium on Graph Drawing and Network Visualization, 14466:18–33. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-49275-4_2.","mla":"De Nooijer, Phoebe, et al. “Removing Popular Faces in Curve Arrangements.” 31st International Symposium on Graph Drawing and Network Visualization, vol. 14466, Springer Nature, 2024, pp. 18–33, doi:10.1007/978-3-031-49275-4_2.","short":"P. De Nooijer, S. Terziadis, A. Weinberger, Z. Masárová, T. Mchedlidze, M. Löffler, G. Rote, in:, 31st International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2024, pp. 18–33."},"publication":"31st International Symposium on Graph Drawing and Network Visualization","article_processing_charge":"No","day":"06","scopus_import":"1","oa_version":"Preprint","intvolume":" 14466","title":"Removing popular faces in curve arrangements","status":"public","_id":"14888","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"A face in a curve arrangement is called popular if it is bounded by the same curve multiple times. Motivated by the automatic generation of curved nonogram puzzles, we investigate possibilities to eliminate the popular faces in an arrangement by inserting a single additional curve. This turns out to be NP-hard; however, it becomes tractable when the number of popular faces is small: We present a probabilistic FPT-approach in the number of popular faces.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference"}]