[{"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:59Z","file_size":7247468,"date_created":"2020-02-18T07:21:16Z","file_name":"2020_eLife_Narasimhan.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7494","checksum":"2052daa4be5019534f3a42f200a09f32"}],"publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"ec_funded":1,"volume":9,"pmid":1,"oa_version":"Published Version","abstract":[{"text":"In plants, clathrin mediated endocytosis (CME) represents the major route for cargo internalisation from the cell surface. It has been assumed to operate in an evolutionary conserved manner as in yeast and animals. Here we report characterisation of ultrastructure, dynamics and mechanisms of plant CME as allowed by our advancement in electron microscopy and quantitative live imaging techniques. Arabidopsis CME appears to follow the constant curvature model and the bona fide CME population generates vesicles of a predominantly hexagonal-basket type; larger and with faster kinetics than in other models. Contrary to the existing paradigm, actin is dispensable for CME events at the plasma membrane but plays a unique role in collecting endocytic vesicles, sorting of internalised cargos and directional endosome movement that itself actively promote CME events. Internalized vesicles display a strongly delayed and sequential uncoating. These unique features highlight the independent evolution of the plant CME mechanism during the autonomous rise of multicellularity in eukaryotes.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"intvolume":" 9","month":"01","scopus_import":"1","ddc":["570","580"],"date_updated":"2023-08-18T06:33:07Z","department":[{"_id":"JiFr"},{"_id":"GaTk"},{"_id":"EM-Fac"},{"_id":"SyCr"}],"file_date_updated":"2020-07-14T12:47:59Z","_id":"7490","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","publication":"eLife","day":"23","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2020-02-16T23:00:50Z","date_published":"2020-01-23T00:00:00Z","doi":"10.7554/eLife.52067","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Narasimhan M, Johnson AJ, Prizak R, Kaufmann W, Tan S, Casillas Perez BE, Friml J. 2020. Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. eLife. 9, e52067.","chicago":"Narasimhan, Madhumitha, Alexander J Johnson, Roshan Prizak, Walter Kaufmann, Shutang Tan, Barbara E Casillas Perez, and Jiří Friml. “Evolutionarily Unique Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.52067.","ama":"Narasimhan M, Johnson AJ, Prizak R, et al. Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. eLife. 2020;9. doi:10.7554/eLife.52067","apa":"Narasimhan, M., Johnson, A. J., Prizak, R., Kaufmann, W., Tan, S., Casillas Perez, B. E., & Friml, J. (2020). Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.52067","short":"M. Narasimhan, A.J. Johnson, R. Prizak, W. Kaufmann, S. Tan, B.E. Casillas Perez, J. Friml, ELife 9 (2020).","ieee":"M. Narasimhan et al., “Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants,” eLife, vol. 9. eLife Sciences Publications, 2020.","mla":"Narasimhan, Madhumitha, et al. “Evolutionarily Unique Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.” ELife, vol. 9, e52067, eLife Sciences Publications, 2020, doi:10.7554/eLife.52067."},"title":"Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants","article_processing_charge":"No","external_id":{"isi":["000514104100001"],"pmid":["31971511"]},"author":[{"last_name":"Narasimhan","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha"},{"last_name":"Johnson","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","full_name":"Prizak, Roshan"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Casillas Perez","full_name":"Casillas Perez, Barbara E","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"article_number":"e52067","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"}]},{"abstract":[{"lang":"eng","text":"Transcription factors, by binding to specific sequences on the DNA, control the precise spatio-temporal expression of genes inside a cell. However, this specificity is limited, leading to frequent incorrect binding of transcription factors that might have deleterious consequences on the cell. By constructing a biophysical model of TF-DNA binding in the context of gene regulation, I will first explore how regulatory constraints can strongly shape the distribution of a population in sequence space. Then, by directly linking this to a picture of multiple types of transcription factors performing their functions simultaneously inside the cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions between transcription factors and binding sites that lead to erroneous regulatory states -- and understand the constraints this places on the design of regulatory systems. I will then develop a generic theoretical framework to investigate the coevolution of multiple transcription factors and multiple binding sites, in the context of a gene regulatory network that performs a certain function. As a particular tractable version of this problem, I will consider the evolution of two transcription factors when they transmit upstream signals to downstream target genes. Specifically, I will describe the evolutionary steady states and the evolutionary pathways involved, along with their timescales, of a system that initially undergoes a transcription factor duplication event. To connect this important theoretical model to the prominent biological event of transcription factor duplication giving rise to paralogous families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription factors, a major family in humans, and focus on the patterns of evolution that paralogs have undergone in their various protein domains in the recent past. "}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"03","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6072","checksum":"e60a72de35d270b31f1a23d50f224ec0","creator":"rprizak","file_size":20995465,"date_updated":"2020-07-14T12:47:18Z","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","date_created":"2019-03-06T16:05:07Z"},{"file_size":85705272,"date_updated":"2020-07-14T12:47:18Z","creator":"rprizak","file_name":"thesis_v2_merge.zip","title":"Latex files","date_created":"2019-03-06T16:09:39Z","content_type":"application/zip","relation":"source_file","access_level":"closed","checksum":"67c2630333d05ebafef5f018863a8465","file_id":"6073"}],"related_material":{"record":[{"status":"public","id":"1358","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"955"}]},"_id":"6071","type":"dissertation","status":"public","date_updated":"2023-09-22T10:00:48Z","supervisor":[{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"ddc":["576"],"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:18Z","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2019","has_accepted_license":"1","day":"11","page":"189","date_created":"2019-03-06T16:16:10Z","date_published":"2019-03-11T00:00:00Z","doi":"10.15479/at:ista:th6071","project":[{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071.","ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria.","mla":"Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071.","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019.","short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.","ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071","apa":"Prizak, R. (2019). Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","full_name":"Prizak, Roshan"}],"title":"Coevolution of transcription factors and their binding sites in sequence space"},{"oa":1,"publisher":"American Physical Society","quality_controlled":"1","date_created":"2019-03-10T22:59:20Z","date_published":"2019-02-26T00:00:00Z","doi":"10.1103/PhysRevE.99.022423","publication":"Physical Review E","day":"26","year":"2019","isi":1,"article_number":"022423","title":"Receptor crosstalk improves concentration sensing of multiple ligands","external_id":{"isi":["000459916500007"]},"article_processing_charge":"No","author":[{"full_name":"Carballo-Pacheco, Martín","last_name":"Carballo-Pacheco","first_name":"Martín"},{"first_name":"Jonathan","last_name":"Desponds","full_name":"Desponds, Jonathan"},{"last_name":"Gavrilchenko","full_name":"Gavrilchenko, Tatyana","first_name":"Tatyana"},{"first_name":"Andreas","full_name":"Mayer, Andreas","last_name":"Mayer"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan","last_name":"Prizak","full_name":"Prizak, Roshan"},{"full_name":"Reddy, Gautam","last_name":"Reddy","first_name":"Gautam"},{"first_name":"Ilya","full_name":"Nemenman, Ilya","last_name":"Nemenman"},{"first_name":"Thierry","last_name":"Mora","full_name":"Mora, Thierry"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423, American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423.","apa":"Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R., Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423","ama":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 2019;99(2). doi:10.1103/PhysRevE.99.022423","ieee":"M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American Physical Society, 2019.","short":"M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).","chicago":"Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423.","ista":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G, Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 99(2), 022423."},"intvolume":" 99","month":"02","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems, leading to crosstalk between ligand-receptor pairs. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of noncognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway. Here we quantify the optimal precision of sensing the concentrations of multiple ligands by a collection of promiscuous receptors. We demonstrate that crosstalk can improve precision in concentration sensing and discrimination tasks. To achieve superior precision, the additional information about ligand concentrations contained in short binding events of the noncognate ligand should be exploited. We present a proofreading scheme to realize an approximate estimation of multiple ligand concentrations that reaches a precision close to the derived optimal bounds. Our results help rationalize the observed ubiquity of receptor crosstalk in molecular sensing.","lang":"eng"}],"volume":99,"issue":"2","language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"6090","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"date_updated":"2024-02-28T13:12:06Z"},{"quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"doi":"10.1038/s41467-017-00238-8","date_published":"2017-08-09T00:00:00Z","date_created":"2018-12-11T11:49:23Z","has_accepted_license":"1","isi":1,"year":"2017","day":"09","publication":"Nature Communications","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"216","author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar","last_name":"Friedlander","full_name":"Friedlander, Tamar"},{"full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik"}],"publist_id":"6459","external_id":{"isi":["000407198800005"]},"article_processing_charge":"Yes (in subscription journal)","title":"Evolution of new regulatory functions on biophysically realistic fitness landscapes","citation":{"ama":"Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00238-8","apa":"Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8","short":"T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017).","ieee":"T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","mla":"Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.","ista":"Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 8(1), 216.","chicago":"Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","month":"08","intvolume":" 8","abstract":[{"text":"Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.","lang":"eng"}],"oa_version":"Published Version","volume":8,"related_material":{"record":[{"relation":"dissertation_contains","id":"6071","status":"public"}]},"issue":"1","ec_funded":1,"publication_identifier":{"issn":["20411723"]},"publication_status":"published","file":[{"file_id":"5064","checksum":"29a1b5db458048d3bd5c67e0e2a56818","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2017-864-v1+1_s41467-017-00238-8.pdf","date_created":"2018-12-12T10:14:14Z","file_size":998157,"date_updated":"2020-07-14T12:48:16Z","creator":"system"},{"file_name":"IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf","date_created":"2018-12-12T10:14:15Z","file_size":9715993,"date_updated":"2020-07-14T12:48:16Z","creator":"system","checksum":"7b78401e52a576cf3e6bbf8d0abadc17","file_id":"5065","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"864","_id":"955","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:48:16Z","date_updated":"2023-09-22T10:00:49Z","ddc":["539","576"]},{"_id":"1358","status":"public","pubrep_id":"627","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["576"],"date_updated":"2023-09-07T12:53:49Z","department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:44:46Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements."}],"month":"08","intvolume":" 7","scopus_import":1,"file":[{"creator":"system","file_size":861805,"date_updated":"2020-07-14T12:44:46Z","file_name":"IST-2016-627-v1+1_ncomms12307.pdf","date_created":"2018-12-12T10:12:01Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"fe3f3a1526d180b29fe691ab11435b78","file_id":"4919"},{"file_id":"4920","checksum":"164864a1a675f3ad80e9917c27aba07f","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:12:02Z","file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","date_updated":"2020-07-14T12:44:46Z","file_size":1084703,"creator":"system"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":7,"related_material":{"record":[{"status":"public","id":"6071","relation":"dissertation_contains"}]},"ec_funded":1,"article_number":"12307","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms12307.","ista":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307.","mla":"Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications, vol. 7, 12307, Nature Publishing Group, 2016, doi:10.1038/ncomms12307.","apa":"Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., & Tkačik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms12307","ama":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 2016;7. doi:10.1038/ncomms12307","short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).","ieee":"T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” Nature Communications, vol. 7. Nature Publishing Group, 2016."},"title":"Intrinsic limits to gene regulation by global crosstalk","publist_id":"5887","author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar","last_name":"Friedlander","full_name":"Friedlander, Tamar"},{"full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"}],"quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"day":"04","publication":"Nature Communications","has_accepted_license":"1","year":"2016","doi":"10.1038/ncomms12307","date_published":"2016-08-04T00:00:00Z","date_created":"2018-12-11T11:51:34Z"},{"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5167","checksum":"3cbe8623174709a8ceec2103246f8fe0","file_size":536154,"date_updated":"2020-07-14T12:45:20Z","creator":"system","file_name":"IST-2016-419-v1+1_Ezard_et_al-2014-Functional_Ecology.pdf","date_created":"2018-12-12T10:15:45Z"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":28,"issue":"3","oa_version":"Published Version","abstract":[{"text":"Summary: Phenotypes are often environmentally dependent, which requires organisms to track environmental change. The challenge for organisms is to construct phenotypes using the most accurate environmental cue. Here, we use a quantitative genetic model of adaptation by additive genetic variance, within- and transgenerational plasticity via linear reaction norms and indirect genetic effects respectively. We show how the relative influence on the eventual phenotype of these components depends on the predictability of environmental change (fast or slow, sinusoidal or stochastic) and the developmental lag τ between when the environment is perceived and when selection acts. We then decompose expected mean fitness into three components (variance load, adaptation and fluctuation load) to study the fitness costs of within- and transgenerational plasticity. A strongly negative maternal effect coefficient m minimizes the variance load, but a strongly positive m minimises the fluctuation load. The adaptation term is maximized closer to zero, with positive or negative m preferred under different environmental scenarios. Phenotypic plasticity is higher when τ is shorter and when the environment changes frequently between seasonal extremes. Expected mean population fitness is highest away from highest observed levels of phenotypic plasticity. Within- and transgenerational plasticity act in concert to deliver well-adapted phenotypes, which emphasizes the need to study both simultaneously when investigating phenotypic evolution.","lang":"eng"}],"month":"06","intvolume":" 28","scopus_import":1,"ddc":["570"],"date_updated":"2021-01-12T06:54:00Z","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:20Z","_id":"1909","status":"public","pubrep_id":"419","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"01","publication":"Functional Ecology","has_accepted_license":"1","year":"2014","doi":"10.1111/1365-2435.12207","date_published":"2014-06-01T00:00:00Z","date_created":"2018-12-11T11:54:40Z","page":"693 - 701","acknowledgement":"Engineering and Physical Sciences Research Council. Grant Number: EP/H031928/1","publisher":"Wiley-Blackwell","oa":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology. Wiley-Blackwell, 2014. https://doi.org/10.1111/1365-2435.12207.","ista":"Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 28(3), 693–701.","mla":"Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology, vol. 28, no. 3, Wiley-Blackwell, 2014, pp. 693–701, doi:10.1111/1365-2435.12207.","apa":"Ezard, T., Prizak, R., & Hoyle, R. (2014). The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. Wiley-Blackwell. https://doi.org/10.1111/1365-2435.12207","ama":"Ezard T, Prizak R, Hoyle R. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 2014;28(3):693-701. doi:10.1111/1365-2435.12207","ieee":"T. Ezard, R. Prizak, and R. Hoyle, “The fitness costs of adaptation via phenotypic plasticity and maternal effects,” Functional Ecology, vol. 28, no. 3. Wiley-Blackwell, pp. 693–701, 2014.","short":"T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701."},"title":"The fitness costs of adaptation via phenotypic plasticity and maternal effects","publist_id":"5186","author":[{"full_name":"Ezard, Thomas","last_name":"Ezard","first_name":"Thomas"},{"full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rebecca","full_name":"Hoyle, Rebecca","last_name":"Hoyle"}]},{"file":[{"date_created":"2018-12-12T10:11:31Z","file_name":"IST-2018-934-v1+1_Prizak_et_al-2014-Ecology_and_Evolution.pdf","creator":"system","date_updated":"2020-07-14T12:46:38Z","file_size":621582,"file_id":"4886","checksum":"e32abf75a248e7a11811fd7f60858769","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":4,"issue":"15","oa_version":"Published Version","abstract":[{"text":"Transgenerational effects are broader than only parental relationships. Despite mounting evidence that multigenerational effects alter phenotypic and life-history traits, our understanding of how they combine to determine fitness is not well developed because of the added complexity necessary to study them. Here, we derive a quantitative genetic model of adaptation to an extraordinary new environment by an additive genetic component, phenotypic plasticity, maternal and grandmaternal effects. We show how, at equilibrium, negative maternal and negative grandmaternal effects maximize expected population mean fitness. We define negative transgenerational effects as those that have a negative effect on trait expression in the subsequent generation, that is, they slow, or potentially reverse, the expected evolutionary dynamic. When maternal effects are positive, negative grandmaternal effects are preferred. As expected under Mendelian inheritance, the grandmaternal effects have a lower impact on fitness than the maternal effects, but this dual inheritance model predicts a more complex relationship between maternal and grandmaternal effects to constrain phenotypic variance and so maximize expected population mean fitness in the offspring.","lang":"eng"}],"month":"07","intvolume":" 4","scopus_import":1,"ddc":["530","571"],"date_updated":"2021-01-12T08:01:30Z","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:46:38Z","_id":"537","status":"public","pubrep_id":"934","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"19","publication":"Ecology and Evolution","has_accepted_license":"1","year":"2014","date_published":"2014-07-19T00:00:00Z","doi":"10.1002/ece3.1150","date_created":"2018-12-11T11:47:02Z","page":"3139 - 3145","publisher":"Wiley-Blackwell","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Prizak R, Ezard T, Hoyle R. 2014. Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. 4(15), 3139–3145.","chicago":"Prizak, Roshan, Thomas Ezard, and Rebecca Hoyle. “Fitness Consequences of Maternal and Grandmaternal Effects.” Ecology and Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1002/ece3.1150.","ama":"Prizak R, Ezard T, Hoyle R. Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. 2014;4(15):3139-3145. doi:10.1002/ece3.1150","apa":"Prizak, R., Ezard, T., & Hoyle, R. (2014). Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.1150","ieee":"R. Prizak, T. Ezard, and R. Hoyle, “Fitness consequences of maternal and grandmaternal effects,” Ecology and Evolution, vol. 4, no. 15. Wiley-Blackwell, pp. 3139–3145, 2014.","short":"R. Prizak, T. Ezard, R. Hoyle, Ecology and Evolution 4 (2014) 3139–3145.","mla":"Prizak, Roshan, et al. “Fitness Consequences of Maternal and Grandmaternal Effects.” Ecology and Evolution, vol. 4, no. 15, Wiley-Blackwell, 2014, pp. 3139–45, doi:10.1002/ece3.1150."},"title":"Fitness consequences of maternal and grandmaternal effects","publist_id":"7280","author":[{"first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan","last_name":"Prizak"},{"first_name":"Thomas","full_name":"Ezard, Thomas","last_name":"Ezard"},{"last_name":"Hoyle","full_name":"Hoyle, Rebecca","first_name":"Rebecca"}]}]