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Moll, Nucleic Acids Research 46 (2018) 2918–2931.","mla":"Nikolic, Nela, et al. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” Nucleic Acids Research, vol. 46, no. 6, Oxford University Press, 2018, pp. 2918–31, doi:10.1093/nar/gky079."},"page":"2918-2931","date_published":"2018-04-06T00:00:00Z","scopus_import":"1","day":"06","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"438","title":"Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations","ddc":["576"],"status":"public","intvolume":" 46","pubrep_id":"971","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2018-971-v1+1_2018_Nikoloc_Autoregulation_of.pdf","creator":"system","file_size":5027978,"content_type":"application/pdf","file_id":"5151","relation":"main_file","checksum":"3ff4f545c27e11a4cd20ccb30778793e","date_created":"2018-12-12T10:15:30Z","date_updated":"2020-07-14T12:46:27Z"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The MazF toxin sequence-specifically cleaves single-stranded RNA upon various stressful conditions, and it is activated as a part of the mazEF toxin–antitoxin module in Escherichia coli. Although autoregulation of mazEF expression through the MazE antitoxin-dependent transcriptional repression has been biochemically characterized, less is known about post-transcriptional autoregulation, as well as how both of these autoregulatory features affect growth of single cells during conditions that promote MazF production. Here, we demonstrate post-transcriptional autoregulation of mazF expression dynamics by MazF cleaving its own transcript. Single-cell analyses of bacterial populations during ectopic MazF production indicated that two-level autoregulation of mazEF expression influences cell-to-cell growth rate heterogeneity. The increase in growth rate heterogeneity is governed by the MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both autoregulatory features grant rapid exit from the stress caused by mazF overexpression. Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads to increased temporal variability in length of individual cells during ectopic mazF overexpression, as explained by a stochastic model indicating that mazEF mRNA cleavage underlies temporal fluctuations in MazF levels during stress."}],"issue":"6"},{"month":"08","doi":"10.7554/eLife.35684","language":[{"iso":"eng"}],"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":{"isi":["000441388200001"]},"oa":1,"project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety"}],"quality_controlled":"1","isi":1,"publist_id":"7792","file_date_updated":"2020-07-14T12:44:43Z","article_number":"e35684","related_material":{"record":[{"id":"5586","status":"public","relation":"popular_science"}]},"author":[{"full_name":"Picard, Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518","first_name":"Marion A","last_name":"Picard"},{"first_name":"Celine","last_name":"Cosseau","full_name":"Cosseau, Celine"},{"last_name":"Ferré","first_name":"Sabrina","full_name":"Ferré, Sabrina"},{"full_name":"Quack, Thomas","first_name":"Thomas","last_name":"Quack"},{"first_name":"Christoph","last_name":"Grevelding","full_name":"Grevelding, Christoph"},{"first_name":"Yohann","last_name":"Couté","full_name":"Couté, Yohann"},{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"volume":7,"date_created":"2018-12-11T11:44:47Z","date_updated":"2024-02-21T13:45:12Z","year":"2018","acknowledgement":"We are grateful to Lu Dabing (Soochow University, Suzhou, China) for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for providing optimal environment to bioinformatic analyses, and to the Vicoso lab for comments on the manuscript.","publisher":"eLife Sciences Publications","department":[{"_id":"BeVi"}],"publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"13","scopus_import":"1","date_published":"2018-08-13T00:00:00Z","citation":{"short":"M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B. Vicoso, ELife 7 (2018).","mla":"Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” ELife, vol. 7, e35684, eLife Sciences Publications, 2018, doi:10.7554/eLife.35684.","chicago":"Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.35684.","ama":"Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 2018;7. doi:10.7554/eLife.35684","ieee":"M. A. L. Picard et al., “Evolution of gene dosage on the Z-chromosome of schistosome parasites,” eLife, vol. 7. eLife Sciences Publications, 2018.","apa":"Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté, Y., & Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome parasites. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.35684","ista":"Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B. 2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 7, e35684."},"publication":"eLife","article_type":"original","abstract":[{"lang":"eng","text":"XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. "}],"type":"journal_article","file":[{"content_type":"application/pdf","file_size":3158125,"creator":"dernst","access_level":"open_access","file_name":"2018_eLife_Picard.pdf","checksum":"d6331d4385b1fffd6b47b45d5949d841","date_created":"2018-12-17T11:55:05Z","date_updated":"2020-07-14T12:44:43Z","relation":"main_file","file_id":"5695"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"131","intvolume":" 7","status":"public","title":"Evolution of gene dosage on the Z-chromosome of schistosome parasites","ddc":["570"]},{"file_date_updated":"2020-07-14T12:47:07Z","abstract":[{"text":"This package contains data for the publication \"Nonlinear decoding of a complex movie from the mammalian retina\" by Deny S. et al, PLOS Comput Biol (2018). \r\n\r\nThe data consists of\r\n(i) 91 spike sorted, isolated rat retinal ganglion cells that pass stability and quality criteria, recorded on the multi-electrode array, in response to the presentation of the complex movie with many randomly moving dark discs. The responses are represented as 648000 x 91 binary matrix, where the first index indicates the timebin of duration 12.5 ms, and the second index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike in the particular time bin.\r\n(ii) README file and a graphical illustration of the structure of the experiment, specifying how the 648000 timebins are split into epochs where 1, 2, 4, or 10 discs were displayed, and which stimulus segments are exact repeats or unique ball trajectories.\r\n(iii) a 648000 x 400 matrix of luminance traces for each of the 20 x 20 positions (\"sites\") in the movie frame, with time that is locked to the recorded raster. The luminance traces are produced as described in the manuscript by filtering the raw disc movie with a small gaussian spatial kernel. ","lang":"eng"}],"type":"research_data","datarep_id":"98","file":[{"relation":"main_file","file_id":"5590","date_created":"2018-12-12T13:02:24Z","date_updated":"2020-07-14T12:47:07Z","checksum":"6808748837b9afbbbabc2a356ca2b88a","file_name":"IST-2018-98-v1+1_BBalls_area2_tile2_20x20.mat","access_level":"open_access","file_size":1142543971,"content_type":"application/octet-stream","creator":"system"},{"file_id":"5591","relation":"main_file","date_created":"2018-12-12T13:02:25Z","date_updated":"2020-07-14T12:47:07Z","checksum":"d6d6cd07743038fe3a12352983fcf9dd","file_name":"IST-2018-98-v1+2_ExperimentStructure.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":702336},{"access_level":"open_access","file_name":"IST-2018-98-v1+3_GoodLocations_area2_20x20.mat","content_type":"application/octet-stream","file_size":432,"creator":"system","relation":"main_file","file_id":"5592","checksum":"0c9cfb4dab35bb3dc25a04395600b1c8","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:26Z"},{"file_size":986,"content_type":"text/plain","creator":"system","access_level":"open_access","file_name":"IST-2018-98-v1+4_README.txt","checksum":"2a83b011012e21e934b4596285b1a183","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:26Z","relation":"main_file","file_id":"5593"}],"oa_version":"Published Version","date_updated":"2024-02-21T13:45:26Z","date_created":"2018-12-12T12:31:39Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"292"}]},"author":[{"full_name":"Deny, Stephane","first_name":"Stephane","last_name":"Deny"},{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"},{"last_name":"Botella-Soler","first_name":"Vicente","full_name":"Botella-Soler, Vicente"},{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","last_name":"Martius","first_name":"Georg S","full_name":"Martius, Georg S"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"department":[{"_id":"ChLa"},{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","title":"Nonlinear decoding of a complex movie from the mammalian retina","ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5584","year":"2018","has_accepted_license":"1","article_processing_charge":"No","month":"03","day":"29","keyword":["retina","decoding","regression","neural networks","complex stimulus"],"doi":"10.15479/AT:ISTA:98","date_published":"2018-03-29T00:00:00Z","project":[{"call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26"}],"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"short":"S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).","mla":"Deny, Stephane, et al. Nonlinear Decoding of a Complex Movie from the Mammalian Retina. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:98.","chicago":"Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:98.","ama":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. 2018. doi:10.15479/AT:ISTA:98","apa":"Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., & Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:98","ieee":"S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina.” Institute of Science and Technology Austria, 2018.","ista":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina, Institute of Science and Technology Austria, 10.15479/AT:ISTA:98."}}]