[{"acknowledgement":"We thank Jens Elgeti and Silvia Fre for fruitful discussions.","oa_version":"None","abstract":[{"lang":"eng","text":"The regulation of cell growth in animal tissues is a question of critical importance: most tissues contain different types of cells in interconversion and the fraction of each type has to be controlled in a precise way, by mechanisms that remain unclear. Here, we provide a theoretical framework for the homeostasis of stem-cell-containing epithelial tissues using mechanical equations, which describe the size of the tissue and kinetic equations, which describe the interconversions of the cell populations. We show that several features, such as the evolution of stem cell fractions during intestinal development, the shape of a developing intestinal wall, as well as the increase in the proliferative compartment in cancer initiation, can be studied and understood from generic modelling which does not rely on a particular regulatory mechanism. Finally, inspired by recent experiments, we propose a model where cell division rates are regulated by the mechanical stresses in the epithelial sheet. We show that pressure-controlled growth can, in addition to the previous features, also explain with few parameters the formation of stem cell compartments as well as the morphologies observed when a colonic crypt becomes cancerous. We also discuss optimal strategies of wound healing, in connection with experiments on the cornea."}],"intvolume":" 11","month":"04","publisher":"Royal Society of London","language":[{"iso":"eng"}],"publication":"Journal of the Royal Society Interface","day":"06","publication_status":"published","year":"2014","date_created":"2018-12-11T11:49:14Z","date_published":"2014-04-06T00:00:00Z","volume":11,"doi":"10.1098/rsif.2013.0895","issue":"93","_id":"926","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"ista":"Hannezo EB, Prost J, Joanny J. 2014. Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. 11(93).","chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Growth Homeostatic Regulation and Stem Cell Dynamics in Tissues.” Journal of the Royal Society Interface. Royal Society of London, 2014. https://doi.org/10.1098/rsif.2013.0895.","ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Growth homeostatic regulation and stem cell dynamics in tissues,” Journal of the Royal Society Interface, vol. 11, no. 93. Royal Society of London, 2014.","short":"E.B. Hannezo, J. Prost, J. Joanny, Journal of the Royal Society Interface 11 (2014).","apa":"Hannezo, E. B., Prost, J., & Joanny, J. (2014). Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. Royal Society of London. https://doi.org/10.1098/rsif.2013.0895","ama":"Hannezo EB, Prost J, Joanny J. Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. 2014;11(93). doi:10.1098/rsif.2013.0895","mla":"Hannezo, Edouard B., et al. “Growth Homeostatic Regulation and Stem Cell Dynamics in Tissues.” Journal of the Royal Society Interface, vol. 11, no. 93, Royal Society of London, 2014, doi:10.1098/rsif.2013.0895."},"date_updated":"2021-01-12T08:21:57Z","title":"Growth homeostatic regulation and stem cell dynamics in tissues","article_processing_charge":"No","publist_id":"6516","author":[{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Prost, Jacques","last_name":"Prost","first_name":"Jacques"},{"first_name":"Jean","full_name":"Joanny, Jean","last_name":"Joanny"}]},{"issue":"6","volume":156,"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2014.01.029","open_access":"1"}],"month":"03","intvolume":" 156","abstract":[{"text":"Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T08:22:36Z","extern":"1","type":"journal_article","article_type":"original","status":"public","_id":"9458","page":"1286-1297","doi":"10.1016/j.cell.2014.01.029","date_published":"2014-03-13T00:00:00Z","date_created":"2021-06-04T12:00:16Z","year":"2014","day":"13","publication":"Cell","quality_controlled":"1","publisher":"Elsevier","oa":1,"author":[{"first_name":"Jason T.","full_name":"Huff, Jason T.","last_name":"Huff"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"}],"article_processing_charge":"No","external_id":{"pmid":["24630728"]},"title":"Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes","citation":{"mla":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:10.1016/j.cell.2014.01.029.","short":"J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.","ieee":"J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” Cell, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014.","ama":"Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 2014;156(6):1286-1297. doi:10.1016/j.cell.2014.01.029","apa":"Huff, J. T., & Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.01.029","chicago":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell. Elsevier, 2014. https://doi.org/10.1016/j.cell.2014.01.029.","ista":"Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of Sciences, vol. 111, no. 45, National Academy of Sciences, 2014, pp. 16166–71, doi:10.1073/pnas.1418564111.","ieee":"Z. Mérai et al., “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes,” Proceedings of the National Academy of Sciences, vol. 111, no. 45. National Academy of Sciences, pp. 16166–16171, 2014.","short":"Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171.","ama":"Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 2014;111(45):16166-16171. doi:10.1073/pnas.1418564111","apa":"Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1418564111","chicago":"Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1418564111.","ista":"Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 111(45), 16166–16171."},"title":"The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes","external_id":{"pmid":["25344531"]},"article_processing_charge":"No","author":[{"first_name":"Zsuzsanna","full_name":"Mérai, Zsuzsanna","last_name":"Mérai"},{"first_name":"Nina","full_name":"Chumak, Nina","last_name":"Chumak"},{"first_name":"Marcelina","last_name":"García-Aguilar","full_name":"García-Aguilar, Marcelina"},{"full_name":"Hsieh, Tzung-Fu","last_name":"Hsieh","first_name":"Tzung-Fu"},{"full_name":"Nishimura, Toshiro","last_name":"Nishimura","first_name":"Toshiro"},{"first_name":"Vera K.","last_name":"Schoft","full_name":"Schoft, Vera K."},{"full_name":"Bindics, János","last_name":"Bindics","first_name":"János"},{"last_name":"Ślusarz","full_name":"Ślusarz, Lucyna","first_name":"Lucyna"},{"full_name":"Arnoux, Stéphanie","last_name":"Arnoux","first_name":"Stéphanie"},{"first_name":"Susanne","full_name":"Opravil, Susanne","last_name":"Opravil"},{"last_name":"Mechtler","full_name":"Mechtler, Karl","first_name":"Karl"},{"last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"},{"first_name":"Robert L.","last_name":"Fischer","full_name":"Fischer, Robert L."},{"full_name":"Tamaru, Hisashi","last_name":"Tamaru","first_name":"Hisashi"}],"oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","publication":"Proceedings of the National Academy of Sciences","day":"11","year":"2014","date_created":"2021-06-07T07:23:43Z","date_published":"2014-11-11T00:00:00Z","doi":"10.1073/pnas.1418564111","page":"16166-16171","_id":"9479","status":"public","type":"journal_article","article_type":"original","extern":"1","date_updated":"2021-12-14T08:23:26Z","department":[{"_id":"DaZi"}],"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction.","lang":"eng"}],"intvolume":" 111","month":"11","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1418564111","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"volume":111,"issue":"45"},{"_id":"9662","status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2021-08-09T12:32:24Z","oa_version":"Preprint","pmid":1,"abstract":[{"text":"Fractionation of isotopes among distinct molecules or phases is a quantum effect which is often exploited to obtain insights on reaction mechanisms, biochemical, geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios in atomistic simulations is challenging, because one needs to perform a thermodynamic integration with respect to the isotope mass, along with time-consuming path integral calculations. By re-formulating the problem as a particle exchange in the ring polymer partition function, we derive new estimators giving direct access to the differential partitioning of isotopes, which can simplify the calculations by avoiding thermodynamic integration. We demonstrate the efficiency of these estimators by applying them to investigate the isotope fractionation ratios in the gas-phase Zundel cation, and in a few simple hydrocarbons.","lang":"eng"}],"month":"12","intvolume":" 141","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1412.1308","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"publication_status":"published","volume":141,"issue":"24","article_number":"244112","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"apa":"Cheng, B., & Ceriotti, M. (2014). Direct path integral estimators for isotope fractionation ratios. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4904293","ama":"Cheng B, Ceriotti M. Direct path integral estimators for isotope fractionation ratios. The Journal of Chemical Physics. 2014;141(24). doi:10.1063/1.4904293","ieee":"B. Cheng and M. Ceriotti, “Direct path integral estimators for isotope fractionation ratios,” The Journal of Chemical Physics, vol. 141, no. 24. AIP Publishing, 2014.","short":"B. Cheng, M. Ceriotti, The Journal of Chemical Physics 141 (2014).","mla":"Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for Isotope Fractionation Ratios.” The Journal of Chemical Physics, vol. 141, no. 24, 244112, AIP Publishing, 2014, doi:10.1063/1.4904293.","ista":"Cheng B, Ceriotti M. 2014. Direct path integral estimators for isotope fractionation ratios. The Journal of Chemical Physics. 141(24), 244112.","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for Isotope Fractionation Ratios.” The Journal of Chemical Physics. AIP Publishing, 2014. https://doi.org/10.1063/1.4904293."},"title":"Direct path integral estimators for isotope fractionation ratios","author":[{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"first_name":"Michele","last_name":"Ceriotti","full_name":"Ceriotti, Michele"}],"external_id":{"arxiv":["1412.1308"],"pmid":["25554138"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"AIP Publishing","oa":1,"day":"28","publication":"The Journal of Chemical Physics","year":"2014","doi":"10.1063/1.4904293","date_published":"2014-12-28T00:00:00Z","date_created":"2021-07-15T09:22:49Z"},{"article_number":"216806","citation":{"mla":"Higginbotham, Andrew P., et al. “Antilocalization of Coulomb Blockade in a Ge/Si Nanowire.” APS Physics, Physical Review Letters, vol. 112, no. 21, 216806, American Physical Society, 2014, doi:10.1103/PhysRevLett.112.216806.","ieee":"A. P. Higginbotham et al., “Antilocalization of coulomb blockade in a Ge/Si nanowire,” APS Physics, Physical Review Letters, vol. 112, no. 21. American Physical Society, 2014.","short":"A.P. Higginbotham, F. Kuemmeth, T. Larsen, M. Fitzpatrick, J. Yao, H. Yan, C. Lieber, C. Marcus, APS Physics, Physical Review Letters 112 (2014).","apa":"Higginbotham, A. P., Kuemmeth, F., Larsen, T., Fitzpatrick, M., Yao, J., Yan, H., … Marcus, C. (2014). Antilocalization of coulomb blockade in a Ge/Si nanowire. APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.112.216806","ama":"Higginbotham AP, Kuemmeth F, Larsen T, et al. Antilocalization of coulomb blockade in a Ge/Si nanowire. APS Physics, Physical Review Letters. 2014;112(21). doi:10.1103/PhysRevLett.112.216806","chicago":"Higginbotham, Andrew P, Ferdinand Kuemmeth, Thorvald Larsen, Mattias Fitzpatrick, Jun Yao, Hao Yan, Charles Lieber, and Charles Marcus. “Antilocalization of Coulomb Blockade in a Ge/Si Nanowire.” APS Physics, Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.112.216806.","ista":"Higginbotham AP, Kuemmeth F, Larsen T, Fitzpatrick M, Yao J, Yan H, Lieber C, Marcus C. 2014. Antilocalization of coulomb blockade in a Ge/Si nanowire. APS Physics, Physical Review Letters. 112(21), 216806."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Higginbotham","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P"},{"last_name":"Kuemmeth","full_name":"Kuemmeth, Ferdinand","first_name":"Ferdinand"},{"first_name":"Thorvald","last_name":"Larsen","full_name":"Larsen, Thorvald"},{"first_name":"Mattias","full_name":"Fitzpatrick, Mattias","last_name":"Fitzpatrick"},{"first_name":"Jun","last_name":"Yao","full_name":"Yao, Jun"},{"last_name":"Yan","full_name":"Yan, Hao","first_name":"Hao"},{"full_name":"Lieber, Charles","last_name":"Lieber","first_name":"Charles"},{"first_name":"Charles","full_name":"Marcus, Charles","last_name":"Marcus"}],"publist_id":"7957","external_id":{"arxiv":["1401.2948"]},"title":"Antilocalization of coulomb blockade in a Ge/Si nanowire","acknowledgement":"Research supported by the Danish National Research Foundation, the Office of Science at the U.S. Department of Energy, the National Science Foundation (PHY-1104528), and the Defense Advanced Research Projects Agency through the QuEST Program.","publisher":"American Physical Society","quality_controlled":"1","oa":1,"year":"2014","day":"29","publication":"APS Physics, Physical Review Letters","doi":"10.1103/PhysRevLett.112.216806","date_published":"2014-05-29T00:00:00Z","date_created":"2018-12-11T11:44:36Z","_id":"97","type":"journal_article","status":"public","date_updated":"2021-01-12T08:22:19Z","extern":"1","abstract":[{"text":"The distribution of Coulomb blockade peak heights as a function of magnetic field is investigated experimentally in a Ge-Si nanowire quantum dot. Strong spin-orbit coupling in this hole-gas system leads to antilocalization of Coulomb blockade peaks, consistent with theory. In particular, the peak height distribution has its maximum away from zero at zero magnetic field, with an average that decreases with increasing field. Magnetoconductance in the open-wire regime places a bound on the spin-orbit length (lso < 20 nm), consistent with values extracted in the Coulomb blockade regime (lso < 25 nm).","lang":"eng"}],"oa_version":"None","main_file_link":[{"url":"https://arxiv.org/abs/1401.2948","open_access":"1"}],"month":"05","intvolume":" 112","publication_status":"published","language":[{"iso":"eng"}],"issue":"21","volume":112},{"file_date_updated":"2020-07-14T12:45:24Z","department":[{"_id":"JoCs"}],"date_updated":"2023-02-23T14:06:14Z","ddc":["570"],"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":"435","_id":"2004","related_material":{"record":[{"status":"public","id":"9722","relation":"research_data"}]},"volume":9,"issue":"11","license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"publication_status":"published","file":[{"date_updated":"2020-07-14T12:45:24Z","file_size":829363,"creator":"system","date_created":"2018-12-12T10:10:58Z","file_name":"IST-2016-435-v1+1_journal.pone.0111430.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4850","checksum":"a2289b843f7463eb1233f9ce45e6a943"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"11","intvolume":" 9","abstract":[{"lang":"eng","text":"We have assembled a network of cell-fate determining transcription factors that play a key role in the specification of the ventral neuronal subtypes of the spinal cord on the basis of published transcriptional interactions. Asynchronous Boolean modelling of the network was used to compare simulation results with reported experimental observations. Such comparison highlighted the need to include additional regulatory connections in order to obtain the fixed point attractors of the model associated with the five known progenitor cell types located in the ventral spinal cord. The revised gene regulatory network reproduced previously observed cell state switches between progenitor cells observed in knock-out animal models or in experiments where the transcription factors were overexpressed. Furthermore the network predicted the inhibition of Irx3 by Nkx2.2 and this prediction was tested experimentally. Our results provide evidence for the existence of an as yet undescribed inhibitory connection which could potentially have significance beyond the ventral spinal cord. The work presented in this paper demonstrates the strength of Boolean modelling for identifying gene regulatory networks."}],"oa_version":"Published Version","author":[{"first_name":"Anna","last_name":"Lovrics","full_name":"Lovrics, Anna"},{"last_name":"Gao","full_name":"Gao, Yu","first_name":"Yu"},{"first_name":"Bianka","last_name":"Juhász","full_name":"Juhász, Bianka"},{"first_name":"István","last_name":"Bock","full_name":"Bock, István"},{"first_name":"Helen","full_name":"Byrne, Helen","last_name":"Byrne"},{"first_name":"András","last_name":"Dinnyés","full_name":"Dinnyés, András"},{"full_name":"Kovács, Krisztián","last_name":"Kovács","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztián"}],"publist_id":"5072","title":"Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord","citation":{"mla":"Lovrics, Anna, et al. “Boolean Modelling Reveals New Regulatory Connections between Transcription Factors Orchestrating the Development of the Ventral Spinal Cord.” PLoS One, vol. 9, no. 11, e111430, Public Library of Science, 2014, doi:10.1371/journal.pone.0111430.","ama":"Lovrics A, Gao Y, Juhász B, et al. Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. PLoS One. 2014;9(11). doi:10.1371/journal.pone.0111430","apa":"Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H., Dinnyés, A., & Kovács, K. (2014). Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0111430","ieee":"A. Lovrics et al., “Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord,” PLoS One, vol. 9, no. 11. Public Library of Science, 2014.","short":"A. Lovrics, Y. Gao, B. Juhász, I. Bock, H. Byrne, A. Dinnyés, K. Kovács, PLoS One 9 (2014).","chicago":"Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen Byrne, András Dinnyés, and Krisztián Kovács. “Boolean Modelling Reveals New Regulatory Connections between Transcription Factors Orchestrating the Development of the Ventral Spinal Cord.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0111430.","ista":"Lovrics A, Gao Y, Juhász B, Bock I, Byrne H, Dinnyés A, Kovács K. 2014. Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. PLoS One. 9(11), e111430."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"article_number":"e111430","date_published":"2014-11-14T00:00:00Z","doi":"10.1371/journal.pone.0111430","date_created":"2018-12-11T11:55:09Z","has_accepted_license":"1","year":"2014","day":"14","publication":"PLoS One","quality_controlled":"1","publisher":"Public Library of Science","oa":1},{"date_created":"2021-07-26T14:35:00Z","related_material":{"record":[{"id":"2004","status":"public","relation":"used_in_publication"}]},"doi":"10.1371/journal.pone.0111430.s006","date_published":"2014-11-14T00:00:00Z","year":"2014","day":"14","publisher":"Public Library of Science","month":"11","oa_version":"Published Version","article_processing_charge":"No","author":[{"first_name":"Anna","full_name":"Lovrics, Anna","last_name":"Lovrics"},{"first_name":"Yu","full_name":"Gao, Yu","last_name":"Gao"},{"first_name":"Bianka","last_name":"Juhász","full_name":"Juhász, Bianka"},{"first_name":"István","last_name":"Bock","full_name":"Bock, István"},{"full_name":"Byrne, Helen M.","last_name":"Byrne","first_name":"Helen M."},{"last_name":"Dinnyés","full_name":"Dinnyés, András","first_name":"András"},{"first_name":"Krisztián","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","last_name":"Kovács","full_name":"Kovács, Krisztián"}],"department":[{"_id":"JoCs"}],"title":"Transition probability between TF expression states when Dbx2 inhibits Nkx2.2","date_updated":"2023-02-23T10:24:07Z","citation":{"mla":"Lovrics, Anna, et al. Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2. Public Library of Science, 2014, doi:10.1371/journal.pone.0111430.s006.","ama":"Lovrics A, Gao Y, Juhász B, et al. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. 2014. doi:10.1371/journal.pone.0111430.s006","apa":"Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H. M., Dinnyés, A., & Kovács, K. (2014). Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. Public Library of Science. https://doi.org/10.1371/journal.pone.0111430.s006","ieee":"A. Lovrics et al., “Transition probability between TF expression states when Dbx2 inhibits Nkx2.2.” Public Library of Science, 2014.","short":"A. Lovrics, Y. Gao, B. Juhász, I. Bock, H.M. Byrne, A. Dinnyés, K. Kovács, (2014).","chicago":"Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen M. Byrne, András Dinnyés, and Krisztián Kovács. “Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2.” Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0111430.s006.","ista":"Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács K. 2014. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2, Public Library of Science, 10.1371/journal.pone.0111430.s006."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9722"},{"scopus_import":1,"intvolume":" 10","month":"09","abstract":[{"text":"A fundamental question in biology is the following: what is the time scale that is needed for evolutionary innovations? There are many results that characterize single steps in terms of the fixation time of new mutants arising in populations of certain size and structure. But here we ask a different question, which is concerned with the much longer time scale of evolutionary trajectories: how long does it take for a population exploring a fitness landscape to find target sequences that encode new biological functions? Our key variable is the length, (Formula presented.) of the genetic sequence that undergoes adaptation. In computer science there is a crucial distinction between problems that require algorithms which take polynomial or exponential time. The latter are considered to be intractable. Here we develop a theoretical approach that allows us to estimate the time of evolution as function of (Formula presented.) We show that adaptation on many fitness landscapes takes time that is exponential in (Formula presented.) even if there are broad selection gradients and many targets uniformly distributed in sequence space. These negative results lead us to search for specific mechanisms that allow evolution to work on polynomial time scales. We study a regeneration process and show that it enables evolution to work in polynomial time.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"issue":"9","related_material":{"record":[{"relation":"research_data","id":"9739","status":"public"}]},"volume":10,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":1399093,"date_updated":"2020-07-14T12:45:26Z","file_name":"IST-2016-440-v1+1_journal.pcbi.1003818.pdf","date_created":"2018-12-12T10:11:35Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"712d4c5787ddf97809cfc962507f0738","file_id":"4890"}],"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)"},"type":"journal_article","pubrep_id":"440","status":"public","_id":"2039","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:26Z","date_updated":"2023-02-23T14:06:36Z","ddc":["510"],"oa":1,"quality_controlled":"1","publisher":"Public Library of Science","date_created":"2018-12-11T11:55:22Z","date_published":"2014-09-11T00:00:00Z","doi":"10.1371/journal.pcbi.1003818","year":"2014","has_accepted_license":"1","publication":"PLoS Computational Biology","day":"11","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"article_number":"7p","publist_id":"5012","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Adlam, Ben","last_name":"Adlam","first_name":"Ben"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"title":"The time scale of evolutionary innovation","citation":{"apa":"Chatterjee, K., Pavlogiannis, A., Adlam, B., & Nowak, M. (2014). The time scale of evolutionary innovation. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003818","ama":"Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. The time scale of evolutionary innovation. PLoS Computational Biology. 2014;10(9). doi:10.1371/journal.pcbi.1003818","ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Nowak, “The time scale of evolutionary innovation,” PLoS Computational Biology, vol. 10, no. 9. Public Library of Science, 2014.","short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Nowak, PLoS Computational Biology 10 (2014).","mla":"Chatterjee, Krishnendu, et al. “The Time Scale of Evolutionary Innovation.” PLoS Computational Biology, vol. 10, no. 9, 7p, Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003818.","ista":"Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. 2014. The time scale of evolutionary innovation. PLoS Computational Biology. 10(9), 7p.","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Nowak. “The Time Scale of Evolutionary Innovation.” PLoS Computational Biology. Public Library of Science, 2014. https://doi.org/10.1371/journal.pcbi.1003818."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"department":[{"_id":"SyCr"}],"date_updated":"2023-02-23T14:06:46Z","type":"journal_article","article_type":"original","status":"public","_id":"2161","volume":68,"issue":"10","related_material":{"record":[{"relation":"research_data","id":"9742","status":"public"}]},"ec_funded":1,"publication_identifier":{"issn":["0340-5443"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 68","abstract":[{"lang":"eng","text":"Repeated pathogen exposure is a common threat in colonies of social insects, posing selection pressures on colony members to respond with improved disease-defense performance. We here tested whether experience gained by repeated tending of low-level fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary brood care in the clonal ant, Platythyrea punctata. We trained ants individually over nine consecutive trials to either sham-treated or fungus-exposed larvae. We then compared the larval grooming behavior of naive and trained ants and measured how effectively they removed infectious fungal conidiospores from the fungus-exposed larvae. We found that the ants changed the duration of larval grooming in response to both, larval treatment and their level of experience: (1) sham-treated larvae received longer grooming than the fungus-exposed larvae and (2) trained ants performed less self-grooming but longer larval grooming than naive ants, which was true for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants that groomed the fungus-exposed larvae for longer periods removed a higher number of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced ants performed longer larval grooming, they were more effective in fungal removal, thus making them better caretakers under pathogen attack of the colony. By studying this clonal ant, we can thus conclude that even in the absence of genetic variation between colony members, differences in experience levels of brood care may affect performance of sanitary brood care in social insects."}],"oa_version":"None","author":[{"id":"ca9c6ca9-e8aa-11ec-a586-b9471ede0494","first_name":"Claudia","last_name":"Westhus","full_name":"Westhus, Claudia"},{"full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883","last_name":"Ugelvig","first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Edouard","last_name":"Tourdot","full_name":"Tourdot, Edouard"},{"last_name":"Heinze","full_name":"Heinze, Jürgen","first_name":"Jürgen"},{"full_name":"Doums, Claudie","last_name":"Doums","first_name":"Claudie"},{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"4823","article_processing_charge":"No","title":"Increased grooming after repeated brood care provides sanitary benefits in a clonal ant","citation":{"chicago":"Westhus, Claudia, Line V Ugelvig, Edouard Tourdot, Jürgen Heinze, Claudie Doums, and Sylvia Cremer. “Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant.” Behavioral Ecology and Sociobiology. Springer, 2014. https://doi.org/10.1007/s00265-014-1778-8.","ista":"Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. 2014. Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. Behavioral Ecology and Sociobiology. 68(10), 1701–1710.","mla":"Westhus, Claudia, et al. “Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant.” Behavioral Ecology and Sociobiology, vol. 68, no. 10, Springer, 2014, pp. 1701–10, doi:10.1007/s00265-014-1778-8.","apa":"Westhus, C., Ugelvig, L. V., Tourdot, E., Heinze, J., Doums, C., & Cremer, S. (2014). Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. Behavioral Ecology and Sociobiology. Springer. https://doi.org/10.1007/s00265-014-1778-8","ama":"Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. Behavioral Ecology and Sociobiology. 2014;68(10):1701-1710. doi:10.1007/s00265-014-1778-8","ieee":"C. Westhus, L. V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, and S. Cremer, “Increased grooming after repeated brood care provides sanitary benefits in a clonal ant,” Behavioral Ecology and Sociobiology, vol. 68, no. 10. Springer, pp. 1701–1710, 2014.","short":"C. Westhus, L.V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, S. Cremer, Behavioral Ecology and Sociobiology 68 (2014) 1701–1710."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"CR-118/3-1","name":"Host-Parasite Coevolution","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425"}],"page":"1701 - 1710","doi":"10.1007/s00265-014-1778-8","date_published":"2014-07-23T00:00:00Z","date_created":"2018-12-11T11:56:03Z","year":"2014","day":"23","publication":"Behavioral Ecology and Sociobiology","quality_controlled":"1","publisher":"Springer","acknowledgement":"We thank Katrin Kellner for colony establishment and characterization, Mike Bidochka for the fungal strain, Meghan Vyleta for fungal strain characterization, Martina Klatt and Simon Tragust for help in the laboratory, Dimitri Missoh for developing the software BioLogic, and Mark Brown and Raphaël Jeanson for discussion and help with data analysis. The study was funded by the European Research Council (ERC Starting Grant to SC; Marie Curie IEF to LVU) and the German Research Foundation DFG (to SC and to JH), and CW received funding by the doctoral school Diversité du Vivant (Cotutelle project to CD and SC).\r\n"},{"acknowledgement":"The project was supported by Leverhulme Trust.","oa":1,"quality_controlled":"1","publisher":"Royal Society, The","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","day":"17","year":"2014","date_created":"2018-12-11T11:55:21Z","date_published":"2014-09-17T00:00:00Z","doi":"10.1098/rspb.2014.1679","article_number":"20141679","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Lagator, Mato, et al. “Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794, 20141679, Royal Society, The, 2014, doi:10.1098/rspb.2014.1679.","ama":"Lagator M, Colegrave N, Neve P. Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Proceedings of the Royal Society of London Series B Biological Sciences. 2014;281(1794). doi:10.1098/rspb.2014.1679","apa":"Lagator, M., Colegrave, N., & Neve, P. (2014). Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2014.1679","short":"M. Lagator, N. Colegrave, P. Neve, Proceedings of the Royal Society of London Series B Biological Sciences 281 (2014).","ieee":"M. Lagator, N. Colegrave, and P. Neve, “Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794. Royal Society, The, 2014.","chicago":"Lagator, Mato, Nick Colegrave, and Paul Neve. “Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2014. https://doi.org/10.1098/rspb.2014.1679.","ista":"Lagator M, Colegrave N, Neve P. 2014. Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Proceedings of the Royal Society of London Series B Biological Sciences. 281(1794), 20141679."},"title":"Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses","author":[{"last_name":"Lagator","full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato"},{"first_name":"Nick","full_name":"Colegrave, Nick","last_name":"Colegrave"},{"last_name":"Neve","full_name":"Neve, Paul","first_name":"Paul"}],"publist_id":"5019","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":" In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments. "}],"intvolume":" 281","month":"09","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211454/"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","volume":281,"issue":"1794","related_material":{"record":[{"relation":"research_data","status":"public","id":"9741"}]},"_id":"2036","status":"public","type":"journal_article","date_updated":"2023-02-23T14:06:44Z","department":[{"_id":"CaGu"}]}]