[{"doi":"10.1088/1742-5468/2013/03/P03011","article_processing_charge":"No","volume":2013,"day":"12","acknowledgement":"his work was supported in part by NSF Grants IIS-0613435 and PHY-0957573, by NIH Grants R01 EY14196 and P50 GM071508, by the Fannie and John Hertz Foundation, by the Human Frontiers Science Program, by the Swartz Foundation, and by the WM Keck Foundation.\r\n","publication":"Journal of Statistical Mechanics Theory and Experiment","intvolume":"      2013","date_published":"2013-03-12T00:00:00Z","publist_id":"3942","title":"The simplest maximum entropy model for collective behavior in a neural network","article_number":"P03011","oa":1,"citation":{"ama":"Tkačik G, Marre O, Mora T, Amodei D, Berry M, Bialek W. The simplest maximum entropy model for collective behavior in a neural network. <i>Journal of Statistical Mechanics Theory and Experiment</i>. 2013;2013(3). doi:<a href=\"https://doi.org/10.1088/1742-5468/2013/03/P03011\">10.1088/1742-5468/2013/03/P03011</a>","ista":"Tkačik G, Marre O, Mora T, Amodei D, Berry M, Bialek W. 2013. The simplest maximum entropy model for collective behavior in a neural network. Journal of Statistical Mechanics Theory and Experiment. 2013(3), P03011.","ieee":"G. Tkačik, O. Marre, T. Mora, D. Amodei, M. Berry, and W. Bialek, “The simplest maximum entropy model for collective behavior in a neural network,” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2013, no. 3. IOP Publishing Ltd., 2013.","short":"G. Tkačik, O. Marre, T. Mora, D. Amodei, M. Berry, W. Bialek, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).","mla":"Tkačik, Gašper, et al. “The Simplest Maximum Entropy Model for Collective Behavior in a Neural Network.” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2013, no. 3, P03011, IOP Publishing Ltd., 2013, doi:<a href=\"https://doi.org/10.1088/1742-5468/2013/03/P03011\">10.1088/1742-5468/2013/03/P03011</a>.","apa":"Tkačik, G., Marre, O., Mora, T., Amodei, D., Berry, M., &#38; Bialek, W. (2013). The simplest maximum entropy model for collective behavior in a neural network. <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1742-5468/2013/03/P03011\">https://doi.org/10.1088/1742-5468/2013/03/P03011</a>","chicago":"Tkačik, Gašper, Olivier Marre, Thierry Mora, Dario Amodei, Michael Berry, and William Bialek. “The Simplest Maximum Entropy Model for Collective Behavior in a Neural Network.” <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing Ltd., 2013. <a href=\"https://doi.org/10.1088/1742-5468/2013/03/P03011\">https://doi.org/10.1088/1742-5468/2013/03/P03011</a>."},"date_created":"2018-12-11T11:59:55Z","quality_controlled":"1","arxiv":1,"author":[{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"first_name":"Thierry","full_name":"Mora, Thierry","last_name":"Mora"},{"first_name":"Dario","last_name":"Amodei","full_name":"Amodei, Dario"},{"last_name":"Berry","full_name":"Berry, Michael","first_name":"Michael"},{"first_name":"William","full_name":"Bialek, William","last_name":"Bialek"}],"status":"public","date_updated":"2021-01-12T07:00:14Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Recent work emphasizes that the maximum entropy principle provides a bridge between statistical mechanics models for collective behavior in neural networks and experiments on networks of real neurons. Most of this work has focused on capturing the measured correlations among pairs of neurons. Here we suggest an alternative, constructing models that are consistent with the distribution of global network activity, i.e. the probability that K out of N cells in the network generate action potentials in the same small time bin. The inverse problem that we need to solve in constructing the model is analytically tractable, and provides a natural 'thermodynamics' for the network in the limit of large N. We analyze the responses of neurons in a small patch of the retina to naturalistic stimuli, and find that the implied thermodynamics is very close to an unusual critical point, in which the entropy (in proper units) is exactly equal to the energy. © 2013 IOP Publishing Ltd and SISSA Medialab srl.\r\n","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.6319"}],"scopus_import":1,"month":"03","year":"2013","department":[{"_id":"GaTk"}],"article_type":"original","publisher":"IOP Publishing Ltd.","type":"journal_article","oa_version":"Preprint","_id":"2850","issue":"3","external_id":{"arxiv":["1207.6319"]},"publication_status":"published"},{"publication_status":"published","quality_controlled":"1","issue":"3","_id":"2851","oa_version":"None","type":"journal_article","date_created":"2018-12-11T11:59:56Z","citation":{"mla":"Berry, Michael, et al. “A Simple Method for Estimating the Entropy of Neural Activity.” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2013, no. 3, P03015, IOP Publishing Ltd., 2013, doi:<a href=\"https://doi.org/10.1088/1742-5468/2013/03/P03015\">10.1088/1742-5468/2013/03/P03015</a>.","chicago":"Berry, Michael, Gašper Tkačik, Julien Dubuis, Olivier Marre, and Ravá Da Silveira. “A Simple Method for Estimating the Entropy of Neural Activity.” <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing Ltd., 2013. <a href=\"https://doi.org/10.1088/1742-5468/2013/03/P03015\">https://doi.org/10.1088/1742-5468/2013/03/P03015</a>.","apa":"Berry, M., Tkačik, G., Dubuis, J., Marre, O., &#38; Da Silveira, R. (2013). A simple method for estimating the entropy of neural activity. <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1742-5468/2013/03/P03015\">https://doi.org/10.1088/1742-5468/2013/03/P03015</a>","ieee":"M. Berry, G. Tkačik, J. Dubuis, O. Marre, and R. Da Silveira, “A simple method for estimating the entropy of neural activity,” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2013, no. 3. IOP Publishing Ltd., 2013.","ista":"Berry M, Tkačik G, Dubuis J, Marre O, Da Silveira R. 2013. A simple method for estimating the entropy of neural activity. Journal of Statistical Mechanics Theory and Experiment. 2013(3), P03015.","short":"M. Berry, G. Tkačik, J. Dubuis, O. Marre, R. Da Silveira, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).","ama":"Berry M, Tkačik G, Dubuis J, Marre O, Da Silveira R. A simple method for estimating the entropy of neural activity. <i>Journal of Statistical Mechanics Theory and Experiment</i>. 2013;2013(3). doi:<a href=\"https://doi.org/10.1088/1742-5468/2013/03/P03015\">10.1088/1742-5468/2013/03/P03015</a>"},"article_number":"P03015","publisher":"IOP Publishing Ltd.","department":[{"_id":"GaTk"}],"title":"A simple method for estimating the entropy of neural activity","publist_id":"3941","year":"2013","month":"03","scopus_import":1,"date_published":"2013-03-12T00:00:00Z","intvolume":"      2013","abstract":[{"lang":"eng","text":"The number of possible activity patterns in a population of neurons grows exponentially with the size of the population. Typical experiments explore only a tiny fraction of the large space of possible activity patterns in the case of populations with more than 10 or 20 neurons. It is thus impossible, in this undersampled regime, to estimate the probabilities with which most of the activity patterns occur. As a result, the corresponding entropy - which is a measure of the computational power of the neural population - cannot be estimated directly. We propose a simple scheme for estimating the entropy in the undersampled regime, which bounds its value from both below and above. The lower bound is the usual 'naive' entropy of the experimental frequencies. The upper bound results from a hybrid approximation of the entropy which makes use of the naive estimate, a maximum entropy fit, and a coverage adjustment. We apply our simple scheme to artificial data, in order to check their accuracy; we also compare its performance to those of several previously defined entropy estimators. We then apply it to actual measurements of neural activity in populations with up to 100 cells. Finally, we discuss the similarities and differences between the proposed simple estimation scheme and various earlier methods. © 2013 IOP Publishing Ltd and SISSA Medialab srl."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"day":"12","publication":"Journal of Statistical Mechanics Theory and Experiment","date_updated":"2021-01-12T07:00:14Z","volume":2013,"status":"public","author":[{"last_name":"Berry","full_name":"Berry, Michael","first_name":"Michael"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"first_name":"Julien","full_name":"Dubuis, Julien","last_name":"Dubuis"},{"last_name":"Marre","full_name":"Marre, Olivier","first_name":"Olivier"},{"first_name":"Ravá","last_name":"Da Silveira","full_name":"Da Silveira, Ravá"}],"doi":"10.1088/1742-5468/2013/03/P03015"},{"date_updated":"2023-10-18T06:43:23Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3619501/","open_access":"1"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9751"}]},"abstract":[{"lang":"eng","text":"High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared with its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent parasite transmission to nearby relatives. We found that bacterial suicide provides large benefits to survivors at marginal costs to committers. The cost of suicide was low, because infected cells are moribund, rapidly dying upon phage infection, such that no more opportunity for reproduction remains. As a consequence of its marginal cost, host suicide was selectively favoured even when relatedness between committers and survivors approached zero. Altogether, our findings demonstrate that low-cost suicide can evolve with ease, represents an effective host-defence strategy, and seems to be widespread among microbes. Moreover, low-cost suicide might also occur in higher organisms as exemplified by infected social insect workers leaving the colony to die in isolation."}],"scopus_import":"1","status":"public","author":[{"first_name":"Dominik","full_name":"Refardt, Dominik","last_name":"Refardt"},{"last_name":"Bergmiller","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kümmerli, Rolf","last_name":"Kümmerli","first_name":"Rolf"}],"publisher":"The Royal Society","type":"journal_article","oa_version":"Submitted Version","publication_status":"published","external_id":{"pmid":["23516238"]},"_id":"2853","issue":"1759","publication_identifier":{"eissn":["1471-2954"]},"month":"05","year":"2013","department":[{"_id":"CaGu"}],"article_type":"original","day":"22","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","volume":280,"pmid":1,"intvolume":"       280","date_published":"2013-05-22T00:00:00Z","doi":"10.1098/rspb.2012.3035","article_processing_charge":"No","oa":1,"citation":{"chicago":"Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society, 2013. <a href=\"https://doi.org/10.1098/rspb.2012.3035\">https://doi.org/10.1098/rspb.2012.3035</a>.","apa":"Refardt, D., Bergmiller, T., &#38; Kümmerli, R. (2013). Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2012.3035\">https://doi.org/10.1098/rspb.2012.3035</a>","mla":"Refardt, Dominik, et al. “Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 280, no. 1759, The Royal Society, 2013, doi:<a href=\"https://doi.org/10.1098/rspb.2012.3035\">10.1098/rspb.2012.3035</a>.","ista":"Refardt D, Bergmiller T, Kümmerli R. 2013. Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection. Proceedings of the Royal Society of London Series B Biological Sciences. 280(1759).","short":"D. Refardt, T. Bergmiller, R. Kümmerli, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013).","ieee":"D. Refardt, T. Bergmiller, and R. Kümmerli, “Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 280, no. 1759. The Royal Society, 2013.","ama":"Refardt D, Bergmiller T, Kümmerli R. Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2013;280(1759). doi:<a href=\"https://doi.org/10.1098/rspb.2012.3035\">10.1098/rspb.2012.3035</a>"},"date_created":"2018-12-11T11:59:56Z","quality_controlled":"1","publist_id":"3939","title":"Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection"},{"page":"640 - 657","publist_id":"3938","title":"Strategy improvement for concurrent reachability and turn based stochastic safety games","oa":1,"quality_controlled":"1","date_created":"2018-12-11T11:59:57Z","citation":{"ieee":"K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Strategy improvement for concurrent reachability and turn based stochastic safety games,” <i>Journal of Computer and System Sciences</i>, vol. 79, no. 5. Elsevier, pp. 640–657, 2013.","short":"K. Chatterjee, L. De Alfaro, T.A. Henzinger, Journal of Computer and System Sciences 79 (2013) 640–657.","ista":"Chatterjee K, De Alfaro L, Henzinger TA. 2013. Strategy improvement for concurrent reachability and turn based stochastic safety games. Journal of Computer and System Sciences. 79(5), 640–657.","ama":"Chatterjee K, De Alfaro L, Henzinger TA. Strategy improvement for concurrent reachability and turn based stochastic safety games. <i>Journal of Computer and System Sciences</i>. 2013;79(5):640-657. doi:<a href=\"https://doi.org/10.1016/j.jcss.2012.12.001\">10.1016/j.jcss.2012.12.001</a>","chicago":"Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Strategy Improvement for Concurrent Reachability and Turn Based Stochastic Safety Games.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.jcss.2012.12.001\">https://doi.org/10.1016/j.jcss.2012.12.001</a>.","apa":"Chatterjee, K., De Alfaro, L., &#38; Henzinger, T. A. (2013). Strategy improvement for concurrent reachability and turn based stochastic safety games. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2012.12.001\">https://doi.org/10.1016/j.jcss.2012.12.001</a>","mla":"Chatterjee, Krishnendu, et al. “Strategy Improvement for Concurrent Reachability and Turn Based Stochastic Safety Games.” <i>Journal of Computer and System Sciences</i>, vol. 79, no. 5, Elsevier, 2013, pp. 640–57, doi:<a href=\"https://doi.org/10.1016/j.jcss.2012.12.001\">10.1016/j.jcss.2012.12.001</a>."},"file_date_updated":"2020-07-14T12:45:51Z","doi":"10.1016/j.jcss.2012.12.001","ec_funded":1,"article_processing_charge":"No","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"volume":79,"publication":"Journal of Computer and System Sciences","day":"01","acknowledgement":"This work was partially supported in part by the NSF grants CCR-0132780, CNS-0720884, CCR-0225610, by the Swiss National Science Foundation, ERC Start Grant Graph Games (Project No. 279307), FWF NFN Grant S11407-N23 (RiSE), and a Microsoft faculty fellows","date_published":"2013-08-01T00:00:00Z","has_accepted_license":"1","intvolume":"        79","year":"2013","month":"08","project":[{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"article_type":"original","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"pubrep_id":"388","publisher":"Elsevier","issue":"5","_id":"2854","publication_status":"published","file":[{"file_id":"5370","creator":"system","relation":"main_file","file_name":"IST-2015-388-v1+1_1-s2.0-S0022000012001778-main.pdf","file_size":425488,"checksum":"6d3ee12cceb946a0abe69594b6a22409","date_created":"2018-12-12T10:18:48Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:51Z"}],"type":"journal_article","oa_version":"Published Version","ddc":["000"],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"De Alfaro, Luca","last_name":"De Alfaro","first_name":"Luca"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T07:00:16Z","scopus_import":1,"abstract":[{"text":"We consider concurrent games played on graphs. At every round of a game, each player simultaneously and independently selects a move; the moves jointly determine the transition to a successor state. Two basic objectives are the safety objective to stay forever in a given set of states, and its dual, the reachability objective to reach a given set of states. First, we present a simple proof of the fact that in concurrent reachability games, for all ε&gt;0, memoryless ε-optimal strategies exist. A memoryless strategy is independent of the history of plays, and an ε-optimal strategy achieves the objective with probability within ε of the value of the game. In contrast to previous proofs of this fact, our proof is more elementary and more combinatorial. Second, we present a strategy-improvement (a.k.a. policy-iteration) algorithm for concurrent games with reachability objectives. Finally, we present a strategy-improvement algorithm for turn-based stochastic games (where each player selects moves in turns) with safety objectives. Our algorithms yield sequences of player-1 strategies which ensure probabilities of winning that converge monotonically (from below) to the value of the game. © 2012 Elsevier Inc.","lang":"eng"}]},{"publication":"Cell Reports","day":"28","volume":3,"intvolume":"         3","has_accepted_license":"1","date_published":"2013-03-28T00:00:00Z","doi":"10.1016/j.celrep.2013.02.002","file_date_updated":"2020-07-14T12:45:51Z","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"oa":1,"date_created":"2018-12-11T11:59:57Z","citation":{"ama":"Hippenmeyer S, Johnson R, Luo L. Mosaic analysis with double markers reveals cell type specific paternal growth dominance. <i>Cell Reports</i>. 2013;3(3):960-967. doi:<a href=\"https://doi.org/10.1016/j.celrep.2013.02.002\">10.1016/j.celrep.2013.02.002</a>","short":"S. Hippenmeyer, R. Johnson, L. Luo, Cell Reports 3 (2013) 960–967.","ieee":"S. Hippenmeyer, R. Johnson, and L. Luo, “Mosaic analysis with double markers reveals cell type specific paternal growth dominance,” <i>Cell Reports</i>, vol. 3, no. 3. Cell Press, pp. 960–967, 2013.","ista":"Hippenmeyer S, Johnson R, Luo L. 2013. Mosaic analysis with double markers reveals cell type specific paternal growth dominance. Cell Reports. 3(3), 960–967.","apa":"Hippenmeyer, S., Johnson, R., &#38; Luo, L. (2013). Mosaic analysis with double markers reveals cell type specific paternal growth dominance. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2013.02.002\">https://doi.org/10.1016/j.celrep.2013.02.002</a>","chicago":"Hippenmeyer, Simon, Randy Johnson, and Liqun Luo. “Mosaic Analysis with Double Markers Reveals Cell Type Specific Paternal Growth Dominance.” <i>Cell Reports</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.celrep.2013.02.002\">https://doi.org/10.1016/j.celrep.2013.02.002</a>.","mla":"Hippenmeyer, Simon, et al. “Mosaic Analysis with Double Markers Reveals Cell Type Specific Paternal Growth Dominance.” <i>Cell Reports</i>, vol. 3, no. 3, Cell Press, 2013, pp. 960–67, doi:<a href=\"https://doi.org/10.1016/j.celrep.2013.02.002\">10.1016/j.celrep.2013.02.002</a>."},"quality_controlled":"1","publist_id":"3937","page":"960 - 967","title":"Mosaic analysis with double markers reveals cell type specific paternal growth dominance","date_updated":"2021-01-12T07:00:16Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Genomic imprinting leads to preferred expression of either the maternal or paternal alleles of a subset of genes. Imprinting is essential for mammalian development, and its deregulation causes many diseases. However, the functional relevance of imprinting at the cellular level is poorly understood for most imprinted genes. We used mosaic analysis with double markers (MADM) in mice to create uniparental disomies (UPDs) and to visualize imprinting effects with single-cell resolution. Although chromosome 12 UPD did not produce detectable phenotypes, chromosome 7 UPD caused highly significant paternal growth dominance in the liver and lung, but not in the brain or heart. A single gene on chromosome 7, encoding the secreted insulin-like growth factor 2 (IGF2), accounts for most of the paternal dominance effect. Mosaic analyses implied additional imprinted loci on chromosome 7 acting cell autonomously to transmit the IGF2 signal. Our study reveals chromosome- and cell-type specificity of genomic imprinting effects.","lang":"eng"}],"scopus_import":1,"status":"public","author":[{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Johnson","full_name":"Johnson, Randy","first_name":"Randy"},{"full_name":"Luo, Liqun","last_name":"Luo","first_name":"Liqun"}],"publisher":"Cell Press","pubrep_id":"405","type":"journal_article","file":[{"file_name":"IST-2016-405-v1+1_1-s2.0-S2211124713000612-main.pdf","relation":"main_file","creator":"system","file_id":"5274","date_updated":"2020-07-14T12:45:51Z","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:17:20Z","checksum":"6e977b918e81384cd571ec5a9d812289","file_size":1907211}],"oa_version":"Published Version","ddc":["570"],"publication_status":"published","_id":"2855","issue":"3","month":"03","year":"2013","department":[{"_id":"SiHi"}]},{"doi":"10.1038/nn.3346","date_published":"2013-03-03T00:00:00Z","intvolume":"        16","pmid":1,"volume":16,"publication":"Nature Neuroscience","day":"03","acknowledgement":"National Science Foundation grants CHE-0233882 and CHE-0840505 (to the College of Chemistry at the University of California, Berkeley), a postdoctoral fellowship of the European Molecular Biology Organization (H.J.)","title":"Optical control of metabotropic glutamate receptors","publist_id":"3936","page":"507 - 516","quality_controlled":"1","citation":{"ama":"Levitz J, Pantoja C, Gaub B, et al. Optical control of metabotropic glutamate receptors. <i>Nature Neuroscience</i>. 2013;16:507-516. doi:<a href=\"https://doi.org/10.1038/nn.3346\">10.1038/nn.3346</a>","ieee":"J. Levitz <i>et al.</i>, “Optical control of metabotropic glutamate receptors,” <i>Nature Neuroscience</i>, vol. 16. Nature Publishing Group, pp. 507–516, 2013.","ista":"Levitz J, Pantoja C, Gaub B, Janovjak HL, Reiner A, Hoagland A, Schoppik D, Kane B, Stawski P, Schier A, Trauner D, Isacoff E. 2013. Optical control of metabotropic glutamate receptors. Nature Neuroscience. 16, 507–516.","short":"J. Levitz, C. Pantoja, B. Gaub, H.L. Janovjak, A. Reiner, A. Hoagland, D. Schoppik, B. Kane, P. Stawski, A. Schier, D. Trauner, E. Isacoff, Nature Neuroscience 16 (2013) 507–516.","mla":"Levitz, Joshua, et al. “Optical Control of Metabotropic Glutamate Receptors.” <i>Nature Neuroscience</i>, vol. 16, Nature Publishing Group, 2013, pp. 507–16, doi:<a href=\"https://doi.org/10.1038/nn.3346\">10.1038/nn.3346</a>.","apa":"Levitz, J., Pantoja, C., Gaub, B., Janovjak, H. L., Reiner, A., Hoagland, A., … Isacoff, E. (2013). Optical control of metabotropic glutamate receptors. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nn.3346\">https://doi.org/10.1038/nn.3346</a>","chicago":"Levitz, Joshua, Carlos Pantoja, Benjamin Gaub, Harald L Janovjak, Andreas Reiner, Adam Hoagland, David Schoppik, et al. “Optical Control of Metabotropic Glutamate Receptors.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nn.3346\">https://doi.org/10.1038/nn.3346</a>."},"date_created":"2018-12-11T11:59:57Z","oa":1,"author":[{"full_name":"Levitz, Joshua","last_name":"Levitz","first_name":"Joshua"},{"first_name":"Carlos","last_name":"Pantoja","full_name":"Pantoja, Carlos"},{"first_name":"Benjamin","last_name":"Gaub","full_name":"Gaub, Benjamin"},{"orcid":"0000-0002-8023-9315","last_name":"Janovjak","full_name":"Janovjak, Harald L","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Reiner","full_name":"Reiner, Andreas","first_name":"Andreas"},{"last_name":"Hoagland","full_name":"Hoagland, Adam","first_name":"Adam"},{"first_name":"David","full_name":"Schoppik, David","last_name":"Schoppik"},{"last_name":"Kane","full_name":"Kane, Brian","first_name":"Brian"},{"first_name":"Philipp","last_name":"Stawski","full_name":"Stawski, Philipp"},{"first_name":"Alexander","full_name":"Schier, Alexander","last_name":"Schier"},{"full_name":"Trauner, Dirk","last_name":"Trauner","first_name":"Dirk"},{"full_name":"Isacoff, Ehud","last_name":"Isacoff","first_name":"Ehud"}],"status":"public","scopus_import":1,"abstract":[{"lang":"eng","text":"G protein–coupled receptors (GPCRs), the largest family of membrane signaling proteins, respond to neurotransmitters, hormones and small environmental molecules. The neuronal function of many GPCRs has been difficult to resolve because of an inability to gate them with subtype specificity, spatial precision, speed and reversibility. To address this, we developed an approach for opto-chemical engineering of native GPCRs. We applied this to the metabotropic glutamate receptors (mGluRs) to generate light-agonized and light-antagonized mGluRs (LimGluRs). The light-agonized LimGluR2, on which we focused, was fast, bistable and supported multiple rounds of on/off switching. Light gated two of the primary neuronal functions of mGluR2: suppression of excitability and inhibition of neurotransmitter release. We found that the light-antagonized tool LimGluR2-block was able to manipulate negative feedback of synaptically released glutamate on transmitter release. We generalized the optical control to two additional family members: mGluR3 and mGluR6. This system worked in rodent brain slices and in zebrafish in vivo, where we found that mGluR2 modulated the threshold for escape behavior. These light-gated mGluRs pave the way for determining the roles of mGluRs in synaptic plasticity, memory and disease."}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681425/","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T07:00:16Z","department":[{"_id":"HaJa"}],"month":"03","year":"2013","_id":"2856","external_id":{"pmid":["23455609"]},"publication_status":"published","oa_version":"Submitted Version","type":"journal_article","publisher":"Nature Publishing Group"},{"_id":"2857","alternative_title":["MIMB"],"publication_status":"published","type":"journal_article","file":[{"date_updated":"2020-07-14T12:45:51Z","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:12:34Z","file_size":336734,"checksum":"1701f0d989f27ddac471b19a894ec0d1","file_name":"IST-2017-834-v1+1_szobota.pdf","relation":"main_file","creator":"system","file_id":"4952"}],"oa_version":"Submitted Version","ddc":["570"],"pubrep_id":"834","publisher":"Springer","department":[{"_id":"HaJa"}],"month":"02","year":"2013","project":[{"grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)"},{"name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564"}],"scopus_import":1,"abstract":[{"lang":"eng","text":"In the vibrant field of optogenetics, optics and genetic targeting are combined to commandeer cellular functions, such as the neuronal action potential, by optically stimulating light-sensitive ion channels expressed in the cell membrane. One broadly applicable manifestation of this approach are covalently attached photochromic tethered ligands (PTLs) that allow activating ligand-gated ion channels with outstanding spatial and temporal resolution. Here, we describe all steps towards the successful development and application of PTL-gated ion channels in cell lines and primary cells. The basis for these experiments forms a combination of molecular modeling, genetic engineering, cell culture, and electrophysiology. The light-gated glutamate receptor (LiGluR), which consists of the PTL-functionalized GluK2 receptor, serves as a model."}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:00:17Z","author":[{"first_name":"Stephanie","full_name":"Szobota, Stephanie","last_name":"Szobota"},{"full_name":"Mckenzie, Catherine","last_name":"Mckenzie","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","first_name":"Catherine"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak"}],"status":"public","quality_controlled":"1","citation":{"mla":"Szobota, Stephanie, et al. “Optical Control of Ligand-Gated Ion Channels.” <i>Methods in Molecular Biology</i>, vol. 998, Springer, 2013, pp. 417–35, doi:<a href=\"https://doi.org/10.1007/978-1-62703-351-0_32\">10.1007/978-1-62703-351-0_32</a>.","apa":"Szobota, S., Mckenzie, C., &#38; Janovjak, H. L. (2013). Optical control of ligand-gated ion channels. <i>Methods in Molecular Biology</i>. Springer. <a href=\"https://doi.org/10.1007/978-1-62703-351-0_32\">https://doi.org/10.1007/978-1-62703-351-0_32</a>","chicago":"Szobota, Stephanie, Catherine Mckenzie, and Harald L Janovjak. “Optical Control of Ligand-Gated Ion Channels.” <i>Methods in Molecular Biology</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/978-1-62703-351-0_32\">https://doi.org/10.1007/978-1-62703-351-0_32</a>.","ama":"Szobota S, Mckenzie C, Janovjak HL. Optical control of ligand-gated ion channels. <i>Methods in Molecular Biology</i>. 2013;998:417-435. doi:<a href=\"https://doi.org/10.1007/978-1-62703-351-0_32\">10.1007/978-1-62703-351-0_32</a>","short":"S. Szobota, C. Mckenzie, H.L. Janovjak, Methods in Molecular Biology 998 (2013) 417–435.","ieee":"S. Szobota, C. Mckenzie, and H. L. Janovjak, “Optical control of ligand-gated ion channels,” <i>Methods in Molecular Biology</i>, vol. 998. Springer, pp. 417–435, 2013.","ista":"Szobota S, Mckenzie C, Janovjak HL. 2013. Optical control of ligand-gated ion channels. Methods in Molecular Biology. 998, 417–435."},"date_created":"2018-12-11T11:59:57Z","oa":1,"title":"Optical control of ligand-gated ion channels","page":"417 - 435","publist_id":"3932","date_published":"2013-02-22T00:00:00Z","intvolume":"       998","has_accepted_license":"1","volume":998,"publication":"Methods in Molecular Biology","day":"22","ec_funded":1,"file_date_updated":"2020-07-14T12:45:51Z","doi":"10.1007/978-1-62703-351-0_32"},{"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-07T11:40:43Z","scopus_import":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1400"}]},"abstract":[{"lang":"eng","text":"Tumor growth is caused by the acquisition of driver mutations, which enhance the net reproductive rate of cells. Driver mutations may increase cell division, reduce cell death, or allow cells to overcome density-limiting effects. We study the dynamics of tumor growth as one additional driver mutation is acquired. Our models are based on two-type branching processes that terminate in either tumor disappearance or tumor detection. In our first model, both cell types grow exponentially, with a faster rate for cells carrying the additional driver. We find that the additional driver mutation does not affect the survival probability of the lesion, but can substantially reduce the time to reach the detectable size if the lesion is slow growing. In our second model, cells lacking the additional driver cannot exceed a fixed carrying capacity, due to density limitations. In this case, the time to detection depends strongly on this carrying capacity. Our model provides a quantitative framework for studying tumor dynamics during different stages of progression. We observe that early, small lesions need additional drivers, while late stage metastases are only marginally affected by them. These results help to explain why additional driver mutations are typically not detected in fast-growing metastases."}],"status":"public","author":[{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","last_name":"Reiter"},{"full_name":"Božić, Ivana","last_name":"Božić","first_name":"Ivana"},{"first_name":"Benjamin","id":"135B5B70-E9D2-11E9-BD74-BB415DA2B523","full_name":"Allen, Benjamin","last_name":"Allen"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"publisher":"Wiley-Blackwell","pubrep_id":"415","publication_status":"published","_id":"2858","issue":"1","ddc":["570"],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:51Z","checksum":"e2955b3889f8a823c3d5a72cb16f8957","file_size":1172037,"date_created":"2018-12-12T10:15:50Z","file_name":"IST-2016-415-v1+1_Reiter_et_al-2013-Evolutionary_Applications.pdf","file_id":"5173","creator":"system","relation":"main_file"}],"project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"}],"month":"01","year":"2013","department":[{"_id":"KrCh"}],"day":"01","publication":"Evolutionary Applications","volume":6,"date_published":"2013-01-01T00:00:00Z","has_accepted_license":"1","intvolume":"         6","file_date_updated":"2020-07-14T12:45:51Z","doi":"10.1111/eva.12020","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"oa":1,"quality_controlled":"1","date_created":"2018-12-11T11:59:58Z","citation":{"apa":"Reiter, J., Božić, I., Allen, B., Chatterjee, K., &#38; Nowak, M. (2013). The effect of one additional driver mutation on tumor progression. <i>Evolutionary Applications</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/eva.12020\">https://doi.org/10.1111/eva.12020</a>","chicago":"Reiter, Johannes, Ivana Božić, Benjamin Allen, Krishnendu Chatterjee, and Martin Nowak. “The Effect of One Additional Driver Mutation on Tumor Progression.” <i>Evolutionary Applications</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/eva.12020\">https://doi.org/10.1111/eva.12020</a>.","mla":"Reiter, Johannes, et al. “The Effect of One Additional Driver Mutation on Tumor Progression.” <i>Evolutionary Applications</i>, vol. 6, no. 1, Wiley-Blackwell, 2013, pp. 34–45, doi:<a href=\"https://doi.org/10.1111/eva.12020\">10.1111/eva.12020</a>.","ama":"Reiter J, Božić I, Allen B, Chatterjee K, Nowak M. The effect of one additional driver mutation on tumor progression. <i>Evolutionary Applications</i>. 2013;6(1):34-45. doi:<a href=\"https://doi.org/10.1111/eva.12020\">10.1111/eva.12020</a>","short":"J. Reiter, I. Božić, B. Allen, K. Chatterjee, M. Nowak, Evolutionary Applications 6 (2013) 34–45.","ista":"Reiter J, Božić I, Allen B, Chatterjee K, Nowak M. 2013. The effect of one additional driver mutation on tumor progression. Evolutionary Applications. 6(1), 34–45.","ieee":"J. Reiter, I. Božić, B. Allen, K. Chatterjee, and M. Nowak, “The effect of one additional driver mutation on tumor progression,” <i>Evolutionary Applications</i>, vol. 6, no. 1. Wiley-Blackwell, pp. 34–45, 2013."},"page":"34 - 45","publist_id":"3931","title":"The effect of one additional driver mutation on tumor progression"},{"date_created":"2018-12-11T11:59:58Z","citation":{"short":"P. Bendich, H. Edelsbrunner, D. Morozov, A. Patel, Homology, Homotopy and Applications 15 (2013) 51–72.","ista":"Bendich P, Edelsbrunner H, Morozov D, Patel A. 2013. Homology and robustness of level and interlevel sets. Homology, Homotopy and Applications. 15(1), 51–72.","ieee":"P. Bendich, H. Edelsbrunner, D. Morozov, and A. Patel, “Homology and robustness of level and interlevel sets,” <i>Homology, Homotopy and Applications</i>, vol. 15, no. 1. International Press, pp. 51–72, 2013.","ama":"Bendich P, Edelsbrunner H, Morozov D, Patel A. Homology and robustness of level and interlevel sets. <i>Homology, Homotopy and Applications</i>. 2013;15(1):51-72. doi:<a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">10.4310/HHA.2013.v15.n1.a3</a>","chicago":"Bendich, Paul, Herbert Edelsbrunner, Dmitriy Morozov, and Amit Patel. “Homology and Robustness of Level and Interlevel Sets.” <i>Homology, Homotopy and Applications</i>. International Press, 2013. <a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">https://doi.org/10.4310/HHA.2013.v15.n1.a3</a>.","apa":"Bendich, P., Edelsbrunner, H., Morozov, D., &#38; Patel, A. (2013). Homology and robustness of level and interlevel sets. <i>Homology, Homotopy and Applications</i>. International Press. <a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">https://doi.org/10.4310/HHA.2013.v15.n1.a3</a>","mla":"Bendich, Paul, et al. “Homology and Robustness of Level and Interlevel Sets.” <i>Homology, Homotopy and Applications</i>, vol. 15, no. 1, International Press, 2013, pp. 51–72, doi:<a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">10.4310/HHA.2013.v15.n1.a3</a>."},"arxiv":1,"quality_controlled":"1","oa":1,"title":"Homology and robustness of level and interlevel sets","page":"51 - 72","publist_id":"3930","intvolume":"        15","date_published":"2013-05-01T00:00:00Z","publication":"Homology, Homotopy and Applications","day":"01","volume":15,"doi":"10.4310/HHA.2013.v15.n1.a3","type":"journal_article","oa_version":"Preprint","publication_status":"published","external_id":{"arxiv":["1102.3389"]},"issue":"1","_id":"2859","publisher":"International Press","department":[{"_id":"HeEd"}],"month":"05","year":"2013","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1102.3389v1"}],"abstract":[{"text":"Given a continuous function f:X-R on a topological space, we consider the preimages of intervals and their homology groups and show how to read the ranks of these groups from the extended persistence diagram of f. In addition, we quantify the robustness of the homology classes under perturbations of f using well groups, and we show how to read the ranks of these groups from the same extended persistence diagram. The special case X=R3 has ramifications in the fields of medical imaging and scientific visualization.","lang":"eng"}],"scopus_import":1,"date_updated":"2021-01-12T07:00:18Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","author":[{"id":"43F6EC54-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","full_name":"Bendich, Paul","last_name":"Bendich"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"first_name":"Dmitriy","last_name":"Morozov","full_name":"Morozov, Dmitriy"},{"full_name":"Patel, Amit","last_name":"Patel","id":"34A254A0-F248-11E8-B48F-1D18A9856A87","first_name":"Amit"}]},{"publisher":"Elsevier","publication_status":"published","issue":"1","_id":"2860","file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:52Z","checksum":"0e18cb8561153ddb50bb5af16e7c9e97","file_size":2637837,"date_created":"2019-01-23T08:08:07Z","file_name":"2013_Neuron_Dupret.pdf","file_id":"5877","creator":"dernst","relation":"main_file"}],"oa_version":"Published Version","ddc":["570"],"type":"journal_article","project":[{"grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"}],"year":"2013","month":"03","department":[{"_id":"JoCs"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T07:00:19Z","scopus_import":1,"abstract":[{"text":"In the hippocampus, cell assemblies forming mnemonic representations of space are thought to arise as a result of changes in functional connections of pyramidal cells. We have found that CA1 interneuron circuits are also reconfigured during goal-oriented spatial learning through modification of inputs from pyramidal cells. As learning progressed, new pyramidal assemblies expressed in theta cycles alternated with previously established ones, and eventually overtook them. The firing patterns of interneurons developed a relationship to new, learning-related assemblies: some interneurons associated their activity with new pyramidal assemblies while some others dissociated from them. These firing associations were explained by changes in the weight of monosynaptic inputs received by interneurons from new pyramidal assemblies, as these predicted the associational changes. Spatial learning thus engages circuit modifications in the hippocampus that incorporate a redistribution of inhibitory activity that might assist in the segregation of competing pyramidal cell assembly patterns in space and time.","lang":"eng"}],"status":"public","author":[{"first_name":"David","full_name":"Dupret, David","last_name":"Dupret"},{"last_name":"O'Neill","full_name":"O'Neill, Joseph","first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L"}],"oa":1,"quality_controlled":"1","citation":{"short":"D. Dupret, J. O’Neill, J.L. Csicsvari, Neuron 78 (2013) 166–180.","ieee":"D. Dupret, J. O’Neill, and J. L. Csicsvari, “Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning,” <i>Neuron</i>, vol. 78, no. 1. Elsevier, pp. 166–180, 2013.","ista":"Dupret D, O’Neill J, Csicsvari JL. 2013. Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning. Neuron. 78(1), 166–180.","ama":"Dupret D, O’Neill J, Csicsvari JL. Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning. <i>Neuron</i>. 2013;78(1):166-180. doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.01.033\">10.1016/j.neuron.2013.01.033</a>","chicago":"Dupret, David, Joseph O’Neill, and Jozsef L Csicsvari. “Dynamic Reconfiguration of Hippocampal Interneuron Circuits during Spatial Learning.” <i>Neuron</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.neuron.2013.01.033\">https://doi.org/10.1016/j.neuron.2013.01.033</a>.","apa":"Dupret, D., O’Neill, J., &#38; Csicsvari, J. L. (2013). Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2013.01.033\">https://doi.org/10.1016/j.neuron.2013.01.033</a>","mla":"Dupret, David, et al. “Dynamic Reconfiguration of Hippocampal Interneuron Circuits during Spatial Learning.” <i>Neuron</i>, vol. 78, no. 1, Elsevier, 2013, pp. 166–80, doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.01.033\">10.1016/j.neuron.2013.01.033</a>."},"date_created":"2018-12-11T11:59:59Z","publist_id":"3929","page":"166 - 180","title":"Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning","publication":"Neuron","day":"21","acknowledgement":"D.D. and J.C. were supported by a MRC Intramural Programme Grant U138197111","volume":78,"date_published":"2013-03-21T00:00:00Z","intvolume":"        78","has_accepted_license":"1","file_date_updated":"2020-07-14T12:45:52Z","doi":"10.1016/j.neuron.2013.01.033","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1},{"publisher":"IOP Publishing Ltd.","article_number":"125101","date_created":"2018-12-11T11:59:59Z","citation":{"ama":"Botella Soler V, Oteo J, Ros J, Glendinning P. Lyapunov exponent and topological entropy plateaus in piecewise linear maps. <i>Journal of Physics A: Mathematical and Theoretical</i>. 2013;46(12). doi:<a href=\"https://doi.org/10.1088/1751-8113/46/12/125101\">10.1088/1751-8113/46/12/125101</a>","ieee":"V. Botella Soler, J. Oteo, J. Ros, and P. Glendinning, “Lyapunov exponent and topological entropy plateaus in piecewise linear maps,” <i>Journal of Physics A: Mathematical and Theoretical</i>, vol. 46, no. 12. IOP Publishing Ltd., 2013.","short":"V. Botella Soler, J. Oteo, J. Ros, P. Glendinning, Journal of Physics A: Mathematical and Theoretical 46 (2013).","ista":"Botella Soler V, Oteo J, Ros J, Glendinning P. 2013. Lyapunov exponent and topological entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical and Theoretical. 46(12), 125101.","mla":"Botella Soler, Vicente, et al. “Lyapunov Exponent and Topological Entropy Plateaus in Piecewise Linear Maps.” <i>Journal of Physics A: Mathematical and Theoretical</i>, vol. 46, no. 12, 125101, IOP Publishing Ltd., 2013, doi:<a href=\"https://doi.org/10.1088/1751-8113/46/12/125101\">10.1088/1751-8113/46/12/125101</a>.","apa":"Botella Soler, V., Oteo, J., Ros, J., &#38; Glendinning, P. (2013). Lyapunov exponent and topological entropy plateaus in piecewise linear maps. <i>Journal of Physics A: Mathematical and Theoretical</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1751-8113/46/12/125101\">https://doi.org/10.1088/1751-8113/46/12/125101</a>","chicago":"Botella Soler, Vicente, José Oteo, Javier Ros, and Paul Glendinning. “Lyapunov Exponent and Topological Entropy Plateaus in Piecewise Linear Maps.” <i>Journal of Physics A: Mathematical and Theoretical</i>. IOP Publishing Ltd., 2013. <a href=\"https://doi.org/10.1088/1751-8113/46/12/125101\">https://doi.org/10.1088/1751-8113/46/12/125101</a>."},"type":"journal_article","oa_version":"None","issue":"12","_id":"2861","publication_status":"published","quality_controlled":"1","month":"03","year":"2013","publist_id":"3928","title":"Lyapunov exponent and topological entropy plateaus in piecewise linear maps","department":[{"_id":"GaTk"}],"volume":46,"date_updated":"2021-01-12T07:00:19Z","publication":"Journal of Physics A: Mathematical and Theoretical","day":"29","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"text":"We consider a two-parameter family of piecewise linear maps in which the moduli of the two slopes take different values. We provide numerical evidence of the existence of some parameter regions in which the Lyapunov exponent and the topological entropy remain constant. Analytical proof of this phenomenon is also given for certain cases. Surprisingly however, the systems with that property are not conjugate as we prove by using kneading theory.","lang":"eng"}],"intvolume":"        46","scopus_import":1,"date_published":"2013-03-29T00:00:00Z","doi":"10.1088/1751-8113/46/12/125101","author":[{"first_name":"Vicente","id":"421234E8-F248-11E8-B48F-1D18A9856A87","full_name":"Botella Soler, Vicente","last_name":"Botella Soler","orcid":"0000-0002-8790-1914"},{"first_name":"José","last_name":"Oteo","full_name":"Oteo, José"},{"first_name":"Javier","last_name":"Ros","full_name":"Ros, Javier"},{"last_name":"Glendinning","full_name":"Glendinning, Paul","first_name":"Paul"}],"status":"public"},{"citation":{"ista":"Tay H, Schulze S, Compagnon J, Foley F, Heisenberg C-PJ, Yost HJ, Abdelilah Seyfried S, Amack J. 2013. Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle. Development. 140(7), 1550–1559.","short":"H. Tay, S. Schulze, J. Compagnon, F. Foley, C.-P.J. Heisenberg, H.J. Yost, S. Abdelilah Seyfried, J. Amack, Development 140 (2013) 1550–1559.","ieee":"H. Tay <i>et al.</i>, “Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle,” <i>Development</i>, vol. 140, no. 7. Company of Biologists, pp. 1550–1559, 2013.","ama":"Tay H, Schulze S, Compagnon J, et al. Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle. <i>Development</i>. 2013;140(7):1550-1559. doi:<a href=\"https://doi.org/10.1242/dev.087130\">10.1242/dev.087130</a>","mla":"Tay, Hwee, et al. “Lethal Giant Larvae 2 Regulates Development of the Ciliated Organ Kupffer’s Vesicle.” <i>Development</i>, vol. 140, no. 7, Company of Biologists, 2013, pp. 1550–59, doi:<a href=\"https://doi.org/10.1242/dev.087130\">10.1242/dev.087130</a>.","chicago":"Tay, Hwee, Sabrina Schulze, Julien Compagnon, Fiona Foley, Carl-Philipp J Heisenberg, H Joseph Yost, Salim Abdelilah Seyfried, and Jeffrey Amack. “Lethal Giant Larvae 2 Regulates Development of the Ciliated Organ Kupffer’s Vesicle.” <i>Development</i>. Company of Biologists, 2013. <a href=\"https://doi.org/10.1242/dev.087130\">https://doi.org/10.1242/dev.087130</a>.","apa":"Tay, H., Schulze, S., Compagnon, J., Foley, F., Heisenberg, C.-P. J., Yost, H. J., … Amack, J. (2013). Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.087130\">https://doi.org/10.1242/dev.087130</a>"},"date_created":"2018-12-11T11:59:59Z","quality_controlled":"1","oa":1,"title":"Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle","page":"1550 - 1559","publist_id":"3927","intvolume":"       140","date_published":"2013-04-01T00:00:00Z","volume":140,"acknowledgement":"Deposited in PMC for release after 12 months. We thank members of the Amack lab for helpful discussions and Mahendra Sonawane for donating reagents.","publication":"Development","day":"01","pmid":1,"doi":"10.1242/dev.087130","oa_version":"Submitted Version","type":"journal_article","issue":"7","_id":"2862","publication_status":"published","external_id":{"pmid":["23482490"]},"publisher":"Company of Biologists","department":[{"_id":"CaHe"}],"year":"2013","month":"04","abstract":[{"text":"Motile cilia perform crucial functions during embryonic development and throughout adult life. Development of organs containing motile cilia involves regulation of cilia formation (ciliogenesis) and formation of a luminal space (lumenogenesis) in which cilia generate fluid flows. Control of ciliogenesis and lumenogenesis is not yet fully understood, and it remains unclear whether these processes are coupled. In the zebrafish embryo, lethal giant larvae 2 (lgl2) is expressed prominently in ciliated organs. Lgl proteins are involved in establishing cell polarity and have been implicated in vesicle trafficking. Here, we identified a role for Lgl2 in development of ciliated epithelia in Kupffer's vesicle, which directs left-right asymmetry of the embryo; the otic vesicles, which give rise to the inner ear; and the pronephric ducts of the kidney. Using Kupffer's vesicle as a model ciliated organ, we found that depletion of Lgl2 disrupted lumen formation and reduced cilia number and length. Immunofluorescence and time-lapse imaging of Kupffer's vesicle morphogenesis in Lgl2-deficient embryos suggested cell adhesion defects and revealed loss of the adherens junction component E-cadherin at lateral membranes. Genetic interaction experiments indicate that Lgl2 interacts with Rab11a to regulate E-cadherin and mediate lumen formation that is uncoupled from cilia formation. These results uncover new roles and interactions for Lgl2 that are crucial for both lumenogenesis and ciliogenesis and indicate that these processes are genetically separable in zebrafish.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596994/"}],"scopus_import":1,"date_updated":"2021-01-12T07:00:20Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Hwee","full_name":"Tay, Hwee","last_name":"Tay"},{"first_name":"Sabrina","last_name":"Schulze","full_name":"Schulze, Sabrina"},{"first_name":"Julien","id":"2E3E0988-F248-11E8-B48F-1D18A9856A87","last_name":"Compagnon","full_name":"Compagnon, Julien"},{"first_name":"Fiona","last_name":"Foley","full_name":"Foley, Fiona"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"},{"last_name":"Yost","full_name":"Yost, H Joseph","first_name":"H Joseph"},{"full_name":"Abdelilah Seyfried, Salim","last_name":"Abdelilah Seyfried","first_name":"Salim"},{"first_name":"Jeffrey","last_name":"Amack","full_name":"Amack, Jeffrey"}],"status":"public"},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1371/journal.pcbi.1002922","file_date_updated":"2020-07-14T12:45:52Z","has_accepted_license":"1","intvolume":"         9","date_published":"2013-03-01T00:00:00Z","publication":"PLoS Computational Biology","day":"01","volume":9,"title":"Stimulus-dependent maximum entropy models of neural population codes","publist_id":"3926","date_created":"2018-12-11T12:00:00Z","citation":{"ama":"Granot Atedgi E, Tkačik G, Segev R, Schneidman E. Stimulus-dependent maximum entropy models of neural population codes. <i>PLoS Computational Biology</i>. 2013;9(3). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1002922\">10.1371/journal.pcbi.1002922</a>","ieee":"E. Granot Atedgi, G. Tkačik, R. Segev, and E. Schneidman, “Stimulus-dependent maximum entropy models of neural population codes,” <i>PLoS Computational Biology</i>, vol. 9, no. 3. Public Library of Science, 2013.","short":"E. Granot Atedgi, G. Tkačik, R. Segev, E. Schneidman, PLoS Computational Biology 9 (2013).","ista":"Granot Atedgi E, Tkačik G, Segev R, Schneidman E. 2013. Stimulus-dependent maximum entropy models of neural population codes. PLoS Computational Biology. 9(3), e1002922.","mla":"Granot Atedgi, Einat, et al. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” <i>PLoS Computational Biology</i>, vol. 9, no. 3, e1002922, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1002922\">10.1371/journal.pcbi.1002922</a>.","apa":"Granot Atedgi, E., Tkačik, G., Segev, R., &#38; Schneidman, E. (2013). Stimulus-dependent maximum entropy models of neural population codes. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1002922\">https://doi.org/10.1371/journal.pcbi.1002922</a>","chicago":"Granot Atedgi, Einat, Gašper Tkačik, Ronen Segev, and Elad Schneidman. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” <i>PLoS Computational Biology</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pcbi.1002922\">https://doi.org/10.1371/journal.pcbi.1002922</a>."},"quality_controlled":"1","oa":1,"article_number":"e1002922","status":"public","author":[{"last_name":"Granot Atedgi","full_name":"Granot Atedgi, Einat","first_name":"Einat"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik"},{"last_name":"Segev","full_name":"Segev, Ronen","first_name":"Ronen"},{"last_name":"Schneidman","full_name":"Schneidman, Elad","first_name":"Elad"}],"abstract":[{"lang":"eng","text":"Neural populations encode information about their stimulus in a collective fashion, by joint activity patterns of spiking and silence. A full account of this mapping from stimulus to neural activity is given by the conditional probability distribution over neural codewords given the sensory input. For large populations, direct sampling of these distributions is impossible, and so we must rely on constructing appropriate models. We show here that in a population of 100 retinal ganglion cells in the salamander retina responding to temporal white-noise stimuli, dependencies between cells play an important encoding role. We introduce the stimulus-dependent maximum entropy (SDME) model—a minimal extension of the canonical linear-nonlinear model of a single neuron, to a pairwise-coupled neural population. We find that the SDME model gives a more accurate account of single cell responses and in particular significantly outperforms uncoupled models in reproducing the distributions of population codewords emitted in response to a stimulus. We show how the SDME model, in conjunction with static maximum entropy models of population vocabulary, can be used to estimate information-theoretic quantities like average surprise and information transmission in a neural population."}],"scopus_import":1,"date_updated":"2021-01-12T07:00:20Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaTk"}],"year":"2013","month":"03","file":[{"checksum":"5a30876c193209fa05b26db71845dd16","file_size":1548120,"date_created":"2018-12-12T10:14:45Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:52Z","creator":"system","file_id":"5099","relation":"main_file","file_name":"IST-2013-120-v1+1_journal.pcbi.1002922.pdf"}],"type":"journal_article","oa_version":"Published Version","ddc":["570"],"publication_status":"published","issue":"3","_id":"2863","publisher":"Public Library of Science","pubrep_id":"120"},{"page":"149 - 158","publist_id":"3882","title":"Auxin reflux between the endodermis and pericycle promotes lateral root initiation","oa":1,"citation":{"apa":"Marhavý, P., Vanstraelen, M., De Rybel, B., Zhaojun, D., Bennett, M., Beeckman, T., &#38; Benková, E. (2013). Auxin reflux between the endodermis and pericycle promotes lateral root initiation. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2012.303\">https://doi.org/10.1038/emboj.2012.303</a>","chicago":"Marhavý, Peter, Marleen Vanstraelen, Bert De Rybel, Ding Zhaojun, Malcolm Bennett, Tom Beeckman, and Eva Benková. “Auxin Reflux between the Endodermis and Pericycle Promotes Lateral Root Initiation.” <i>EMBO Journal</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1038/emboj.2012.303\">https://doi.org/10.1038/emboj.2012.303</a>.","mla":"Marhavý, Peter, et al. “Auxin Reflux between the Endodermis and Pericycle Promotes Lateral Root Initiation.” <i>EMBO Journal</i>, vol. 32, no. 1, Wiley-Blackwell, 2013, pp. 149–58, doi:<a href=\"https://doi.org/10.1038/emboj.2012.303\">10.1038/emboj.2012.303</a>.","ama":"Marhavý P, Vanstraelen M, De Rybel B, et al. Auxin reflux between the endodermis and pericycle promotes lateral root initiation. <i>EMBO Journal</i>. 2013;32(1):149-158. doi:<a href=\"https://doi.org/10.1038/emboj.2012.303\">10.1038/emboj.2012.303</a>","short":"P. Marhavý, M. Vanstraelen, B. De Rybel, D. Zhaojun, M. Bennett, T. Beeckman, E. Benková, EMBO Journal 32 (2013) 149–158.","ieee":"P. Marhavý <i>et al.</i>, “Auxin reflux between the endodermis and pericycle promotes lateral root initiation,” <i>EMBO Journal</i>, vol. 32, no. 1. Wiley-Blackwell, pp. 149–158, 2013.","ista":"Marhavý P, Vanstraelen M, De Rybel B, Zhaojun D, Bennett M, Beeckman T, Benková E. 2013. Auxin reflux between the endodermis and pericycle promotes lateral root initiation. EMBO Journal. 32(1), 149–158."},"date_created":"2018-12-11T12:00:07Z","quality_controlled":"1","doi":"10.1038/emboj.2012.303","ec_funded":1,"day":"09","publication":"EMBO Journal","volume":32,"pmid":1,"intvolume":"        32","date_published":"2013-01-09T00:00:00Z","project":[{"name":"Hormonal cross-talk in plant organogenesis","call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362"}],"month":"01","year":"2013","department":[{"_id":"EvBe"}],"publisher":"Wiley-Blackwell","type":"journal_article","oa_version":"Submitted Version","external_id":{"pmid":["23178590"]},"publication_status":"published","issue":"1","_id":"2880","status":"public","author":[{"full_name":"Marhavy, Peter","last_name":"Marhavy","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"first_name":"Marleen","full_name":"Vanstraelen, Marleen","last_name":"Vanstraelen"},{"full_name":"De Rybel, Bert","last_name":"De Rybel","first_name":"Bert"},{"first_name":"Ding","full_name":"Zhaojun, Ding","last_name":"Zhaojun"},{"first_name":"Malcolm","full_name":"Bennett, Malcolm","last_name":"Bennett"},{"first_name":"Tom","full_name":"Beeckman, Tom","last_name":"Beeckman"},{"orcid":"0000-0002-8510-9739","last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T07:00:27Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545298/","open_access":"1"}],"abstract":[{"lang":"eng","text":"Lateral root (LR) formation is initiated when pericycle cells accumulate auxin, thereby acquiring founder cell (FC) status and triggering asymmetric cell divisions, giving rise to a new primordium. How this auxin maximum in pericycle cells builds up and remains focused is not understood. We report that the endodermis plays an active role in the regulation of auxin accumulation and is instructive for FCs to progress during the LR initiation (LRI) phase. We describe the functional importance of a PIN3 (PIN-formed) auxin efflux carrier-dependent hormone reflux pathway between overlaying endodermal and pericycle FCs. Disrupting this reflux pathway causes dramatic defects in the progress of FCs towards the next initiation phase. Our data identify an unexpected regulatory function for the endodermis in LRI as part of the fine-tuning mechanism that appears to act as a check point in LR organogenesis after FCs are specified."}],"scopus_import":1},{"intvolume":"       110","date_published":"2013-02-26T00:00:00Z","volume":110,"day":"26","publication":"PNAS","pmid":1,"doi":"10.1073/pnas.1300107110","date_created":"2018-12-11T12:00:07Z","citation":{"chicago":"Löfke, Christian, Marta Zwiewka, Ingo Heilmann, Marc Van Montagu, Thomas Teichmann, and Jiří Friml. “Asymmetric Gibberellin Signaling Regulates Vacuolar Trafficking of PIN Auxin Transporters during Root Gravitropism.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1300107110\">https://doi.org/10.1073/pnas.1300107110</a>.","apa":"Löfke, C., Zwiewka, M., Heilmann, I., Van Montagu, M., Teichmann, T., &#38; Friml, J. (2013). Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1300107110\">https://doi.org/10.1073/pnas.1300107110</a>","mla":"Löfke, Christian, et al. “Asymmetric Gibberellin Signaling Regulates Vacuolar Trafficking of PIN Auxin Transporters during Root Gravitropism.” <i>PNAS</i>, vol. 110, no. 9, National Academy of Sciences, 2013, pp. 3627–32, doi:<a href=\"https://doi.org/10.1073/pnas.1300107110\">10.1073/pnas.1300107110</a>.","ieee":"C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, and J. Friml, “Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism,” <i>PNAS</i>, vol. 110, no. 9. National Academy of Sciences, pp. 3627–3632, 2013.","ista":"Löfke C, Zwiewka M, Heilmann I, Van Montagu M, Teichmann T, Friml J. 2013. Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism. PNAS. 110(9), 3627–3632.","short":"C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, J. Friml, PNAS 110 (2013) 3627–3632.","ama":"Löfke C, Zwiewka M, Heilmann I, Van Montagu M, Teichmann T, Friml J. Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism. <i>PNAS</i>. 2013;110(9):3627-3632. doi:<a href=\"https://doi.org/10.1073/pnas.1300107110\">10.1073/pnas.1300107110</a>"},"quality_controlled":"1","oa":1,"title":"Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism","publist_id":"3879","page":"3627 - 3632","abstract":[{"lang":"eng","text":"Gravitropic bending of plant organs is mediated by an asymmetric signaling of the plant hormone auxin between the upper and lower side of the respective organ. Here, we show that also another plant hormone, gibberellic acid (GA), shows asymmetric action during gravitropic responses. Immunodetection using an antibody against GA and monitoring GA signaling output by downstream degradation of DELLA proteins revealed an asymmetric GA distribution and response with the maximum at the lower side of gravistimulated roots. Genetic or pharmacological manipulation of GA levels or response affects gravity-mediated auxin redistribution and root bending response. The higher GA levels at the lower side of the root correlate with increased amounts of PIN-FORMED2 (PIN2) auxin transporter at the plasma membrane. The observed increase in PIN2 stability is caused by a specific GA effect on trafficking of PIN proteins to lytic vacuoles that presumably occurs downstream of brefeldin A-sensitive endosomes. Our results suggest that asymmetric auxin distribution instructive for gravity-induced differential growth is consolidated by the asymmetric action of GA that stabilizes the PIN-dependent auxin stream along the lower side of gravistimulated roots."}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587205/"}],"scopus_import":1,"date_updated":"2021-01-12T07:00:27Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Löfke, Christian","last_name":"Löfke","first_name":"Christian"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"last_name":"Heilmann","full_name":"Heilmann, Ingo","first_name":"Ingo"},{"full_name":"Van Montagu, Marc","last_name":"Van Montagu","first_name":"Marc"},{"first_name":"Thomas","last_name":"Teichmann","full_name":"Teichmann, Thomas"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"status":"public","type":"journal_article","oa_version":"Submitted Version","issue":"9","_id":"2882","external_id":{"pmid":["23391733"]},"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"month":"02","year":"2013"},{"intvolume":"        25","date_published":"2013-01-01T00:00:00Z","publication":"Plant Cell","acknowledgement":"We would thank Vincent Vincenzetti and Laurence Charrier for excellent technical assistance, A. von Arnim for the donation of BRET vectors, E. Spalding for TWD1-CFP, TWD1-CFP/29-1-GFP/ER-YFP, and ABCB4-GFP lines, M. Palmgren for discussion and support, and E. Martinoia for TT12 cDNA, support, and mentorship. Imaging data were partially collected at the Center for Advanced Bioimaging, University of Copenhagen, Denmark. This work was supported by grants from the Novartis Foundation (to M.G.), from the Danish Research School for Biotechnology (to M.G. and A.S.), from the Forschungskredit of the University of Zurich (to A.B.), from the Pool de Recherche of the University of Fribourg (to M.G.), and from the Swiss National Funds (to M.G.). M.G. dedicates this work to his father, who passed away during the resubmission process.","day":"01","volume":25,"pmid":1,"doi":"10.1105/tpc.112.105999","date_created":"2018-12-11T12:00:08Z","citation":{"mla":"Wang, Bangjun, et al. “Arabidopsis TWISTED DWARF1 Functionally Interacts with Auxin Exporter ABCB1 on the Root Plasma Membrane.” <i>Plant Cell</i>, vol. 25, no. 1, American Society of Plant Biologists, 2013, pp. 202–14, doi:<a href=\"https://doi.org/10.1105/tpc.112.105999\">10.1105/tpc.112.105999</a>.","apa":"Wang, B., Bailly, A., Zwiewk, M., Henrichs, S., Azzarello, E., Mancuso, S., … Geisler, M. (2013). Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.112.105999\">https://doi.org/10.1105/tpc.112.105999</a>","chicago":"Wang, Bangjun, Aurélien Bailly, Marta Zwiewk, Sina Henrichs, Elisa Azzarello, Stefano Mancuso, Masayoshi Maeshima, Jiří Friml, Alexander Schulz, and Markus Geisler. “Arabidopsis TWISTED DWARF1 Functionally Interacts with Auxin Exporter ABCB1 on the Root Plasma Membrane.” <i>Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.112.105999\">https://doi.org/10.1105/tpc.112.105999</a>.","ama":"Wang B, Bailly A, Zwiewk M, et al. Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane. <i>Plant Cell</i>. 2013;25(1):202-214. doi:<a href=\"https://doi.org/10.1105/tpc.112.105999\">10.1105/tpc.112.105999</a>","ieee":"B. Wang <i>et al.</i>, “Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane,” <i>Plant Cell</i>, vol. 25, no. 1. American Society of Plant Biologists, pp. 202–214, 2013.","ista":"Wang B, Bailly A, Zwiewk M, Henrichs S, Azzarello E, Mancuso S, Maeshima M, Friml J, Schulz A, Geisler M. 2013. Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane. Plant Cell. 25(1), 202–214.","short":"B. Wang, A. Bailly, M. Zwiewk, S. Henrichs, E. Azzarello, S. Mancuso, M. Maeshima, J. Friml, A. Schulz, M. Geisler, Plant Cell 25 (2013) 202–214."},"quality_controlled":"1","oa":1,"title":"Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane","page":"202 - 214","publist_id":"3878","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584535/","open_access":"1"}],"abstract":[{"text":"Plant architecture is influenced by the polar, cell-to-cell transport of auxin that is primarily provided and regulated by plasma membrane efflux catalysts of the PIN-FORMED and B family of ABC transporter (ABCB) classes. The latter were shown to require the functionality of the FK506 binding protein42 TWISTED DWARF1 (TWD1), although underlying mechanisms are unclear. By genetic manipulation of TWD1 expression, we show here that TWD1 affects shootward root auxin reflux and, thus, downstream developmental traits, such as epidermal twisting and gravitropism of the root. Using immunological assays, we demonstrate a predominant lateral, mainly outward-facing, plasma membrane location for TWD1 in the root epidermis characterized by the lateral marker ABC transporter G36/PLEIOTROPIC DRUG-RESISTANCE8/PENETRATION3. At these epidermal plasma membrane domains, TWD1 colocalizes with nonpolar ABCB1. In planta bioluminescence resonance energy transfer analysis was used to verify specific ABC transporter B1 (ABCB1)-TWD1 interaction. Our data support a model in which TWD1 promotes lateral ABCB-mediated auxin efflux via protein-protein interaction at the plasma membrane, minimizing reflux from the root apoplast into the cytoplasm.","lang":"eng"}],"scopus_import":1,"date_updated":"2021-01-12T07:00:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"status":"public","author":[{"full_name":"Wang, Bangjun","last_name":"Wang","first_name":"Bangjun"},{"last_name":"Bailly","full_name":"Bailly, Aurélien","first_name":"Aurélien"},{"last_name":"Zwiewk","full_name":"Zwiewk, Marta","first_name":"Marta"},{"first_name":"Sina","last_name":"Henrichs","full_name":"Henrichs, Sina"},{"last_name":"Azzarello","full_name":"Azzarello, Elisa","first_name":"Elisa"},{"first_name":"Stefano","full_name":"Mancuso, Stefano","last_name":"Mancuso"},{"first_name":"Masayoshi","last_name":"Maeshima","full_name":"Maeshima, Masayoshi"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"full_name":"Schulz, Alexander","last_name":"Schulz","first_name":"Alexander"},{"first_name":"Markus","full_name":"Geisler, Markus","last_name":"Geisler"}],"oa_version":"Submitted Version","type":"journal_article","publication_status":"published","external_id":{"pmid":["23321285"]},"issue":"1","_id":"2883","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"month":"01","year":"2013"},{"publist_id":"3877","project":[{"name":"Analysis of the Formation and Function of Different Cell Protusion Types During Cell Migration in Vivo","_id":"252064B8-B435-11E9-9278-68D0E5697425","grant_number":"HE_3231/6-1"},{"grant_number":"I 812-B12","_id":"2527D5CC-B435-11E9-9278-68D0E5697425","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","call_identifier":"FWF"}],"page":"147 - 150","month":"02","year":"2013","department":[{"_id":"CaHe"}],"title":"Cell adhesion mechanics of zebrafish gastrulation","publisher":"Éditions Médicales et Scientifiques","oa_version":"None","type":"journal_article","citation":{"ieee":"J.-L. Maître <i>et al.</i>, “Cell adhesion mechanics of zebrafish gastrulation,” <i>Medecine Sciences</i>, vol. 29, no. 2. Éditions Médicales et Scientifiques, pp. 147–150, 2013.","short":"J.-L. Maître, H. Berthoumieux, G. Krens, G. Salbreux, F. Julicher, E. Paluch, C.-P.J. Heisenberg, Medecine Sciences 29 (2013) 147–150.","ista":"Maître J-L, Berthoumieux H, Krens G, Salbreux G, Julicher F, Paluch E, Heisenberg C-PJ. 2013. Cell adhesion mechanics of zebrafish gastrulation. Medecine Sciences. 29(2), 147–150.","ama":"Maître J-L, Berthoumieux H, Krens G, et al. Cell adhesion mechanics of zebrafish gastrulation. <i>Medecine Sciences</i>. 2013;29(2):147-150. doi:<a href=\"https://doi.org/10.1051/medsci/2013292011\">10.1051/medsci/2013292011</a>","mla":"Maître, Jean-Léon, et al. “Cell Adhesion Mechanics of Zebrafish Gastrulation.” <i>Medecine Sciences</i>, vol. 29, no. 2, Éditions Médicales et Scientifiques, 2013, pp. 147–50, doi:<a href=\"https://doi.org/10.1051/medsci/2013292011\">10.1051/medsci/2013292011</a>.","chicago":"Maître, Jean-Léon, Hélène Berthoumieux, Gabriel Krens, Guillaume Salbreux, Frank Julicher, Ewa Paluch, and Carl-Philipp J Heisenberg. “Cell Adhesion Mechanics of Zebrafish Gastrulation.” <i>Medecine Sciences</i>. Éditions Médicales et Scientifiques, 2013. <a href=\"https://doi.org/10.1051/medsci/2013292011\">https://doi.org/10.1051/medsci/2013292011</a>.","apa":"Maître, J.-L., Berthoumieux, H., Krens, G., Salbreux, G., Julicher, F., Paluch, E., &#38; Heisenberg, C.-P. J. (2013). Cell adhesion mechanics of zebrafish gastrulation. <i>Medecine Sciences</i>. Éditions Médicales et Scientifiques. <a href=\"https://doi.org/10.1051/medsci/2013292011\">https://doi.org/10.1051/medsci/2013292011</a>"},"date_created":"2018-12-11T12:00:08Z","publication_status":"published","quality_controlled":"1","_id":"2884","issue":"2","doi":"10.1051/medsci/2013292011","status":"public","author":[{"full_name":"Maître, Jean-Léon","last_name":"Maître","orcid":"0000-0002-3688-1474","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","first_name":"Jean-Léon"},{"last_name":"Berthoumieux","full_name":"Berthoumieux, Hélène","first_name":"Hélène"},{"full_name":"Krens, Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996","first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Guillaume","last_name":"Salbreux","full_name":"Salbreux, Guillaume"},{"first_name":"Frank","last_name":"Julicher","full_name":"Julicher, Frank"},{"full_name":"Paluch, Ewa","last_name":"Paluch","first_name":"Ewa"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"}],"day":"01","publication":"Medecine Sciences","date_updated":"2021-01-12T07:00:28Z","volume":29,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"intvolume":"        29","date_published":"2013-02-01T00:00:00Z","scopus_import":1},{"page":"1 - 228","publist_id":"3874","month":"01","year":"2013","department":[{"_id":"ToHe"}],"title":"Mathematical and Engineering Methods in Computer Science","publisher":"Springer","type":"conference_editor","oa_version":"None","date_created":"2018-12-11T12:00:08Z","citation":{"ama":"Kucera A, Henzinger TA, Nesetril J, Vojnar T, Antos D, eds. <i>Mathematical and Engineering Methods in Computer Science</i>. Vol 7721. Springer; 2013:1-228. doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6\">10.1007/978-3-642-36046-6</a>","ista":"Kucera A, Henzinger TA, Nesetril J, Vojnar T, Antos D eds. 2013. Mathematical and Engineering Methods in Computer Science, Springer,p.","short":"A. Kucera, T.A. Henzinger, J. Nesetril, T. Vojnar, D. Antos, eds., Mathematical and Engineering Methods in Computer Science, Springer, 2013.","ieee":"A. Kucera, T. A. Henzinger, J. Nesetril, T. Vojnar, and D. Antos, Eds., <i>Mathematical and Engineering Methods in Computer Science</i>, vol. 7721. Springer, 2013, pp. 1–228.","mla":"Kucera, Antonin, et al., editors. <i>Mathematical and Engineering Methods in Computer Science</i>. Vol. 7721, Springer, 2013, pp. 1–228, doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6\">10.1007/978-3-642-36046-6</a>.","apa":"Kucera, A., Henzinger, T. A., Nesetril, J., Vojnar, T., &#38; Antos, D. (Eds.). (2013). <i>Mathematical and Engineering Methods in Computer Science</i> (Vol. 7721, pp. 1–228). Presented at the MEMICS: Mathematical and Engineering methods in computer science, Znojmo, Czech Republic: Springer. <a href=\"https://doi.org/10.1007/978-3-642-36046-6\">https://doi.org/10.1007/978-3-642-36046-6</a>","chicago":"Kucera, Antonin, Thomas A Henzinger, Jaroslav Nesetril, Tomas Vojnar, and David Antos, eds. <i>Mathematical and Engineering Methods in Computer Science</i>. Vol. 7721. Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36046-6\">https://doi.org/10.1007/978-3-642-36046-6</a>."},"publication_status":"published","quality_controlled":"1","alternative_title":["LNCS"],"conference":{"start_date":"2012-10-25","name":"MEMICS: Mathematical and Engineering methods in computer science","location":"Znojmo, Czech Republic","end_date":"2012-10-28"},"_id":"2885","doi":"10.1007/978-3-642-36046-6","status":"public","day":"09","acknowledgement":"Red Hat Czech Republic, Y Soft","volume":7721,"series_title":"Lecture Notes in Computer Science","date_updated":"2019-08-02T12:37:55Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"editor":[{"first_name":"Antonin","last_name":"Kucera","full_name":"Kucera, Antonin"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Nesetril, Jaroslav","last_name":"Nesetril","first_name":"Jaroslav"},{"first_name":"Tomas","last_name":"Vojnar","full_name":"Vojnar, Tomas"},{"last_name":"Antos","full_name":"Antos, David","first_name":"David"}],"intvolume":"      7721","abstract":[{"lang":"eng","text":"This volume contains the post-proceedings of the 8th Doctoral Workshop on Mathematical and Engineering Methods in Computer Science, MEMICS 2012, held in Znojmo, Czech Republic, in October, 2012. The 13 thoroughly revised papers were carefully selected out of 31 submissions and are presented together with 6 invited papers. The topics covered by the papers include: computer-aided analysis and verification, applications of game theory in computer science, networks and security, modern trends of graph theory in computer science, electronic systems design and testing, and quantum information processing."}],"date_published":"2013-01-09T00:00:00Z"},{"title":"Controllable-choice message sequence graphs","publist_id":"3873","page":"118 - 130","date_created":"2018-12-11T12:00:09Z","citation":{"chicago":"Chmelik, Martin, and Vojtěch Řehák. “Controllable-Choice Message Sequence Graphs.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36046-6_12\">https://doi.org/10.1007/978-3-642-36046-6_12</a>.","apa":"Chmelik, M., &#38; Řehák, V. (2013). Controllable-choice message sequence graphs. Presented at the MEMICS: Mathematical and Engineering Methods in Computer Science, Znojmo, Czech Republic: Springer. <a href=\"https://doi.org/10.1007/978-3-642-36046-6_12\">https://doi.org/10.1007/978-3-642-36046-6_12</a>","mla":"Chmelik, Martin, and Vojtěch Řehák. <i>Controllable-Choice Message Sequence Graphs</i>. Vol. 7721, Springer, 2013, pp. 118–30, doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6_12\">10.1007/978-3-642-36046-6_12</a>.","short":"M. Chmelik, V. Řehák, 7721 (2013) 118–130.","ieee":"M. Chmelik and V. Řehák, “Controllable-choice message sequence graphs,” vol. 7721. Springer, pp. 118–130, 2013.","ista":"Chmelik M, Řehák V. 2013. Controllable-choice message sequence graphs. 7721, 118–130.","ama":"Chmelik M, Řehák V. Controllable-choice message sequence graphs. 2013;7721:118-130. doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6_12\">10.1007/978-3-642-36046-6_12</a>"},"quality_controlled":"1","conference":{"location":"Znojmo, Czech Republic","end_date":"2012-10-28","start_date":"2012-10-25","name":"MEMICS: Mathematical and Engineering Methods in Computer Science"},"oa":1,"ec_funded":1,"doi":"10.1007/978-3-642-36046-6_12","intvolume":"      7721","date_published":"2013-01-09T00:00:00Z","day":"09","volume":7721,"department":[{"_id":"KrCh"}],"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"grant_number":"S11407","call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"month":"01","year":"2013","oa_version":"Submitted Version","type":"conference","publication_status":"published","alternative_title":["LNCS"],"_id":"2886","publisher":"Springer","status":"public","author":[{"full_name":"Chmelik, Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"first_name":"Vojtěch","full_name":"Řehák, Vojtěch","last_name":"Řehák"}],"main_file_link":[{"url":"http://arxiv.org/abs/1209.4499","open_access":"1"}],"abstract":[{"lang":"eng","text":"We focus on the realizability problem of Message Sequence Graphs (MSG), i.e. the problem whether a given MSG specification is correctly distributable among parallel components communicating via messages. This fundamental problem of MSG is known to be undecidable. We introduce a well motivated restricted class of MSG, so called controllable-choice MSG, and show that all its models are realizable and moreover it is decidable whether a given MSG model is a member of this class. In more detail, this class of MSG specifications admits a deadlock-free realization by overloading existing messages with additional bounded control data. We also show that the presented class is the largest known subclass of MSG that allows for deadlock-free realization."}],"scopus_import":1,"series_title":"Lecture Notes in Computer Science","date_updated":"2020-08-11T10:09:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}]},{"title":"Genotypic recognition and spatial responses by rice roots","page":"2670 - 2675","publist_id":"3872","quality_controlled":"1","date_created":"2018-12-11T12:00:09Z","citation":{"ista":"Fang S, Clark R, Zheng Y, Iyer Pascuzzi A, Weitz J, Kochian L, Edelsbrunner H, Liao H, Benfey P. 2013. Genotypic recognition and spatial responses by rice roots. PNAS. 110(7), 2670–2675.","short":"S. Fang, R. Clark, Y. Zheng, A. Iyer Pascuzzi, J. Weitz, L. Kochian, H. Edelsbrunner, H. Liao, P. Benfey, PNAS 110 (2013) 2670–2675.","ieee":"S. Fang <i>et al.</i>, “Genotypic recognition and spatial responses by rice roots,” <i>PNAS</i>, vol. 110, no. 7. National Academy of Sciences, pp. 2670–2675, 2013.","ama":"Fang S, Clark R, Zheng Y, et al. Genotypic recognition and spatial responses by rice roots. <i>PNAS</i>. 2013;110(7):2670-2675. doi:<a href=\"https://doi.org/10.1073/pnas.1222821110\">10.1073/pnas.1222821110</a>","chicago":"Fang, Suqin, Randy Clark, Ying Zheng, Anjali Iyer Pascuzzi, Joshua Weitz, Leon Kochian, Herbert Edelsbrunner, Hong Liao, and Philip Benfey. “Genotypic Recognition and Spatial Responses by Rice Roots.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1222821110\">https://doi.org/10.1073/pnas.1222821110</a>.","apa":"Fang, S., Clark, R., Zheng, Y., Iyer Pascuzzi, A., Weitz, J., Kochian, L., … Benfey, P. (2013). Genotypic recognition and spatial responses by rice roots. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1222821110\">https://doi.org/10.1073/pnas.1222821110</a>","mla":"Fang, Suqin, et al. “Genotypic Recognition and Spatial Responses by Rice Roots.” <i>PNAS</i>, vol. 110, no. 7, National Academy of Sciences, 2013, pp. 2670–75, doi:<a href=\"https://doi.org/10.1073/pnas.1222821110\">10.1073/pnas.1222821110</a>."},"oa":1,"article_processing_charge":"No","doi":"10.1073/pnas.1222821110","date_published":"2013-02-12T00:00:00Z","intvolume":"       110","pmid":1,"volume":110,"day":"12","publication":"PNAS","article_type":"original","department":[{"_id":"HeEd"}],"month":"02","year":"2013","_id":"2887","issue":"7","publication_status":"published","external_id":{"pmid":["23362379"]},"oa_version":"Published Version","type":"journal_article","publisher":"National Academy of Sciences","author":[{"first_name":"Suqin","last_name":"Fang","full_name":"Fang, Suqin"},{"first_name":"Randy","full_name":"Clark, Randy","last_name":"Clark"},{"first_name":"Ying","last_name":"Zheng","full_name":"Zheng, Ying"},{"first_name":"Anjali","full_name":"Iyer Pascuzzi, Anjali","last_name":"Iyer Pascuzzi"},{"last_name":"Weitz","full_name":"Weitz, Joshua","first_name":"Joshua"},{"last_name":"Kochian","full_name":"Kochian, Leon","first_name":"Leon"},{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"first_name":"Hong","last_name":"Liao","full_name":"Liao, Hong"},{"last_name":"Benfey","full_name":"Benfey, Philip","first_name":"Philip"}],"status":"public","scopus_import":1,"abstract":[{"text":"Root system growth and development is highly plastic and is influenced by the surrounding environment. Roots frequently grow in heterogeneous environments that include interactions from neighboring plants and physical impediments in the rhizosphere. To investigate how planting density and physical objects affect root system growth, we grew rice in a transparent gel system in close proximity with another plant or a physical object. Root systems were imaged and reconstructed in three dimensions. Root-root interaction strength was calculated using quantitative metrics that characterize the extent towhich the reconstructed root systems overlap each other. Surprisingly, we found the overlap of root systems of the same genotype was significantly higher than that of root systems of different genotypes. Root systems of the same genotype tended to grow toward each other but those of different genotypes appeared to avoid each other. Shoot separation experiments excluded the possibility of aerial interactions, suggesting root communication. Staggered plantings indicated that interactions likely occur at root tips in close proximity. Recognition of obstacles also occurred through root tips, but through physical contact in a size-dependent manner. These results indicate that root systems use two different forms of communication to recognize objects and alter root architecture: root-root recognition, possibly mediated through root exudates, and root-object recognition mediated by physical contact at the root tips. This finding suggests that root tips act as local sensors that integrate rhizosphere information into global root architectural changes.","lang":"eng"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574932/","open_access":"1"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:00:29Z"}]