[{"ddc":["576"],"external_id":{"isi":["000321524500001"]},"quality_controlled":"1","publisher":"BioMed Central","publication_status":"published","publication":"BMC Evolutionary Biology","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)"},"volume":13,"file":[{"access_level":"open_access","file_name":"IST-2015-397-v1+1_1471-2148-13-54.pdf","file_size":518729,"content_type":"application/pdf","checksum":"029c7e0b198c19312b66ecce3cabb22f","creator":"system","date_updated":"2020-07-14T12:45:40Z","file_id":"5268","date_created":"2018-12-12T10:17:15Z","relation":"main_file"}],"day":"26","status":"public","corr_author":"1","publist_id":"4514","month":"02","license":"https://creativecommons.org/licenses/by/4.0/","doi":"10.1186/1471-2148-13-54","file_date_updated":"2020-07-14T12:45:40Z","pubrep_id":"397","year":"2013","article_processing_charge":"No","intvolume":"        13","author":[{"id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Kupczok, Anne","last_name":"Kupczok","first_name":"Anne"},{"full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","orcid":"0000-0002-4624-4612","first_name":"Jonathan P"}],"scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Probabilistic models for CRISPR spacer content evolution ","type":"journal_article","oa_version":"Published Version","date_created":"2018-12-11T11:57:31Z","isi":1,"oa":1,"issue":"1","has_accepted_license":"1","language":[{"iso":"eng"}],"citation":{"mla":"Kupczok, Anne, and Jonathan P. Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1, BioMed Central, 2013, pp. 54–54, doi:<a href=\"https://doi.org/10.1186/1471-2148-13-54\">10.1186/1471-2148-13-54</a>.","short":"A. Kupczok, J.P. Bollback, BMC Evolutionary Biology 13 (2013) 54–54.","apa":"Kupczok, A., &#38; Bollback, J. P. (2013). Probabilistic models for CRISPR spacer content evolution . <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-13-54\">https://doi.org/10.1186/1471-2148-13-54</a>","ista":"Kupczok A, Bollback JP. 2013. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 13(1), 54–54.","chicago":"Kupczok, Anne, and Jonathan P Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” <i>BMC Evolutionary Biology</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1471-2148-13-54\">https://doi.org/10.1186/1471-2148-13-54</a>.","ieee":"A. Kupczok and J. P. Bollback, “Probabilistic models for CRISPR spacer content evolution ,” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1. BioMed Central, pp. 54–54, 2013.","ama":"Kupczok A, Bollback JP. Probabilistic models for CRISPR spacer content evolution . <i>BMC Evolutionary Biology</i>. 2013;13(1):54-54. doi:<a href=\"https://doi.org/10.1186/1471-2148-13-54\">10.1186/1471-2148-13-54</a>"},"department":[{"_id":"JoBo"}],"date_published":"2013-02-26T00:00:00Z","page":"54 - 54","_id":"2412","date_updated":"2025-09-29T14:15:59Z","abstract":[{"lang":"eng","text":"Background: The CRISPR/Cas system is known to act as an adaptive and heritable immune system in Eubacteria and Archaea. Immunity is encoded in an array of spacer sequences. Each spacer can provide specific immunity to invasive elements that carry the same or a similar sequence. Even in closely related strains, spacer content is very dynamic and evolves quickly. Standard models of nucleotide evolutioncannot be applied to quantify its rate of change since processes other than single nucleotide changes determine its evolution.Methods We present probabilistic models that are specific for spacer content evolution. They account for the different processes of insertion and deletion. Insertions can be constrained to occur on one end only or are allowed to occur throughout the array. One deletion event can affect one spacer or a whole fragment of adjacent spacers. Parameters of the underlying models are estimated for a pair of arrays by maximum likelihood using explicit ancestor enumeration.Results Simulations show that parameters are well estimated on average under the models presented here. There is a bias in the rate estimation when including fragment deletions. The models also estimate times between pairs of strains. But with increasing time, spacer overlap goes to zero, and thus there is an upper bound on the distance that can be estimated. Spacer content similarities are displayed in a distance based phylogeny using the estimated times.We use the presented models to analyze different Yersinia pestis data sets and find that the results among them are largely congruent. The models also capture the variation in diversity of spacers among the data sets. A comparison of spacer-based phylogenies and Cas gene phylogenies shows that they resolve very different time scales for this data set.Conclusions The simulations and data analyses show that the presented models are useful for quantifying spacer content evolution and for displaying spacer content similarities of closely related strains in a phylogeny. This allows for comparisons of different CRISPR arrays or for comparisons between CRISPR arrays and nucleotide substitution rates."}]},{"date_published":"2013-08-01T00:00:00Z","citation":{"ama":"Valderrama M, Botella Soler V, Le Van Quyen M. Neuronal oscillations scale up and scale down the brain dynamics . In: Meyer M, Pesenson Z, eds. <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>. Wiley; 2013. doi:<a href=\"https://doi.org/10.1002/9783527671632.ch08\">10.1002/9783527671632.ch08</a>","ieee":"M. Valderrama, V. Botella Soler, and M. Le Van Quyen, “Neuronal oscillations scale up and scale down the brain dynamics ,” in <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>, M. Meyer and Z. Pesenson, Eds. Wiley, 2013.","ista":"Valderrama M, Botella Soler V, Le Van Quyen M. 2013.Neuronal oscillations scale up and scale down the brain dynamics . In: Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Reviews of Nonlinear Dynamics and Complexity, .","chicago":"Valderrama, Mario, Vicente Botella Soler, and Michel Le Van Quyen. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .” In <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>, edited by Misha Meyer and Z. Pesenson. Wiley, 2013. <a href=\"https://doi.org/10.1002/9783527671632.ch08\">https://doi.org/10.1002/9783527671632.ch08</a>.","mla":"Valderrama, Mario, et al. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .” <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>, edited by Misha Meyer and Z. Pesenson, Wiley, 2013, doi:<a href=\"https://doi.org/10.1002/9783527671632.ch08\">10.1002/9783527671632.ch08</a>.","short":"M. Valderrama, V. Botella Soler, M. Le Van Quyen, in:, M. Meyer, Z. Pesenson (Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, Wiley, 2013.","apa":"Valderrama, M., Botella Soler, V., &#38; Le Van Quyen, M. (2013). Neuronal oscillations scale up and scale down the brain dynamics . In M. Meyer &#38; Z. Pesenson (Eds.), <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>. Wiley. <a href=\"https://doi.org/10.1002/9783527671632.ch08\">https://doi.org/10.1002/9783527671632.ch08</a>"},"department":[{"_id":"GaTk"}],"abstract":[{"text":"Progress in understanding the global brain dynamics has remained slow to date in large part because of the highly multiscale nature of brain activity. Indeed, normal brain dynamics is characterized by complex interactions between multiple levels: from the microscopic scale of single neurons to the mesoscopic level of local groups of neurons, and finally to the macroscopic level of the whole brain. Among the most difficult tasks are those of identifying which scales are significant for a given particular function and describing how the scales affect each other. It is important to realize that the scales of time and space are linked together, or even intertwined, and that causal inference is far more ambiguous between than within levels. We approach this problem from the perspective of our recent work on simultaneous recording from micro- and macroelectrodes in the human brain. We propose a physiological description of these multilevel interactions, based on phase–amplitude coupling of neuronal oscillations that operate at multiple frequencies and on different spatial scales. Specifically, the amplitude of the oscillations on a particular spatial scale is modulated by phasic variations in neuronal excitability induced by lower frequency oscillations that emerge on a larger spatial scale. Following this general principle, it is possible to scale up or scale down the multiscale brain dynamics. It is expected that large-scale network oscillations in the low-frequency range, mediating downward effects, may play an important role in attention and consciousness.","lang":"eng"}],"_id":"2413","date_updated":"2025-06-03T11:46:23Z","month":"08","language":[{"iso":"eng"}],"doi":"10.1002/9783527671632.ch08","oa_version":"None","date_created":"2018-12-11T11:57:31Z","publist_id":"4513","type":"book_chapter","publication":"Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain","publisher":"Wiley","alternative_title":["Reviews of Nonlinear Dynamics and Complexity"],"publication_status":"published","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Neuronal oscillations scale up and scale down the brain dynamics ","publication_identifier":{"eisbn":["9783527671632"],"isbn":["9783527411986 "]},"scopus_import":"1","year":"2013","article_processing_charge":"No","quality_controlled":"1","author":[{"full_name":"Valderrama, Mario","last_name":"Valderrama","first_name":"Mario"},{"id":"421234E8-F248-11E8-B48F-1D18A9856A87","full_name":"Botella Soler, Vicente","first_name":"Vicente","orcid":"0000-0002-8790-1914","last_name":"Botella Soler"},{"first_name":"Michel","last_name":"Le Van Quyen","full_name":"Le Van Quyen, Michel"}],"editor":[{"last_name":"Meyer","first_name":"Misha","full_name":"Meyer, Misha"},{"full_name":"Pesenson, Z.","first_name":"Z.","last_name":"Pesenson"}]},{"publication_status":"published","publisher":"Wiley","volume":200,"publication":"New Phytologist","status":"public","day":"01","acknowledgement":"The authors thank Dr Christian Luschnig (University of Natural Resources and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds and, last but not least, to Dr David Morris for critical reading of the manuscript. We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance. This work was supported by the Grant Agency of the Czech Republic (P305/11/0797 to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European Research Council starting independent research grant ERC-2011-StG-20101109-PSDP (to J.F.).","external_id":{"isi":["000330955300012"]},"quality_controlled":"1","month":"12","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"doi":"10.1111/nph.12437","publist_id":"4460","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/nph.12437"}],"scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Defining the selectivity of processes along the auxin response chain: A study using auxin analogues","article_processing_charge":"No","year":"2013","article_type":"original","intvolume":"       200","author":[{"first_name":"Sibu","orcid":"0000-0002-1998-6741","last_name":"Simon","full_name":"Simon, Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kubeš, Martin","first_name":"Martin","last_name":"Kubeš"},{"id":"3028BD74-F248-11E8-B48F-1D18A9856A87","full_name":"Baster, Pawel","first_name":"Pawel","last_name":"Baster"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"},{"last_name":"Dobrev","first_name":"Petre","full_name":"Dobrev, Petre"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"full_name":"Zažímalová, Eva","first_name":"Eva","last_name":"Zažímalová"}],"language":[{"iso":"eng"}],"_id":"2443","abstract":[{"text":"The mode of action of auxin is based on its non-uniform distribution within tissues and organs. Despite the wide use of several auxin analogues in research and agriculture, little is known about the specificity of different auxin-related transport and signalling processes towards these compounds. Using seedlings of Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2), the physiological activity of several auxin analogues was investigated, together with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis and to be transported across the plasma membrane. This study shows that the specificity criteria for different auxin-related processes vary widely. Notably, the special behaviour of some synthetic auxin analogues suggests that they might be useful tools in investigations of the molecular mechanism of auxin action. Thus, due to their differential stimulatory effects on DR5 expression, indole-3-propionic (IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate between transcriptional and non-transcriptional pathways of auxin signalling. The results demonstrate that the major determinants for the auxin-like physiological potential of a particular compound are very complex and involve its chemical and metabolic stability, its ability to distribute in tissues in a polar manner and its activity towards auxin signalling machinery.","lang":"eng"}],"date_updated":"2025-09-29T14:15:18Z","department":[{"_id":"JiFr"}],"citation":{"ieee":"S. Simon <i>et al.</i>, “Defining the selectivity of processes along the auxin response chain: A study using auxin analogues,” <i>New Phytologist</i>, vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.","ama":"Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. 2013;200(4):1034-1048. doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>","chicago":"Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>. Wiley, 2013. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>.","ista":"Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová E. 2013. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. 200(4), 1034–1048.","apa":"Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová, E. (2013). Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>","mla":"Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>, vol. 200, no. 4, Wiley, 2013, pp. 1034–48, doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>.","short":"S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek, E. Zažímalová, New Phytologist 200 (2013) 1034–1048."},"page":"1034 - 1048","date_published":"2013-12-01T00:00:00Z","type":"journal_article","date_created":"2018-12-11T11:57:41Z","oa_version":"Published Version","oa":1,"isi":1,"issue":"4"},{"title":"Faster algorithms for Markov decision processes with low treewidth","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"name":"CAV: Computer Aided Verification","end_date":"2013-07-19","start_date":"2013-07-13","location":"St. Petersburg, Russia"},"scopus_import":1,"alternative_title":["LNCS"],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"last_name":"Ła̧Cki","first_name":"Jakub","full_name":"Ła̧Cki, Jakub"}],"intvolume":"      8044","year":"2013","abstract":[{"text":"We consider two core algorithmic problems for probabilistic verification: the maximal end-component decomposition and the almost-sure reachability set computation for Markov decision processes (MDPs). For MDPs with treewidth k, we present two improved static algorithms for both the problems that run in time O(n·k 2.38·2k ) and O(m·logn· k), respectively, where n is the number of states and m is the number of edges, significantly improving the previous known O(n·k·√n· k) bound for low treewidth. We also present decremental algorithms for both problems for MDPs with constant treewidth that run in amortized logarithmic time, which is a huge improvement over the previously known algorithms that require amortized linear time.","lang":"eng"}],"_id":"2444","date_updated":"2020-08-11T10:09:47Z","page":"543 - 558","citation":{"ieee":"K. Chatterjee and J. Ła̧Cki, “Faster algorithms for Markov decision processes with low treewidth,” vol. 8044. Springer, pp. 543–558, 2013.","ama":"Chatterjee K, Ła̧Cki J. Faster algorithms for Markov decision processes with low treewidth. 2013;8044:543-558. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">10.1007/978-3-642-39799-8_36</a>","chicago":"Chatterjee, Krishnendu, and Jakub Ła̧Cki. “Faster Algorithms for Markov Decision Processes with Low Treewidth.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">https://doi.org/10.1007/978-3-642-39799-8_36</a>.","ista":"Chatterjee K, Ła̧Cki J. 2013. Faster algorithms for Markov decision processes with low treewidth. 8044, 543–558.","apa":"Chatterjee, K., &#38; Ła̧Cki, J. (2013). Faster algorithms for Markov decision processes with low treewidth. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">https://doi.org/10.1007/978-3-642-39799-8_36</a>","mla":"Chatterjee, Krishnendu, and Jakub Ła̧Cki. <i>Faster Algorithms for Markov Decision Processes with Low Treewidth</i>. Vol. 8044, Springer, 2013, pp. 543–58, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">10.1007/978-3-642-39799-8_36</a>.","short":"K. Chatterjee, J. Ła̧Cki, 8044 (2013) 543–558."},"department":[{"_id":"KrCh"}],"date_published":"2013-07-01T00:00:00Z","language":[{"iso":"eng"}],"oa":1,"date_created":"2018-12-11T11:57:42Z","oa_version":"Preprint","type":"conference","status":"public","day":"01","arxiv":1,"series_title":"Lecture Notes in Computer Science","volume":8044,"publication_status":"published","publisher":"Springer","quality_controlled":"1","external_id":{"arxiv":["1304.0084"]},"doi":"10.1007/978-3-642-39799-8_36","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","grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"month":"07","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1304.0084"}],"ec_funded":1,"publist_id":"4459"},{"scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis","conference":{"start_date":"2013-07-13","location":"St. Petersburg, Russia","end_date":"2013-07-19","name":"CAV: Computer Aided Verification"},"alternative_title":["LNCS"],"author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gaiser","first_name":"Andreas","full_name":"Gaiser, Andreas"},{"full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","orcid":"0000-0002-8122-2881","first_name":"Jan"}],"intvolume":"      8044","year":"2013","language":[{"iso":"eng"}],"_id":"2446","date_updated":"2020-08-11T10:09:47Z","abstract":[{"text":"The model-checking problem for probabilistic systems crucially relies on the translation of LTL to deterministic Rabin automata (DRW). Our recent Safraless translation [KE12, GKE12] for the LTL(F,G) fragment produces smaller automata as compared to the traditional approach. In this work, instead of DRW we consider deterministic automata with acceptance condition given as disjunction of generalized Rabin pairs (DGRW). The Safraless translation of LTL(F,G) formulas to DGRW results in smaller automata as compared to DRW. We present algorithms for probabilistic model-checking as well as game solving for DGRW conditions. Our new algorithms lead to improvement both in terms of theoretical bounds as well as practical evaluation. We compare PRISM with and without our new translation, and show that the new translation leads to significant improvements.","lang":"eng"}],"citation":{"apa":"Chatterjee, K., Gaiser, A., &#38; Kretinsky, J. (2013). Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">https://doi.org/10.1007/978-3-642-39799-8_37</a>","short":"K. Chatterjee, A. Gaiser, J. Kretinsky, 8044 (2013) 559–575.","mla":"Chatterjee, Krishnendu, et al. <i>Automata with Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis</i>. Vol. 8044, Springer, 2013, pp. 559–75, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">10.1007/978-3-642-39799-8_37</a>.","ama":"Chatterjee K, Gaiser A, Kretinsky J. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 2013;8044:559-575. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">10.1007/978-3-642-39799-8_37</a>","ieee":"K. Chatterjee, A. Gaiser, and J. Kretinsky, “Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis,” vol. 8044. Springer, pp. 559–575, 2013.","chicago":"Chatterjee, Krishnendu, Andreas Gaiser, and Jan Kretinsky. “Automata with Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">https://doi.org/10.1007/978-3-642-39799-8_37</a>.","ista":"Chatterjee K, Gaiser A, Kretinsky J. 2013. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 8044, 559–575."},"date_published":"2013-07-01T00:00:00Z","page":"559 - 575","department":[{"_id":"KrCh"}],"oa":1,"type":"conference","date_created":"2018-12-11T11:57:42Z","oa_version":"Preprint","arxiv":1,"status":"public","day":"01","publication_status":"published","publisher":"Springer","series_title":"Lecture Notes in Computer Science","volume":8044,"external_id":{"arxiv":["1304.5281"]},"quality_controlled":"1","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","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"doi":"10.1007/978-3-642-39799-8_37","month":"07","ec_funded":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1304.5281"}],"publist_id":"4457"},{"oa_version":"Submitted Version","date_created":"2018-12-11T11:57:43Z","type":"conference","oa":1,"_id":"2447","abstract":[{"text":"Separation logic (SL) has gained widespread popularity because of its ability to succinctly express complex invariants of a program’s heap configurations. Several specialized provers have been developed for decidable SL fragments. However, these provers cannot be easily extended or combined with solvers for other theories that are important in program verification, e.g., linear arithmetic. In this paper, we present a reduction of decidable SL fragments to a decidable first-order theory that fits well into the satisfiability modulo theories (SMT) framework. We show how to use this reduction to automate satisfiability, entailment, frame inference, and abduction problems for separation logic using SMT solvers. Our approach provides a simple method of integrating separation logic into existing verification tools that provide SMT backends, and an elegant way of combining SL fragments with other decidable first-order theories. We implemented this approach in a verification tool and applied it to heap-manipulating programs whose verification involves reasoning in theory combinations.\r\n","lang":"eng"}],"date_updated":"2020-08-11T10:09:47Z","citation":{"chicago":"Piskac, Ruzica, Thomas Wies, and Damien Zufferey. “Automating Separation Logic Using SMT.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">https://doi.org/10.1007/978-3-642-39799-8_54</a>.","ista":"Piskac R, Wies T, Zufferey D. 2013. Automating separation logic using SMT. 8044, 773–789.","ama":"Piskac R, Wies T, Zufferey D. Automating separation logic using SMT. 2013;8044:773-789. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">10.1007/978-3-642-39799-8_54</a>","ieee":"R. Piskac, T. Wies, and D. Zufferey, “Automating separation logic using SMT,” vol. 8044. Springer, pp. 773–789, 2013.","apa":"Piskac, R., Wies, T., &#38; Zufferey, D. (2013). Automating separation logic using SMT. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">https://doi.org/10.1007/978-3-642-39799-8_54</a>","short":"R. Piskac, T. Wies, D. Zufferey, 8044 (2013) 773–789.","mla":"Piskac, Ruzica, et al. <i>Automating Separation Logic Using SMT</i>. Vol. 8044, Springer, 2013, pp. 773–89, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">10.1007/978-3-642-39799-8_54</a>."},"date_published":"2013-07-01T00:00:00Z","department":[{"_id":"ToHe"}],"page":"773 - 789","language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"No","year":"2013","intvolume":"      8044","author":[{"first_name":"Ruzica","last_name":"Piskac","full_name":"Piskac, Ruzica"},{"last_name":"Wies","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","full_name":"Wies, Thomas"},{"id":"4397AC76-F248-11E8-B48F-1D18A9856A87","full_name":"Zufferey, Damien","last_name":"Zufferey","orcid":"0000-0002-3197-8736","first_name":"Damien"}],"alternative_title":["LNCS"],"title":"Automating separation logic using SMT","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"start_date":"2013-07-13","location":"St. Petersburg, Russia","end_date":"2013-07-19","name":"CAV: Computer Aided Verification"},"scopus_import":1,"publist_id":"4456","month":"07","file_date_updated":"2020-07-14T12:45:41Z","doi":"10.1007/978-3-642-39799-8_54","quality_controlled":"1","ddc":["000"],"volume":8044,"series_title":"Lecture Notes in Computer Science","publication_status":"published","publisher":"Springer","status":"public","day":"01","file":[{"file_name":"2013_CAV_Piskac.pdf","access_level":"open_access","file_size":309182,"checksum":"2e866932ab688f47ecd504acb4d5c7d4","content_type":"application/pdf","creator":"dernst","date_updated":"2020-07-14T12:45:41Z","file_id":"7859","relation":"main_file","date_created":"2020-05-15T11:13:01Z"}]},{"external_id":{"pmid":["23857365"]},"quality_controlled":"1","status":"public","day":"10","pmid":1,"publication_status":"published","publisher":"Taylor & Francis","volume":8,"publication":"Plant Signaling & Behavior","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091088/","open_access":"1"}],"ec_funded":1,"publist_id":"4455","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"doi":"10.4161/psb.25688","month":"07","article_type":"original","intvolume":"         8","author":[{"full_name":"Remy, Estelle","last_name":"Remy","first_name":"Estelle"},{"full_name":"Baster, Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","last_name":"Baster","first_name":"Pawel"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"full_name":"Duque, Paula","last_name":"Duque","first_name":"Paula"}],"article_processing_charge":"No","year":"2013","scopus_import":"1","title":"ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"issue":"10","article_number":"e25688","type":"journal_article","date_created":"2018-12-11T11:57:43Z","oa_version":"Submitted Version","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Cell-to-cell directional flow of the phytohormone auxin is primarily established by polar localization of the PIN auxin transporters, a process tightly regulated at multiple levels by auxin itself. We recently reported that, in the context of strong auxin flows, activity of the vacuolar ZIFL1.1 transporter is required for fine-tuning of polar auxin transport rates in the Arabidopsis root. In particular, ZIFL1.1 function protects plasma-membrane stability of the PIN2 carrier in epidermal root tip cells under conditions normally triggering PIN2 degradation. Here, we show that ZIFL1.1 activity at the root tip also promotes PIN1 plasma-membrane abundance in central cylinder cells, thus supporting the notion that ZIFL1.1 acts as a general positive modulator of polar auxin transport in roots."}],"_id":"2448","date_updated":"2025-04-15T07:48:02Z","citation":{"apa":"Remy, E., Baster, P., Friml, J., &#38; Duque, P. (2013). ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.4161/psb.25688\">https://doi.org/10.4161/psb.25688</a>","mla":"Remy, Estelle, et al. “ZIFL1.1 Transporter Modulates Polar Auxin Transport by Stabilizing Membrane Abundance of Multiple PINs in Arabidopsis Root Tip.” <i>Plant Signaling &#38; Behavior</i>, vol. 8, no. 10, e25688, Taylor &#38; Francis, 2013, doi:<a href=\"https://doi.org/10.4161/psb.25688\">10.4161/psb.25688</a>.","short":"E. Remy, P. Baster, J. Friml, P. Duque, Plant Signaling &#38; Behavior 8 (2013).","ama":"Remy E, Baster P, Friml J, Duque P. ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. <i>Plant Signaling &#38; Behavior</i>. 2013;8(10). doi:<a href=\"https://doi.org/10.4161/psb.25688\">10.4161/psb.25688</a>","ieee":"E. Remy, P. Baster, J. Friml, and P. Duque, “ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip,” <i>Plant Signaling &#38; Behavior</i>, vol. 8, no. 10. Taylor &#38; Francis, 2013.","chicago":"Remy, Estelle, Pawel Baster, Jiří Friml, and Paula Duque. “ZIFL1.1 Transporter Modulates Polar Auxin Transport by Stabilizing Membrane Abundance of Multiple PINs in Arabidopsis Root Tip.” <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis, 2013. <a href=\"https://doi.org/10.4161/psb.25688\">https://doi.org/10.4161/psb.25688</a>.","ista":"Remy E, Baster P, Friml J, Duque P. 2013. ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. Plant Signaling &#38; Behavior. 8(10), e25688."},"department":[{"_id":"JiFr"}],"date_published":"2013-07-10T00:00:00Z"},{"corr_author":"1","publist_id":"4454","month":"11","doi":"10.1093/mp/sst044","external_id":{"isi":["000327541200010"]},"quality_controlled":"1","publication_status":"published","publisher":"Cell Press","volume":6,"publication":"Molecular Plant","status":"public","day":"01","type":"journal_article","oa_version":"None","date_created":"2018-12-11T11:57:44Z","isi":1,"issue":"6","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Intracellular protein routing is mediated by vesicular transport which is tightly regulated in eukaryotes. The protein and lipid homeostasis depends on coordinated delivery of de novo synthesized or recycled cargoes to the plasma membrane by exocytosis and their subsequent removal by rerouting them for recycling or degradation. Here, we report the characterization of protein affected trafficking 3 (pat3) mutant that we identified by an epifluorescence-based forward genetic screen for mutants defective in subcellular distribution of Arabidopsis auxin transporter PIN1–GFP. While pat3 displays largely normal plant morphology and development in nutrient-rich conditions, it shows strong ectopic intracellular accumulations of different plasma membrane cargoes in structures that resemble prevacuolar compartments (PVC) with an aberrant morphology. Genetic mapping revealed that pat3 is defective in vacuolar protein sorting 35A (VPS35A), a putative subunit of the retromer complex that mediates retrograde trafficking between the PVC and trans-Golgi network. Similarly, a mutant defective in another retromer subunit, vps29, shows comparable subcellular defects in PVC morphology and protein accumulation. Thus, our data provide evidence that the retromer components VPS35A and VPS29 are essential for normal PVC morphology and normal trafficking of plasma membrane proteins in plants. In addition, we show that, out of the three VPS35 retromer subunits present in Arabidopsis thaliana genome, the VPS35 homolog A plays a prevailing role in trafficking to the lytic vacuole, presenting another level of complexity in the retromer-dependent vacuolar sorting. "}],"_id":"2449","date_updated":"2025-09-29T14:14:22Z","date_published":"2013-11-01T00:00:00Z","citation":{"chicago":"Nodzyński, Tomasz, Murguel Feraru, Sibylle Hirsch, Riet De Rycke, Claudiu Nicuales, Jelle Van Leene, Geert De Jaeger, Steffen Vanneste, and Jiří Friml. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function in Arabidopsis.” <i>Molecular Plant</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1093/mp/sst044\">https://doi.org/10.1093/mp/sst044</a>.","ista":"Nodzyński T, Feraru M, Hirsch S, De Rycke R, Nicuales C, Van Leene J, De Jaeger G, Vanneste S, Friml J. 2013. Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant. 6(6), 1849–1862.","ama":"Nodzyński T, Feraru M, Hirsch S, et al. Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. <i>Molecular Plant</i>. 2013;6(6):1849-1862. doi:<a href=\"https://doi.org/10.1093/mp/sst044\">10.1093/mp/sst044</a>","ieee":"T. Nodzyński <i>et al.</i>, “Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis,” <i>Molecular Plant</i>, vol. 6, no. 6. Cell Press, pp. 1849–1862, 2013.","apa":"Nodzyński, T., Feraru, M., Hirsch, S., De Rycke, R., Nicuales, C., Van Leene, J., … Friml, J. (2013). Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. <i>Molecular Plant</i>. Cell Press. <a href=\"https://doi.org/10.1093/mp/sst044\">https://doi.org/10.1093/mp/sst044</a>","mla":"Nodzyński, Tomasz, et al. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function in Arabidopsis.” <i>Molecular Plant</i>, vol. 6, no. 6, Cell Press, 2013, pp. 1849–62, doi:<a href=\"https://doi.org/10.1093/mp/sst044\">10.1093/mp/sst044</a>.","short":"T. Nodzyński, M. Feraru, S. Hirsch, R. De Rycke, C. Nicuales, J. Van Leene, G. De Jaeger, S. Vanneste, J. Friml, Molecular Plant 6 (2013) 1849–1862."},"department":[{"_id":"JiFr"}],"page":"1849 - 1862","article_processing_charge":"No","year":"2013","author":[{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"last_name":"Feraru","first_name":"Murguel","full_name":"Feraru, Murguel"},{"first_name":"Sibylle","last_name":"Hirsch","full_name":"Hirsch, Sibylle"},{"last_name":"De Rycke","first_name":"Riet","full_name":"De Rycke, Riet"},{"full_name":"Nicuales, Claudiu","first_name":"Claudiu","last_name":"Nicuales"},{"first_name":"Jelle","last_name":"Van Leene","full_name":"Van Leene, Jelle"},{"last_name":"De Jaeger","first_name":"Geert","full_name":"De Jaeger, Geert"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"intvolume":"         6","scopus_import":"1","title":"Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"main_file_link":[{"url":"https://arxiv.org/abs/1011.3434","open_access":"1"}],"issue":"680","oa":1,"date_created":"2018-12-11T11:45:24Z","publist_id":"7659","type":"journal_article","doi":"10.1515/crelle.2012.039","abstract":[{"text":"For given non-zero integers a, b, q we investigate the density of solutions (x; y) ∈ ℤ2 to the binary cubic congruence ax2 + by3 ≡ 0 mod q, and use it to establish the Manin conjecture for a singular del Pezzo surface of degree 2 defined over ℚ.","lang":"eng"}],"_id":"245","date_updated":"2021-01-12T06:57:33Z","date_published":"2013-07-01T00:00:00Z","citation":{"apa":"Baier, S., &#38; Browning, T. D. (2013). Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. <i>Journal Fur Die Reine Und Angewandte Mathematik</i>. Walter de Gruyter. <a href=\"https://doi.org/10.1515/crelle.2012.039\">https://doi.org/10.1515/crelle.2012.039</a>","short":"S. Baier, T.D. Browning, Journal Fur Die Reine Und Angewandte Mathematik (2013) 69–151.","mla":"Baier, Stephan, and Timothy D. Browning. “Inhomogeneous Cubic Congruences and Rational Points on Del Pezzo Surfaces.” <i>Journal Fur Die Reine Und Angewandte Mathematik</i>, no. 680, Walter de Gruyter, 2013, pp. 69–151, doi:<a href=\"https://doi.org/10.1515/crelle.2012.039\">10.1515/crelle.2012.039</a>.","ieee":"S. Baier and T. D. Browning, “Inhomogeneous cubic congruences and rational points on del Pezzo surfaces,” <i>Journal fur die Reine und Angewandte Mathematik</i>, no. 680. Walter de Gruyter, pp. 69–151, 2013.","ama":"Baier S, Browning TD. Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. <i>Journal fur die Reine und Angewandte Mathematik</i>. 2013;(680):69-151. doi:<a href=\"https://doi.org/10.1515/crelle.2012.039\">10.1515/crelle.2012.039</a>","chicago":"Baier, Stephan, and Timothy D Browning. “Inhomogeneous Cubic Congruences and Rational Points on Del Pezzo Surfaces.” <i>Journal Fur Die Reine Und Angewandte Mathematik</i>. Walter de Gruyter, 2013. <a href=\"https://doi.org/10.1515/crelle.2012.039\">https://doi.org/10.1515/crelle.2012.039</a>.","ista":"Baier S, Browning TD. 2013. Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. (680), 69–151."},"page":"69 - 151","month":"07","author":[{"full_name":"Baier, Stephan","first_name":"Stephan","last_name":"Baier"},{"full_name":"Timothy Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","last_name":"Browning","first_name":"Timothy D"}],"quality_controlled":0,"year":"2013","extern":1,"title":"Inhomogeneous cubic congruences and rational points on del Pezzo surfaces","status":"public","day":"01","publication":"Journal fur die Reine und Angewandte Mathematik","publication_status":"published","publisher":"Walter de Gruyter"},{"quality_controlled":0,"author":[{"full_name":"Liu, Junli","first_name":"Junli","last_name":"Liu"},{"full_name":"Menhi, Saher","last_name":"Menhi","first_name":"Saher"},{"full_name":"Topping, Jennifer","first_name":"Jennifer","last_name":"Topping"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lindsey","first_name":"Keith","full_name":"Lindsey, Keith"}],"intvolume":"         4","year":"2013","extern":1,"day":"01","status":"public","title":"Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development","publication":"Frontiers in Plant Science","volume":4,"publisher":"Frontiers Research Foundation","publication_status":"published","issue":"75","publist_id":"4453","date_created":"2018-12-11T11:57:44Z","type":"journal_article","doi":"10.3389/fpls.2013.00075","citation":{"short":"J. Liu, S. Menhi, J. Topping, J. Friml, K. Lindsey, Frontiers in Plant Science 4 (2013).","mla":"Liu, Junli, et al. “Interaction of PLS and PIN and Hormonal Crosstalk in Arabidopsis Root Development.” <i>Frontiers in Plant Science</i>, vol. 4, no. 75, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fpls.2013.00075\">10.3389/fpls.2013.00075</a>.","apa":"Liu, J., Menhi, S., Topping, J., Friml, J., &#38; Lindsey, K. (2013). Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2013.00075\">https://doi.org/10.3389/fpls.2013.00075</a>","ista":"Liu J, Menhi S, Topping J, Friml J, Lindsey K. 2013. Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. Frontiers in Plant Science. 4(75).","chicago":"Liu, Junli, Saher Menhi, Jennifer Topping, Jiří Friml, and Keith Lindsey. “Interaction of PLS and PIN and Hormonal Crosstalk in Arabidopsis Root Development.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fpls.2013.00075\">https://doi.org/10.3389/fpls.2013.00075</a>.","ieee":"J. Liu, S. Menhi, J. Topping, J. Friml, and K. Lindsey, “Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development,” <i>Frontiers in Plant Science</i>, vol. 4, no. 75. Frontiers Research Foundation, 2013.","ama":"Liu J, Menhi S, Topping J, Friml J, Lindsey K. Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. <i>Frontiers in Plant Science</i>. 2013;4(75). doi:<a href=\"https://doi.org/10.3389/fpls.2013.00075\">10.3389/fpls.2013.00075</a>"},"date_published":"2013-04-01T00:00:00Z","_id":"2450","date_updated":"2021-01-12T06:57:34Z","abstract":[{"text":"Understanding how hormones and genes interact to coordinate plant growth is a major challenge in developmental biology. The activities of auxin, ethylene, and cytokinin depend on cellular context and exhibit either synergistic or antagonistic interactions. Here we use experimentation and network construction to elucidate the role of the interaction of the POLARIS peptide (PLS) and the auxin efflux carrier PIN proteins in the crosstalk of three hormones (auxin, ethylene, and cytokinin) in Arabidopsis root development. In ethylene hypersignaling mutants such as polaris (pls), we show experimentally that expression of both PIN1 and PIN2 significantly increases. This relationship is analyzed in the context of the crosstalk between auxin, ethylene, and cytokinin: in pls, endogenous auxin, ethylene and cytokinin concentration decreases, approximately remains unchanged and increases, respectively. Experimental data are integrated into a hormonal crosstalk network through combination with information in literature. Network construction reveals that the regulation of both PIN1 and PIN2 is predominantly via ethylene signaling. In addition, it is deduced that the relationship between cytokinin and PIN1 and PIN2 levels implies a regulatory role of cytokinin in addition to its regulation to auxin, ethylene, and PLS levels. We discuss how the network of hormones and genes coordinates plant growth by simultaneously regulating the activities of auxin, ethylene, and cytokinin signaling pathways.hormonal crosstalk, root development, auxin flux, PIN proteins, PLS protein, signaling network","lang":"eng"}],"month":"04"},{"month":"02","date_updated":"2021-01-12T06:57:34Z","_id":"2452","abstract":[{"text":"Background: Abundance and distribution of the plant hormone auxin play important roles in plant development. Besides other metabolic processes, various auxin carriers control the cellular level of active auxin and, hence, are major regulators of cellular auxin homeostasis. Despite the developmental importance of auxin transporters, a simple medium-to-high throughput approach to assess carrier activities is still missing. Here we show that carrier driven depletion of cellular auxin correlates with reduced nuclear auxin signaling in tobacco Bright Yellow-2 (BY-2) cell cultures.Results: We developed an easy to use transient single-cell-based system to detect carrier activity. We use the relative changes in signaling output of the auxin responsive promoter element DR5 to indirectly visualize auxin carrier activity. The feasibility of the transient approach was demonstrated by pharmacological and genetic interference with auxin signaling and transport. As a proof of concept, we provide visual evidence that the prominent auxin transport proteins PIN-FORMED (PIN)2 and PIN5 regulate cellular auxin homeostasis at the plasma membrane and endoplasmic reticulum (ER), respectively. Our data suggest that PIN2 and PIN5 have different sensitivities to the auxin transport inhibitor 1-naphthylphthalamic acid (NPA). Also the putative PIN-LIKES (PILS) auxin carrier activity at the ER is insensitive to NPA in our system, indicating that NPA blocks intercellular, but not intracellular auxin transport.Conclusions: This single-cell-based system is a useful tool by which the activity of putative auxin carriers, such as PINs, PILS and WALLS ARE THIN1 (WAT1), can be indirectly visualized in a medium-to-high throughput manner. Moreover, our single cell system might be useful to investigate also other hormonal signaling pathways, such as cytokinin.","lang":"eng"}],"citation":{"apa":"Barbez, E., Laňková, M., Pařezová, M., Maizel, A., Zažímalová, E., Petrášek, J., … Kleine Vehn, J. (2013). Single-cell-based system to monitor carrier driven cellular auxin homeostasis. <i>BMC Plant Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2229-13-20\">https://doi.org/10.1186/1471-2229-13-20</a>","mla":"Barbez, Elke, et al. “Single-Cell-Based System to Monitor Carrier Driven Cellular Auxin Homeostasis.” <i>BMC Plant Biology</i>, vol. 13, no. 1, BioMed Central, 2013, doi:<a href=\"https://doi.org/10.1186/1471-2229-13-20\">10.1186/1471-2229-13-20</a>.","short":"E. Barbez, M. Laňková, M. Pařezová, A. Maizel, E. Zažímalová, J. Petrášek, J. Friml, J. Kleine Vehn, BMC Plant Biology 13 (2013).","ieee":"E. Barbez <i>et al.</i>, “Single-cell-based system to monitor carrier driven cellular auxin homeostasis,” <i>BMC Plant Biology</i>, vol. 13, no. 1. BioMed Central, 2013.","ama":"Barbez E, Laňková M, Pařezová M, et al. Single-cell-based system to monitor carrier driven cellular auxin homeostasis. <i>BMC Plant Biology</i>. 2013;13(1). doi:<a href=\"https://doi.org/10.1186/1471-2229-13-20\">10.1186/1471-2229-13-20</a>","chicago":"Barbez, Elke, Martina Laňková, Markéta Pařezová, Alexis Maizel, Eva Zažímalová, Jan Petrášek, Jiří Friml, and Jürgen Kleine Vehn. “Single-Cell-Based System to Monitor Carrier Driven Cellular Auxin Homeostasis.” <i>BMC Plant Biology</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1471-2229-13-20\">https://doi.org/10.1186/1471-2229-13-20</a>.","ista":"Barbez E, Laňková M, Pařezová M, Maizel A, Zažímalová E, Petrášek J, Friml J, Kleine Vehn J. 2013. Single-cell-based system to monitor carrier driven cellular auxin homeostasis. BMC Plant Biology. 13(1)."},"date_published":"2013-02-01T00:00:00Z","doi":"10.1186/1471-2229-13-20","type":"journal_article","date_created":"2018-12-11T11:57:45Z","publist_id":"4451","issue":"1","publication_status":"published","publisher":"BioMed Central","volume":13,"publication":"BMC Plant Biology","status":"public","title":"Single-cell-based system to monitor carrier driven cellular auxin homeostasis","day":"01","extern":1,"year":"2013","quality_controlled":0,"author":[{"first_name":"Elke","last_name":"Barbez","full_name":"Barbez, Elke"},{"last_name":"Laňková","first_name":"Martina","full_name":"Laňková, Martina"},{"first_name":"Markéta","last_name":"Pařezová","full_name":"Pařezová, Markéta"},{"last_name":"Maizel","first_name":"Alexis","full_name":"Maizel, Alexis"},{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine-Vehn, Jürgen"}],"intvolume":"        13"},{"day":"01","status":"public","title":"Origin and evolution of PIN auxin transporters in the green lineage","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"Trends in Plant Science","volume":18,"publisher":"Cell Press","publication_status":"published","intvolume":"        18","author":[{"first_name":"Tom","last_name":"Viaene","full_name":"Viaene, Tom"},{"full_name":"Delwiche, Charles","first_name":"Charles","last_name":"Delwiche"},{"full_name":"Rensing, Stefan","last_name":"Rensing","first_name":"Stefan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí"}],"quality_controlled":"1","year":"2013","extern":"1","doi":"10.1016/j.tplants.2012.08.009","page":"5 - 10","citation":{"ista":"Viaene T, Delwiche C, Rensing S, Friml J. 2013. Origin and evolution of PIN auxin transporters in the green lineage. Trends in Plant Science. 18(1), 5–10.","chicago":"Viaene, Tom, Charles Delwiche, Stefan Rensing, and Jiří Friml. “Origin and Evolution of PIN Auxin Transporters in the Green Lineage.” <i>Trends in Plant Science</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.tplants.2012.08.009\">https://doi.org/10.1016/j.tplants.2012.08.009</a>.","ama":"Viaene T, Delwiche C, Rensing S, Friml J. Origin and evolution of PIN auxin transporters in the green lineage. <i>Trends in Plant Science</i>. 2013;18(1):5-10. doi:<a href=\"https://doi.org/10.1016/j.tplants.2012.08.009\">10.1016/j.tplants.2012.08.009</a>","ieee":"T. Viaene, C. Delwiche, S. Rensing, and J. Friml, “Origin and evolution of PIN auxin transporters in the green lineage,” <i>Trends in Plant Science</i>, vol. 18, no. 1. Cell Press, pp. 5–10, 2013.","mla":"Viaene, Tom, et al. “Origin and Evolution of PIN Auxin Transporters in the Green Lineage.” <i>Trends in Plant Science</i>, vol. 18, no. 1, Cell Press, 2013, pp. 5–10, doi:<a href=\"https://doi.org/10.1016/j.tplants.2012.08.009\">10.1016/j.tplants.2012.08.009</a>.","short":"T. Viaene, C. Delwiche, S. Rensing, J. Friml, Trends in Plant Science 18 (2013) 5–10.","apa":"Viaene, T., Delwiche, C., Rensing, S., &#38; Friml, J. (2013). Origin and evolution of PIN auxin transporters in the green lineage. <i>Trends in Plant Science</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tplants.2012.08.009\">https://doi.org/10.1016/j.tplants.2012.08.009</a>"},"date_published":"2013-01-01T00:00:00Z","date_updated":"2021-01-12T06:57:36Z","_id":"2457","month":"01","language":[{"iso":"eng"}],"issue":"1","publist_id":"4446","oa_version":"None","date_created":"2018-12-11T11:57:46Z","type":"journal_article"},{"type":"journal_article","publist_id":"7658","date_created":"2018-12-11T11:45:25Z","issue":"9","month":"09","date_published":"2013-09-01T00:00:00Z","citation":{"ista":"Browning TD, Munshi R. 2013. Rational points on singular intersections of quadrics. Compositio Mathematica. 149(9), 1457–1494.","chicago":"Browning, Timothy D, and Ritabrata Munshi. “Rational Points on Singular Intersections of Quadrics.” <i>Compositio Mathematica</i>. Cambridge University Press, 2013. <a href=\"https://doi.org/10.1112/S0010437X13007185\">https://doi.org/10.1112/S0010437X13007185</a>.","ieee":"T. D. Browning and R. Munshi, “Rational points on singular intersections of quadrics,” <i>Compositio Mathematica</i>, vol. 149, no. 9. Cambridge University Press, pp. 1457–1494, 2013.","ama":"Browning TD, Munshi R. Rational points on singular intersections of quadrics. <i>Compositio Mathematica</i>. 2013;149(9):1457-1494. doi:<a href=\"https://doi.org/10.1112/S0010437X13007185\">10.1112/S0010437X13007185</a>","mla":"Browning, Timothy D., and Ritabrata Munshi. “Rational Points on Singular Intersections of Quadrics.” <i>Compositio Mathematica</i>, vol. 149, no. 9, Cambridge University Press, 2013, pp. 1457–94, doi:<a href=\"https://doi.org/10.1112/S0010437X13007185\">10.1112/S0010437X13007185</a>.","short":"T.D. Browning, R. Munshi, Compositio Mathematica 149 (2013) 1457–1494.","apa":"Browning, T. D., &#38; Munshi, R. (2013). Rational points on singular intersections of quadrics. <i>Compositio Mathematica</i>. Cambridge University Press. <a href=\"https://doi.org/10.1112/S0010437X13007185\">https://doi.org/10.1112/S0010437X13007185</a>"},"page":"1457 - 1494","_id":"246","abstract":[{"text":"Given an intersection of two quadrics X Pm1, with m &gt; 9, the quantitative arithmetic of the set X(Q) is investigated under the assumption that the singular locus of X consists of a pair of conjugate singular points defined over Q(i).","lang":"eng"}],"date_updated":"2021-01-12T06:57:37Z","doi":"10.1112/S0010437X13007185","extern":1,"year":"2013","acknowledgement":"EP/E053262/1\tEngineering and Physical Sciences Research Council","author":[{"first_name":"Timothy D","last_name":"Browning","orcid":"0000-0002-8314-0177","full_name":"Timothy Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ritabrata","last_name":"Munshi","full_name":"Munshi, Ritabrata"}],"quality_controlled":0,"intvolume":"       149","publisher":"Cambridge University Press","publication_status":"published","publication":"Compositio Mathematica","volume":149,"day":"01","title":"Rational points on singular intersections of quadrics","status":"public"},{"intvolume":"        32","author":[{"full_name":"Ando, Ryoichi","first_name":"Ryoichi","last_name":"Ando"},{"full_name":"Thuerey, Nils","first_name":"Nils","last_name":"Thuerey"},{"first_name":"Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J"}],"year":"2013","article_processing_charge":"No","title":"Highly adaptive liquid simulations on tetrahedral meshes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","issue":"4","oa":1,"isi":1,"oa_version":"Submitted Version","date_created":"2018-12-11T11:57:50Z","type":"journal_article","article_number":"103","department":[{"_id":"ChWo"}],"date_published":"2013-07-01T00:00:00Z","citation":{"apa":"Ando, R., Thuerey, N., &#38; Wojtan, C. (2013). Highly adaptive liquid simulations on tetrahedral meshes. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461982\">https://doi.org/10.1145/2461912.2461982</a>","short":"R. Ando, N. Thuerey, C. Wojtan, ACM Transactions on Graphics 32 (2013).","mla":"Ando, Ryoichi, et al. “Highly Adaptive Liquid Simulations on Tetrahedral Meshes.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, 103, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461982\">10.1145/2461912.2461982</a>.","ieee":"R. Ando, N. Thuerey, and C. Wojtan, “Highly adaptive liquid simulations on tetrahedral meshes,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","ama":"Ando R, Thuerey N, Wojtan C. Highly adaptive liquid simulations on tetrahedral meshes. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461982\">10.1145/2461912.2461982</a>","chicago":"Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “Highly Adaptive Liquid Simulations on Tetrahedral Meshes.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461982\">https://doi.org/10.1145/2461912.2461982</a>.","ista":"Ando R, Thuerey N, Wojtan C. 2013. Highly adaptive liquid simulations on tetrahedral meshes. ACM Transactions on Graphics. 32(4), 103."},"_id":"2466","date_updated":"2025-09-29T14:13:52Z","abstract":[{"text":"We introduce a new method for efficiently simulating liquid with extreme amounts of spatial adaptivity. Our method combines several key components to drastically speed up the simulation of large-scale fluid phenomena: We leverage an alternative Eulerian tetrahedral mesh discretization to significantly reduce the complexity of the pressure solve while increasing the robustness with respect to element quality and removing the possibility of locking. Next, we enable subtle free-surface phenomena by deriving novel second-order boundary conditions consistent with our discretization. We couple this discretization with a spatially adaptive Fluid-Implicit Particle (FLIP) method, enabling efficient, robust, minimally-dissipative simulations that can undergo sharp changes in spatial resolution while minimizing artifacts. Along the way, we provide a new method for generating a smooth and detailed surface from a set of particles with variable sizes. Finally, we explore several new sizing functions for determining spatially adaptive simulation resolutions, and we show how to couple them to our simulator. We combine each of these elements to produce a simulation algorithm that is capable of creating animations at high maximum resolutions while avoiding common pitfalls like inaccurate boundary conditions and inefficient computation.","lang":"eng"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"quality_controlled":"1","ddc":["000"],"external_id":{"isi":["000321840100072"]},"day":"01","status":"public","file":[{"file_id":"5279","date_created":"2018-12-12T10:17:25Z","relation":"main_file","access_level":"open_access","file_name":"IST-2016-605-v1+1_tetflip_fixed.pdf","file_size":8601561,"content_type":"application/pdf","checksum":"aeea6b0ff2b27c695aeb8408c7d2fc50","creator":"system","date_updated":"2020-07-14T12:45:41Z"}],"publication":"ACM Transactions on Graphics","volume":32,"publisher":"ACM","publication_status":"published","publist_id":"4436","doi":"10.1145/2461912.2461982","file_date_updated":"2020-07-14T12:45:41Z","pubrep_id":"605","month":"07"},{"date_published":"2013-07-01T00:00:00Z","citation":{"short":"G. Bernstein, C. Wojtan, ACM Transactions on Graphics 32 (2013).","mla":"Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology Change for Arbitrary Surfaces.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, 34, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2462027\">10.1145/2461912.2462027</a>.","apa":"Bernstein, G., &#38; Wojtan, C. (2013). Putting holes in holey geometry: Topology change for arbitrary surfaces. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2462027\">https://doi.org/10.1145/2461912.2462027</a>","ista":"Bernstein G, Wojtan C. 2013. Putting holes in holey geometry: Topology change for arbitrary surfaces. ACM Transactions on Graphics. 32(4), 34.","chicago":"Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology Change for Arbitrary Surfaces.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2462027\">https://doi.org/10.1145/2461912.2462027</a>.","ieee":"G. Bernstein and C. Wojtan, “Putting holes in holey geometry: Topology change for arbitrary surfaces,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","ama":"Bernstein G, Wojtan C. Putting holes in holey geometry: Topology change for arbitrary surfaces. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2462027\">10.1145/2461912.2462027</a>"},"department":[{"_id":"ChWo"}],"date_updated":"2025-09-29T14:13:25Z","_id":"2467","abstract":[{"lang":"eng","text":"This paper presents a method for computing topology changes for triangle meshes in an interactive geometric modeling environment. Most triangle meshes in practice do not exhibit desirable geometric properties, so we develop a solution that is independent of standard assumptions and robust to geometric errors. Specifically, we provide the first method for topology change applicable to arbitrary non-solid, non-manifold, non-closed, self-intersecting surfaces. We prove that this new method for topology change produces the expected conventional results when applied to solid (closed, manifold, non-self-intersecting) surfaces---that is, we prove a backwards-compatibility property relative to prior work. Beyond solid surfaces, we present empirical evidence that our method remains tolerant to a variety of surface aberrations through the incorporation of a novel error correction scheme. Finally, we demonstrate how topology change applied to non-solid objects enables wholly new and useful behaviors."}],"has_accepted_license":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:57:50Z","oa_version":"Submitted Version","type":"journal_article","article_number":"34","issue":"4","isi":1,"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Putting holes in holey geometry: Topology change for arbitrary surfaces","scopus_import":"1","year":"2013","article_processing_charge":"No","intvolume":"        32","author":[{"last_name":"Bernstein","first_name":"Gilbert","full_name":"Bernstein, Gilbert"},{"orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"month":"07","doi":"10.1145/2461912.2462027","pubrep_id":"604","file_date_updated":"2020-07-14T12:45:41Z","publist_id":"4435","publication":"ACM Transactions on Graphics","volume":32,"publisher":"ACM","publication_status":"published","day":"01","status":"public","file":[{"date_updated":"2020-07-14T12:45:41Z","creator":"system","checksum":"9c8425d62246996ca632c5a01870515b","content_type":"application/pdf","file_size":3514674,"access_level":"open_access","file_name":"IST-2016-604-v1+1_toptop2013.pdf","date_created":"2018-12-12T10:09:43Z","relation":"main_file","file_id":"4768"}],"quality_controlled":"1","ddc":["000"],"external_id":{"isi":["000321840100003"]}},{"scopus_import":"1","title":"Liquid surface tracking with error compensation","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2013","article_processing_charge":"No","intvolume":"        32","author":[{"id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","full_name":"Bojsen-Hansen, Morten","orcid":"0000-0002-4417-3224","last_name":"Bojsen-Hansen","first_name":"Morten"},{"last_name":"Wojtan","orcid":"0000-0001-6646-5546","first_name":"Christopher J","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"ChWo"}],"date_published":"2013-07-01T00:00:00Z","citation":{"ieee":"M. Bojsen-Hansen and C. Wojtan, “Liquid surface tracking with error compensation,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","ama":"Bojsen-Hansen M, Wojtan C. Liquid surface tracking with error compensation. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461991\">10.1145/2461912.2461991</a>","ista":"Bojsen-Hansen M, Wojtan C. 2013. Liquid surface tracking with error compensation. ACM Transactions on Graphics. 32(4), 68.","chicago":"Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error Compensation.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461991\">https://doi.org/10.1145/2461912.2461991</a>.","short":"M. Bojsen-Hansen, C. Wojtan, ACM Transactions on Graphics 32 (2013).","mla":"Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error Compensation.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, 68, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461991\">10.1145/2461912.2461991</a>.","apa":"Bojsen-Hansen, M., &#38; Wojtan, C. (2013). Liquid surface tracking with error compensation. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461991\">https://doi.org/10.1145/2461912.2461991</a>"},"abstract":[{"lang":"eng","text":"Our work concerns the combination of an Eulerian liquid simulation with a high-resolution surface tracker (e.g. the level set method or a Lagrangian triangle mesh). The naive application of a high-resolution surface tracker to a low-resolution velocity field can produce many visually disturbing physical and topological artifacts that limit their use in practice. We address these problems by defining an error function which compares the current state of the surface tracker to the set of physically valid surface states. By reducing this error with a gradient descent technique, we introduce a novel physics-based surface fairing method. Similarly, by treating this error function as a potential energy, we derive a new surface correction force that mimics the vortex sheet equations. We demonstrate our results with both level set and mesh-based surface trackers."}],"_id":"2468","date_updated":"2025-09-29T14:12:53Z","type":"journal_article","article_number":"68","date_created":"2018-12-11T11:57:50Z","oa_version":"Submitted Version","oa":1,"isi":1,"issue":"4","publisher":"ACM","publication_status":"published","publication":"ACM Transactions on Graphics","volume":32,"file":[{"relation":"main_file","date_created":"2018-12-12T10:09:37Z","file_id":"4761","creator":"system","date_updated":"2020-07-14T12:45:41Z","content_type":"application/pdf","checksum":"53d905e0180e23ef3e813b969ffed4e1","file_size":5813685,"access_level":"open_access","file_name":"IST-2016-603-v1+1_liquidError_web.pdf"}],"day":"01","status":"public","ddc":["000"],"external_id":{"isi":["000321840100037"]},"quality_controlled":"1","month":"07","doi":"10.1145/2461912.2461991","file_date_updated":"2020-07-14T12:45:41Z","pubrep_id":"603","corr_author":"1","publist_id":"4434"},{"scopus_import":"1","title":"Three functions of cadherins in cell adhesion","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Jean-Léon","orcid":"0000-0002-3688-1474","last_name":"Maître","full_name":"Maître, Jean-Léon","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"intvolume":"        23","article_processing_charge":"No","year":"2013","language":[{"iso":"eng"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Cadherins are transmembrane proteins that mediate cell–cell adhesion in animals. By regulating contact formation and stability, cadherins play a crucial role in tissue morphogenesis and homeostasis. Here, we review the three major  unctions of cadherins in cell–cell contact formation and stability. Two of those functions lead to a decrease in interfacial ension at the forming cell–cell contact, thereby promoting contact expansion — first, by providing adhesion tension that lowers interfacial tension at the cell–cell contact, and second, by signaling to the actomyosin cytoskeleton in order to reduce cortex tension and thus interfacial tension at the contact. The third function of cadherins in cell–cell contact formation is to stabilize the contact by resisting mechanical forces that pull on the contact."}],"_id":"2469","date_updated":"2025-09-29T14:12:25Z","department":[{"_id":"CaHe"}],"citation":{"chicago":"Maître, Jean-Léon, and Carl-Philipp J Heisenberg. “Three Functions of Cadherins in Cell Adhesion.” <i>Current Biology</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">https://doi.org/10.1016/j.cub.2013.06.019</a>.","ista":"Maître J-L, Heisenberg C-PJ. 2013. Three functions of cadherins in cell adhesion. Current Biology. 23(14), R626–R633.","ama":"Maître J-L, Heisenberg C-PJ. Three functions of cadherins in cell adhesion. <i>Current Biology</i>. 2013;23(14):R626-R633. doi:<a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">10.1016/j.cub.2013.06.019</a>","ieee":"J.-L. Maître and C.-P. J. Heisenberg, “Three functions of cadherins in cell adhesion,” <i>Current Biology</i>, vol. 23, no. 14. Cell Press, pp. R626–R633, 2013.","apa":"Maître, J.-L., &#38; Heisenberg, C.-P. J. (2013). Three functions of cadherins in cell adhesion. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">https://doi.org/10.1016/j.cub.2013.06.019</a>","short":"J.-L. Maître, C.-P.J. Heisenberg, Current Biology 23 (2013) R626–R633.","mla":"Maître, Jean-Léon, and Carl-Philipp J. Heisenberg. “Three Functions of Cadherins in Cell Adhesion.” <i>Current Biology</i>, vol. 23, no. 14, Cell Press, 2013, pp. R626–33, doi:<a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">10.1016/j.cub.2013.06.019</a>."},"date_published":"2013-07-22T00:00:00Z","page":"R626 - R633","oa":1,"isi":1,"issue":"14","type":"journal_article","date_created":"2018-12-11T11:57:51Z","oa_version":"Published Version","file":[{"checksum":"6a424b2f007b41d4955a9135793b2162","content_type":"application/pdf","date_updated":"2020-07-14T12:45:41Z","creator":"dernst","access_level":"open_access","file_name":"2013_CurrentBiology_Maitre.pdf","file_size":247320,"date_created":"2019-01-24T15:40:22Z","relation":"main_file","file_id":"5881"}],"status":"public","day":"22","pmid":1,"publication_status":"published","publisher":"Cell Press","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)"},"volume":23,"publication":"Current Biology","ddc":["570"],"external_id":{"pmid":["23885883"],"isi":["000322414200018"]},"quality_controlled":"1","file_date_updated":"2020-07-14T12:45:41Z","doi":"10.1016/j.cub.2013.06.019","month":"07","corr_author":"1","publist_id":"4433"},{"date_created":"2018-12-11T11:45:25Z","publist_id":"7657","type":"journal_article","issue":"3","_id":"247","abstract":[{"lang":"eng","text":"An improved estimate is provided for the number of Fq-rational points on a geometrically irreducible, projective, cubic hypersurface that is not equal to a cone."}],"date_updated":"2021-01-12T06:57:40Z","page":"500 - 502","citation":{"short":"T.D. Browning, Canadian Mathematical Bulletin 56 (2013) 500–502.","mla":"Browning, Timothy D. “The Lang-Weil Estimate for Cubic Hypersurfaces.” <i>Canadian Mathematical Bulletin</i>, vol. 56, no. 3, Unknown, 2013, pp. 500–02, doi:<a href=\"https://doi.org/10.4153/CMB-2011-177-4\">10.4153/CMB-2011-177-4</a>.","apa":"Browning, T. D. (2013). The Lang-Weil estimate for cubic hypersurfaces. <i>Canadian Mathematical Bulletin</i>. Unknown. <a href=\"https://doi.org/10.4153/CMB-2011-177-4\">https://doi.org/10.4153/CMB-2011-177-4</a>","ieee":"T. D. Browning, “The Lang-Weil estimate for cubic hypersurfaces,” <i>Canadian Mathematical Bulletin</i>, vol. 56, no. 3. Unknown, pp. 500–502, 2013.","ama":"Browning TD. The Lang-Weil estimate for cubic hypersurfaces. <i>Canadian Mathematical Bulletin</i>. 2013;56(3):500-502. doi:<a href=\"https://doi.org/10.4153/CMB-2011-177-4\">10.4153/CMB-2011-177-4</a>","ista":"Browning TD. 2013. The Lang-Weil estimate for cubic hypersurfaces. Canadian Mathematical Bulletin. 56(3), 500–502.","chicago":"Browning, Timothy D. “The Lang-Weil Estimate for Cubic Hypersurfaces.” <i>Canadian Mathematical Bulletin</i>. Unknown, 2013. <a href=\"https://doi.org/10.4153/CMB-2011-177-4\">https://doi.org/10.4153/CMB-2011-177-4</a>."},"date_published":"2013-08-31T00:00:00Z","month":"08","doi":"10.4153/CMB-2011-177-4","year":"2013","extern":1,"author":[{"last_name":"Browning","orcid":"0000-0002-8314-0177","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Timothy Browning"}],"intvolume":"        56","quality_controlled":0,"acknowledgement":"EP/E053262/1\tEngineering and Physical Sciences Research Council","volume":56,"publication":"Canadian Mathematical Bulletin","publication_status":"published","publisher":"Unknown","status":"public","title":"The Lang-Weil estimate for cubic hypersurfaces","day":"31"},{"author":[{"full_name":"Čovanová, Milada","last_name":"Čovanová","first_name":"Milada"},{"last_name":"Sauer","first_name":"Michael","full_name":"Sauer, Michael"},{"full_name":"Rychtář, Jan","first_name":"Jan","last_name":"Rychtář"},{"first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"full_name":"Zažímalová, Eva","first_name":"Eva","last_name":"Zažímalová"}],"intvolume":"         8","article_processing_charge":"No","year":"2013","title":"Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","issue":"7","isi":1,"oa":1,"date_created":"2018-12-11T11:57:51Z","oa_version":"Published Version","article_number":"e70050","type":"journal_article","_id":"2470","date_updated":"2025-09-29T14:11:54Z","abstract":[{"lang":"eng","text":"Background:Auxin binding protein 1 (ABP1) is a putative auxin receptor and its function is indispensable for plant growth and development. ABP1 has been shown to be involved in auxin-dependent regulation of cell division and expansion, in plasma-membrane-related processes such as changes in transmembrane potential, and in the regulation of clathrin-dependent endocytosis. However, the ABP1-regulated downstream pathway remains elusive.Methodology/Principal Findings:Using auxin transport assays and quantitative analysis of cellular morphology we show that ABP1 regulates auxin efflux from tobacco BY-2 cells. The overexpression of ABP1can counterbalance increased auxin efflux and auxin starvation phenotypes caused by the overexpression of PIN auxin efflux carrier. Relevant mechanism involves the ABP1-controlled vesicle trafficking processes, including positive regulation of endocytosis of PIN auxin efflux carriers, as indicated by fluorescence recovery after photobleaching (FRAP) and pharmacological manipulations.Conclusions/Significance:The findings indicate the involvement of ABP1 in control of rate of auxin transport across plasma membrane emphasizing the role of ABP1 in regulation of PIN activity at the plasma membrane, and highlighting the relevance of ABP1 for the formation of developmentally important, PIN-dependent auxin gradients."}],"date_published":"2013-07-23T00:00:00Z","citation":{"short":"M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, E. Zažímalová, PLoS One 8 (2013).","mla":"Čovanová, Milada, et al. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent Auxin Transport in Tobacco Cells.” <i>PLoS One</i>, vol. 8, no. 7, e70050, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0070050\">10.1371/journal.pone.0070050</a>.","apa":"Čovanová, M., Sauer, M., Rychtář, J., Friml, J., Petrášek, J., &#38; Zažímalová, E. (2013). Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0070050\">https://doi.org/10.1371/journal.pone.0070050</a>","ista":"Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. 2013. Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. PLoS One. 8(7), e70050.","chicago":"Čovanová, Milada, Michael Sauer, Jan Rychtář, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent Auxin Transport in Tobacco Cells.” <i>PLoS One</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0070050\">https://doi.org/10.1371/journal.pone.0070050</a>.","ieee":"M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, and E. Zažímalová, “Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells,” <i>PLoS One</i>, vol. 8, no. 7. Public Library of Science, 2013.","ama":"Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. <i>PLoS One</i>. 2013;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0070050\">10.1371/journal.pone.0070050</a>"},"department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","quality_controlled":"1","external_id":{"isi":["000325211000181"]},"ddc":["570"],"status":"public","day":"23","file":[{"date_created":"2018-12-12T10:08:21Z","relation":"main_file","file_id":"4681","checksum":"2d47ef47616ef4de1d517d146548184e","content_type":"application/pdf","creator":"system","date_updated":"2020-07-14T12:45:41Z","access_level":"open_access","file_name":"IST-2016-413-v1+1_journal.pone.0070050.pdf","file_size":2294955}],"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)"},"volume":8,"publication":"PLoS One","publication_status":"published","publisher":"Public Library of Science","publist_id":"4432","file_date_updated":"2020-07-14T12:45:41Z","pubrep_id":"413","doi":"10.1371/journal.pone.0070050","month":"07"},{"doi":"10.1371/journal.pone.0070013","pubrep_id":"414","file_date_updated":"2020-07-14T12:45:41Z","month":"07","publist_id":"4430","day":"30","status":"public","file":[{"file_name":"IST-2016-414-v1+1_journal.pone.0070013.pdf","access_level":"open_access","file_size":1323666,"content_type":"application/pdf","checksum":"c0c96cc76ed7ef0d036a31a7e33c9a37","creator":"system","date_updated":"2020-07-14T12:45:41Z","file_id":"5124","relation":"main_file","date_created":"2018-12-12T10:15:07Z"}],"publication":"PLoS One","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)"},"volume":8,"publisher":"Public Library of Science","publication_status":"published","quality_controlled":"1","ddc":["570"],"external_id":{"isi":["000323114200054"]},"date_published":"2013-07-30T00:00:00Z","department":[{"_id":"HaJa"}],"citation":{"apa":"Sanchez-Romero, I., Ariza, A., Wilson, K., Skjøt, M., Vind, J., De Maria, L., … Sánchez Ruiz, J. (2013). Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0070013\">https://doi.org/10.1371/journal.pone.0070013</a>","short":"I. Sanchez-Romero, A. Ariza, K. Wilson, M. Skjøt, J. Vind, L. De Maria, L. Skov, J. Sánchez Ruiz, PLoS One 8 (2013).","mla":"Sanchez-Romero, Inmaculada, et al. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” <i>PLoS One</i>, vol. 8, no. 7, e70013, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0070013\">10.1371/journal.pone.0070013</a>.","ieee":"I. Sanchez-Romero <i>et al.</i>, “Mechanism of protein kinetic stabilization by engineered disulfide crosslinks,” <i>PLoS One</i>, vol. 8, no. 7. Public Library of Science, 2013.","ama":"Sanchez-Romero I, Ariza A, Wilson K, et al. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. <i>PLoS One</i>. 2013;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0070013\">10.1371/journal.pone.0070013</a>","chicago":"Sanchez-Romero, Inmaculada, Antonio Ariza, Keith Wilson, Michael Skjøt, Jesper Vind, Leonardo De Maria, Lars Skov, and Jose Sánchez Ruiz. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” <i>PLoS One</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0070013\">https://doi.org/10.1371/journal.pone.0070013</a>.","ista":"Sanchez-Romero I, Ariza A, Wilson K, Skjøt M, Vind J, De Maria L, Skov L, Sánchez Ruiz J. 2013. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. 8(7), e70013."},"abstract":[{"text":"The impact of disulfide bonds on protein stability goes beyond simple equilibrium thermodynamics effects associated with the conformational entropy of the unfolded state. Indeed, disulfide crosslinks may play a role in the prevention of dysfunctional association and strongly affect the rates of irreversible enzyme inactivation, highly relevant in biotechnological applications. While these kinetic-stability effects remain poorly understood, by analogy with proposed mechanisms for processes of protein aggregation and fibrillogenesis, we propose that they may be determined by the properties of sparsely-populated, partially-unfolded intermediates. Here we report the successful design, on the basis of high temperature molecular-dynamics simulations, of six thermodynamically and kinetically stabilized variants of phytase from Citrobacter braakii (a biotechnologically important enzyme) with one, two or three engineered disulfides. Activity measurements and 3D crystal structure determination demonstrate that the engineered crosslinks do not cause dramatic alterations in the native structure. The inactivation kinetics for all the variants displays a strongly non-Arrhenius temperature dependence, with the time-scale for the irreversible denaturation process reaching a minimum at a given temperature within the range of the denaturation transition. We show this striking feature to be a signature of a key role played by a partially unfolded, intermediate state/ensemble. Energetic and mutational analyses confirm that the intermediate is highly unfolded (akin to a proposed critical intermediate in the misfolding of the prion protein), a result that explains the observed kinetic stabilization. Our results provide a rationale for the kinetic-stability consequences of disulfide-crosslink engineering and an experimental methodology to arrive at energetic/structural descriptions of the sparsely populated and elusive intermediates that play key roles in irreversible protein denaturation.","lang":"eng"}],"_id":"2471","date_updated":"2025-09-29T14:10:56Z","has_accepted_license":"1","language":[{"iso":"eng"}],"issue":"7","oa":1,"isi":1,"date_created":"2018-12-11T11:57:51Z","oa_version":"Published Version","type":"journal_article","article_number":"e70013","title":"Mechanism of protein kinetic stabilization by engineered disulfide crosslinks","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","author":[{"id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","full_name":"Sanchez Romero, Inmaculada","last_name":"Sanchez Romero","first_name":"Inmaculada"},{"last_name":"Ariza","first_name":"Antonio","full_name":"Ariza, Antonio"},{"full_name":"Wilson, Keith","last_name":"Wilson","first_name":"Keith"},{"last_name":"Skjøt","first_name":"Michael","full_name":"Skjøt, Michael"},{"full_name":"Vind, Jesper","first_name":"Jesper","last_name":"Vind"},{"full_name":"De Maria, Leonardo","last_name":"De Maria","first_name":"Leonardo"},{"first_name":"Lars","last_name":"Skov","full_name":"Skov, Lars"},{"full_name":"Sánchez Ruiz, Jose","first_name":"Jose","last_name":"Sánchez Ruiz"}],"intvolume":"         8","year":"2013","article_processing_charge":"No"}]