[{"scopus_import":"1","article_processing_charge":"No","article_type":"letter_note","publication":"Information and Computation","_id":"11758","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","date_created":"2022-08-08T11:25:34Z","volume":222,"title":"38th International Colloquium on Automata, Languages and Programming","day":"01","date_updated":"2023-02-23T10:09:19Z","month":"01","oa_version":"None","type":"journal_article","page":"1","author":[{"last_name":"Aceto","first_name":"Luca","full_name":"Aceto, Luca"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H"},{"full_name":"Sgall, Jiří","first_name":"Jiří","last_name":"Sgall"}],"citation":{"ieee":"L. Aceto, M. H. Henzinger, and J. Sgall, “38th International Colloquium on Automata, Languages and Programming,” <i>Information and Computation</i>, vol. 222, no. 1. Elsevier, p. 1, 2013.","chicago":"Aceto, Luca, Monika H Henzinger, and Jiří Sgall. “38th International Colloquium on Automata, Languages and Programming.” <i>Information and Computation</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.ic.2012.11.002\">https://doi.org/10.1016/j.ic.2012.11.002</a>.","short":"L. Aceto, M.H. Henzinger, J. Sgall, Information and Computation 222 (2013) 1.","ama":"Aceto L, Henzinger MH, Sgall J. 38th International Colloquium on Automata, Languages and Programming. <i>Information and Computation</i>. 2013;222(1):1. doi:<a href=\"https://doi.org/10.1016/j.ic.2012.11.002\">10.1016/j.ic.2012.11.002</a>","mla":"Aceto, Luca, et al. “38th International Colloquium on Automata, Languages and Programming.” <i>Information and Computation</i>, vol. 222, no. 1, Elsevier, 2013, p. 1, doi:<a href=\"https://doi.org/10.1016/j.ic.2012.11.002\">10.1016/j.ic.2012.11.002</a>.","ista":"Aceto L, Henzinger MH, Sgall J. 2013. 38th International Colloquium on Automata, Languages and Programming. Information and Computation. 222(1), 1.","apa":"Aceto, L., Henzinger, M. H., &#38; Sgall, J. (2013). 38th International Colloquium on Automata, Languages and Programming. <i>Information and Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ic.2012.11.002\">https://doi.org/10.1016/j.ic.2012.11.002</a>"},"language":[{"iso":"eng"}],"issue":"1","intvolume":"       222","extern":"1","status":"public","quality_controlled":"1","doi":"10.1016/j.ic.2012.11.002","date_published":"2013-01-01T00:00:00Z","publication_status":"published","publication_identifier":{"issn":["0890-5401"]}},{"year":"2013","_id":"11759","date_updated":"2022-09-12T09:36:15Z","abstract":[{"text":"Matching markets play a prominent role in economic theory. A prime example of such a market is the sponsored search market. Here, as in other markets of that kind, market equilibria correspond to feasible, envy free, and bidder optimal outcomes. For settings without budgets such an outcome always exists and can be computed in polynomial-time by the so-called Hungarian Method. Moreover, every mechanism that computes such an outcome is incentive compatible. We show that the Hungarian Method can be modified so that it finds a feasible, envy free, and bidder optimal outcome for settings with budgets. We also show that in settings with budgets no mechanism that computes such an outcome can be incentive compatible for all inputs. For inputs in general position, however, the presented mechanism—as any other mechanism that computes such an outcome for settings with budgets—is incentive compatible.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","month":"02","page":"67-73","date_created":"2022-08-08T11:29:08Z","volume":113,"status":"public","external_id":{"arxiv":["0912.1934"]},"citation":{"short":"P. Dütting, M.H. Henzinger, I. Weber, Information Processing Letters 113 (2013) 67–73.","ieee":"P. Dütting, M. H. Henzinger, and I. Weber, “Sponsored search, market equilibria, and the Hungarian Method,” <i>Information Processing Letters</i>, vol. 113, no. 3. Elsevier, pp. 67–73, 2013.","chicago":"Dütting, Paul, Monika H Henzinger, and Ingmar Weber. “Sponsored Search, Market Equilibria, and the Hungarian Method.” <i>Information Processing Letters</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.ipl.2012.11.006\">https://doi.org/10.1016/j.ipl.2012.11.006</a>.","mla":"Dütting, Paul, et al. “Sponsored Search, Market Equilibria, and the Hungarian Method.” <i>Information Processing Letters</i>, vol. 113, no. 3, Elsevier, 2013, pp. 67–73, doi:<a href=\"https://doi.org/10.1016/j.ipl.2012.11.006\">10.1016/j.ipl.2012.11.006</a>.","ista":"Dütting P, Henzinger MH, Weber I. 2013. Sponsored search, market equilibria, and the Hungarian Method. Information Processing Letters. 113(3), 67–73.","apa":"Dütting, P., Henzinger, M. H., &#38; Weber, I. (2013). Sponsored search, market equilibria, and the Hungarian Method. <i>Information Processing Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ipl.2012.11.006\">https://doi.org/10.1016/j.ipl.2012.11.006</a>","ama":"Dütting P, Henzinger MH, Weber I. Sponsored search, market equilibria, and the Hungarian Method. <i>Information Processing Letters</i>. 2013;113(3):67-73. doi:<a href=\"https://doi.org/10.1016/j.ipl.2012.11.006\">10.1016/j.ipl.2012.11.006</a>"},"intvolume":"       113","extern":"1","publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/0912.1934"}],"date_published":"2013-02-15T00:00:00Z","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","article_processing_charge":"No","article_type":"original","publication":"Information Processing Letters","day":"15","author":[{"full_name":"Dütting, Paul","first_name":"Paul","last_name":"Dütting"},{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger"},{"first_name":"Ingmar","last_name":"Weber","full_name":"Weber, Ingmar"}],"arxiv":1,"title":"Sponsored search, market equilibria, and the Hungarian Method","language":[{"iso":"eng"}],"issue":"3","publication_identifier":{"issn":["0020-0190"]},"quality_controlled":"1","doi":"10.1016/j.ipl.2012.11.006"},{"publication_identifier":{"issn":["1611-3349"],"isbn":["9783642450457"]},"doi":"10.1007/978-3-642-45046-4_13","quality_controlled":"1","conference":{"start_date":"2013-12-01","location":"Cambridge, MA, USA","name":"WINE: International Conference on Web and Internet Economics","end_date":"2013-12-14"},"language":[{"iso":"eng"}],"author":[{"first_name":"Paul","last_name":"Dütting","full_name":"Dütting, Paul"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H"},{"full_name":"Starnberger, Martin","first_name":"Martin","last_name":"Starnberger"}],"day":"01","title":"Valuation compressions in VCG-based combinatorial auctions","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","publication":"9th International Conference on Web and Internet Economics","article_processing_charge":"No","scopus_import":"1","publication_status":"published","oa":1,"date_published":"2013-12-01T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1310.3153","open_access":"1"}],"alternative_title":["LNCS"],"status":"public","external_id":{"arxiv":["1310.3153"]},"extern":"1","intvolume":"      8289","citation":{"short":"P. Dütting, M.H. Henzinger, M. Starnberger, in:, 9th International Conference on Web and Internet Economics, Springer Nature, 2013, pp. 146–159.","chicago":"Dütting, Paul, Monika H Henzinger, and Martin Starnberger. “Valuation Compressions in VCG-Based Combinatorial Auctions.” In <i>9th International Conference on Web and Internet Economics</i>, 8289:146–159. Springer Nature, 2013. <a href=\"https://doi.org/10.1007/978-3-642-45046-4_13\">https://doi.org/10.1007/978-3-642-45046-4_13</a>.","ieee":"P. Dütting, M. H. Henzinger, and M. Starnberger, “Valuation compressions in VCG-based combinatorial auctions,” in <i>9th International Conference on Web and Internet Economics</i>, Cambridge, MA, USA, 2013, vol. 8289, pp. 146–159.","apa":"Dütting, P., Henzinger, M. H., &#38; Starnberger, M. (2013). Valuation compressions in VCG-based combinatorial auctions. In <i>9th International Conference on Web and Internet Economics</i> (Vol. 8289, pp. 146–159). Cambridge, MA, USA: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-45046-4_13\">https://doi.org/10.1007/978-3-642-45046-4_13</a>","ista":"Dütting P, Henzinger MH, Starnberger M. 2013. Valuation compressions in VCG-based combinatorial auctions. 9th International Conference on Web and Internet Economics. WINE: International Conference on Web and Internet Economics, LNCS, vol. 8289, 146–159.","mla":"Dütting, Paul, et al. “Valuation Compressions in VCG-Based Combinatorial Auctions.” <i>9th International Conference on Web and Internet Economics</i>, vol. 8289, Springer Nature, 2013, pp. 146–159, doi:<a href=\"https://doi.org/10.1007/978-3-642-45046-4_13\">10.1007/978-3-642-45046-4_13</a>.","ama":"Dütting P, Henzinger MH, Starnberger M. Valuation compressions in VCG-based combinatorial auctions. In: <i>9th International Conference on Web and Internet Economics</i>. Vol 8289. Springer Nature; 2013:146–159. doi:<a href=\"https://doi.org/10.1007/978-3-642-45046-4_13\">10.1007/978-3-642-45046-4_13</a>"},"page":"146–159","type":"conference","month":"12","oa_version":"Preprint","date_updated":"2023-02-13T11:20:42Z","abstract":[{"lang":"eng","text":"The focus of classic mechanism design has been on truthful direct-revelation mechanisms. In the context of combinatorial auctions the truthful direct-revelation mechanism that maximizes social welfare is the VCG mechanism. For many valuation spaces computing the allocation and payments of the VCG mechanism, however, is a computationally hard problem. We thus study the performance of the VCG mechanism when bidders are forced to choose bids from a subspace of the valuation space for which the VCG outcome can be computed efficiently. We prove improved upper bounds on the welfare loss for restrictions to additive bids and upper and lower bounds for restrictions to non-additive bids. These bounds show that the welfare loss increases in expressiveness. All our bounds apply to equilibrium concepts that can be computed in polynomial time as well as to learning outcomes."}],"volume":8289,"date_created":"2022-08-11T11:05:14Z","year":"2013","_id":"11791"},{"abstract":[{"text":"We study the problem of maximizing a monotone submodular function with viability constraints. This problem originates from computational biology, where we are given a phylogenetic tree over a set of species and a directed graph, the so-called food web, encoding viability constraints between these species. These food webs usually have constant depth. The goal is to select a subset of k species that satisfies the viability constraints and has maximal phylogenetic diversity. As this problem is known to be NP-hard, we investigate approximation algorithm. We present the first constant factor approximation algorithm if the depth is constant. Its approximation ratio is (1−1𝑒√). This algorithm not only applies to phylogenetic trees with viability constraints but for arbitrary monotone submodular set functions with viability constraints. Second, we show that there is no (1 − 1/e + ε)-approximation algorithm for our problem setting (even for additive functions) and that there is no approximation algorithm for a slight extension of this setting.","lang":"eng"}],"date_updated":"2023-02-21T16:28:24Z","type":"conference","month":"09","oa_version":"Preprint","page":"409 - 420","date_created":"2022-08-11T11:18:19Z","volume":8125,"year":"2013","_id":"11792","publication_status":"published","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1611.05753","open_access":"1"}],"date_published":"2013-09-01T00:00:00Z","external_id":{"arxiv":["1611.05753"]},"status":"public","alternative_title":["LNCS"],"citation":{"ieee":"W. Dvořák, M. H. Henzinger, and D. P. Williamson, “Maximizing a submodular function with viability constraints,” in <i>21st Annual European Symposium on Algorithms</i>, Sophia Antipolis, France, 2013, vol. 8125, pp. 409–420.","chicago":"Dvořák, Wolfgang, Monika H Henzinger, and David P. Williamson. “Maximizing a Submodular Function with Viability Constraints.” In <i>21st Annual European Symposium on Algorithms</i>, 8125:409–20. Springer Nature, 2013. <a href=\"https://doi.org/10.1007/978-3-642-40450-4_35\">https://doi.org/10.1007/978-3-642-40450-4_35</a>.","short":"W. Dvořák, M.H. Henzinger, D.P. Williamson, in:, 21st Annual European Symposium on Algorithms, Springer Nature, 2013, pp. 409–420.","ama":"Dvořák W, Henzinger MH, Williamson DP. Maximizing a submodular function with viability constraints. In: <i>21st Annual European Symposium on Algorithms</i>. Vol 8125. Springer Nature; 2013:409-420. doi:<a href=\"https://doi.org/10.1007/978-3-642-40450-4_35\">10.1007/978-3-642-40450-4_35</a>","mla":"Dvořák, Wolfgang, et al. “Maximizing a Submodular Function with Viability Constraints.” <i>21st Annual European Symposium on Algorithms</i>, vol. 8125, Springer Nature, 2013, pp. 409–20, doi:<a href=\"https://doi.org/10.1007/978-3-642-40450-4_35\">10.1007/978-3-642-40450-4_35</a>.","ista":"Dvořák W, Henzinger MH, Williamson DP. 2013. Maximizing a submodular function with viability constraints. 21st Annual European Symposium on Algorithms. ESA: European Symposium on Algorithms, LNCS, vol. 8125, 409–420.","apa":"Dvořák, W., Henzinger, M. H., &#38; Williamson, D. P. (2013). Maximizing a submodular function with viability constraints. In <i>21st Annual European Symposium on Algorithms</i> (Vol. 8125, pp. 409–420). Sophia Antipolis, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-40450-4_35\">https://doi.org/10.1007/978-3-642-40450-4_35</a>"},"related_material":{"record":[{"relation":"later_version","status":"public","id":"11792"}]},"extern":"1","intvolume":"      8125","day":"01","author":[{"first_name":"Wolfgang","last_name":"Dvořák","full_name":"Dvořák, Wolfgang"},{"first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530"},{"last_name":"Williamson","first_name":"David P.","full_name":"Williamson, David P."}],"title":"Maximizing a submodular function with viability constraints","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","scopus_import":"1","article_processing_charge":"No","publication":"21st Annual European Symposium on Algorithms","publication_identifier":{"isbn":["9783642404498"],"issn":["1611-3349"]},"quality_controlled":"1","doi":"10.1007/978-3-642-40450-4_35","language":[{"iso":"eng"}],"conference":{"end_date":"2013-09-04","location":"Sophia Antipolis, France","name":"ESA: European Symposium on Algorithms","start_date":"2013-09-02"}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","publication":"40th International Colloquium on Automata, Languages, and Programming","scopus_import":"1","article_processing_charge":"No","author":[{"last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"first_name":"Sebastian","last_name":"Krinninger","full_name":"Krinninger, Sebastian"},{"last_name":"Nanongkai","first_name":"Danupon","full_name":"Nanongkai, Danupon"}],"day":"01","title":"Sublinear-time maintenance of breadth-first spanning tree in partially dynamic networks","arxiv":1,"conference":{"end_date":"2013-07-12","start_date":"2013-07-08","location":"Riga, Latvia","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783642392115"],"issn":["1611-3349"]},"doi":"10.1007/978-3-642-39212-2_53","quality_controlled":"1","year":"2013","_id":"11793","page":"607–619","abstract":[{"lang":"eng","text":"We study the problem of maintaining a breadth-first spanning tree (BFS tree) in partially dynamic distributed networks modeling a sequence of either failures or additions of communication links (but not both). We show (1 + ε)-approximation algorithms whose amortized time (over some number of link changes) is sublinear in D, the maximum diameter of the network. This breaks the Θ(D) time bound of recomputing “from scratch”.\r\n\r\nOur technique also leads to a (1 + ε)-approximate incremental algorithm for single-source shortest paths (SSSP) in the sequential (usual RAM) model. Prior to our work, the state of the art was the classic exact algorithm of [9] that is optimal under some assumptions [27]. Our result is the first to show that, in the incremental setting, this bound can be beaten in certain cases if a small approximation is allowed."}],"date_updated":"2023-02-21T16:28:26Z","type":"conference","month":"07","oa_version":"Preprint","volume":7966,"date_created":"2022-08-11T11:25:13Z","alternative_title":["LNCS"],"status":"public","external_id":{"arxiv":["1512.08147"]},"related_material":{"record":[{"id":"11793","status":"public","relation":"later_version"}]},"intvolume":"      7966","extern":"1","citation":{"ama":"Henzinger MH, Krinninger S, Nanongkai D. Sublinear-time maintenance of breadth-first spanning tree in partially dynamic networks. In: <i>40th International Colloquium on Automata, Languages, and Programming</i>. Vol 7966. Springer Nature; 2013:607–619. doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_53\">10.1007/978-3-642-39212-2_53</a>","mla":"Henzinger, Monika H., et al. “Sublinear-Time Maintenance of Breadth-First Spanning Tree in Partially Dynamic Networks.” <i>40th International Colloquium on Automata, Languages, and Programming</i>, vol. 7966, Springer Nature, 2013, pp. 607–619, doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_53\">10.1007/978-3-642-39212-2_53</a>.","ista":"Henzinger MH, Krinninger S, Nanongkai D. 2013. Sublinear-time maintenance of breadth-first spanning tree in partially dynamic networks. 40th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LNCS, vol. 7966, 607–619.","apa":"Henzinger, M. H., Krinninger, S., &#38; Nanongkai, D. (2013). Sublinear-time maintenance of breadth-first spanning tree in partially dynamic networks. In <i>40th International Colloquium on Automata, Languages, and Programming</i> (Vol. 7966, pp. 607–619). Riga, Latvia: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_53\">https://doi.org/10.1007/978-3-642-39212-2_53</a>","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Sublinear-time maintenance of breadth-first spanning tree in partially dynamic networks,” in <i>40th International Colloquium on Automata, Languages, and Programming</i>, Riga, Latvia, 2013, vol. 7966, pp. 607–619.","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Sublinear-Time Maintenance of Breadth-First Spanning Tree in Partially Dynamic Networks.” In <i>40th International Colloquium on Automata, Languages, and Programming</i>, 7966:607–619. Springer Nature, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_53\">https://doi.org/10.1007/978-3-642-39212-2_53</a>.","short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 40th International Colloquium on Automata, Languages, and Programming, Springer Nature, 2013, pp. 607–619."},"oa":1,"publication_status":"published","date_published":"2013-07-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1512.08147"}]},{"author":[{"full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","last_name":"Goodrich","first_name":"Carl Peter"},{"full_name":"Ellenbroek, Wouter G.","first_name":"Wouter G.","last_name":"Ellenbroek"},{"full_name":"Liu, Andrea J.","last_name":"Liu","first_name":"Andrea J."}],"day":"08","abstract":[{"lang":"eng","text":"In 2005, Wyart et al. [Europhys. Lett., 2005, 72, 486] showed that the low frequency vibrational properties of jammed amorphous sphere packings can be understood in terms of a length scale, called l*, that diverges as the system becomes marginally unstable. Despite the tremendous success of this theory, it has been difficult to connect the counting argument that defines l* to other length scales that diverge near the jamming transition. We present an alternate derivation of l* based on the onset of rigidity. This phenomenological approach reveals the physical mechanism underlying the length scale and is relevant to a range of systems for which the original argument breaks down. It also allows us to present the first direct numerical measurement of l*."}],"date_updated":"2021-01-12T08:15:27Z","oa_version":"None","type":"journal_article","month":"10","volume":9,"title":"Stability of jammed packings I: The rigidity length scale","article_number":"10993","date_created":"2020-04-30T11:43:42Z","publisher":"Royal Society of Chemistry","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","publication":"Soft Matter","_id":"7774","article_processing_charge":"No","article_type":"original","publication_status":"published","publication_identifier":{"issn":["1744-683X","1744-6848"]},"doi":"10.1039/c3sm51095f","date_published":"2013-10-08T00:00:00Z","quality_controlled":"1","status":"public","intvolume":"         9","extern":"1","language":[{"iso":"eng"}],"citation":{"short":"C.P. Goodrich, W.G. Ellenbroek, A.J. Liu, Soft Matter 9 (2013).","ieee":"C. P. Goodrich, W. G. Ellenbroek, and A. J. Liu, “Stability of jammed packings I: The rigidity length scale,” <i>Soft Matter</i>, vol. 9, no. 46. Royal Society of Chemistry, 2013.","chicago":"Goodrich, Carl Peter, Wouter G. Ellenbroek, and Andrea J. Liu. “Stability of Jammed Packings I: The Rigidity Length Scale.” <i>Soft Matter</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3sm51095f\">https://doi.org/10.1039/c3sm51095f</a>.","ista":"Goodrich CP, Ellenbroek WG, Liu AJ. 2013. Stability of jammed packings I: The rigidity length scale. Soft Matter. 9(46), 10993.","mla":"Goodrich, Carl Peter, et al. “Stability of Jammed Packings I: The Rigidity Length Scale.” <i>Soft Matter</i>, vol. 9, no. 46, 10993, Royal Society of Chemistry, 2013, doi:<a href=\"https://doi.org/10.1039/c3sm51095f\">10.1039/c3sm51095f</a>.","apa":"Goodrich, C. P., Ellenbroek, W. G., &#38; Liu, A. J. (2013). Stability of jammed packings I: The rigidity length scale. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3sm51095f\">https://doi.org/10.1039/c3sm51095f</a>","ama":"Goodrich CP, Ellenbroek WG, Liu AJ. Stability of jammed packings I: The rigidity length scale. <i>Soft Matter</i>. 2013;9(46). doi:<a href=\"https://doi.org/10.1039/c3sm51095f\">10.1039/c3sm51095f</a>"},"issue":"46"},{"publication_status":"published","publication_identifier":{"issn":["1744-683X","1744-6848"]},"date_published":"2013-10-08T00:00:00Z","doi":"10.1039/c3sm51096d","quality_controlled":"1","status":"public","extern":"1","intvolume":"         9","language":[{"iso":"eng"}],"citation":{"apa":"Schoenholz, S. S., Goodrich, C. P., Kogan, O., Liu, A. J., &#38; Nagel, S. R. (2013). Stability of jammed packings II: The transverse length scale. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3sm51096d\">https://doi.org/10.1039/c3sm51096d</a>","ista":"Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. 2013. Stability of jammed packings II: The transverse length scale. Soft Matter. 9(46), 11000.","mla":"Schoenholz, Samuel S., et al. “Stability of Jammed Packings II: The Transverse Length Scale.” <i>Soft Matter</i>, vol. 9, no. 46, 11000, Royal Society of Chemistry, 2013, doi:<a href=\"https://doi.org/10.1039/c3sm51096d\">10.1039/c3sm51096d</a>.","ama":"Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. Stability of jammed packings II: The transverse length scale. <i>Soft Matter</i>. 2013;9(46). doi:<a href=\"https://doi.org/10.1039/c3sm51096d\">10.1039/c3sm51096d</a>","short":"S.S. Schoenholz, C.P. Goodrich, O. Kogan, A.J. Liu, S.R. Nagel, Soft Matter 9 (2013).","chicago":"Schoenholz, Samuel S., Carl Peter Goodrich, Oleg Kogan, Andrea J. Liu, and Sidney R. Nagel. “Stability of Jammed Packings II: The Transverse Length Scale.” <i>Soft Matter</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3sm51096d\">https://doi.org/10.1039/c3sm51096d</a>.","ieee":"S. S. Schoenholz, C. P. Goodrich, O. Kogan, A. J. Liu, and S. R. Nagel, “Stability of jammed packings II: The transverse length scale,” <i>Soft Matter</i>, vol. 9, no. 46. Royal Society of Chemistry, 2013."},"issue":"46","author":[{"last_name":"Schoenholz","first_name":"Samuel S.","full_name":"Schoenholz, Samuel S."},{"orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter","last_name":"Goodrich","first_name":"Carl Peter"},{"last_name":"Kogan","first_name":"Oleg","full_name":"Kogan, Oleg"},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"},{"full_name":"Nagel, Sidney R.","last_name":"Nagel","first_name":"Sidney R."}],"date_updated":"2021-01-12T08:15:27Z","day":"08","abstract":[{"lang":"eng","text":"As a function of packing fraction at zero temperature and applied stress, an amorphous packing of spheres exhibits a jamming transition where the system is sensitive to boundary conditions even in the thermodynamic limit. Upon further compression, the system should become insensitive to boundary conditions provided it is sufficiently large. Here we explore the linear response to a large class of boundary perturbations in 2 and 3 dimensions. We consider each finite packing with periodic-boundary conditions as the basis of an infinite square or cubic lattice and study properties of vibrational modes at arbitrary wave vector. We find that the stability of such modes can be understood in terms of a competition between plane waves and the anomalous vibrational modes associated with the jamming transition; infinitesimal boundary perturbations become irrelevant for systems that are larger than a length scale that characterizes the transverse excitations. This previously identified length diverges at the jamming transition."}],"month":"10","type":"journal_article","oa_version":"None","volume":9,"title":"Stability of jammed packings II: The transverse length scale","article_number":"11000","date_created":"2020-04-30T11:43:58Z","publisher":"Royal Society of Chemistry","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","publication":"Soft Matter","_id":"7775","article_processing_charge":"No","article_type":"original"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","year":"2013","_id":"7785","publication":"Neuron","article_type":"original","article_processing_charge":"No","author":[{"full_name":"Joo, William J.","first_name":"William J.","last_name":"Joo"},{"orcid":"0000-0001-9242-5601","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","full_name":"Sweeney, Lora Beatrice Jaeger","last_name":"Sweeney","first_name":"Lora Beatrice Jaeger"},{"last_name":"Liang","first_name":"Liang","full_name":"Liang, Liang"},{"full_name":"Luo, Liqun","first_name":"Liqun","last_name":"Luo"}],"page":"673-686","month":"05","oa_version":"None","type":"journal_article","date_updated":"2024-01-31T10:15:25Z","day":"22","abstract":[{"text":"Neural circuit assembly requires selection of specific cell fates, axonal trajectories, and synaptic targets. By analyzing the function of a secreted semaphorin, Sema-2b, in Drosophila olfactory receptor neuron (ORN) development, we identified multiple molecular and cellular mechanisms that link these events. Notch signaling limits Sema-2b expression to ventromedial ORN classes, within which Sema-2b cell-autonomously sensitizes ORN axons to external semaphorins. Central-brain-derived Sema-2a and Sema-2b attract Sema-2b-expressing axons to the ventromedial trajectory. In addition, Sema-2b/PlexB-mediated axon-axon interactions consolidate this trajectory choice and promote ventromedial axon-bundle formation. Selecting the correct developmental trajectory is ultimately essential for proper target choice. These findings demonstrate that Sema-2b couples ORN axon guidance to postsynaptic target neuron dendrite patterning well before the final target selection phase, and exemplify how a single guidance molecule can drive consecutive stages of neural circuit assembly with the help of sophisticated spatial and temporal regulation.","lang":"eng"}],"title":"Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting","volume":78,"date_created":"2020-04-30T13:19:59Z","status":"public","extern":"1","intvolume":"        78","issue":"4","citation":{"short":"W.J. Joo, L.B. Sweeney, L. Liang, L. Luo, Neuron 78 (2013) 673–686.","ieee":"W. J. Joo, L. B. Sweeney, L. Liang, and L. Luo, “Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting,” <i>Neuron</i>, vol. 78, no. 4. Elsevier, pp. 673–686, 2013.","chicago":"Joo, William J., Lora B. Sweeney, Liang Liang, and Liqun Luo. “Linking Cell Fate, Trajectory Choice, and Target Selection: Genetic Analysis of Sema-2b in Olfactory Axon Targeting.” <i>Neuron</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.neuron.2013.03.022\">https://doi.org/10.1016/j.neuron.2013.03.022</a>.","mla":"Joo, William J., et al. “Linking Cell Fate, Trajectory Choice, and Target Selection: Genetic Analysis of Sema-2b in Olfactory Axon Targeting.” <i>Neuron</i>, vol. 78, no. 4, Elsevier, 2013, pp. 673–86, doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.03.022\">10.1016/j.neuron.2013.03.022</a>.","ista":"Joo WJ, Sweeney LB, Liang L, Luo L. 2013. Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting. Neuron. 78(4), 673–686.","apa":"Joo, W. J., Sweeney, L. B., Liang, L., &#38; Luo, L. (2013). Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2013.03.022\">https://doi.org/10.1016/j.neuron.2013.03.022</a>","ama":"Joo WJ, Sweeney LB, Liang L, Luo L. Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting. <i>Neuron</i>. 2013;78(4):673-686. doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.03.022\">10.1016/j.neuron.2013.03.022</a>"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0896-6273"]},"publication_status":"published","date_published":"2013-05-22T00:00:00Z","doi":"10.1016/j.neuron.2013.03.022","quality_controlled":"1"},{"date_published":"2013-07-18T00:00:00Z","ddc":["570"],"publication_status":"published","oa":1,"has_accepted_license":"1","extern":"1","intvolume":"         7","citation":{"ieee":"T. P. Vogels <i>et al.</i>, “Inhibitory synaptic plasticity: Spike timing-dependence and putative network function,” <i>Frontiers in Neural Circuits</i>, vol. 7. Frontiers Media, 2013.","chicago":"Vogels, Tim P, R. C. Froemke, N. Doyon, M. Gilson, J. S. Haas, R. Liu, A. Maffei, et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence and Putative Network Function.” <i>Frontiers in Neural Circuits</i>. Frontiers Media, 2013. <a href=\"https://doi.org/10.3389/fncir.2013.00119\">https://doi.org/10.3389/fncir.2013.00119</a>.","short":"T.P. Vogels, R.C. Froemke, N. Doyon, M. Gilson, J.S. Haas, R. Liu, A. Maffei, P. Miller, C.J. Wierenga, M.A. Woodin, F. Zenke, H. Sprekeler, Frontiers in Neural Circuits 7 (2013).","ama":"Vogels TP, Froemke RC, Doyon N, et al. Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. <i>Frontiers in Neural Circuits</i>. 2013;7. doi:<a href=\"https://doi.org/10.3389/fncir.2013.00119\">10.3389/fncir.2013.00119</a>","ista":"Vogels TP, Froemke RC, Doyon N, Gilson M, Haas JS, Liu R, Maffei A, Miller P, Wierenga CJ, Woodin MA, Zenke F, Sprekeler H. 2013. Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. Frontiers in Neural Circuits. 7, 119.","mla":"Vogels, Tim P., et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence and Putative Network Function.” <i>Frontiers in Neural Circuits</i>, vol. 7, 119, Frontiers Media, 2013, doi:<a href=\"https://doi.org/10.3389/fncir.2013.00119\">10.3389/fncir.2013.00119</a>.","apa":"Vogels, T. P., Froemke, R. C., Doyon, N., Gilson, M., Haas, J. S., Liu, R., … Sprekeler, H. (2013). Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. <i>Frontiers in Neural Circuits</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fncir.2013.00119\">https://doi.org/10.3389/fncir.2013.00119</a>"},"external_id":{"pmid":["23882186"]},"status":"public","volume":7,"date_created":"2020-06-25T13:23:50Z","file_date_updated":"2020-07-16T11:23:40Z","month":"07","type":"journal_article","oa_version":"Published Version","date_updated":"2021-01-12T08:16:38Z","abstract":[{"lang":"eng","text":"While the plasticity of excitatory synaptic connections in the brain has been widely studied, the plasticity of inhibitory connections is much less understood. Here, we present recent experimental and theoretical findings concerning the rules of spike timing-dependent inhibitory plasticity and their putative network function. This is a summary of a workshop at the COSYNE conference 2012."}],"_id":"8030","year":"2013","doi":"10.3389/fncir.2013.00119","quality_controlled":"1","publication_identifier":{"eissn":["1662-5110"]},"language":[{"iso":"eng"}],"article_number":"119","title":"Inhibitory synaptic plasticity: Spike timing-dependence and putative network function","author":[{"full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","first_name":"Tim P","last_name":"Vogels"},{"first_name":"R. C.","last_name":"Froemke","full_name":"Froemke, R. C."},{"first_name":"N.","last_name":"Doyon","full_name":"Doyon, N."},{"full_name":"Gilson, M.","first_name":"M.","last_name":"Gilson"},{"last_name":"Haas","first_name":"J. S.","full_name":"Haas, J. S."},{"last_name":"Liu","first_name":"R.","full_name":"Liu, R."},{"last_name":"Maffei","first_name":"A.","full_name":"Maffei, A."},{"last_name":"Miller","first_name":"P.","full_name":"Miller, P."},{"first_name":"C. J.","last_name":"Wierenga","full_name":"Wierenga, C. J."},{"first_name":"M. A.","last_name":"Woodin","full_name":"Woodin, M. A."},{"full_name":"Zenke, F.","last_name":"Zenke","first_name":"F."},{"full_name":"Sprekeler, H.","last_name":"Sprekeler","first_name":"H."}],"license":"https://creativecommons.org/licenses/by/3.0/","file":[{"checksum":"9c321cb12977d84048712eefa7f0c497","date_updated":"2020-07-16T11:23:40Z","file_id":"8123","access_level":"open_access","date_created":"2020-07-16T11:23:40Z","success":1,"file_name":"2013_FrontNeurCirc_Vogels.pdf","creator":"cziletti","content_type":"application/pdf","relation":"main_file","file_size":1530469}],"day":"18","publication":"Frontiers in Neural Circuits","article_type":"original","tmp":{"short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","image":"/images/cc_by.png"},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Frontiers Media","pmid":1},{"publication_status":"published","quality_controlled":0,"date_published":"2013-12-01T00:00:00Z","doi":"10.1016/j.jsb.2013.10.015","status":"public","citation":{"apa":"Schur, F. K., Hagen, W., De Marco, A., &#38; Briggs, J. (2013). Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging. <i>Journal of Structural Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jsb.2013.10.015\">https://doi.org/10.1016/j.jsb.2013.10.015</a>","mla":"Schur, Florian KM, et al. “Determination of Protein Structure at 8.5Å Resolution Using Cryo-Electron Tomography and Sub-Tomogram Averaging.” <i>Journal of Structural Biology</i>, vol. 184, no. 3, Academic Press, 2013, pp. 394–400, doi:<a href=\"https://doi.org/10.1016/j.jsb.2013.10.015\">10.1016/j.jsb.2013.10.015</a>.","ista":"Schur FK, Hagen W, De Marco A, Briggs J. 2013. Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging. Journal of Structural Biology. 184(3), 394–400.","ama":"Schur FK, Hagen W, De Marco A, Briggs J. Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging. <i>Journal of Structural Biology</i>. 2013;184(3):394-400. doi:<a href=\"https://doi.org/10.1016/j.jsb.2013.10.015\">10.1016/j.jsb.2013.10.015</a>","short":"F.K. Schur, W. Hagen, A. De Marco, J. Briggs, Journal of Structural Biology 184 (2013) 394–400.","chicago":"Schur, Florian KM, Wim Hagen, Alex De Marco, and John Briggs. “Determination of Protein Structure at 8.5Å Resolution Using Cryo-Electron Tomography and Sub-Tomogram Averaging.” <i>Journal of Structural Biology</i>. Academic Press, 2013. <a href=\"https://doi.org/10.1016/j.jsb.2013.10.015\">https://doi.org/10.1016/j.jsb.2013.10.015</a>.","ieee":"F. K. Schur, W. Hagen, A. De Marco, and J. Briggs, “Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging,” <i>Journal of Structural Biology</i>, vol. 184, no. 3. Academic Press, pp. 394–400, 2013."},"issue":"3","extern":1,"intvolume":"       184","abstract":[{"lang":"eng","text":"Cryo-electron tomography combined with image processing by sub-tomogram averaging is unique in its power to resolve the structures of proteins and macromolecular complexes in situ. Limitations of the method, including the low signal to noise ratio within individual images from cryo-tomographic datasets and difficulties in determining the defocus at which the data was collected, mean that to date the very best structures obtained by sub-tomogram averaging are limited to a resolution of approximately 15. Å. Here, by optimizing data collection and defocus determination steps, we have determined the structure of assembled Mason-Pfizer monkey virus Gag protein using sub-tomogram averaging to a resolution of 8.5. Å. At this resolution alpha-helices can be directly and clearly visualized. These data demonstrate for the first time that high-resolution structural information can be obtained from cryo-electron tomograms using sub-tomogram averaging. Sub-tomogram averaging has the potential to allow detailed studies of unsolved and biologically relevant structures under biologically relevant conditions."}],"date_updated":"2021-01-12T08:16:54Z","day":"01","type":"journal_article","month":"12","author":[{"last_name":"Schur","first_name":"Florian","full_name":"Florian Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"},{"first_name":"Wim","last_name":"Hagen","full_name":"Hagen, Wim J"},{"last_name":"De Marco","first_name":"Alex","full_name":"De Marco, Alex"},{"full_name":"Briggs, John A","last_name":"Briggs","first_name":"John"}],"page":"394 - 400","date_created":"2018-12-11T11:48:37Z","publist_id":"6839","volume":184,"title":"Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging","year":"2013","publisher":"Academic Press","acknowledgement":"The M-PMV ΔPro CANC tubes imaged in this study were a kind gift from Pavel Ulbrich and Tomas Ruml, Institute of Chemical Technology, Prague. The cryo-EM grids were prepared by Tanmay Bharat. This study was technically supported by EMBL’s IT services unit and by Frank Thommen. We thank Martin Schorb and Svetlana Dodonova for discussions and advice; Khanh Huy Bui for advice and scripts to streamline tomogram reconstruction; and Giulia Zanetti, Tanmay Bharat, and Martin Beck for comments on the manuscript. This study was supported by Deutsche Forschungsgemeinschaft grant BR 3635/2-1 to JAGB.","publication":"Journal of Structural Biology","_id":"810"},{"publication":"Journal of Cell Science","_id":"811","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)"},"publisher":"Company of Biologists","acknowledgement":"This work was supported in part by the Deutsche Forschungsgemeinschaft [grants within programs SFB621 to K.R., and FOR629 and SFB629 to T.E.B.S.]. Deposited in PMC for immediate release.\nWe thank Brigitte Denker and Gerd Landsberg for excellent technical assistance. We are grateful to Robert Geffers (HZI Braunschweig, Germany) for microarray analyses and to Mirko Himmel (UKE Hamburg, Germany) for valuable advice on FRAP analysis.","year":"2013","volume":126,"title":"Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation","date_created":"2018-12-11T11:48:38Z","publist_id":"6840","author":[{"last_name":"Steffen","first_name":"Anika","full_name":"Steffen, Anika"},{"last_name":"Ladwein","first_name":"Markus","full_name":"Ladwein, Markus"},{"full_name":"Georgi Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","first_name":"Georgi A","last_name":"Dimchev"},{"first_name":"Anke","last_name":"Hein","full_name":"Hein, Anke"},{"first_name":"Lisa","last_name":"Schwenkmezger","full_name":"Schwenkmezger, Lisa"},{"last_name":"Arens","first_name":"Stefan","full_name":"Arens, Stefan"},{"first_name":"Kathrin","last_name":"Ladwein","full_name":"Ladwein, Kathrin I"},{"full_name":"Holleboom, J. Margit","last_name":"Holleboom","first_name":"J."},{"first_name":"Florian","last_name":"Schur","full_name":"Florian Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"},{"last_name":"Small","first_name":"John","full_name":"Small, John V"},{"first_name":"Janett","last_name":"Schwarz","full_name":"Schwarz, Janett"},{"full_name":"Gerhard, Ralf","first_name":"Ralf","last_name":"Gerhard"},{"last_name":"Faix","first_name":"Jan","full_name":"Faix, Jan"},{"first_name":"Theresia","last_name":"Stradal","full_name":"Stradal, Theresia E"},{"full_name":"Brakebusch, Cord H","first_name":"Cord","last_name":"Brakebusch"},{"full_name":"Rottner, Klemens","first_name":"Klemens","last_name":"Rottner"}],"page":"4572 - 4588","date_updated":"2021-01-12T08:16:57Z","abstract":[{"text":"Cell migration is commonly accompanied by protrusion of membrane ruffles and lamellipodia. In two-dimensional migration, protrusion of these thin sheets of cytoplasm is considered relevant to both exploration of new space and initiation of nascent adhesion to the substratum. Lamellipodium formation can be potently stimulated by Rho GTPases of the Rac subfamily, but alsoby RhoG or Cdc42. Here we describe viable fibroblast cell lines geneticallydeficient for Rac1 that lack detectable levels of Rac2 and Rac3. Rac-deficient cells were devoid of apparent lamellipodia, but these structures were restored by expression of either Rac subfamily member, but not by Cdc42 or RhoG. Cells deficient in Rac showed strong reduction in wound closure and random cell migration and a notable loss of sensitivity to a chemotactic gradient. Despite these defects, Rac-deficient cells were able to spread, formed filopodia and established focal adhesions. Spreading in these cells was achieved by the extension of filopodia followed by the advancement of cytoplasmic veils between them. The number and size of focal adhesions as well as their intensity were largely unaffected by genetic removal of Rac1. However, Rac deficiency increased the mobility of different components in focal adhesions, potentially explaining how Rac - although not essential - can contribute to focal adhesion assembly. Together, our data demonstrate that Rac signaling is essential for lamellipodium protrusion and for efficient cell migration, but not for spreading or filopodium formation. Our findings also suggest that Rac GTPases are crucial to the establishment or maintenance of polarity in chemotactic migration.","lang":"eng"}],"day":"01","month":"01","type":"journal_article","intvolume":"       126","extern":1,"citation":{"ama":"Steffen A, Ladwein M, Dimchev GA, et al. Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. <i>Journal of Cell Science</i>. 2013;126(20):4572-4588. doi:<a href=\"https://doi.org/10.1242/jcs.118232\">10.1242/jcs.118232</a>","apa":"Steffen, A., Ladwein, M., Dimchev, G. A., Hein, A., Schwenkmezger, L., Arens, S., … Rottner, K. (2013). Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.118232\">https://doi.org/10.1242/jcs.118232</a>","ista":"Steffen A, Ladwein M, Dimchev GA, Hein A, Schwenkmezger L, Arens S, Ladwein K, Holleboom J, Schur FK, Small J, Schwarz J, Gerhard R, Faix J, Stradal T, Brakebusch C, Rottner K. 2013. Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. Journal of Cell Science. 126(20), 4572–4588.","mla":"Steffen, Anika, et al. “Rac Function Is Crucial for Cell Migration but Is Not Required for Spreading and Focal Adhesion Formation.” <i>Journal of Cell Science</i>, vol. 126, no. 20, Company of Biologists, 2013, pp. 4572–88, doi:<a href=\"https://doi.org/10.1242/jcs.118232\">10.1242/jcs.118232</a>.","chicago":"Steffen, Anika, Markus Ladwein, Georgi A Dimchev, Anke Hein, Lisa Schwenkmezger, Stefan Arens, Kathrin Ladwein, et al. “Rac Function Is Crucial for Cell Migration but Is Not Required for Spreading and Focal Adhesion Formation.” <i>Journal of Cell Science</i>. Company of Biologists, 2013. <a href=\"https://doi.org/10.1242/jcs.118232\">https://doi.org/10.1242/jcs.118232</a>.","ieee":"A. Steffen <i>et al.</i>, “Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation,” <i>Journal of Cell Science</i>, vol. 126, no. 20. Company of Biologists, pp. 4572–4588, 2013.","short":"A. Steffen, M. Ladwein, G.A. Dimchev, A. Hein, L. Schwenkmezger, S. Arens, K. Ladwein, J. Holleboom, F.K. Schur, J. Small, J. Schwarz, R. Gerhard, J. Faix, T. Stradal, C. Brakebusch, K. Rottner, Journal of Cell Science 126 (2013) 4572–4588."},"issue":"20","status":"public","doi":"10.1242/jcs.118232","date_published":"2013-01-01T00:00:00Z","quality_controlled":0,"publication_status":"published"},{"quality_controlled":0,"doi":"10.1091/mbc.E12-12-0857","date_published":"2013-09-15T00:00:00Z","publication_status":"published","citation":{"short":"S. Koestler, A. Steffen, M. Nemethova, M. Winterhoff, N. Luo, J. Holleboom, J. Krupp, S. Jacob, M. Vinzenz, F.K. Schur, K. Schlüter, P. Gunning, C. Winkler, C. Schmeiser, J. Faix, T. Stradal, J. Small, K. Rottner, Molecular Biology of the Cell 24 (2013) 2861–2875.","ieee":"S. Koestler <i>et al.</i>, “Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin,” <i>Molecular Biology of the Cell</i>, vol. 24, no. 18. American Society for Biology, pp. 2861–2875, 2013.","chicago":"Koestler, Stefan, Anika Steffen, Maria Nemethova, Moritz Winterhoff, Ningning Luo, J. Holleboom, Jessica Krupp, et al. “Arp2/3 Complex Is Essential for Actin Network Treadmilling as Well as for Targeting of Capping Protein and Cofilin.” <i>Molecular Biology of the Cell</i>. American Society for Biology, 2013. <a href=\"https://doi.org/10.1091/mbc.E12-12-0857\">https://doi.org/10.1091/mbc.E12-12-0857</a>.","mla":"Koestler, Stefan, et al. “Arp2/3 Complex Is Essential for Actin Network Treadmilling as Well as for Targeting of Capping Protein and Cofilin.” <i>Molecular Biology of the Cell</i>, vol. 24, no. 18, American Society for Biology, 2013, pp. 2861–75, doi:<a href=\"https://doi.org/10.1091/mbc.E12-12-0857\">10.1091/mbc.E12-12-0857</a>.","ista":"Koestler S, Steffen A, Nemethova M, Winterhoff M, Luo N, Holleboom J, Krupp J, Jacob S, Vinzenz M, Schur FK, Schlüter K, Gunning P, Winkler C, Schmeiser C, Faix J, Stradal T, Small J, Rottner K. 2013. Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. Molecular Biology of the Cell. 24(18), 2861–2875.","apa":"Koestler, S., Steffen, A., Nemethova, M., Winterhoff, M., Luo, N., Holleboom, J., … Rottner, K. (2013). Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. <i>Molecular Biology of the Cell</i>. American Society for Biology. <a href=\"https://doi.org/10.1091/mbc.E12-12-0857\">https://doi.org/10.1091/mbc.E12-12-0857</a>","ama":"Koestler S, Steffen A, Nemethova M, et al. Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. <i>Molecular Biology of the Cell</i>. 2013;24(18):2861-2875. doi:<a href=\"https://doi.org/10.1091/mbc.E12-12-0857\">10.1091/mbc.E12-12-0857</a>"},"issue":"18","intvolume":"        24","extern":1,"status":"public","publist_id":"6841","date_created":"2018-12-11T11:48:38Z","volume":24,"title":"Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin","day":"15","abstract":[{"text":"Lamellipodia are sheet-like protrusions formed during migration or phagocytosis and comprise a network of actin filaments. Filament formation in this network is initiated by nucleation/branching through the actin-related protein 2/3 (Arp2/3) complex downstream of its activator, suppressor of cAMP receptor/WASP-family verprolin homologous (Scar/WAVE), but the relative relevance of Arp2/3-mediated branching versus actin filament elongation is unknown. Here we use instantaneous interference with Arp2/3 complex function in live fibroblasts with established lamellipodia. This allows direct examination of both the fate of elongating filaments upon instantaneous suppression of Arp2/3 complex activity and the consequences of this treatment on the dynamics of other lamellipodial regulators. We show that Arp2/3 complex is an essential organizer of treadmilling actin filament arrays but has little effect on the net rate of actin filament turnover at the cell periphery. In addition, Arp2/3 complex serves as key upstream factor for the recruitment of modulators of lamellipodia formation such as capping protein or cofilin. Arp2/3 complex is thus decisive for filament organization and geometry within the network not only by generating branches and novel filament ends, but also by directing capping or severing activities to the lamellipodium. Arp2/3 complex is also crucial to lamellipodia-based migration of keratocytes.","lang":"eng"}],"date_updated":"2021-01-12T08:17:00Z","month":"09","type":"journal_article","author":[{"first_name":"Stefan","last_name":"Koestler","full_name":"Koestler, Stefan A"},{"first_name":"Anika","last_name":"Steffen","full_name":"Steffen, Anika"},{"id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","full_name":"Maria Nemethova","last_name":"Nemethova","first_name":"Maria"},{"last_name":"Winterhoff","first_name":"Moritz","full_name":"Winterhoff, Moritz"},{"full_name":"Luo, Ningning","first_name":"Ningning","last_name":"Luo"},{"first_name":"J.","last_name":"Holleboom","full_name":"Holleboom, J. Margit"},{"first_name":"Jessica","last_name":"Krupp","full_name":"Krupp, Jessica"},{"full_name":"Jacob, Sonja","last_name":"Jacob","first_name":"Sonja"},{"first_name":"Marlene","last_name":"Vinzenz","full_name":"Vinzenz, Marlene"},{"last_name":"Schur","first_name":"Florian","full_name":"Florian Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schlüter, Kai","last_name":"Schlüter","first_name":"Kai"},{"full_name":"Gunning, Peter W","last_name":"Gunning","first_name":"Peter"},{"full_name":"Winkler, Christoph","last_name":"Winkler","first_name":"Christoph"},{"full_name":"Schmeiser, Christian","first_name":"Christian","last_name":"Schmeiser"},{"first_name":"Jan","last_name":"Faix","full_name":"Faix, Jan"},{"first_name":"Theresia","last_name":"Stradal","full_name":"Stradal, Theresia E"},{"full_name":"Small, John V","first_name":"John","last_name":"Small"},{"last_name":"Rottner","first_name":"Klemens","full_name":"Rottner, Klemens"}],"page":"2861 - 2875","publication":"Molecular Biology of the Cell","_id":"812","year":"2013","publisher":"American Society for Biology","acknowledgement":"This work was supported in part by Deutsche Forschungsgemeinschaft Grants RO2414/3-1 (to K.R.) and FA330/6-1 (to J.F.), Austrian \nScience Fund Projects FWF 1516-B09 and FWF P21292-B09 (to  J.V.S.),  the Vienna  Science  and  Technology  Fund  (WWTF,  to \nJ.V.S.  and  C.S.),  and  Australian  National  Health  and  Medical \nResearch Council Grant APP1004175 (to P.W.G.). We thank J. Adams, \nR. Chisholm, A. Hall, L. Machesky, H. G. Mannherz, D. Schafer, and \nR.   Wedlich-Söldner   for   expression   constructs   and   B.   Denker, \nP. Hagendorff, and G. Landsberg for technical assistance."},{"author":[{"full_name":"Petricevic, Branka","first_name":"Branka","last_name":"Petricevic"},{"full_name":"Laengle, Johannes","first_name":"Johannes","last_name":"Laengle"},{"full_name":"Singer, Josef","first_name":"Josef","last_name":"Singer"},{"first_name":"Monika","last_name":"Sachet","full_name":"Sachet, Monika"},{"orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87","full_name":"Fazekas, Judit","first_name":"Judit","last_name":"Fazekas"},{"first_name":"Guenther","last_name":"Steger","full_name":"Steger, Guenther"},{"first_name":"Rupert","last_name":"Bartsch","full_name":"Bartsch, Rupert"},{"last_name":"Jensen-Jarolim","first_name":"Erika","full_name":"Jensen-Jarolim, Erika"},{"first_name":"Michael","last_name":"Bergmann","full_name":"Bergmann, Michael"}],"day":"12","file":[{"success":1,"file_name":"2013_JoTM_Petricevic.pdf","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":777311,"date_updated":"2020-08-10T13:45:19Z","file_id":"8247","access_level":"open_access","date_created":"2020-08-10T13:45:19Z"}],"title":"Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients","article_number":"307","publisher":"Springer Nature","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","pmid":1,"publication":"Journal of Translational Medicine","article_processing_charge":"No","tmp":{"short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","image":"/images/cc_by.png"},"publication_identifier":{"issn":["1479-5876"]},"doi":"10.1186/1479-5876-11-307","quality_controlled":"1","language":[{"iso":"eng"}],"abstract":[{"text":"Background: Monoclonal antibodies (mAb), such as trastuzumab are a valuable addition to breast cancer therapy.\r\nData obtained from neoadjuvant settings revealed that antibody-dependent cell-mediated cytotoxicity (ADCC) is a\r\nmajor mechanism of action for the mAb trastuzumab. Conflicting results still call into question whether disease\r\nprogression, prolonged treatment or concomitant chemotherapy influences ADCC and related immunological\r\nphenomena.\r\nMethods: We analyzed the activity of ADCC and antibody-dependent cell-mediated phagocytosis (ADCP) of\r\nperipheral blood mononuclear cells (PBMCs) from human epidermal growth factor receptor 2 (HER2/neu) positive\r\nbreast cancer patients receiving trastuzumab therapy either in an adjuvant (n = 13) or metastatic (n = 15) setting as\r\nwell as from trastuzumab treatment-naive (t-naive) HER2/neu negative patients (n = 15). PBMCs from healthy volunteers\r\n(n = 24) were used as controls. ADCC and ADCP activity was correlated with the expression of antibody binding\r\nFc-gamma receptor (FcγR)I (CD64), FcγRII (CD32) and FcγRIII (CD16) on CD14+ (monocytes) and CD56+ (NK) cells, as well as the expression of CD107a+ (LAMP-1) on CD56+ cells and the total amount of CD4+CD25+FOXP3+ (Treg) cells. In metastatic patients, markers were correlated with progression-free survival (PFS).\r\nResults: ADCC activity was significantly down regulated in metastatic, adjuvant and t-naive patient cohorts as compared to healthy controls. Reduced ADCC activity was inversely correlated with the expression of CD107a on CD56+\r\ncells in adjuvant patients. ADCC and ADCP activity of the patient cohorts were similar, regardless of treatment duration\r\nor additional chemotherapy. PFS in metastatic patients inversely correlated with the number of peripheral Treg cells.\r\nConclusion: The reduction of ADCC in patients as compared to healthy controls calls for adjuvant strategies, such as\r\nimmune-enhancing agents, to improve the activity of trastuzumab. However, efficacy of trastuzumab-specific ADCC\r\nand ADCP appears not to be affected by treatment duration, disease progression or concomitant chemotherapy. This\r\nfinding supports the application of trastuzumab at any stage of the disease.","lang":"eng"}],"date_updated":"2022-08-25T14:52:39Z","oa_version":"None","month":"12","type":"journal_article","volume":11,"file_date_updated":"2020-08-10T13:45:19Z","date_created":"2020-08-10T11:54:34Z","year":"2013","_id":"8245","oa":1,"publication_status":"published","has_accepted_license":"1","date_published":"2013-12-12T00:00:00Z","ddc":["570"],"external_id":{"pmid":["24330813"]},"status":"public","extern":"1","intvolume":"        11","citation":{"mla":"Petricevic, Branka, et al. “Trastuzumab Mediates Antibody-Dependent Cell-Mediated Cytotoxicity and Phagocytosis to the Same Extent in Both Adjuvant and Metastatic HER2/Neu Breast Cancer Patients.” <i>Journal of Translational Medicine</i>, vol. 11, 307, Springer Nature, 2013, doi:<a href=\"https://doi.org/10.1186/1479-5876-11-307\">10.1186/1479-5876-11-307</a>.","ista":"Petricevic B, Laengle J, Singer J, Sachet M, Singer J, Steger G, Bartsch R, Jensen-Jarolim E, Bergmann M. 2013. Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. Journal of Translational Medicine. 11, 307.","apa":"Petricevic, B., Laengle, J., Singer, J., Sachet, M., Singer, J., Steger, G., … Bergmann, M. (2013). Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. <i>Journal of Translational Medicine</i>. Springer Nature. <a href=\"https://doi.org/10.1186/1479-5876-11-307\">https://doi.org/10.1186/1479-5876-11-307</a>","ama":"Petricevic B, Laengle J, Singer J, et al. Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. <i>Journal of Translational Medicine</i>. 2013;11. doi:<a href=\"https://doi.org/10.1186/1479-5876-11-307\">10.1186/1479-5876-11-307</a>","short":"B. Petricevic, J. Laengle, J. Singer, M. Sachet, J. Singer, G. Steger, R. Bartsch, E. Jensen-Jarolim, M. Bergmann, Journal of Translational Medicine 11 (2013).","ieee":"B. Petricevic <i>et al.</i>, “Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients,” <i>Journal of Translational Medicine</i>, vol. 11. Springer Nature, 2013.","chicago":"Petricevic, Branka, Johannes Laengle, Josef Singer, Monika Sachet, Judit Singer, Guenther Steger, Rupert Bartsch, Erika Jensen-Jarolim, and Michael Bergmann. “Trastuzumab Mediates Antibody-Dependent Cell-Mediated Cytotoxicity and Phagocytosis to the Same Extent in Both Adjuvant and Metastatic HER2/Neu Breast Cancer Patients.” <i>Journal of Translational Medicine</i>. Springer Nature, 2013. <a href=\"https://doi.org/10.1186/1479-5876-11-307\">https://doi.org/10.1186/1479-5876-11-307</a>."}},{"status":"public","intvolume":"         4","citation":{"chicago":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fpls.2013.00451\">https://doi.org/10.3389/fpls.2013.00451</a>.","ieee":"J. O’Brien and E. Benková, “Cytokinin cross talking during biotic and abiotic stress responses,” <i>Frontiers in Plant Science</i>, vol. 4. Frontiers Research Foundation, 2013.","short":"J. O’Brien, E. Benková, Frontiers in Plant Science 4 (2013).","ama":"O’Brien J, Benková E. Cytokinin cross talking during biotic and abiotic stress responses. <i>Frontiers in Plant Science</i>. 2013;4. doi:<a href=\"https://doi.org/10.3389/fpls.2013.00451\">10.3389/fpls.2013.00451</a>","apa":"O’Brien, J., &#38; Benková, E. (2013). Cytokinin cross talking during biotic and abiotic stress responses. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2013.00451\">https://doi.org/10.3389/fpls.2013.00451</a>","mla":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” <i>Frontiers in Plant Science</i>, vol. 4, 451, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fpls.2013.00451\">10.3389/fpls.2013.00451</a>.","ista":"O’Brien J, Benková E. 2013. Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. 4, 451."},"publication_status":"published","oa":1,"has_accepted_license":"1","date_published":"2013-11-19T00:00:00Z","ddc":["580"],"year":"2013","_id":"827","abstract":[{"lang":"eng","text":"As sessile organisms, plants have to be able to adapt to a continuously changing environment. Plants that perceive some of these changes as stress signals activate signaling pathways to modulate their development and to enable them to survive. The complex responses to environmental cues are to a large extent mediated by plant hormones that together orchestrate the final plant response. The phytohormone cytokinin is involved in many plant developmental processes. Recently, it has been established that cytokinin plays an important role in stress responses, but does not act alone. Indeed, the hormonal control of plant development and stress adaptation is the outcome of a complex network of multiple synergistic and antagonistic interactions between various hormones. Here, we review the recent findings on the cytokinin function as part of this hormonal network. We focus on the importance of the crosstalk between cytokinin and other hormones, such as abscisic acid, jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development and stress adaptation. Finally, the impact of the current research in the biotechnological industry will be discussed."}],"date_updated":"2021-01-12T08:17:50Z","type":"journal_article","oa_version":"Published Version","month":"11","volume":4,"file_date_updated":"2020-07-14T12:48:11Z","date_created":"2018-12-11T11:48:43Z","project":[{"name":"Hormonal cross-talk in plant organogenesis","call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362"}],"language":[{"iso":"eng"}],"doi":"10.3389/fpls.2013.00451","quality_controlled":"1","publisher":"Frontiers Research Foundation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"EvBe"}],"publication":"Frontiers in Plant Science","ec_funded":1,"scopus_import":1,"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)"},"author":[{"full_name":"O'Brien, José","last_name":"O'Brien","first_name":"José"},{"last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"file":[{"creator":"dernst","file_size":953299,"relation":"main_file","content_type":"application/pdf","file_name":"2013_FrontiersPlant_OBrien.pdf","access_level":"open_access","date_created":"2019-01-31T10:40:38Z","checksum":"fdc25ddd1bf9a99b99f662cdbafeddd4","file_id":"5903","date_updated":"2020-07-14T12:48:11Z"}],"day":"19","title":"Cytokinin cross talking during biotic and abiotic stress responses","article_number":"451","publist_id":"6821"},{"doi":"10.3389/fpls.2013.00537","quality_controlled":"1","language":[{"iso":"eng"}],"project":[{"grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis","call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425"}],"article_number":"537","title":"Systems approaches to study root architecture dynamics","publist_id":"6820","author":[{"last_name":"Cuesta","first_name":"Candela","orcid":"0000-0003-1923-2410","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","full_name":"Cuesta, Candela"},{"orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","full_name":"Wabnik, Krzysztof T","first_name":"Krzysztof T","last_name":"Wabnik"},{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_size":710835,"creator":"dernst","file_name":"2013_FrontiersPlant_Cuesta.pdf","date_created":"2019-01-31T10:36:43Z","access_level":"open_access","date_updated":"2020-07-14T12:48:11Z","file_id":"5902","checksum":"0185b3c4d7df9a94bd3ce5a66d213506"}],"day":"26","publication":"Frontiers in Plant Science","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)"},"scopus_import":1,"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Frontiers Research Foundation","department":[{"_id":"EvBe"}],"ddc":["580"],"date_published":"2013-12-26T00:00:00Z","publication_status":"published","oa":1,"has_accepted_license":"1","intvolume":"         4","citation":{"short":"C. Cuesta, K.T. Wabnik, E. Benková, Frontiers in Plant Science 4 (2013).","ieee":"C. Cuesta, K. T. Wabnik, and E. Benková, “Systems approaches to study root architecture dynamics,” <i>Frontiers in Plant Science</i>, vol. 4. Frontiers Research Foundation, 2013.","chicago":"Cuesta, Candela, Krzysztof T Wabnik, and Eva Benková. “Systems Approaches to Study Root Architecture Dynamics.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fpls.2013.00537\">https://doi.org/10.3389/fpls.2013.00537</a>.","mla":"Cuesta, Candela, et al. “Systems Approaches to Study Root Architecture Dynamics.” <i>Frontiers in Plant Science</i>, vol. 4, 537, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fpls.2013.00537\">10.3389/fpls.2013.00537</a>.","ista":"Cuesta C, Wabnik KT, Benková E. 2013. Systems approaches to study root architecture dynamics. Frontiers in Plant Science. 4, 537.","apa":"Cuesta, C., Wabnik, K. T., &#38; Benková, E. (2013). Systems approaches to study root architecture dynamics. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2013.00537\">https://doi.org/10.3389/fpls.2013.00537</a>","ama":"Cuesta C, Wabnik KT, Benková E. Systems approaches to study root architecture dynamics. <i>Frontiers in Plant Science</i>. 2013;4. doi:<a href=\"https://doi.org/10.3389/fpls.2013.00537\">10.3389/fpls.2013.00537</a>"},"status":"public","volume":4,"date_created":"2018-12-11T11:48:43Z","file_date_updated":"2020-07-14T12:48:11Z","oa_version":"Published Version","type":"journal_article","month":"12","abstract":[{"lang":"eng","text":"The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed."}],"date_updated":"2021-01-12T08:17:52Z","_id":"828","year":"2013"},{"article_type":"original","scopus_import":"1","article_processing_charge":"No","publication":"The Plant journal for cell and molecular biology","pmid":1,"publisher":"Wiley-Blackwell","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6818","title":"An integrative model of the control of ovule primordia formation","day":"19","author":[{"full_name":"Galbiati, Francesca","first_name":"Francesca","last_name":"Galbiati"},{"full_name":"Sinha Roy, Dola","first_name":"Dola","last_name":"Sinha Roy"},{"last_name":"Simonini","first_name":"Sara","full_name":"Simonini, Sara"},{"full_name":"Cucinotta, Mara","last_name":"Cucinotta","first_name":"Mara"},{"last_name":"Ceccato","first_name":"Luca","full_name":"Ceccato, Luca"},{"first_name":"Candela","last_name":"Cuesta","full_name":"Cuesta, Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1923-2410"},{"full_name":"Šimášková, Mária","last_name":"Šimášková","first_name":"Mária"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"},{"last_name":"Kamiuchi","first_name":"Yuri","full_name":"Kamiuchi, Yuri"},{"full_name":"Aida, Mitsuhiro","first_name":"Mitsuhiro","last_name":"Aida"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"first_name":"Rüdiger","last_name":"Simon","full_name":"Simon, Rüdiger"},{"full_name":"Masiero, Simona","last_name":"Masiero","first_name":"Simona"},{"full_name":"Colombo, Lucia","first_name":"Lucia","last_name":"Colombo"}],"issue":"3","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1111/tpj.12309","_id":"830","year":"2013","acknowledgement":"The project and F.G. were supported by the CARIPLO Foundation (project 2009-2990) and COST (European Cooperation in Science and Technology) action HAPRECI (Harnessing Plant Reproduction for Crop Improvement). E.B. and C.C. were supported by the European Research Council through a ‘Starting Independent Research’ grant (ERC-2007-Stg-207362-HCPO). We thank A.P. MacCabe (Consejo Superior de Investigaciones Científicas, Valencia, Spain) for critical reading of the manuscript.","date_created":"2018-12-11T11:48:44Z","volume":76,"type":"journal_article","month":"09","oa_version":"None","date_updated":"2022-03-21T07:17:26Z","abstract":[{"text":"Upon hormonal signaling, ovules develop as lateral organs from the placenta. Ovule numbers ultimately determine the number of seeds that develop, and thereby contribute to the final seed yield in crop plants. We demonstrate here that CUP-SHAPED COTYLEDON 1 (CUC1), CUC2 and AINTEGUMENTA (ANT) have additive effects on ovule primordia formation. We show that expression of the CUC1 and CUC2 genes is required to redundantly regulate expression of PINFORMED1 (PIN1), which in turn is required for ovule primordia formation. Furthermore, our results suggest that the auxin response factor MONOPTEROS (MP/ARF5) may directly bind ANT, CUC1 and CUC2 and promote their transcription. Based on our findings, we propose an integrative model to describe the molecular mechanisms of the early stages of ovule development.","lang":"eng"}],"page":"446 - 455","citation":{"short":"F. Galbiati, D. Sinha Roy, S. Simonini, M. Cucinotta, L. Ceccato, C. Cuesta, M. Šimášková, E. Benková, Y. Kamiuchi, M. Aida, D. Weijers, R. Simon, S. Masiero, L. Colombo, The Plant Journal for Cell and Molecular Biology 76 (2013) 446–455.","chicago":"Galbiati, Francesca, Dola Sinha Roy, Sara Simonini, Mara Cucinotta, Luca Ceccato, Candela Cuesta, Mária Šimášková, et al. “An Integrative Model of the Control of Ovule Primordia Formation.” <i>The Plant Journal for Cell and Molecular Biology</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/tpj.12309\">https://doi.org/10.1111/tpj.12309</a>.","ieee":"F. Galbiati <i>et al.</i>, “An integrative model of the control of ovule primordia formation,” <i>The Plant journal for cell and molecular biology</i>, vol. 76, no. 3. Wiley-Blackwell, pp. 446–455, 2013.","apa":"Galbiati, F., Sinha Roy, D., Simonini, S., Cucinotta, M., Ceccato, L., Cuesta, C., … Colombo, L. (2013). An integrative model of the control of ovule primordia formation. <i>The Plant Journal for Cell and Molecular Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/tpj.12309\">https://doi.org/10.1111/tpj.12309</a>","ista":"Galbiati F, Sinha Roy D, Simonini S, Cucinotta M, Ceccato L, Cuesta C, Šimášková M, Benková E, Kamiuchi Y, Aida M, Weijers D, Simon R, Masiero S, Colombo L. 2013. An integrative model of the control of ovule primordia formation. The Plant journal for cell and molecular biology. 76(3), 446–455.","mla":"Galbiati, Francesca, et al. “An Integrative Model of the Control of Ovule Primordia Formation.” <i>The Plant Journal for Cell and Molecular Biology</i>, vol. 76, no. 3, Wiley-Blackwell, 2013, pp. 446–55, doi:<a href=\"https://doi.org/10.1111/tpj.12309\">10.1111/tpj.12309</a>.","ama":"Galbiati F, Sinha Roy D, Simonini S, et al. An integrative model of the control of ovule primordia formation. <i>The Plant journal for cell and molecular biology</i>. 2013;76(3):446-455. doi:<a href=\"https://doi.org/10.1111/tpj.12309\">10.1111/tpj.12309</a>"},"extern":"1","intvolume":"        76","external_id":{"pmid":["23941199"]},"status":"public","date_published":"2013-09-19T00:00:00Z","publication_status":"published"},{"acknowledgement":"This work was supported by an FEBS Long‐Term Fellowship (BP), an Intra‐European Fellowship for Career Development under the 7th framework of the European Commission (IEF‐2008‐220506 to BP), an EMBO Long‐Term Fellowship (BP), an European Reintegration Grant under the 7th framework of the European Commission (ERG‐2010‐276662 to BP) and the Swedish Research Council (VR 621‐2010‐5720 to IS, GS and KL). AMM, APF, AL, LRB, SP, NM, DMW, MO, JRK and MJB acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC) and Engineering and Physical Sciences Research Council (EPSRC) funding to the Centre for Plant Integrative Biology (CPIB); BBSRC Professorial Research Fellowship funding to DMW and MJB; Belgian Scientific policy (BELSPO contract MARS) to TB and MJB. We thank Bert de Rybel for his help in Multisite Gateway cloning.","publisher":"Nature Publishing Group","year":"2013","_id":"831","publication":"Molecular Systems Biology","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"author":[{"last_name":"Péret","first_name":"Benjamin","full_name":"Péret, Benjamin"},{"first_name":"Alistair","last_name":"Middleton","full_name":"Middleton, Alistair M"},{"last_name":"French","first_name":"Andrew","full_name":"French, Andrew P"},{"last_name":"Larrieu","first_name":"Antoine","full_name":"Larrieu, Antoine"},{"full_name":"Bishopp, Anthony","last_name":"Bishopp","first_name":"Anthony"},{"full_name":"Njo, Maria","last_name":"Njo","first_name":"Maria"},{"last_name":"Wells","first_name":"Darren","full_name":"Wells, Darren M"},{"last_name":"Porco","first_name":"Silvana","full_name":"Porco, Silvana"},{"first_name":"Nathan","last_name":"Mellor","full_name":"Mellor, Nathan"},{"last_name":"Band","first_name":"Leah","full_name":"Band, Leah R"},{"full_name":"Casimiro, Ilda","first_name":"Ilda","last_name":"Casimiro"},{"last_name":"Kleine Vehn","first_name":"Jürgen","full_name":"Kleine-Vehn, Jürgen"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"full_name":"Sairanen, Ilkka","first_name":"Ilkka","last_name":"Sairanen"},{"last_name":"Mallet","first_name":"Romain","full_name":"Mallet, Romain"},{"first_name":"Göran","last_name":"Sandberg","full_name":"Sandberg, Göran"},{"last_name":"Ljung","first_name":"Karin","full_name":"Ljung, Karin"},{"last_name":"Beeckman","first_name":"Tom","full_name":"Beeckman, Tom"},{"first_name":"Eva","last_name":"Benková","full_name":"Eva Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml"},{"first_name":"Eric","last_name":"Kramer","full_name":"Kramer, Eric"},{"full_name":"King, John R","last_name":"King","first_name":"John"},{"full_name":"De Smet, Ive","last_name":"De Smet","first_name":"Ive"},{"full_name":"Pridmore, Tony","last_name":"Pridmore","first_name":"Tony"},{"first_name":"Markus","last_name":"Owen","full_name":"Owen, Markus"},{"full_name":"Bennett, Malcolm J","last_name":"Bennett","first_name":"Malcolm"}],"type":"journal_article","month":"10","day":"22","abstract":[{"text":"In Arabidopsis, lateral roots originate from pericycle cells deep within the primary root. New lateral root primordia (LRP) have to emerge through several overlaying tissues. Here, we report that auxin produced in new LRP is transported towards the outer tissues where it triggers cell separation by inducing both the auxin influx carrier LAX3 and cell-wall enzymes. LAX3 is expressed in just two cell files overlaying new LRP. To understand how this striking pattern of LAX3 expression is regulated, we developed a mathematical model that captures the network regulating its expression and auxin transport within realistic three-dimensional cell and tissue geometries. Our model revealed that, for the LAX3 spatial expression to be robust to natural variations in root tissue geometry, an efflux carrier is required--later identified to be PIN3. To prevent LAX3 from being transiently expressed in multiple cell files, PIN3 and LAX3 must be induced consecutively, which we later demonstrated to be the case. Our study exemplifies how mathematical models can be used to direct experiments to elucidate complex developmental processes.","lang":"eng"}],"date_updated":"2021-01-12T08:18:03Z","title":"Sequential induction of auxin efflux and influx carriers regulates lateral root emergence","volume":9,"date_created":"2018-12-11T11:48:44Z","publist_id":"6817","status":"public","extern":1,"intvolume":"         9","citation":{"ista":"Péret B, Middleton A, French A, Larrieu A, Bishopp A, Njo M, Wells D, Porco S, Mellor N, Band L, Casimiro I, Kleine Vehn J, Vanneste S, Sairanen I, Mallet R, Sandberg G, Ljung K, Beeckman T, Benková E, Friml J, Kramer E, King J, De Smet I, Pridmore T, Owen M, Bennett M. 2013. Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology. 9.","mla":"Péret, Benjamin, et al. “Sequential Induction of Auxin Efflux and Influx Carriers Regulates Lateral Root Emergence.” <i>Molecular Systems Biology</i>, vol. 9, Nature Publishing Group, 2013, doi:<a href=\"https://doi.org/10.1038/msb.2013.43\">10.1038/msb.2013.43</a>.","apa":"Péret, B., Middleton, A., French, A., Larrieu, A., Bishopp, A., Njo, M., … Bennett, M. (2013). Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. <i>Molecular Systems Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/msb.2013.43\">https://doi.org/10.1038/msb.2013.43</a>","ama":"Péret B, Middleton A, French A, et al. Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. <i>Molecular Systems Biology</i>. 2013;9. doi:<a href=\"https://doi.org/10.1038/msb.2013.43\">10.1038/msb.2013.43</a>","short":"B. Péret, A. Middleton, A. French, A. Larrieu, A. Bishopp, M. Njo, D. Wells, S. Porco, N. Mellor, L. Band, I. Casimiro, J. Kleine Vehn, S. Vanneste, I. Sairanen, R. Mallet, G. Sandberg, K. Ljung, T. Beeckman, E. Benková, J. Friml, E. Kramer, J. King, I. De Smet, T. Pridmore, M. Owen, M. Bennett, Molecular Systems Biology 9 (2013).","ieee":"B. Péret <i>et al.</i>, “Sequential induction of auxin efflux and influx carriers regulates lateral root emergence,” <i>Molecular Systems Biology</i>, vol. 9. Nature Publishing Group, 2013.","chicago":"Péret, Benjamin, Alistair Middleton, Andrew French, Antoine Larrieu, Anthony Bishopp, Maria Njo, Darren Wells, et al. “Sequential Induction of Auxin Efflux and Influx Carriers Regulates Lateral Root Emergence.” <i>Molecular Systems Biology</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/msb.2013.43\">https://doi.org/10.1038/msb.2013.43</a>."},"publication_status":"published","date_published":"2013-10-22T00:00:00Z","doi":"10.1038/msb.2013.43","quality_controlled":0},{"volume":57,"title":"Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin","date_created":"2020-09-18T10:09:05Z","author":[{"first_name":"Jens D.","last_name":"Haller","full_name":"Haller, Jens D."},{"first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"page":"263-280","oa_version":"None","month":"10","type":"journal_article","day":"09","date_updated":"2021-01-12T08:19:26Z","abstract":[{"lang":"eng","text":"Solid-state NMR provides insight into protein motion over time scales ranging from picoseconds to seconds. While in solution state the methodology to measure protein dynamics is well established, there is currently no such consensus protocol for measuring dynamics in solids. In this article, we perform a detailed investigation of measurement protocols for fast motions, i.e. motions ranging from picoseconds to a few microseconds, which is the range covered by dipolar coupling and relaxation experiments. We perform a detailed theoretical investigation how dipolar couplings and relaxation data can provide information about amplitudes and time scales of local motion. We show that the measurement of dipolar couplings is crucial for obtaining accurate motional parameters, while systematic errors are found when only relaxation data are used. Based on this realization, we investigate how the REDOR experiment can provide such data in a very accurate manner. We identify that with accurate rf calibration, and explicit consideration of rf field inhomogeneities, one can obtain highly accurate absolute order parameters. We then perform joint model-free analyses of 6 relaxation data sets and dipolar couplings, based on previously existing, as well as new data sets on microcrystalline ubiquitin. We show that nanosecond motion can be detected primarily in loop regions, and compare solid-state data to solution-state relaxation and RDC analyses. The protocols investigated here will serve as a useful basis towards the establishment of a routine protocol for the characterization of ps–μs motions in proteins by solid-state NMR."}],"_id":"8461","publication":"Journal of Biomolecular NMR","article_type":"original","article_processing_charge":"No","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","date_published":"2013-10-09T00:00:00Z","doi":"10.1007/s10858-013-9787-x","quality_controlled":"1","publication_identifier":{"issn":["0925-2738","1573-5001"]},"publication_status":"published","keyword":["Spectroscopy","Biochemistry"],"extern":"1","intvolume":"        57","issue":"3","citation":{"short":"J.D. Haller, P. Schanda, Journal of Biomolecular NMR 57 (2013) 263–280.","ieee":"J. D. Haller and P. Schanda, “Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin,” <i>Journal of Biomolecular NMR</i>, vol. 57, no. 3. Springer Nature, pp. 263–280, 2013.","chicago":"Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental Approaches and Application to Crystalline Ubiquitin.” <i>Journal of Biomolecular NMR</i>. Springer Nature, 2013. <a href=\"https://doi.org/10.1007/s10858-013-9787-x\">https://doi.org/10.1007/s10858-013-9787-x</a>.","mla":"Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental Approaches and Application to Crystalline Ubiquitin.” <i>Journal of Biomolecular NMR</i>, vol. 57, no. 3, Springer Nature, 2013, pp. 263–80, doi:<a href=\"https://doi.org/10.1007/s10858-013-9787-x\">10.1007/s10858-013-9787-x</a>.","ista":"Haller JD, Schanda P. 2013. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR. 57(3), 263–280.","apa":"Haller, J. D., &#38; Schanda, P. (2013). Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. <i>Journal of Biomolecular NMR</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10858-013-9787-x\">https://doi.org/10.1007/s10858-013-9787-x</a>","ama":"Haller JD, Schanda P. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. <i>Journal of Biomolecular NMR</i>. 2013;57(3):263-280. doi:<a href=\"https://doi.org/10.1007/s10858-013-9787-x\">10.1007/s10858-013-9787-x</a>"},"language":[{"iso":"eng"}],"status":"public"},{"doi":"10.1016/j.jmb.2013.04.028","date_published":"2013-08-09T00:00:00Z","quality_controlled":"1","publication_status":"published","publication_identifier":{"issn":["0022-2836"]},"extern":"1","intvolume":"       425","keyword":["Molecular Biology"],"citation":{"apa":"Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Gabel, F., Forge, V., … Brutscher, B. (2013). Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">https://doi.org/10.1016/j.jmb.2013.04.028</a>","ista":"Rennella E, Cutuil T, Schanda P, Ayala I, Gabel F, Forge V, Corazza A, Esposito G, Brutscher B. 2013. Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal of Molecular Biology. 425(15), 2722–2736.","mla":"Rennella, E., et al. “Oligomeric States along the Folding Pathways of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” <i>Journal of Molecular Biology</i>, vol. 425, no. 15, Elsevier, 2013, pp. 2722–36, doi:<a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">10.1016/j.jmb.2013.04.028</a>.","ama":"Rennella E, Cutuil T, Schanda P, et al. Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. <i>Journal of Molecular Biology</i>. 2013;425(15):2722-2736. doi:<a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">10.1016/j.jmb.2013.04.028</a>","short":"E. Rennella, T. Cutuil, P. Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza, G. Esposito, B. Brutscher, Journal of Molecular Biology 425 (2013) 2722–2736.","chicago":"Rennella, E., T. Cutuil, Paul Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza, G. Esposito, and B. Brutscher. “Oligomeric States along the Folding Pathways of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” <i>Journal of Molecular Biology</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">https://doi.org/10.1016/j.jmb.2013.04.028</a>.","ieee":"E. Rennella <i>et al.</i>, “Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure,” <i>Journal of Molecular Biology</i>, vol. 425, no. 15. Elsevier, pp. 2722–2736, 2013."},"language":[{"iso":"eng"}],"issue":"15","status":"public","title":"Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure","volume":425,"date_created":"2020-09-18T10:09:12Z","page":"2722-2736","author":[{"last_name":"Rennella","first_name":"E.","full_name":"Rennella, E."},{"full_name":"Cutuil, T.","first_name":"T.","last_name":"Cutuil"},{"orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda"},{"full_name":"Ayala, I.","first_name":"I.","last_name":"Ayala"},{"first_name":"F.","last_name":"Gabel","full_name":"Gabel, F."},{"last_name":"Forge","first_name":"V.","full_name":"Forge, V."},{"last_name":"Corazza","first_name":"A.","full_name":"Corazza, A."},{"full_name":"Esposito, G.","last_name":"Esposito","first_name":"G."},{"last_name":"Brutscher","first_name":"B.","full_name":"Brutscher, B."}],"day":"09","abstract":[{"text":"The transition of proteins from their soluble functional state to amyloid fibrils and aggregates is associated with the onset of several human diseases. Protein aggregation often requires some structural reshaping and the subsequent formation of intermolecular contacts. Therefore, the study of the conformation of excited protein states and their ability to form oligomers is of primary importance for understanding the molecular basis of amyloid fibril formation. Here, we investigated the oligomerization processes that occur along the folding of the amyloidogenic human protein β2-microglobulin. The combination of real-time two-dimensional NMR data with real-time small-angle X-ray scattering measurements allowed us to derive thermodynamic and kinetic information on protein oligomerization of different conformational states populated along the folding pathways. In particular, we could demonstrate that a long-lived folding intermediate (I-state) has a higher propensity to oligomerize compared to the native state. Our data agree well with a simple five-state kinetic model that involves only monomeric and dimeric species. The dimers have an elongated shape with the dimerization interface located at the apical side of β2-microglobulin close to Pro32, the residue that has a trans conformation in the I-state and a cis conformation in the native (N) state. Our experimental data suggest that partial unfolding in the apical half of the protein close to Pro32 leads to an excited state conformation with enhanced propensity for oligomerization. This excited state becomes more populated in the transient I-state due to the destabilization of the native conformation by the trans-Pro32 configuration.","lang":"eng"}],"date_updated":"2022-08-25T14:56:24Z","type":"journal_article","oa_version":"None","month":"08","publication":"Journal of Molecular Biology","_id":"8462","article_processing_charge":"No","article_type":"original","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","year":"2013"},{"publication_status":"published","doi":"10.1186/1756-0500-6-310","date_published":"2013-01-01T00:00:00Z","status":"public","language":[{"iso":"eng"}],"citation":{"ama":"Derelle R, Kondrashov F, Arkhipov V, et al. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. <i>BMC Research Notes</i>. 2013;6(1). doi:<a href=\"https://doi.org/10.1186/1756-0500-6-310\">10.1186/1756-0500-6-310</a>","apa":"Derelle, R., Kondrashov, F., Arkhipov, V., Corbel, H., Frantz, A., Gasparini, J., … Baudry, E. (2013). Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. <i>BMC Research Notes</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1756-0500-6-310\">https://doi.org/10.1186/1756-0500-6-310</a>","ista":"Derelle R, Kondrashov F, Arkhipov V, Corbel H, Frantz A, Gasparini J, Jacquin L, Jacob G, Thibault S, Baudry E. 2013. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 6(1).","mla":"Derelle, Romain, et al. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” <i>BMC Research Notes</i>, vol. 6, no. 1, BioMed Central, 2013, doi:<a href=\"https://doi.org/10.1186/1756-0500-6-310\">10.1186/1756-0500-6-310</a>.","chicago":"Derelle, Romain, Fyodor Kondrashov, Vladimir Arkhipov, Hélène Corbel, Adrien Frantz, Julien Gasparini, Lisa Jacquin, Gwenaël Jacob, Sophie Thibault, and Emmanuelle Baudry. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” <i>BMC Research Notes</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1756-0500-6-310\">https://doi.org/10.1186/1756-0500-6-310</a>.","ieee":"R. Derelle <i>et al.</i>, “Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R,” <i>BMC Research Notes</i>, vol. 6, no. 1. BioMed Central, 2013.","short":"R. Derelle, F. Kondrashov, V. Arkhipov, H. Corbel, A. Frantz, J. Gasparini, L. Jacquin, G. Jacob, S. Thibault, E. Baudry, BMC Research Notes 6 (2013)."},"issue":"1","extern":"1","intvolume":"         6","date_updated":"2021-01-12T08:21:25Z","day":"01","abstract":[{"lang":"eng","text":"Background: Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in many birds. Feral pigeons (Columba livia) show two major melanin-based colorations: a red coloration due to pheomelanic pigment and a black coloration due to eumelanic pigment. Furthermore, within each color type, feral pigeons display continuous variation in the amount of melanin pigment present in the feathers, with individuals varying from pure white to a full dark melanic color. Coloration is highly heritable and it has been suggested that it is under natural or sexual selection, or both. Our objective was to investigate whether MC1R allelic variants are associated with plumage color in feral pigeons. Findings. We sequenced 888 bp of the coding sequence of MC1R among pigeons varying both in the type, eumelanin or pheomelanin, and the amount of melanin in their feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution but none of them were associated with a plumage type. It remains possible that non-synonymous substitutions that influence coloration are present in the short MC1R fragment that we did not sequence but this seems unlikely because we analyzed the entire functionally important region of the gene. Conclusions: Our results show that color differences among feral pigeons are probably not attributable to amino acid variation at the MC1R locus. Therefore, variation in regulatory regions of MC1R or variation in other genes may be responsible for the color polymorphism of feral pigeons."}],"oa_version":"None","month":"01","type":"journal_article","author":[{"last_name":"Derelle","first_name":"Romain","full_name":"Derelle, Romain"},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor"},{"full_name":"Arkhipov, Vladimir","first_name":"Vladimir","last_name":"Arkhipov"},{"first_name":"Hélène","last_name":"Corbel","full_name":"Corbel, Hélène"},{"full_name":"Frantz, Adrien","last_name":"Frantz","first_name":"Adrien"},{"first_name":"Julien","last_name":"Gasparini","full_name":"Gasparini, Julien"},{"full_name":"Jacquin, Lisa","last_name":"Jacquin","first_name":"Lisa"},{"full_name":"Jacob, Gwenaël","last_name":"Jacob","first_name":"Gwenaël"},{"first_name":"Sophie","last_name":"Thibault","full_name":"Thibault, Sophie"},{"full_name":"Baudry, Emmanuelle","first_name":"Emmanuelle","last_name":"Baudry"}],"date_created":"2018-12-11T11:49:04Z","publist_id":"6752","volume":6,"title":"Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"BioMed Central","acknowledgement":"Romain Derelle was supported by grant from Plan Nacional 004302 BFU2012-31329. Fyodor A Kondrashov was supported by grants HHMI (Howard Hughes Medical Institute) 003803 and EMBO 003691 EUI-EURYIP-2011-4320.","publication":"BMC Research Notes","_id":"894"}]