[{"date_published":"2015-05-01T00:00:00Z","article_type":"original","publication":"Science Advances","citation":{"ieee":"J. A. Palacci et al., “Artificial rheotaxis,” Science Advances, vol. 1, no. 4. American Association for the Advancement of Science , 2015.","apa":"Palacci, J. A., Sacanna, S., Abramian, A., Barral, J., Hanson, K., Grosberg, A. Y., … Chaikin, P. M. (2015). Artificial rheotaxis. Science Advances. American Association for the Advancement of Science . https://doi.org/10.1126/sciadv.1400214","ista":"Palacci JA, Sacanna S, Abramian A, Barral J, Hanson K, Grosberg AY, Pine DJ, Chaikin PM. 2015. Artificial rheotaxis. Science Advances. 1(4), e1400214.","ama":"Palacci JA, Sacanna S, Abramian A, et al. Artificial rheotaxis. Science Advances. 2015;1(4). doi:10.1126/sciadv.1400214","chicago":"Palacci, Jérémie A, Stefano Sacanna, Anaïs Abramian, Jérémie Barral, Kasey Hanson, Alexander Y. Grosberg, David J. Pine, and Paul M. Chaikin. “Artificial Rheotaxis.” Science Advances. American Association for the Advancement of Science , 2015. https://doi.org/10.1126/sciadv.1400214.","short":"J.A. Palacci, S. Sacanna, A. Abramian, J. Barral, K. Hanson, A.Y. Grosberg, D.J. Pine, P.M. Chaikin, Science Advances 1 (2015).","mla":"Palacci, Jérémie A., et al. “Artificial Rheotaxis.” Science Advances, vol. 1, no. 4, e1400214, American Association for the Advancement of Science , 2015, doi:10.1126/sciadv.1400214."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"date_created":"2021-02-02T13:22:19Z","date_updated":"2021-02-02T13:22:19Z","checksum":"b97d62433581875c1b85210c5f6ae370","success":1,"relation":"main_file","file_id":"9058","content_type":"application/pdf","file_size":2416780,"creator":"cziletti","file_name":"2015_ScienceAdvances_Palacci.pdf","access_level":"open_access"}],"oa_version":"Published Version","ddc":["530"],"status":"public","title":"Artificial rheotaxis","intvolume":" 1","_id":"9057","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","abstract":[{"text":"Motility is a basic feature of living microorganisms, and how it works is often determined by environmental cues. Recent efforts have focused on developing artificial systems that can mimic microorganisms, in particular their self-propulsion. We report on the design and characterization of synthetic self-propelled particles that migrate upstream, known as positive rheotaxis. This phenomenon results from a purely physical mechanism involving the interplay between the polarity of the particles and their alignment by a viscous torque. We show quantitative agreement between experimental data and a simple model of an overdamped Brownian pendulum. The model notably predicts the existence of a stagnation point in a diverging flow. We take advantage of this property to demonstrate that our active particles can sense and predictably organize in an imposed flow. Our colloidal system represents an important step toward the realization of biomimetic microsystems with the ability to sense and respond to environmental changes.","lang":"eng"}],"issue":"4","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1126/sciadv.1400214","quality_controlled":"1","external_id":{"pmid":["26601175"],"arxiv":["1505.05111"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"month":"05","publication_identifier":{"issn":["2375-2548"]},"date_created":"2021-02-02T13:15:02Z","date_updated":"2023-02-23T13:47:52Z","volume":1,"author":[{"full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci","first_name":"Jérémie A"},{"last_name":"Sacanna","first_name":"Stefano","full_name":"Sacanna, Stefano"},{"first_name":"Anaïs","last_name":"Abramian","full_name":"Abramian, Anaïs"},{"full_name":"Barral, Jérémie","last_name":"Barral","first_name":"Jérémie"},{"full_name":"Hanson, Kasey","last_name":"Hanson","first_name":"Kasey"},{"full_name":"Grosberg, Alexander Y.","first_name":"Alexander Y.","last_name":"Grosberg"},{"full_name":"Pine, David J.","last_name":"Pine","first_name":"David J."},{"full_name":"Chaikin, Paul M.","first_name":"Paul M.","last_name":"Chaikin"}],"publication_status":"published","publisher":"American Association for the Advancement of Science ","year":"2015","pmid":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","extern":"1","file_date_updated":"2021-02-02T13:22:19Z","article_number":"e1400214"},{"_id":"906","year":"2015","acknowledgement":"Funding: The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, \"Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)\" and (BFU2012-31329), the European Union and the European Research Council under grant agreement 335980_EinME. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Our author Dr., Prof. Akimenko Vasilii K. (1942–2013) passed away during work on the article. Prof. Akimenko was a leading biochemist in IBPM RAS and active researcher until last days. A number of his work remains unfinished. We mourn premature care of Prof. Akimenko Vasilii. We thank Heinz Himmelbauer and the CRG Genomic Unit for the sequencing.","intvolume":" 10","publisher":"Public Library of Science","publication_status":"published","status":"public","title":"Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer","author":[{"full_name":"Arkhipova, Oksana V","last_name":"Arkhipova","first_name":"Oksana"},{"full_name":"Meer, Margarita V","first_name":"Margarita","last_name":"Meer"},{"last_name":"Mikoulinskaia","first_name":"Galina","full_name":"Mikoulinskaia, Galina V"},{"first_name":"Marina","last_name":"Zakharova","full_name":"Zakharova, Marina V"},{"full_name":"Galushko, Alexander S","last_name":"Galushko","first_name":"Alexander"},{"last_name":"Akimenko","first_name":"Vasilii","full_name":"Akimenko, Vasilii K"},{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov"}],"volume":10,"date_created":"2018-12-11T11:49:08Z","date_updated":"2021-01-12T08:21:48Z","type":"journal_article","issue":"5","publist_id":"6742","abstract":[{"text":"The origin and evolution of novel biochemical functions remains one of the key questions in molecular evolution. We study recently emerged methacrylate reductase function that is thought to have emerged in the last century and reported in Geobacter sulfurreducens strain AM-1. We report the sequence and study the evolution of the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme cytochrome (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex mechanism of biogenesis for chromoproteids of the methacrylate redox system. The homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres are also organized into an operon and their phylogenetic distribution suggested that these two genes tend to be horizontally transferred together. Specifically, the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any of the homologs found in other Geobacter genomes. The acquisition of methacrylate reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene transfer event. However, the new function of the products of mrd and mcc may have evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1.","lang":"eng"}],"extern":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"apa":"Arkhipova, O., Meer, M., Mikoulinskaia, G., Zakharova, M., Galushko, A., Akimenko, V., & Kondrashov, F. (2015). Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0125888","ieee":"O. Arkhipova et al., “Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015.","ista":"Arkhipova O, Meer M, Mikoulinskaia G, Zakharova M, Galushko A, Akimenko V, Kondrashov F. 2015. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 10(5).","ama":"Arkhipova O, Meer M, Mikoulinskaia G, et al. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0125888","chicago":"Arkhipova, Oksana, Margarita Meer, Galina Mikoulinskaia, Marina Zakharova, Alexander Galushko, Vasilii Akimenko, and Fyodor Kondrashov. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0125888.","short":"O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko, F. Kondrashov, PLoS One 10 (2015).","mla":"Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0125888."},"publication":"PLoS One","quality_controlled":0,"date_published":"2015-05-11T00:00:00Z","doi":"10.1371/journal.pone.0125888","month":"05","day":"11"},{"extern":"1","year":"2015","publisher":"American Geophysical Union","publication_status":"published","author":[{"full_name":"Lefauve, Adrien","first_name":"Adrien","last_name":"Lefauve"},{"last_name":"Muller","first_name":"Caroline J","orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J"},{"full_name":"Melet, Angélique","first_name":"Angélique","last_name":"Melet"}],"volume":120,"date_updated":"2022-01-24T13:45:41Z","date_created":"2021-02-15T14:21:49Z","publication_identifier":{"issn":["2169-9275"]},"month":"06","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/2014JC010598"}],"quality_controlled":"1","doi":"10.1002/2014jc010598","language":[{"iso":"eng"}],"type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"The breaking of internal tides is believed to provide a large part of the power needed to mix the abyssal ocean and sustain the meridional overturning circulation. Both the fraction of internal tide energy that is dissipated locally and the resulting vertical mixing distribution are crucial for the ocean state, but remain poorly quantified. Here we present a first worldwide estimate of mixing due to internal tides generated at small‐scale abyssal hills. Our estimate is based on linear wave theory, a nonlinear parameterization for wave breaking and uses quasi‐global small‐scale abyssal hill bathymetry, stratification, and tidal data. We show that a large fraction of abyssal‐hill generated internal tide energy is locally dissipated over mid‐ocean ridges in the Southern Hemisphere. Significant dissipation occurs above ridge crests, and, upon rescaling by the local stratification, follows a monotonic exponential decay with height off the bottom, with a nonuniform decay scale. We however show that a substantial part of the dissipation occurs over the smoother flanks of mid‐ocean ridges, and exhibits a middepth maximum due to the interplay of wave amplitude with stratification. We link the three‐dimensional map of dissipation to abyssal hills characteristics, ocean stratification, and tidal forcing, and discuss its potential implementation in time‐evolving parameterizations for global climate models. Current tidal parameterizations only account for waves generated at large‐scale satellite‐resolved bathymetry. Our results suggest that the presence of small‐scale, mostly unresolved abyssal hills could significantly enhance the spatial inhomogeneity of tidal mixing, particularly above mid‐ocean ridges in the Southern Hemisphere."}],"_id":"9141","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 120","title":"A three-dimensional map of tidal dissipation over abyssal hills","status":"public","oa_version":"Published Version","article_processing_charge":"No","day":"08","citation":{"ama":"Lefauve A, Muller CJ, Melet A. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 2015;120(7):4760-4777. doi:10.1002/2014jc010598","apa":"Lefauve, A., Muller, C. J., & Melet, A. (2015). A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. American Geophysical Union. https://doi.org/10.1002/2014jc010598","ieee":"A. Lefauve, C. J. Muller, and A. Melet, “A three-dimensional map of tidal dissipation over abyssal hills,” Journal of Geophysical Research: Oceans, vol. 120, no. 7. American Geophysical Union, pp. 4760–4777, 2015.","ista":"Lefauve A, Muller CJ, Melet A. 2015. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 120(7), 4760–4777.","short":"A. Lefauve, C.J. Muller, A. Melet, Journal of Geophysical Research: Oceans 120 (2015) 4760–4777.","mla":"Lefauve, Adrien, et al. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans, vol. 120, no. 7, American Geophysical Union, 2015, pp. 4760–77, doi:10.1002/2014jc010598.","chicago":"Lefauve, Adrien, Caroline J Muller, and Angélique Melet. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans. American Geophysical Union, 2015. https://doi.org/10.1002/2014jc010598."},"publication":"Journal of Geophysical Research: Oceans","page":"4760-4777","article_type":"original","date_published":"2015-06-08T00:00:00Z"},{"publication":"eLife","citation":{"apa":"Sehring, I., Recho, P., Denker, E., Kourakis, M., Mathiesen, B., Hannezo, E. B., … Jiang, D. (2015). Assembly and positioning of actomyosin rings by contractility and planar cell polarity. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.09206","ieee":"I. Sehring et al., “Assembly and positioning of actomyosin rings by contractility and planar cell polarity,” eLife, vol. 4. eLife Sciences Publications, 2015.","ista":"Sehring I, Recho P, Denker E, Kourakis M, Mathiesen B, Hannezo EB, Dong B, Jiang D. 2015. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 4, e09206.","ama":"Sehring I, Recho P, Denker E, et al. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 2015;4. doi:10.7554/eLife.09206","chicago":"Sehring, Ivonne, Pierre Recho, Elsa Denker, Matthew Kourakis, Birthe Mathiesen, Edouard B Hannezo, Bo Dong, and Di Jiang. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife. eLife Sciences Publications, 2015. https://doi.org/10.7554/eLife.09206.","short":"I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo, B. Dong, D. Jiang, ELife 4 (2015).","mla":"Sehring, Ivonne, et al. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife, vol. 4, e09206, eLife Sciences Publications, 2015, doi:10.7554/eLife.09206."},"date_published":"2015-10-21T00:00:00Z","day":"21","has_accepted_license":"1","ddc":["539","570"],"title":"Assembly and positioning of actomyosin rings by contractility and planar cell polarity","status":"public","intvolume":" 4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"928","file":[{"relation":"main_file","file_id":"5769","date_updated":"2020-07-14T12:48:15Z","date_created":"2018-12-20T15:50:56Z","checksum":"1e4024b3161adcae4a53a0b3dc8a946e","file_name":"2015_eLife_Sehring.pdf","access_level":"open_access","content_type":"application/pdf","file_size":7202224,"creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"The actomyosin cytoskeleton is a primary force-generating mechanism in morphogenesis, thus a robust spatial control of cytoskeletal positioning is essential. In this report, we demonstrate that actomyosin contractility and planar cell polarity (PCP) interact in post-mitotic Ciona notochord cells to self-assemble and reposition actomyosin rings, which play an essential role for cell elongation. Intriguingly, rings always form at the cells′ anterior edge before migrating towards the center as contractility increases, reflecting a novel dynamical property of the cortex. Our drug and genetic manipulations uncover a tug-of-war between contractility, which localizes cortical flows toward the equator and PCP, which tries to reposition them. We develop a simple model of the physical forces underlying this tug-of-war, which quantitatively reproduces our results. We thus propose a quantitative framework for dissecting the relative contribution of contractility and PCP to the self-assembly and repositioning of cytoskeletal structures, which should be applicable to other morphogenetic events.","lang":"eng"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/eLife.09206","month":"10","publication_status":"published","publisher":"eLife Sciences Publications","year":"2015","date_updated":"2021-01-12T08:21:58Z","date_created":"2018-12-11T11:49:15Z","volume":4,"author":[{"full_name":"Sehring, Ivonne","last_name":"Sehring","first_name":"Ivonne"},{"last_name":"Recho","first_name":"Pierre","full_name":"Recho, Pierre"},{"full_name":"Denker, Elsa","first_name":"Elsa","last_name":"Denker"},{"full_name":"Kourakis, Matthew","first_name":"Matthew","last_name":"Kourakis"},{"last_name":"Mathiesen","first_name":"Birthe","full_name":"Mathiesen, Birthe"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"full_name":"Dong, Bo","first_name":"Bo","last_name":"Dong"},{"last_name":"Jiang","first_name":"Di","full_name":"Jiang, Di"}],"article_number":"e09206","extern":"1","file_date_updated":"2020-07-14T12:48:15Z","publist_id":"6512"},{"doi":"10.1016/j.endm.2015.06.027","language":[{"iso":"eng"}],"external_id":{"arxiv":["1501.04816"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1501.04816","open_access":"1"}],"quality_controlled":"1","month":"11","publication_identifier":{"issn":["1571-0653"]},"author":[{"full_name":"Krivelevich, Michael","first_name":"Michael","last_name":"Krivelevich"},{"full_name":"Kwan, Matthew Alan","orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan","first_name":"Matthew Alan"},{"full_name":"Sudakov, Benny","first_name":"Benny","last_name":"Sudakov"}],"date_updated":"2023-02-23T14:01:28Z","date_created":"2021-06-21T06:40:34Z","volume":49,"year":"2015","publication_status":"published","publisher":"Elsevier","extern":"1","date_published":"2015-11-01T00:00:00Z","publication":"Electronic Notes in Discrete Mathematics","citation":{"ama":"Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 2015;49:181-187. doi:10.1016/j.endm.2015.06.027","ieee":"M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly perturbed digraphs and hypergraphs,” Electronic Notes in Discrete Mathematics, vol. 49. Elsevier, pp. 181–187, 2015.","apa":"Krivelevich, M., Kwan, M. A., & Sudakov, B. (2015). Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2015.06.027","ista":"Krivelevich M, Kwan MA, Sudakov B. 2015. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 49, 181–187.","short":"M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics 49 (2015) 181–187.","mla":"Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics, vol. 49, Elsevier, 2015, pp. 181–87, doi:10.1016/j.endm.2015.06.027.","chicago":"Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics. Elsevier, 2015. https://doi.org/10.1016/j.endm.2015.06.027."},"article_type":"original","page":"181-187","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","_id":"9575","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Cycles and matchings in randomly perturbed digraphs and hypergraphs","intvolume":" 49","abstract":[{"text":"We give several results showing that different discrete structures typically gain certain spanning substructures (in particular, Hamilton cycles) after a modest random perturbation. First, we prove that adding linearly many random edges to a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence of a perfect matching or a loose Hamilton cycle. The proof involves an interesting application of Szemerédi's Regularity Lemma, which might be independently useful. We next prove that digraphs with certain strong expansion properties are pancyclic, and use this to show that adding a linear number of random edges typically makes a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent) number of random edges in a tournament typically ensures the existence of multiple edge-disjoint Hamilton cycles. All our results are tight.","lang":"eng"}],"type":"journal_article"}]