[{"publication_identifier":{"issn":["0027-8424","1091-6490"]},"issue":"2","type":"journal_article","citation":{"apa":"Goodrich, C. P., &#38; Brenner, M. P. (2017). Using active colloids as machines to weave and braid on the micrometer scale. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1608838114\">https://doi.org/10.1073/pnas.1608838114</a>","mla":"Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines to Weave and Braid on the Micrometer Scale.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 2, Proceedings of the National Academy of Sciences, 2017, pp. 257–62, doi:<a href=\"https://doi.org/10.1073/pnas.1608838114\">10.1073/pnas.1608838114</a>.","ieee":"C. P. Goodrich and M. P. Brenner, “Using active colloids as machines to weave and braid on the micrometer scale,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 2. Proceedings of the National Academy of Sciences, pp. 257–262, 2017.","ama":"Goodrich CP, Brenner MP. Using active colloids as machines to weave and braid on the micrometer scale. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(2):257-262. doi:<a href=\"https://doi.org/10.1073/pnas.1608838114\">10.1073/pnas.1608838114</a>","ista":"Goodrich CP, Brenner MP. 2017. Using active colloids as machines to weave and braid on the micrometer scale. Proceedings of the National Academy of Sciences. 114(2), 257–262.","short":"C.P. Goodrich, M.P. Brenner, Proceedings of the National Academy of Sciences 114 (2017) 257–262.","chicago":"Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines to Weave and Braid on the Micrometer Scale.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1608838114\">https://doi.org/10.1073/pnas.1608838114</a>."},"month":"01","status":"public","oa_version":"None","article_processing_charge":"No","volume":114,"year":"2017","publisher":"Proceedings of the National Academy of Sciences","date_updated":"2021-01-12T08:15:20Z","author":[{"last_name":"Goodrich","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"full_name":"Brenner, Michael P.","last_name":"Brenner","first_name":"Michael P."}],"publication_status":"published","intvolume":"       114","doi":"10.1073/pnas.1608838114","page":"257-262","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Using active colloids as machines to weave and braid on the micrometer scale","day":"10","quality_controlled":"1","language":[{"iso":"eng"}],"article_type":"original","fulldoi":"https://doi.org/10.1073/pnas.1608838114","_id":"7758","publication":"Proceedings of the National Academy of Sciences","abstract":[{"text":"Controlling motion at the microscopic scale is a fundamental goal in the development of biologically inspired systems. We show that the motion of active, self-propelled colloids can be sufficiently controlled for use as a tool to assemble complex structures such as braids and weaves out of microscopic filaments. Unlike typical self-assembly paradigms, these structures are held together by geometric constraints rather than adhesive bonds. The out-of-equilibrium assembly that we propose involves precisely controlling the 2D motion of active colloids so that their path has a nontrivial topology. We demonstrate with proof-of-principle Brownian dynamics simulations that, when the colloids are attached to long semiflexible filaments, this motion causes the filaments to braid. The ability of the active particles to provide sufficient force necessary to bend the filaments into a braid depends on a number of factors, including the self-propulsion mechanism, the properties of the filament, and the maximum curvature in the braid. Our work demonstrates that nonequilibrium assembly pathways can be designed using active particles.","lang":"eng"}],"date_created":"2020-04-30T11:39:09Z","date_published":"2017-01-10T00:00:00Z","extern":"1"},{"article_processing_charge":"No","page":"6666-6674","intvolume":"       114","doi":"10.1073/pnas.1701812114","type":"journal_article","issue":"26","month":"06","citation":{"short":"H.C. Barron, T.P. Vogels, T.E. Behrens, M. Ramaswami, Proceedings of the National Academy of Sciences 114 (2017) 6666–6674.","chicago":"Barron, Helen C., Tim P Vogels, Timothy E. Behrens, and Mani Ramaswami. “Inhibitory Engrams in Perception and Memory.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1701812114\">https://doi.org/10.1073/pnas.1701812114</a>.","ista":"Barron HC, Vogels TP, Behrens TE, Ramaswami M. 2017. Inhibitory engrams in perception and memory. Proceedings of the National Academy of Sciences. 114(26), 6666–6674.","ama":"Barron HC, Vogels TP, Behrens TE, Ramaswami M. Inhibitory engrams in perception and memory. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(26):6666-6674. doi:<a href=\"https://doi.org/10.1073/pnas.1701812114\">10.1073/pnas.1701812114</a>","mla":"Barron, Helen C., et al. “Inhibitory Engrams in Perception and Memory.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 26, Proceedings of the National Academy of Sciences, 2017, pp. 6666–74, doi:<a href=\"https://doi.org/10.1073/pnas.1701812114\">10.1073/pnas.1701812114</a>.","ieee":"H. C. Barron, T. P. Vogels, T. E. Behrens, and M. Ramaswami, “Inhibitory engrams in perception and memory,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 26. Proceedings of the National Academy of Sciences, pp. 6666–6674, 2017.","apa":"Barron, H. C., Vogels, T. P., Behrens, T. E., &#38; Ramaswami, M. (2017). Inhibitory engrams in perception and memory. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1701812114\">https://doi.org/10.1073/pnas.1701812114</a>"},"status":"public","day":"27","quality_controlled":"1","article_type":"original","oa":1,"date_created":"2020-06-25T12:56:58Z","_id":"8018","publication":"Proceedings of the National Academy of Sciences","title":"Inhibitory engrams in perception and memory","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495250/","open_access":"1"}],"date_updated":"2021-01-12T08:16:33Z","publisher":"Proceedings of the National Academy of Sciences","year":"2017","volume":114,"publication_status":"published","author":[{"full_name":"Barron, Helen C.","last_name":"Barron","first_name":"Helen C."},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","last_name":"Vogels"},{"full_name":"Behrens, Timothy E.","last_name":"Behrens","first_name":"Timothy E."},{"full_name":"Ramaswami, Mani","last_name":"Ramaswami","first_name":"Mani"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"oa_version":"Published Version","fulldoi":"https://doi.org/10.1073/pnas.1701812114","language":[{"iso":"eng"}],"pmid":1,"extern":"1","date_published":"2017-06-27T00:00:00Z","abstract":[{"text":"Nervous systems use excitatory cell assemblies to encode and represent sensory percepts. Similarly, synaptically connected cell assemblies or \"engrams\" are thought to represent memories of past experience. Multiple lines of recent evidence indicate that brain systems create and use inhibitory replicas of excitatory representations for important cognitive functions. Such matched \"inhibitory engrams\" can form through homeostatic potentiation of inhibition onto postsynaptic cells that show increased levels of excitation. Inhibitory engrams can reduce behavioral responses to familiar stimuli, thereby resulting in behavioral habituation. In addition, by preventing inappropriate activation of excitatory memory engrams, inhibitory engrams can make memories quiescent, stored in a latent form that is available for context-relevant activation. In neural networks with balanced excitatory and inhibitory engrams, the release of innate responses and recall of associative memories can occur through focused disinhibition. Understanding mechanisms that regulate the formation and expression of inhibitory engrams in vivo may help not only to explain key features of cognition but also to provide insight into transdiagnostic traits associated with psychiatric conditions such as autism, schizophrenia, and posttraumatic stress disorder. ","lang":"eng"}],"external_id":{"pmid":["28611219"]}},{"publication_status":"published","author":[{"first_name":"Marjon","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","full_name":"De Vos, Marjon","last_name":"De Vos"},{"id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P","orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P","last_name":"Zagórski"},{"full_name":"Mcnally, Alan","last_name":"Mcnally","first_name":"Alan"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach"}],"scopus_import":"1","publisher":"National Academy of Sciences","date_updated":"2025-07-10T11:55:08Z","volume":114,"year":"2017","oa_version":"Submitted Version","corr_author":"1","publication_identifier":{"issn":["0027-8424"]},"date_published":"2017-10-03T00:00:00Z","abstract":[{"lang":"eng","text":"Polymicrobial infections constitute small ecosystems that accommodate several bacterial species. Commonly, these bacteria are investigated in isolation. However, it is unknown to what extent the isolates interact and whether their interactions alter bacterial growth and ecosystem resilience in the presence and absence of antibiotics. We quantified the complete ecological interaction network for 72 bacterial isolates collected from 23 individuals diagnosed with polymicrobial urinary tract infections and found that most interactions cluster based on evolutionary relatedness. Statistical network analysis revealed that competitive and cooperative reciprocal interactions are enriched in the global network, while cooperative interactions are depleted in the individual host community networks. A population dynamics model parameterized by our measurements suggests that interactions restrict community stability, explaining the observed species diversity of these communities. We further show that the clinical isolates frequently protect each other from clinically relevant antibiotics. Together, these results highlight that ecological interactions are crucial for the growth and survival of bacteria in polymicrobial infection communities and affect their assembly and resilience. "}],"department":[{"_id":"ToBo"}],"fulldoi":"https://doi.org/10.1073/pnas.1713372114","pmid":1,"language":[{"iso":"eng"}],"external_id":{"isi":["000412130500061"],"pmid":["28923953"]},"doi":"10.1073/pnas.1713372114","intvolume":"       114","ec_funded":1,"page":"10666 - 10671","publist_id":"6827","article_processing_charge":"No","isi":1,"month":"10","citation":{"mla":"de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” <i>PNAS</i>, vol. 114, no. 40, National Academy of Sciences, 2017, pp. 10666–71, doi:<a href=\"https://doi.org/10.1073/pnas.1713372114\">10.1073/pnas.1713372114</a>.","ieee":"M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections,” <i>PNAS</i>, vol. 114, no. 40. National Academy of Sciences, pp. 10666–10671, 2017.","apa":"de Vos, M., Zagórski, M. P., Mcnally, A., &#38; Bollenbach, M. T. (2017). Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1713372114\">https://doi.org/10.1073/pnas.1713372114</a>","short":"M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671.","chicago":"Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1713372114\">https://doi.org/10.1073/pnas.1713372114</a>.","ama":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. <i>PNAS</i>. 2017;114(40):10666-10671. doi:<a href=\"https://doi.org/10.1073/pnas.1713372114\">10.1073/pnas.1713372114</a>","ista":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. 2017. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 114(40), 10666–10671."},"status":"public","issue":"40","type":"journal_article","_id":"822","publication":"PNAS","date_created":"2018-12-11T11:48:41Z","project":[{"grant_number":"303507","call_identifier":"FP7","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","name":"Optimality principles in responses to antibiotics"},{"call_identifier":"FWF","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"}],"oa":1,"quality_controlled":"1","day":"03","title":"Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/","open_access":"1"}]},{"oa_version":"Submitted Version","publication_identifier":{"issn":["0027-8424"]},"scopus_import":"1","author":[{"full_name":"Möller, Barbara","last_name":"Möller","first_name":"Barbara"},{"full_name":"Ten Hove, Colette","last_name":"Ten Hove","first_name":"Colette"},{"full_name":"Xiang, Daoquan","last_name":"Xiang","first_name":"Daoquan"},{"full_name":"Williams, Nerys","last_name":"Williams","first_name":"Nerys"},{"first_name":"Lorena","last_name":"López","full_name":"López, Lorena"},{"first_name":"Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","full_name":"Yoshida, Saiko","last_name":"Yoshida"},{"last_name":"Smit","full_name":"Smit, Margot","first_name":"Margot"},{"full_name":"Datla, Raju","last_name":"Datla","first_name":"Raju"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"}],"publication_status":"published","year":"2017","volume":114,"date_updated":"2025-09-11T07:09:58Z","publisher":"National Academy of Sciences","external_id":{"isi":["000396893600033"],"pmid":["28265057"]},"department":[{"_id":"JiFr"}],"abstract":[{"text":"Plant organs are typically organized into three main tissue layers. The middle ground tissue layer comprises the majority of the plant body and serves a wide range of functions, including photosynthesis, selective nutrient uptake and storage, and gravity sensing. Ground tissue patterning and maintenance in Arabidopsis are controlled by a well-established gene network revolving around the key regulator SHORT-ROOT (SHR). In contrast, it is completely unknown how ground tissue identity is first specified from totipotent precursor cells in the embryo. The plant signaling molecule auxin, acting through AUXIN RESPONSE FACTOR (ARF) transcription factors, is critical for embryo patterning. The auxin effector ARF5/MONOPTEROS (MP) acts both cell-autonomously and noncell-autonomously to control embryonic vascular tissue formation and root initiation, respectively. Here we show that auxin response and ARF activity cell-autonomously control the asymmetric division of the first ground tissue cells. By identifying embryonic target genes, we show that MP transcriptionally initiates the ground tissue lineage and acts upstream of the regulatory network that controls ground tissue patterning and maintenance. Strikingly, whereas the SHR network depends on MP, this MP function is, at least in part, SHR independent. Our study therefore identifies auxin response as a regulator of ground tissue specification in the embryonic root, and reveals that ground tissue initiation and maintenance use different regulators and mechanisms. Moreover, our data provide a framework for the simultaneous formation of multiple cell types by the same transcriptional regulator.","lang":"eng"}],"date_published":"2017-03-21T00:00:00Z","language":[{"iso":"eng"}],"pmid":1,"fulldoi":"https://doi.org/10.1073/pnas.1616493114","citation":{"chicago":"Möller, Barbara, Colette Ten Hove, Daoquan Xiang, Nerys Williams, Lorena López, Saiko Yoshida, Margot Smit, Raju Datla, and Dolf Weijers. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1616493114\">https://doi.org/10.1073/pnas.1616493114</a>.","short":"B. Möller, C. Ten Hove, D. Xiang, N. Williams, L. López, S. Yoshida, M. Smit, R. Datla, D. Weijers, PNAS 114 (2017) E2533–E2539.","ista":"Möller B, Ten Hove C, Xiang D, Williams N, López L, Yoshida S, Smit M, Datla R, Weijers D. 2017. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. 114(12), E2533–E2539.","ama":"Möller B, Ten Hove C, Xiang D, et al. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. <i>PNAS</i>. 2017;114(12):E2533-E2539. doi:<a href=\"https://doi.org/10.1073/pnas.1616493114\">10.1073/pnas.1616493114</a>","ieee":"B. Möller <i>et al.</i>, “Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo,” <i>PNAS</i>, vol. 114, no. 12. National Academy of Sciences, pp. E2533–E2539, 2017.","mla":"Möller, Barbara, et al. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” <i>PNAS</i>, vol. 114, no. 12, National Academy of Sciences, 2017, pp. E2533–39, doi:<a href=\"https://doi.org/10.1073/pnas.1616493114\">10.1073/pnas.1616493114</a>.","apa":"Möller, B., Ten Hove, C., Xiang, D., Williams, N., López, L., Yoshida, S., … Weijers, D. (2017). Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1616493114\">https://doi.org/10.1073/pnas.1616493114</a>"},"status":"public","month":"03","type":"journal_article","issue":"12","publist_id":"7076","page":"E2533 - E2539","doi":"10.1073/pnas.1616493114","intvolume":"       114","isi":1,"article_processing_charge":"No","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373392/","open_access":"1"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo","date_created":"2018-12-11T11:47:45Z","publication":"PNAS","_id":"657","quality_controlled":"1","day":"21","oa":1},{"oa_version":"Submitted Version","publication_identifier":{"issn":["0027-8424"]},"publication_status":"published","author":[{"first_name":"Jamie","last_name":"Rickman","full_name":"Rickman, Jamie"},{"last_name":"Düllberg","full_name":"Düllberg, Christian F","orcid":"0000-0001-6335-9748","first_name":"Christian F","id":"459064DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas","full_name":"Cade, Nicholas","last_name":"Cade"},{"last_name":"Griffin","full_name":"Griffin, Lewis","first_name":"Lewis"},{"last_name":"Surrey","full_name":"Surrey, Thomas","first_name":"Thomas"}],"scopus_import":"1","publisher":"National Academy of Sciences","date_updated":"2025-09-11T07:08:20Z","volume":114,"year":"2017","external_id":{"isi":["000397607300065"],"pmid":["28280102"]},"date_published":"2017-03-28T00:00:00Z","abstract":[{"lang":"eng","text":"Growing microtubules are protected from depolymerization by the presence of a GTP or GDP/Pi cap. End-binding proteins of the EB1 family bind to the stabilizing cap, allowing monitoring of its size in real time. The cap size has been shown to correlate with instantaneous microtubule stability. Here we have quantitatively characterized the properties of cap size fluctuations during steadystate growth and have developed a theory predicting their timescale and amplitude from the kinetics of microtubule growth and cap maturation. In contrast to growth speed fluctuations, cap size fluctuations show a characteristic timescale, which is defined by the lifetime of the cap sites. Growth fluctuations affect the amplitude of cap size fluctuations; however, cap size does not affect growth speed, indicating that microtubules are far from instability during most of their time of growth. Our theory provides the basis for a quantitative understanding of microtubule stability fluctuations during steady-state growth."}],"department":[{"_id":"MaLo"}],"fulldoi":"https://doi.org/10.1073/pnas.1620274114","pmid":1,"language":[{"iso":"eng"}],"acknowledgement":"We thank Philippe Cluzel for helpful discussions and Gunnar Pruessner for data analysis advice. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK Grant FC001163, Medical Research Council Grant FC001163, and Wellcome Trust Grant FC001163. This work was also supported by European Research Council Advanced Grant Project 323042 (to C.D. and T.S.).","status":"public","month":"03","citation":{"ieee":"J. Rickman, C. F. Düllberg, N. Cade, L. Griffin, and T. Surrey, “Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation,” <i>PNAS</i>, vol. 114, no. 13. National Academy of Sciences, pp. 3427–3432, 2017.","mla":"Rickman, Jamie, et al. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” <i>PNAS</i>, vol. 114, no. 13, National Academy of Sciences, 2017, pp. 3427–32, doi:<a href=\"https://doi.org/10.1073/pnas.1620274114\">10.1073/pnas.1620274114</a>.","apa":"Rickman, J., Düllberg, C. F., Cade, N., Griffin, L., &#38; Surrey, T. (2017). Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1620274114\">https://doi.org/10.1073/pnas.1620274114</a>","chicago":"Rickman, Jamie, Christian F Düllberg, Nicholas Cade, Lewis Griffin, and Thomas Surrey. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1620274114\">https://doi.org/10.1073/pnas.1620274114</a>.","short":"J. Rickman, C.F. Düllberg, N. Cade, L. Griffin, T. Surrey, PNAS 114 (2017) 3427–3432.","ama":"Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. <i>PNAS</i>. 2017;114(13):3427-3432. doi:<a href=\"https://doi.org/10.1073/pnas.1620274114\">10.1073/pnas.1620274114</a>","ista":"Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. 2017. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 114(13), 3427–3432."},"issue":"13","type":"journal_article","intvolume":"       114","doi":"10.1073/pnas.1620274114","page":"3427 - 3432","publist_id":"7073","article_processing_charge":"No","isi":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5380103/"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation","publication":"PNAS","_id":"660","date_created":"2018-12-11T11:47:46Z","oa":1,"day":"28","quality_controlled":"1"},{"external_id":{"pmid":["28420786"],"isi":["000400358000050"]},"abstract":[{"text":"Humans routinely use conditionally cooperative strategies when interacting in repeated social dilemmas. They are more likely to cooperate if others cooperated before, and are ready to retaliate if others defected. To capture the emergence of reciprocity, most previous models consider subjects who can only choose from a restricted set of representative strategies, or who react to the outcome of the very last round only. As players memorize more rounds, the dimension of the strategy space increases exponentially. This increasing computational complexity renders simulations for individuals with higher cognitive abilities infeasible, especially if multiplayer interactions are taken into account. Here, we take an axiomatic approach instead. We propose several properties that a robust cooperative strategy for a repeated multiplayer dilemma should have. These properties naturally lead to a unique class of cooperative strategies, which contains the classical Win-Stay Lose-Shift rule as a special case. A comprehensive numerical analysis for the prisoner's dilemma and for the public goods game suggests that strategies of this class readily evolve across various memory-n spaces. Our results reveal that successful strategies depend not only on how cooperative others were in the past but also on the respective context of cooperation.","lang":"eng"}],"department":[{"_id":"KrCh"}],"date_published":"2017-05-02T00:00:00Z","pmid":1,"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1073/pnas.1621239114","oa_version":"Published Version","publication_identifier":{"issn":["0027-8424"]},"corr_author":"1","author":[{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe","full_name":"Hilbe, Christian"},{"first_name":"Vaquero","full_name":"Martinez, Vaquero","last_name":"Martinez"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"scopus_import":"1","publication_status":"published","volume":114,"year":"2017","publisher":"National Academy of Sciences","date_updated":"2026-06-18T19:11:14Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5422766/","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Memory-n strategies of direct reciprocity","publication":"PNAS","_id":"671","date_created":"2018-12-11T11:47:50Z","oa":1,"day":"02","quality_controlled":"1","project":[{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407"}],"status":"public","month":"05","citation":{"ieee":"C. Hilbe, V. Martinez, K. Chatterjee, and M. Nowak, “Memory-n strategies of direct reciprocity,” <i>PNAS</i>, vol. 114, no. 18. National Academy of Sciences, pp. 4715–4720, 2017.","mla":"Hilbe, Christian, et al. “Memory-n Strategies of Direct Reciprocity.” <i>PNAS</i>, vol. 114, no. 18, National Academy of Sciences, 2017, pp. 4715–20, doi:<a href=\"https://doi.org/10.1073/pnas.1621239114\">10.1073/pnas.1621239114</a>.","apa":"Hilbe, C., Martinez, V., Chatterjee, K., &#38; Nowak, M. (2017). Memory-n strategies of direct reciprocity. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1621239114\">https://doi.org/10.1073/pnas.1621239114</a>","short":"C. Hilbe, V. Martinez, K. Chatterjee, M. Nowak, PNAS 114 (2017) 4715–4720.","chicago":"Hilbe, Christian, Vaquero Martinez, Krishnendu Chatterjee, and Martin Nowak. “Memory-n Strategies of Direct Reciprocity.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1621239114\">https://doi.org/10.1073/pnas.1621239114</a>.","ista":"Hilbe C, Martinez V, Chatterjee K, Nowak M. 2017. Memory-n strategies of direct reciprocity. PNAS. 114(18), 4715–4720.","ama":"Hilbe C, Martinez V, Chatterjee K, Nowak M. Memory-n strategies of direct reciprocity. <i>PNAS</i>. 2017;114(18):4715-4720. doi:<a href=\"https://doi.org/10.1073/pnas.1621239114\">10.1073/pnas.1621239114</a>"},"issue":"18","type":"journal_article","publist_id":"7053","ec_funded":1,"intvolume":"       114","doi":"10.1073/pnas.1621239114","page":"4715 - 4720","article_processing_charge":"Yes (in subscription journal)","isi":1,"ddc":["000"]},{"department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"abstract":[{"lang":"eng","text":"Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. "}],"date_published":"2017-06-27T00:00:00Z","language":[{"iso":"eng"}],"pmid":1,"fulldoi":"https://doi.org/10.1073/pnas.1704470114","file":[{"file_size":2721544,"creator":"kschuh","file_id":"7223","date_updated":"2020-07-14T12:47:44Z","content_type":"application/pdf","file_name":"2017_PNAS_Miki.pdf","checksum":"2ab75d554f3df4a34d20fa8040589b7e","date_created":"2020-01-03T13:27:29Z","access_level":"open_access","relation":"main_file"}],"external_id":{"isi":["000404108400028"],"pmid":["28607047"]},"scopus_import":"1","author":[{"last_name":"Miki","full_name":"Miki, Takafumi","first_name":"Takafumi"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"first_name":"Gerardo","last_name":"Malagon","full_name":"Malagon, Gerardo"},{"full_name":"Gomez, Laura","last_name":"Gomez","first_name":"Laura"},{"last_name":"Tabuchi","full_name":"Tabuchi, Katsuhiko","first_name":"Katsuhiko"},{"first_name":"Masahiko","last_name":"Watanabe","full_name":"Watanabe, Masahiko"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"},{"first_name":"Alain","full_name":"Marty, Alain","last_name":"Marty"}],"publication_status":"published","year":"2017","volume":114,"date_updated":"2025-09-10T14:00:03Z","has_accepted_license":"1","publisher":"National Academy of Sciences","oa_version":"Published Version","publication_identifier":{"issn":["0027-8424"]},"corr_author":"1","file_date_updated":"2020-07-14T12:47:44Z","date_created":"2018-12-11T11:47:57Z","_id":"693","publication":"PNAS","quality_controlled":"1","day":"27","oa":1,"title":"Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"7013","page":"E5246 - E5255","intvolume":"       114","doi":"10.1073/pnas.1704470114","isi":1,"article_processing_charge":"Yes (in subscription journal)","ddc":["570"],"citation":{"apa":"Miki, T., Kaufmann, W., Malagon, G., Gomez, L., Tabuchi, K., Watanabe, M., … Marty, A. (2017). Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1704470114\">https://doi.org/10.1073/pnas.1704470114</a>","ieee":"T. Miki <i>et al.</i>, “Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses,” <i>PNAS</i>, vol. 114, no. 26. National Academy of Sciences, pp. E5246–E5255, 2017.","mla":"Miki, Takafumi, et al. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” <i>PNAS</i>, vol. 114, no. 26, National Academy of Sciences, 2017, pp. E5246–55, doi:<a href=\"https://doi.org/10.1073/pnas.1704470114\">10.1073/pnas.1704470114</a>.","ista":"Miki T, Kaufmann W, Malagon G, Gomez L, Tabuchi K, Watanabe M, Shigemoto R, Marty A. 2017. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 114(26), E5246–E5255.","ama":"Miki T, Kaufmann W, Malagon G, et al. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. <i>PNAS</i>. 2017;114(26):E5246-E5255. doi:<a href=\"https://doi.org/10.1073/pnas.1704470114\">10.1073/pnas.1704470114</a>","short":"T. Miki, W. Kaufmann, G. Malagon, L. Gomez, K. Tabuchi, M. Watanabe, R. Shigemoto, A. Marty, PNAS 114 (2017) E5246–E5255.","chicago":"Miki, Takafumi, Walter Kaufmann, Gerardo Malagon, Laura Gomez, Katsuhiko Tabuchi, Masahiko Watanabe, Ryuichi Shigemoto, and Alain Marty. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1704470114\">https://doi.org/10.1073/pnas.1704470114</a>."},"month":"06","status":"public","type":"journal_article","issue":"26"},{"scopus_import":"1","author":[{"first_name":"Carl","full_name":"Veller, Carl","last_name":"Veller"},{"full_name":"Hayward, Laura","last_name":"Hayward","first_name":"Laura"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"},{"first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","last_name":"Hilbe","orcid":"0000-0001-5116-955X"}],"publication_status":"published","year":"2017","volume":114,"date_updated":"2025-09-10T11:11:07Z","publisher":"National Academy of Sciences","oa_version":"Submitted Version","publication_identifier":{"issn":["0027-8424"]},"department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts. "}],"date_published":"2017-07-03T00:00:00Z","language":[{"iso":"eng"}],"pmid":1,"fulldoi":"https://doi.org/10.1073/pnas.1702020114","external_id":{"isi":["000404576100017"],"pmid":["28630336"]},"publist_id":"7002","page":"E5396 - E5405","doi":"10.1073/pnas.1702020114","intvolume":"       114","isi":1,"article_processing_charge":"No","status":"public","citation":{"apa":"Veller, C., Hayward, L., Nowak, M., &#38; Hilbe, C. (2017). The red queen and king in finite populations. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1702020114\">https://doi.org/10.1073/pnas.1702020114</a>","mla":"Veller, Carl, et al. “The Red Queen and King in Finite Populations.” <i>PNAS</i>, vol. 114, no. 27, National Academy of Sciences, 2017, pp. E5396–405, doi:<a href=\"https://doi.org/10.1073/pnas.1702020114\">10.1073/pnas.1702020114</a>.","ieee":"C. Veller, L. Hayward, M. Nowak, and C. Hilbe, “The red queen and king in finite populations,” <i>PNAS</i>, vol. 114, no. 27. National Academy of Sciences, pp. E5396–E5405, 2017.","ista":"Veller C, Hayward L, Nowak M, Hilbe C. 2017. The red queen and king in finite populations. PNAS. 114(27), E5396–E5405.","ama":"Veller C, Hayward L, Nowak M, Hilbe C. The red queen and king in finite populations. <i>PNAS</i>. 2017;114(27):E5396-E5405. doi:<a href=\"https://doi.org/10.1073/pnas.1702020114\">10.1073/pnas.1702020114</a>","short":"C. Veller, L. Hayward, M. Nowak, C. Hilbe, PNAS 114 (2017) E5396–E5405.","chicago":"Veller, Carl, Laura Hayward, Martin Nowak, and Christian Hilbe. “The Red Queen and King in Finite Populations.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1702020114\">https://doi.org/10.1073/pnas.1702020114</a>."},"month":"07","issue":"27","type":"journal_article","date_created":"2018-12-11T11:48:00Z","publication":"PNAS","_id":"699","day":"03","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502615/"}],"title":"The red queen and king in finite populations","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"language":[{"iso":"eng"}],"pmid":1,"fulldoi":"https://doi.org/10.1073/pnas.1703817114","department":[{"_id":"GaTk"}],"abstract":[{"lang":"eng","text":"Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here, we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. We show that fish alternate between an “active” mode, in which they are sensitive to the swimming patterns of conspecifics, and a “passive” mode, where they ignore them. Using a model that accounts for these two modes explicitly, we predict behaviors of individual fish with high accuracy, outperforming previous approaches that assumed a single continuous computation by individuals and simple metric or topological weighing of neighbors’ behavior. At the group level, switching between active and passive modes is uncorrelated among fish, but correlated directional swimming behavior still emerges. Our quantitative approach for studying complex, multi-modal individual behavior jointly with emergent group behavior is readily extensible to additional behavioral modes and their neural correlates as well as to other species."}],"date_published":"2017-09-19T00:00:00Z","external_id":{"pmid":["28874581"],"isi":["000411157100063"]},"year":"2017","volume":114,"date_updated":"2025-09-10T10:53:06Z","publisher":"National Academy of Sciences","scopus_import":"1","author":[{"first_name":"Roy","last_name":"Harpaz","full_name":"Harpaz, Roy"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik"},{"last_name":"Schneidman","full_name":"Schneidman, Elad","first_name":"Elad"}],"publication_status":"published","publication_identifier":{"issn":["0027-8424"]},"oa_version":"Submitted Version","day":"19","quality_controlled":"1","oa":1,"date_created":"2018-12-11T11:48:10Z","publication":"PNAS","_id":"725","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617265/","open_access":"1"}],"title":"Discrete modes of social information processing predict individual behavior of fish in a group","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"article_processing_charge":"No","publist_id":"6953","page":"10149 - 10154","intvolume":"       114","doi":"10.1073/pnas.1703817114","issue":"38","type":"journal_article","status":"public","citation":{"mla":"Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” <i>PNAS</i>, vol. 114, no. 38, National Academy of Sciences, 2017, pp. 10149–54, doi:<a href=\"https://doi.org/10.1073/pnas.1703817114\">10.1073/pnas.1703817114</a>.","ieee":"R. Harpaz, G. Tkačik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” <i>PNAS</i>, vol. 114, no. 38. National Academy of Sciences, pp. 10149–10154, 2017.","apa":"Harpaz, R., Tkačik, G., &#38; Schneidman, E. (2017). Discrete modes of social information processing predict individual behavior of fish in a group. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1703817114\">https://doi.org/10.1073/pnas.1703817114</a>","short":"R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 10149–10154.","chicago":"Harpaz, Roy, Gašper Tkačik, and Elad Schneidman. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1703817114\">https://doi.org/10.1073/pnas.1703817114</a>.","ista":"Harpaz R, Tkačik G, Schneidman E. 2017. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 114(38), 10149–10154.","ama":"Harpaz R, Tkačik G, Schneidman E. Discrete modes of social information processing predict individual behavior of fish in a group. <i>PNAS</i>. 2017;114(38):10149-10154. doi:<a href=\"https://doi.org/10.1073/pnas.1703817114\">10.1073/pnas.1703817114</a>"},"month":"09"},{"oa_version":"Published Version","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"author":[{"full_name":"Ragettli, Silvan","last_name":"Ragettli","first_name":"Silvan"},{"last_name":"Immerzeel","full_name":"Immerzeel, Walter W.","first_name":"Walter W."},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti"}],"scopus_import":"1","publication_status":"published","volume":113,"year":"2016","publisher":"Proceedings of the National Academy of Sciences","date_updated":"2023-02-24T10:48:43Z","external_id":{"pmid":["27482082"]},"abstract":[{"lang":"eng","text":"Mountain ranges are the world’s natural water towers and provide water resources for millions of people. However, their hydrological balance and possible future changes in river flow remain poorly understood because of high meteorological variability, physical inaccessibility, and the complex interplay between climate, cryosphere, and hydrological processes. Here, we use a state-of-the art glacio-hydrological model informed by data from high-altitude observations and the latest climate change scenarios to quantify the climate change impact on water resources of two contrasting catchments vulnerable to changes in the cryosphere. The two study catchments are located in the Central Andes of Chile and in the Nepalese Himalaya in close vicinity of densely populated areas. Although both sites reveal a strong decrease in glacier area, they show a remarkably different hydrological response to projected climate change. In the Juncal catchment in Chile, runoff is likely to sharply decrease in the future and the runoff seasonality is sensitive to projected climatic changes. In the Langtang catchment in Nepal, future water availability is on the rise for decades to come with limited shifts between seasons. Owing to the high spatiotemporal resolution of the simulations and process complexity included in the modeling, the response times and the mechanisms underlying the variations in glacier area and river flow can be well constrained. The projections indicate that climate change adaptation in Central Chile should focus on dealing with a reduction in water availability, whereas in Nepal preparedness for flood extremes should be the policy priority."}],"date_published":"2016-08-01T00:00:00Z","extern":"1","pmid":1,"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1073/pnas.1606526113","citation":{"mla":"Ragettli, Silvan, et al. “Contrasting Climate Change Impact on River Flows from High-Altitude Catchments in the Himalayan and Andes Mountains.” <i>PNAS</i>, vol. 113, no. 33, Proceedings of the National Academy of Sciences, 2016, pp. 9222–27, doi:<a href=\"https://doi.org/10.1073/pnas.1606526113\">10.1073/pnas.1606526113</a>.","ieee":"S. Ragettli, W. W. Immerzeel, and F. Pellicciotti, “Contrasting climate change impact on river flows from high-altitude catchments in the Himalayan and Andes Mountains,” <i>PNAS</i>, vol. 113, no. 33. Proceedings of the National Academy of Sciences, pp. 9222–9227, 2016.","apa":"Ragettli, S., Immerzeel, W. W., &#38; Pellicciotti, F. (2016). Contrasting climate change impact on river flows from high-altitude catchments in the Himalayan and Andes Mountains. <i>PNAS</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1606526113\">https://doi.org/10.1073/pnas.1606526113</a>","short":"S. Ragettli, W.W. Immerzeel, F. Pellicciotti, PNAS 113 (2016) 9222–9227.","chicago":"Ragettli, Silvan, Walter W. Immerzeel, and Francesca Pellicciotti. “Contrasting Climate Change Impact on River Flows from High-Altitude Catchments in the Himalayan and Andes Mountains.” <i>PNAS</i>. Proceedings of the National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1606526113\">https://doi.org/10.1073/pnas.1606526113</a>.","ista":"Ragettli S, Immerzeel WW, Pellicciotti F. 2016. Contrasting climate change impact on river flows from high-altitude catchments in the Himalayan and Andes Mountains. PNAS. 113(33), 9222–9227.","ama":"Ragettli S, Immerzeel WW, Pellicciotti F. Contrasting climate change impact on river flows from high-altitude catchments in the Himalayan and Andes Mountains. <i>PNAS</i>. 2016;113(33):9222-9227. doi:<a href=\"https://doi.org/10.1073/pnas.1606526113\">10.1073/pnas.1606526113</a>"},"month":"08","status":"public","type":"journal_article","issue":"33","doi":"10.1073/pnas.1606526113","intvolume":"       113","page":"9222-9227","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Contrasting climate change impact on river flows from high-altitude catchments in the Himalayan and Andes Mountains","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1606526113"}],"keyword":["Multidisciplinary"],"publication":"PNAS","_id":"12618","date_created":"2023-02-20T08:14:58Z","oa":1,"article_type":"original","day":"01","quality_controlled":"1"},{"abstract":[{"text":"Despite the recent rapid progress in cryo-electron microscopy (cryo-EM), there still exist ample opportunities for improvement in sample preparation. Macromolecular complexes may disassociate or adopt nonrandom orientations against the extended air–water interface that exists for a short time before the sample is frozen. We designed a hollow support structure using 3D DNA origami to protect complexes from the detrimental effects of cryo-EM sample preparation. For a first proof-of-principle, we concentrated on the transcription factor p53, which binds to specific DNA sequences on double-stranded DNA. The support structures spontaneously form monolayers of preoriented particles in a thin film of water, and offer advantages in particle picking and sorting. By controlling the position of the binding sequence on a single helix that spans the hollow support structure, we also sought to control the orientation of individual p53 complexes. Although the latter did not yet yield the desired results, the support structures did provide partial information about the relative orientations of individual p53 complexes. We used this information to calculate a tomographic 3D reconstruction, and refined this structure to a final resolution of ∼15 Å. This structure settles an ongoing debate about the symmetry of the p53 tetramer bound to DNA.","lang":"eng"}],"date_published":"2016-10-13T00:00:00Z","extern":"1","pmid":1,"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1073/pnas.1612720113","external_id":{"pmid":["27821763"]},"author":[{"first_name":"Thomas G.","full_name":"Martin, Thomas G.","last_name":"Martin"},{"last_name":"Bharat","full_name":"Bharat, Tanmay A. M.","first_name":"Tanmay A. M."},{"first_name":"Andreas C.","full_name":"Joerger, Andreas C.","last_name":"Joerger"},{"first_name":"Xiao-chen","full_name":"Bai, Xiao-chen","last_name":"Bai"},{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M","full_name":"Praetorius, Florian M","last_name":"Praetorius"},{"full_name":"Fersht, Alan R.","last_name":"Fersht","first_name":"Alan R."},{"first_name":"Hendrik","last_name":"Dietz","full_name":"Dietz, Hendrik"},{"full_name":"Scheres, Sjors H. W.","last_name":"Scheres","first_name":"Sjors H. W."}],"scopus_import":"1","publication_status":"published","volume":113,"year":"2016","publisher":"Proceedings of the National Academy of Sciences","date_updated":"2023-11-07T11:53:06Z","oa_version":"Published Version","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"_id":"14304","publication":"PNAS","date_created":"2023-09-06T12:53:48Z","day":"13","quality_controlled":"1","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Design of a molecular support for cryo-EM structure determination","intvolume":"       113","doi":"10.1073/pnas.1612720113","page":"E7456-E7463","article_processing_charge":"No","status":"public","month":"10","citation":{"short":"T.G. Martin, T.A.M. Bharat, A.C. Joerger, X. Bai, F.M. Praetorius, A.R. Fersht, H. Dietz, S.H.W. Scheres, PNAS 113 (2016) E7456–E7463.","chicago":"Martin, Thomas G., Tanmay A. M. Bharat, Andreas C. Joerger, Xiao-chen Bai, Florian M Praetorius, Alan R. Fersht, Hendrik Dietz, and Sjors H. W. Scheres. “Design of a Molecular Support for Cryo-EM Structure Determination.” <i>PNAS</i>. Proceedings of the National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1612720113\">https://doi.org/10.1073/pnas.1612720113</a>.","ama":"Martin TG, Bharat TAM, Joerger AC, et al. Design of a molecular support for cryo-EM structure determination. <i>PNAS</i>. 2016;113(47):E7456-E7463. doi:<a href=\"https://doi.org/10.1073/pnas.1612720113\">10.1073/pnas.1612720113</a>","ista":"Martin TG, Bharat TAM, Joerger AC, Bai X, Praetorius FM, Fersht AR, Dietz H, Scheres SHW. 2016. Design of a molecular support for cryo-EM structure determination. PNAS. 113(47), E7456–E7463.","mla":"Martin, Thomas G., et al. “Design of a Molecular Support for Cryo-EM Structure Determination.” <i>PNAS</i>, vol. 113, no. 47, Proceedings of the National Academy of Sciences, 2016, pp. E7456–63, doi:<a href=\"https://doi.org/10.1073/pnas.1612720113\">10.1073/pnas.1612720113</a>.","ieee":"T. G. Martin <i>et al.</i>, “Design of a molecular support for cryo-EM structure determination,” <i>PNAS</i>, vol. 113, no. 47. Proceedings of the National Academy of Sciences, pp. E7456–E7463, 2016.","apa":"Martin, T. G., Bharat, T. A. M., Joerger, A. C., Bai, X., Praetorius, F. M., Fersht, A. R., … Scheres, S. H. W. (2016). Design of a molecular support for cryo-EM structure determination. <i>PNAS</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1612720113\">https://doi.org/10.1073/pnas.1612720113</a>"},"issue":"47","type":"journal_article"},{"page":"9745-9750","doi":"10.1073/pnas.1601858113","publication_status":"published","intvolume":"       113","author":[{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","last_name":"Goodrich","full_name":"Goodrich, Carl Peter"},{"last_name":"Liu","full_name":"Liu, Andrea J.","first_name":"Andrea J."},{"full_name":"Sethna, James P.","last_name":"Sethna","first_name":"James P."}],"date_updated":"2021-01-12T08:15:21Z","publisher":"Proceedings of the National Academy of Sciences","year":"2016","volume":113,"article_processing_charge":"No","oa_version":"None","status":"public","month":"08","citation":{"chicago":"Goodrich, Carl Peter, Andrea J. Liu, and James P. Sethna. “Scaling Ansatz for the Jamming Transition.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1601858113\">https://doi.org/10.1073/pnas.1601858113</a>.","short":"C.P. Goodrich, A.J. Liu, J.P. Sethna, Proceedings of the National Academy of Sciences 113 (2016) 9745–9750.","ama":"Goodrich CP, Liu AJ, Sethna JP. Scaling ansatz for the jamming transition. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(35):9745-9750. doi:<a href=\"https://doi.org/10.1073/pnas.1601858113\">10.1073/pnas.1601858113</a>","ista":"Goodrich CP, Liu AJ, Sethna JP. 2016. Scaling ansatz for the jamming transition. Proceedings of the National Academy of Sciences. 113(35), 9745–9750.","ieee":"C. P. Goodrich, A. J. Liu, and J. P. Sethna, “Scaling ansatz for the jamming transition,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 35. Proceedings of the National Academy of Sciences, pp. 9745–9750, 2016.","mla":"Goodrich, Carl Peter, et al. “Scaling Ansatz for the Jamming Transition.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 35, Proceedings of the National Academy of Sciences, 2016, pp. 9745–50, doi:<a href=\"https://doi.org/10.1073/pnas.1601858113\">10.1073/pnas.1601858113</a>.","apa":"Goodrich, C. P., Liu, A. J., &#38; Sethna, J. P. (2016). Scaling ansatz for the jamming transition. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1601858113\">https://doi.org/10.1073/pnas.1601858113</a>"},"type":"journal_article","issue":"35","publication_identifier":{"issn":["0027-8424","1091-6490"]},"extern":"1","date_published":"2016-08-30T00:00:00Z","date_created":"2020-04-30T11:39:53Z","_id":"7760","abstract":[{"lang":"eng","text":"We propose a Widom-like scaling ansatz for the critical jamming transition. Our ansatz for the elastic energy shows that the scaling of the energy, compressive strain, shear strain, system size, pressure, shear stress, bulk modulus, and shear modulus are all related to each other via scaling relations, with only three independent scaling exponents. We extract the values of these exponents from already known numerical or theoretical results, and we numerically verify the resulting predictions of the scaling theory for the energy and residual shear stress. We also derive a scaling relation between pressure and residual shear stress that yields insight into why the shear and bulk moduli scale differently. Our theory shows that the jamming transition exhibits an emergent scale invariance, setting the stage for the potential development of a renormalization group theory for jamming."}],"publication":"Proceedings of the National Academy of Sciences","fulldoi":"https://doi.org/10.1073/pnas.1601858113","quality_controlled":"1","day":"30","article_type":"original","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Scaling ansatz for the jamming transition"},{"date_created":"2020-09-18T10:06:58Z","abstract":[{"lang":"eng","text":"During spore formation in Bacillus subtilis a transenvelope complex is assembled across the double membrane that separates the mother cell and forespore. This complex (called the “A–Q complex”) is required to maintain forespore development and is composed of proteins with remote homology to components of type II, III, and IV secretion systems found in Gram-negative bacteria. Here, we show that one of these proteins, SpoIIIAG, which has remote homology to ring-forming proteins found in type III secretion systems, assembles into an oligomeric ring in the periplasmic-like space between the two membranes. Three-dimensional reconstruction of images generated by cryo-electron microscopy indicates that the SpoIIIAG ring has a cup-and-saucer architecture with a 6-nm central pore. Structural modeling of SpoIIIAG generated a 24-member ring with dimensions similar to those of the EM-derived saucer. Point mutations in the predicted oligomeric interface disrupted ring formation in vitro and impaired forespore gene expression and efficient spore formation in vivo. Taken together, our data provide strong support for the model in which the A–Q transenvelope complex contains a conduit that connects the mother cell and forespore. We propose that a set of stacked rings spans the intermembrane space, as has been found for type III secretion systems."}],"_id":"8452","publication":"Proceedings of the National Academy of Sciences","extern":"1","date_published":"2016-09-28T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","article_type":"original","day":"28","fulldoi":"https://doi.org/10.1073/pnas.1609604113","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis","author":[{"first_name":"Christopher D. A.","full_name":"Rodrigues, Christopher D. A.","last_name":"Rodrigues"},{"first_name":"Xavier","full_name":"Henry, Xavier","last_name":"Henry"},{"full_name":"Neumann, Emmanuelle","last_name":"Neumann","first_name":"Emmanuelle"},{"first_name":"Vilius","last_name":"Kurauskas","full_name":"Kurauskas, Vilius"},{"first_name":"Laure","full_name":"Bellard, Laure","last_name":"Bellard"},{"first_name":"Yann","full_name":"Fichou, Yann","last_name":"Fichou"},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606"},{"first_name":"Guy","last_name":"Schoehn","full_name":"Schoehn, Guy"},{"full_name":"Rudner, David Z.","last_name":"Rudner","first_name":"David Z."},{"first_name":"Cecile","last_name":"Morlot","full_name":"Morlot, Cecile"}],"page":"11585-11590","publication_status":"published","doi":"10.1073/pnas.1609604113","intvolume":"       113","year":"2016","article_processing_charge":"No","volume":113,"date_updated":"2021-01-12T08:19:22Z","publisher":"National Academy of Sciences","month":"09","status":"public","citation":{"mla":"Rodrigues, Christopher D. A., et al. “A Ring-Shaped Conduit Connects the Mother Cell and Forespore during Sporulation in Bacillus Subtilis.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 41, National Academy of Sciences, 2016, pp. 11585–90, doi:<a href=\"https://doi.org/10.1073/pnas.1609604113\">10.1073/pnas.1609604113</a>.","ieee":"C. D. A. Rodrigues <i>et al.</i>, “A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 41. National Academy of Sciences, pp. 11585–11590, 2016.","apa":"Rodrigues, C. D. A., Henry, X., Neumann, E., Kurauskas, V., Bellard, L., Fichou, Y., … Morlot, C. (2016). A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1609604113\">https://doi.org/10.1073/pnas.1609604113</a>","short":"C.D.A. Rodrigues, X. Henry, E. Neumann, V. Kurauskas, L. Bellard, Y. Fichou, P. Schanda, G. Schoehn, D.Z. Rudner, C. Morlot, Proceedings of the National Academy of Sciences 113 (2016) 11585–11590.","chicago":"Rodrigues, Christopher D. A., Xavier Henry, Emmanuelle Neumann, Vilius Kurauskas, Laure Bellard, Yann Fichou, Paul Schanda, Guy Schoehn, David Z. Rudner, and Cecile Morlot. “A Ring-Shaped Conduit Connects the Mother Cell and Forespore during Sporulation in Bacillus Subtilis.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1609604113\">https://doi.org/10.1073/pnas.1609604113</a>.","ista":"Rodrigues CDA, Henry X, Neumann E, Kurauskas V, Bellard L, Fichou Y, Schanda P, Schoehn G, Rudner DZ, Morlot C. 2016. A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis. Proceedings of the National Academy of Sciences. 113(41), 11585–11590.","ama":"Rodrigues CDA, Henry X, Neumann E, et al. A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(41):11585-11590. doi:<a href=\"https://doi.org/10.1073/pnas.1609604113\">10.1073/pnas.1609604113</a>"},"oa_version":"None","type":"journal_article","issue":"41","publication_identifier":{"issn":["0027-8424","1091-6490"]}},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1619074114"}],"title":"Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9473","publication":"Proceedings of the National Academy of Sciences","date_created":"2021-06-07T06:21:39Z","oa":1,"day":"27","quality_controlled":"1","article_type":"original","citation":{"ieee":"P.-H. Hsieh <i>et al.</i>, “Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15132–15137, 2016.","mla":"Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15132–37, doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>.","apa":"Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L., … Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>","short":"P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman, X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.","chicago":"Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman, Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>.","ama":"Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15132-15137. doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>","ista":"Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. 113(52), 15132–15137."},"status":"public","month":"12","issue":"52","type":"journal_article","intvolume":"       113","doi":"10.1073/pnas.1619074114","page":"15132-15137","article_processing_charge":"No","external_id":{"pmid":["27956643"]},"date_published":"2016-12-27T00:00:00Z","extern":"1","abstract":[{"text":"Cytosine DNA methylation regulates the expression of eukaryotic genes and transposons. Methylation is copied by methyltransferases after DNA replication, which results in faithful transmission of methylation patterns during cell division and, at least in flowering plants, across generations. Transgenerational inheritance is mediated by a small group of cells that includes gametes and their progenitors. However, methylation is usually analyzed in somatic tissues that do not contribute to the next generation, and the mechanisms of transgenerational inheritance are inferred from such studies. To gain a better understanding of how DNA methylation is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases. We find that DNA methylation dependency on these enzymes is similar in sperm, vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin in vegetative cells, likely reflecting transcription of heterochromatic transposons in this cell type. We also show that lack of histone H1, which elevates heterochromatic DNA methylation in somatic tissues, does not have this effect in pollen. Instead, levels of CG methylation in wild-type sperm and vegetative cells, as well as in wild-type microspores from which both pollen cell types originate, are substantially higher than in wild-type somatic tissues and similar to those of H1-depleted roots. Our results demonstrate that the mechanisms of methylation maintenance are similar between pollen and somatic cells, but the efficiency of CG methylation is higher in pollen, allowing methylation patterns to be accurately inherited across generations.","lang":"eng"}],"department":[{"_id":"DaZi"},{"_id":"XiFe"}],"fulldoi":"https://doi.org/10.1073/pnas.1619074114","pmid":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","author":[{"full_name":"Hsieh, Ping-Hung","last_name":"Hsieh","first_name":"Ping-Hung"},{"full_name":"He, Shengbo","last_name":"He","first_name":"Shengbo"},{"last_name":"Buttress","full_name":"Buttress, Toby","first_name":"Toby"},{"full_name":"Gao, Hongbo","last_name":"Gao","first_name":"Hongbo"},{"full_name":"Couchman, Matthew","last_name":"Couchman","first_name":"Matthew"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman"},{"orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi"}],"scopus_import":"1","publisher":"National Academy of Sciences","date_updated":"2023-05-08T11:00:40Z","volume":113,"year":"2016"},{"quality_controlled":"1","article_type":"original","day":"27","oa":1,"date_created":"2021-06-07T07:10:59Z","_id":"9477","publication":"Proceedings of the National Academy of Sciences","keyword":["Multidisciplinary"],"title":"DNA demethylation is initiated in the central cells of Arabidopsis and rice","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1619047114"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","page":"15138-15143","doi":"10.1073/pnas.1619047114","intvolume":"       113","type":"journal_article","issue":"52","status":"public","citation":{"ama":"Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15138-15143. doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>","ista":"Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. 113(52), 15138–15143.","short":"K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman, R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy of Sciences 113 (2016) 15138–15143.","chicago":"Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun, Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>.","apa":"Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten, S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>","ieee":"K. Park <i>et al.</i>, “DNA demethylation is initiated in the central cells of Arabidopsis and rice,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.","mla":"Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>."},"month":"12","language":[{"iso":"eng"}],"pmid":1,"fulldoi":"https://doi.org/10.1073/pnas.1619047114","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"abstract":[{"lang":"eng","text":"Cytosine methylation is a DNA modification with important regulatory functions in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive DNA demethylation, which is required for proper gene expression in the endosperm, a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm cell carried in the pollen and a female central cell. Endosperm DNA demethylation is observed specifically on the chromosomes inherited from the central cell in Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase in Arabidopsis. DEMETER is expressed in the central cell before fertilization, suggesting that endosperm demethylation patterns are inherited from the central cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed to contribute to central cell demethylation. However, with the exception of three maize genes, central cell DNA methylation has not been directly measured, leaving the origin and mechanism of endosperm demethylation uncertain. Here, we report genome-wide analysis of DNA methylation in the central cells of Arabidopsis and rice—species that diverged 150 million years ago—as well as in rice egg cells. We find that DNA demethylation in both species is initiated in central cells, which requires DEMETER in Arabidopsis. However, we do not observe a global reduction of CG methylation that would be indicative of lowered MET1 activity; on the contrary, CG methylation efficiency is elevated in female gametes compared with nonsexual tissues. Our results demonstrate that locus-specific, active DNA demethylation in the central cell is the origin of maternal chromosome hypomethylation in the endosperm."}],"extern":"1","date_published":"2016-12-27T00:00:00Z","external_id":{"pmid":["27956642"]},"year":"2016","volume":113,"date_updated":"2023-05-08T11:00:07Z","publisher":"National Academy of Sciences","scopus_import":"1","author":[{"first_name":"Kyunghyuk","last_name":"Park","full_name":"Park, Kyunghyuk"},{"last_name":"Kim","full_name":"Kim, M. Yvonne","first_name":"M. Yvonne"},{"first_name":"Martin","full_name":"Vickers, Martin","last_name":"Vickers"},{"full_name":"Park, Jin-Sup","last_name":"Park","first_name":"Jin-Sup"},{"first_name":"Youbong","full_name":"Hyun, Youbong","last_name":"Hyun"},{"last_name":"Okamoto","full_name":"Okamoto, Takashi","first_name":"Takashi"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel"},{"last_name":"Fischer","full_name":"Fischer, Robert L.","first_name":"Robert L."},{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234"},{"first_name":"Yeonhee","last_name":"Choi","full_name":"Choi, Yeonhee"},{"first_name":"Stefan","last_name":"Scholten","full_name":"Scholten, Stefan"}],"publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"oa_version":"Published Version"},{"quality_controlled":"1","article_type":"original","day":"08","oa":1,"date_created":"2026-07-27T12:30:24Z","publication":"Proceedings of the National Academy of Sciences","_id":"22536","keyword":["carbon dioxide","modeling","FACE","soil moisture","evapotranspiration"],"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1605036113","open_access":"1"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Partitioning direct and indirect effects reveals the response of water-limited ecosystems to elevated CO","article_processing_charge":"No","page":"12757-12762","intvolume":"       113","doi":"10.1073/pnas.1605036113","issue":"45","type":"journal_article","month":"11","citation":{"ista":"Fatichi S, Leuzinger S, Paschalis A, Langley JA, Donnellan Barraclough A, Hovenden MJ. 2016. Partitioning direct and indirect effects reveals the response of water-limited ecosystems to elevated CO. Proceedings of the National Academy of Sciences. 113(45), 12757–12762.","ama":"Fatichi S, Leuzinger S, Paschalis A, Langley JA, Donnellan Barraclough A, Hovenden MJ. Partitioning direct and indirect effects reveals the response of water-limited ecosystems to elevated CO. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(45):12757-12762. doi:<a href=\"https://doi.org/10.1073/pnas.1605036113\">10.1073/pnas.1605036113</a>","chicago":"Fatichi, Simone, Sebastian Leuzinger, Athanasios Paschalis, J. Adam Langley, Alicia Donnellan Barraclough, and Mark J. Hovenden. “Partitioning Direct and Indirect Effects Reveals the Response of Water-Limited Ecosystems to Elevated CO.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1605036113\">https://doi.org/10.1073/pnas.1605036113</a>.","short":"S. Fatichi, S. Leuzinger, A. Paschalis, J.A. Langley, A. Donnellan Barraclough, M.J. Hovenden, Proceedings of the National Academy of Sciences 113 (2016) 12757–12762.","apa":"Fatichi, S., Leuzinger, S., Paschalis, A., Langley, J. A., Donnellan Barraclough, A., &#38; Hovenden, M. J. (2016). Partitioning direct and indirect effects reveals the response of water-limited ecosystems to elevated CO. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1605036113\">https://doi.org/10.1073/pnas.1605036113</a>","ieee":"S. Fatichi, S. Leuzinger, A. Paschalis, J. A. Langley, A. Donnellan Barraclough, and M. J. Hovenden, “Partitioning direct and indirect effects reveals the response of water-limited ecosystems to elevated CO,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 45. National Academy of Sciences, pp. 12757–12762, 2016.","mla":"Fatichi, Simone, et al. “Partitioning Direct and Indirect Effects Reveals the Response of Water-Limited Ecosystems to Elevated CO.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 45, National Academy of Sciences, 2016, pp. 12757–62, doi:<a href=\"https://doi.org/10.1073/pnas.1605036113\">10.1073/pnas.1605036113</a>."},"status":"public","OA_type":"free access","language":[{"iso":"eng"}],"pmid":1,"fulldoi":"https://doi.org/10.1073/pnas.1605036113","abstract":[{"lang":"eng","text":"Increasing concentrations of atmospheric carbon dioxide are expected to affect carbon assimilation and evapotranspiration (ET), ultimately driving changes in plant growth, hydrology, and the global carbon balance. Direct leaf biochemical effects have been widely investigated, whereas indirect effects, although documented, elude explicit quantification in experiments. Here, we used a mechanistic model to investigate the relative contributions of direct (through carbon assimilation) and indirect (via soil moisture savings due to stomatal closure, and changes in leaf area index) effects of elevated CO2 across a variety of ecosystems. We specifically determined which ecosystems and climatic conditions maximize the indirect effects of elevated CO2. The simulations suggest that the indirect effects of elevated CO2 on net primary productivity are large and variable, ranging from less than 10% to more than 100% of the size of direct effects. For ET, indirect effects were, on average, 65% of the size of direct effects. Indirect effects tended to be considerably larger in water-limited ecosystems. As a consequence, the total CO2 effect had a significant, inverse relationship with the wetness index and was directly related to vapor pressure deficit. These results have major implications for our understanding of the CO2 response of ecosystems and for global projections of CO2 fertilization, because, although direct effects are typically understood and easily reproducible in models, simulations of indirect effects are far more challenging and difficult to constrain. Our findings also provide an explanation for the discrepancies between experiments in the total CO2 effect on net primary productivity."}],"extern":"1","date_published":"2016-11-08T00:00:00Z","external_id":{"pmid":["27791074"]},"das_tickbox":"1","year":"2016","volume":113,"date_updated":"2026-08-06T08:08:46Z","publisher":"National Academy of Sciences","scopus_import":"1","OA_place":"publisher","author":[{"last_name":"Fatichi","full_name":"Fatichi, Simone","first_name":"Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6"},{"full_name":"Leuzinger, Sebastian","last_name":"Leuzinger","first_name":"Sebastian"},{"full_name":"Paschalis, Athanasios","last_name":"Paschalis","first_name":"Athanasios"},{"last_name":"Langley","full_name":"Langley, J. Adam","first_name":"J. Adam"},{"last_name":"Donnellan Barraclough","full_name":"Donnellan Barraclough, Alicia","first_name":"Alicia"},{"first_name":"Mark J.","full_name":"Hovenden, Mark J.","last_name":"Hovenden"}],"publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"oa_version":"Published Version"},{"external_id":{"pmid":["26100886"]},"file":[{"date_updated":"2020-07-14T12:47:20Z","file_id":"6119","content_type":"application/pdf","file_name":"2015_PNAS_Fenk.pdf","relation":"main_file","access_level":"open_access","checksum":"3d2da5af8d72467e382a565abc2e003d","date_created":"2019-03-19T14:21:07Z","file_size":2822681,"creator":"kschuh"}],"pmid":1,"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1073/pnas.1423808112","abstract":[{"text":"Carbon dioxide (CO2) gradients are ubiquitous and provide animals with information about their environment, such as the potential presence of prey or predators. The nematode Caenorhabditis elegans avoids elevated CO2, and previous work identified three neuron pairs called “BAG,” “AFD,” and “ASE” that respond to CO2 stimuli. Using in vivo Ca2+ imaging and behavioral analysis, we show that C. elegans can detect CO2 independently of these sensory pathways. Many of the C. elegans sensory neurons we examined, including the AWC olfactory neurons, the ASJ and ASK gustatory neurons, and the ASH and ADL nociceptors, respond to a rise in CO2 with a rise in Ca2+. In contrast, glial sheath cells harboring the sensory endings of C. elegans’ major chemosensory neurons exhibit strong and sustained decreases in Ca2+ in response to high CO2. Some of these CO2 responses appear to be cell intrinsic. Worms therefore may couple detection of CO2 to that of other cues at the earliest stages of sensory processing. We show that C. elegans persistently suppresses oviposition at high CO2. Hermaphrodite-specific neurons (HSNs), the executive neurons driving egg-laying, are tonically inhibited when CO2 is elevated. CO2 modulates the egg-laying system partly through the AWC olfactory neurons: High CO2 tonically activates AWC by a cGMP-dependent mechanism, and AWC output inhibits the HSNs. Our work shows that CO2 is a more complex sensory cue for C. elegans than previously thought, both in terms of behavior and neural circuitry.","lang":"eng"}],"date_published":"2015-07-07T00:00:00Z","extern":"1","publication_identifier":{"issn":["0027-8424","1091-6490"]},"oa_version":"Published Version","volume":112,"year":"2015","publisher":"National Academy of Sciences","has_accepted_license":"1","date_updated":"2021-01-12T08:06:12Z","author":[{"first_name":"Lorenz A.","full_name":"Fenk, Lorenz A.","last_name":"Fenk"},{"full_name":"de Bono, Mario","last_name":"de Bono","orcid":"0000-0001-8347-0443","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity","oa":1,"day":"07","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences","_id":"6118","file_date_updated":"2020-07-14T12:47:20Z","date_created":"2019-03-19T14:15:50Z","issue":"27","type":"journal_article","month":"07","citation":{"apa":"Fenk, L. A., &#38; de Bono, M. (2015). Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1423808112\">https://doi.org/10.1073/pnas.1423808112</a>","ieee":"L. A. Fenk and M. de Bono, “Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity,” <i>Proceedings of the National Academy of Sciences</i>, vol. 112, no. 27. National Academy of Sciences, pp. E3525–E3534, 2015.","mla":"Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes in Neural Activity.” <i>Proceedings of the National Academy of Sciences</i>, vol. 112, no. 27, National Academy of Sciences, 2015, pp. E3525–34, doi:<a href=\"https://doi.org/10.1073/pnas.1423808112\">10.1073/pnas.1423808112</a>.","ista":"Fenk LA, de Bono M. 2015. Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity. Proceedings of the National Academy of Sciences. 112(27), E3525–E3534.","ama":"Fenk LA, de Bono M. Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity. <i>Proceedings of the National Academy of Sciences</i>. 2015;112(27):E3525-E3534. doi:<a href=\"https://doi.org/10.1073/pnas.1423808112\">10.1073/pnas.1423808112</a>","short":"L.A. Fenk, M. de Bono, Proceedings of the National Academy of Sciences 112 (2015) E3525–E3534.","chicago":"Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes in Neural Activity.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1423808112\">https://doi.org/10.1073/pnas.1423808112</a>."},"status":"public","ddc":["570"],"intvolume":"       112","doi":"10.1073/pnas.1423808112","page":"E3525-E3534"},{"type":"journal_article","issue":"30","OA_type":"free access","status":"public","month":"07","citation":{"ista":"Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333.","ama":"Kretz C, Dai M, Soylemez O, et al. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. <i>PNAS</i>. 2015;112(30):9328-9333. doi:<a href=\"https://doi.org/10.1073/pnas.1511328112\">10.1073/pnas.1511328112</a>","short":"C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg, F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333.","chicago":"Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1511328112\">https://doi.org/10.1073/pnas.1511328112</a>.","apa":"Kretz, C., Dai, M., Soylemez, O., Yee, A., Desch, K., Siemieniak, D., … Ginsburg, D. (2015). Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1511328112\">https://doi.org/10.1073/pnas.1511328112</a>","ieee":"C. Kretz <i>et al.</i>, “Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13,” <i>PNAS</i>, vol. 112, no. 30. National Academy of Sciences, pp. 9328–9333, 2015.","mla":"Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” <i>PNAS</i>, vol. 112, no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:<a href=\"https://doi.org/10.1073/pnas.1511328112\">10.1073/pnas.1511328112</a>."},"article_processing_charge":"No","publist_id":"6783","doi":"10.1073/pnas.1511328112","intvolume":"       112","page":"9328 - 9333","title":"Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1511328112","open_access":"1"}],"oa":1,"day":"28","quality_controlled":"1","article_type":"original","publication":"PNAS","_id":"866","date_created":"2018-12-11T11:48:55Z","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"oa_version":"Accepted Version","volume":112,"year":"2015","publisher":"National Academy of Sciences","date_updated":"2026-05-19T13:15:29Z","author":[{"first_name":"Colin","full_name":"Kretz, Colin","last_name":"Kretz"},{"first_name":"Manhong","full_name":"Dai, Manhong","last_name":"Dai"},{"first_name":"Onuralp","full_name":"Soylemez, Onuralp","last_name":"Soylemez"},{"first_name":"Andrew","last_name":"Yee","full_name":"Yee, Andrew"},{"first_name":"Karl","full_name":"Desch, Karl","last_name":"Desch"},{"last_name":"Siemieniak","full_name":"Siemieniak, David","first_name":"David"},{"first_name":"Kärt","full_name":"Tomberg, Kärt","last_name":"Tomberg"},{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"first_name":"Fan","last_name":"Meng","full_name":"Meng, Fan"},{"last_name":"Ginsburg","full_name":"Ginsburg, David","first_name":"David"}],"OA_place":"publisher","scopus_import":"1","publication_status":"published","external_id":{"pmid":[" 26170332"]},"pmid":1,"language":[{"iso":"eng"}],"acknowledgement":"We thank Isabel Wang and Vivian Cheung from the Life Sciences Institute, University of Michigan, for assistance with high- throughput sequencing experiments and valuable discussions. We also thank J. Evan Sadler (Washington University) and Sriram Krishnaswamy (Children’s Hospital of Philadelphia) for helpful discussions. We thank Jeff Weitz (McMaster University), Jim Fredenburgh (McMaster University), and Steve Weiss (University of Michigan) for critical review of the manuscript. C.A.K. was awarded the Judith Graham Pool Fellowship from National Hemophilia Foundation. This work was supported by the National Institutes of Health (R01 HL039693), the National Heart, Lung, and Blood Institute (P01- HL057346), Ministerio de Economía y Competitividad Grants BFU2012- 31329 and Sev-2012-0208, and European Research Council Starting Grant 335980_EinME. D.G. is an investigator of the Howard Hughes Medical In- stitute, and F.A.K. is a Howard Hughes Medical Institute International Early Career Scientist.\r\n","fulldoi":"https://doi.org/10.1073/pnas.1511328112","abstract":[{"lang":"eng","text":"Proteases play important roles in many biologic processes and are key mediators of cancer, inflammation, and thrombosis. However, comprehensive and quantitative techniques to define the substrate specificity profile of proteases are lacking. The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage display library based on a 73-amino acid fragment of VWF was constructed, and the ADAMTS13-dependent change in library complexity was evaluated over reaction time points, using high-throughput sequencing. Reaction rate constants (kcat/KM) were calculated for nearly every possible single amino acid substitution within this fragment. This massively parallel enzyme kinetics analysis detailed the specificity of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues while defining exosite binding domains. These data provided empirical evidence for the propensity for epistasis within VWF and showed strong correlation to conservation across orthologs, highlighting evolutionary selective pressures for VWF."}],"date_published":"2015-07-28T00:00:00Z","extern":"1"},{"language":[{"iso":"eng"}],"pmid":1,"fulldoi":"https://doi.org/10.1073/pnas.1401651112","abstract":[{"text":"We consider the problem of exact and inexact matching of weighted undirected graphs, in which a bijective correspondence is sought to minimize a quadratic weight disagreement. This computationally challenging problem is often relaxed as a convex quadratic program, in which the space of permutations is replaced by the space of doubly stochastic matrices. However, the applicability of such a relaxation is poorly understood. We define a broad class of friendly graphs characterized by an easily verifiable spectral property. We prove that for friendly graphs, the convex relaxation is guaranteed to find the exact isomorphism or certify its inexistence. This result is further extended to approximately isomorphic graphs, for which we develop an explicit bound on the amount of weight disagreement under which the relaxation is guaranteed to find the globally optimal approximate isomorphism. We also show that in many cases, the graph matching problem can be further harmlessly relaxed to a convex quadratic program with only n separable linear equality constraints, which is substantially more efficient than the standard relaxation involving 2n equality and n2 inequality constraints. Finally, we show that our results are still valid for unfriendly graphs if additional information in the form of seeds or attributes is allowed, with the latter satisfying an easy to verify spectral characteristic.","lang":"eng"}],"extern":"1","date_published":"2015-03-10T00:00:00Z","external_id":{"pmid":["25713342"]},"year":"2015","volume":112,"date_updated":"2024-11-12T08:54:37Z","publisher":"National Academy of Sciences","scopus_import":"1","author":[{"first_name":"Yonathan","full_name":"Aflalo, Yonathan","last_name":"Aflalo"},{"first_name":"Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","full_name":"Bronstein, Alexander","last_name":"Bronstein","orcid":"0000-0001-9699-8730"},{"first_name":"Ron","full_name":"Kimmel, Ron","last_name":"Kimmel"}],"publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"oa_version":"None","day":"10","quality_controlled":"1","article_type":"original","date_created":"2024-10-15T11:20:54Z","_id":"18371","publication":"Proceedings of the National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"On convex relaxation of graph isomorphism","article_processing_charge":"No","page":"2942-2947","doi":"10.1073/pnas.1401651112","intvolume":"       112","issue":"10","type":"journal_article","status":"public","citation":{"mla":"Aflalo, Yonathan, et al. “On Convex Relaxation of Graph Isomorphism.” <i>Proceedings of the National Academy of Sciences</i>, vol. 112, no. 10, National Academy of Sciences, 2015, pp. 2942–47, doi:<a href=\"https://doi.org/10.1073/pnas.1401651112\">10.1073/pnas.1401651112</a>.","ieee":"Y. Aflalo, A. M. Bronstein, and R. Kimmel, “On convex relaxation of graph isomorphism,” <i>Proceedings of the National Academy of Sciences</i>, vol. 112, no. 10. National Academy of Sciences, pp. 2942–2947, 2015.","apa":"Aflalo, Y., Bronstein, A. M., &#38; Kimmel, R. (2015). On convex relaxation of graph isomorphism. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1401651112\">https://doi.org/10.1073/pnas.1401651112</a>","chicago":"Aflalo, Yonathan, Alex M. Bronstein, and Ron Kimmel. “On Convex Relaxation of Graph Isomorphism.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1401651112\">https://doi.org/10.1073/pnas.1401651112</a>.","short":"Y. Aflalo, A.M. Bronstein, R. Kimmel, Proceedings of the National Academy of Sciences 112 (2015) 2942–2947.","ista":"Aflalo Y, Bronstein AM, Kimmel R. 2015. On convex relaxation of graph isomorphism. Proceedings of the National Academy of Sciences. 112(10), 2942–2947.","ama":"Aflalo Y, Bronstein AM, Kimmel R. On convex relaxation of graph isomorphism. <i>Proceedings of the National Academy of Sciences</i>. 2015;112(10):2942-2947. doi:<a href=\"https://doi.org/10.1073/pnas.1401651112\">10.1073/pnas.1401651112</a>"},"month":"03"},{"keyword":["multidisciplinary"],"main_file_link":[{"open_access":"1","url":"https://www.pnas.org/content/111/50/17869"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Crucial role of nonspecific interactions in amyloid nucleation","day":"01","article_type":"original","quality_controlled":"1","oa":1,"date_created":"2021-11-29T13:09:53Z","_id":"10382","publication":"Proceedings of the National Academy of Sciences","issue":"50","type":"journal_article","month":"12","citation":{"ama":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions in amyloid nucleation. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(50):17869-17874. doi:<a href=\"https://doi.org/10.1073/pnas.1410159111\">10.1073/pnas.1410159111</a>","ista":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 111(50), 17869–17874.","chicago":"Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1410159111\">https://doi.org/10.1073/pnas.1410159111</a>.","short":"A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National Academy of Sciences 111 (2014) 17869–17874.","apa":"Šarić, A., Chebaro, Y. C., Knowles, T. P. J., &#38; Frenkel, D. (2014). Crucial role of nonspecific interactions in amyloid nucleation. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1410159111\">https://doi.org/10.1073/pnas.1410159111</a>","ieee":"A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of nonspecific interactions in amyloid nucleation,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874, 2014.","mla":"Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:<a href=\"https://doi.org/10.1073/pnas.1410159111\">10.1073/pnas.1410159111</a>."},"status":"public","article_processing_charge":"No","page":"17869-17874","intvolume":"       111","doi":"10.1073/pnas.1410159111","external_id":{"pmid":["25453085"],"arxiv":["1412.0897"]},"language":[{"iso":"eng"}],"acknowledgement":"We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs, for helpful discussions. A.Š. acknowledges support from the Human Frontier Science Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology and Biological Sciences Research Council. D.F. acknowledges European Research Council Advanced Grant 227758.","arxiv":1,"pmid":1,"fulldoi":"https://doi.org/10.1073/pnas.1410159111","abstract":[{"text":"Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. However, it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct. Analogously, it has not been resolved if the amyloid nucleation process is a classical one-step nucleation process or a two-step process involving prenucleation clusters. We use coarse-grained computer simulations to study the effect of nonspecific attractions between peptides on the primary nucleation process underlying amyloid fibrillization. We find that, for peptides that do not attract, the classical one-step nucleation mechanism is possible but only at nonphysiologically high peptide concentrations. At low peptide concentrations, which mimic the physiologically relevant regime, attractive interpeptide interactions are essential for fibril formation. Nucleation then inevitably takes place through a two-step mechanism involving prefibrillar oligomers. We show that oligomers not only help peptides meet each other but also, create an environment that facilitates the conversion of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically does not proceed through the most prevalent oligomers but through an oligomer size that is only observed in rare fluctuations, which is why such aggregates might be hard to capture experimentally. Finally, we find that the nucleation of amyloid fibrils cannot be described by classical nucleation theory: in the two-step mechanism, the critical nucleus size increases with increases in both concentration and interpeptide interactions, which is in direct contrast with predictions from classical nucleation theory.","lang":"eng"}],"extern":"1","date_published":"2014-12-01T00:00:00Z","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"oa_version":"Published Version","year":"2014","volume":111,"date_updated":"2021-11-29T13:29:05Z","publisher":"National Academy of Sciences","scopus_import":"1","author":[{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139"},{"full_name":"Chebaro, Yassmine C.","last_name":"Chebaro","first_name":"Yassmine C."},{"first_name":"Tuomas P. J.","last_name":"Knowles","full_name":"Knowles, Tuomas P. J."},{"last_name":"Frenkel","full_name":"Frenkel, Daan","first_name":"Daan"}],"publication_status":"published"}]