[{"quality_controlled":"1","ec_funded":1,"citation":{"ama":"O’Brien J, Benková E. Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. 2013;4. doi:10.3389/fpls.2013.00451","apa":"O’Brien, J., & Benková, E. (2013). Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2013.00451","chicago":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” Frontiers in Plant Science. Frontiers Research Foundation, 2013. https://doi.org/10.3389/fpls.2013.00451.","short":"J. O’Brien, E. Benková, Frontiers in Plant Science 4 (2013).","ieee":"J. O’Brien and E. Benková, “Cytokinin cross talking during biotic and abiotic stress responses,” Frontiers in Plant Science, vol. 4. Frontiers Research Foundation, 2013.","ista":"O’Brien J, Benková E. 2013. Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. 4, 451.","mla":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” Frontiers in Plant Science, vol. 4, 451, Frontiers Research Foundation, 2013, doi:10.3389/fpls.2013.00451."},"doi":"10.3389/fpls.2013.00451","has_accepted_license":"1","intvolume":" 4","year":"2013","language":[{"iso":"eng"}],"abstract":[{"text":"As sessile organisms, plants have to be able to adapt to a continuously changing environment. Plants that perceive some of these changes as stress signals activate signaling pathways to modulate their development and to enable them to survive. The complex responses to environmental cues are to a large extent mediated by plant hormones that together orchestrate the final plant response. The phytohormone cytokinin is involved in many plant developmental processes. Recently, it has been established that cytokinin plays an important role in stress responses, but does not act alone. Indeed, the hormonal control of plant development and stress adaptation is the outcome of a complex network of multiple synergistic and antagonistic interactions between various hormones. Here, we review the recent findings on the cytokinin function as part of this hormonal network. We focus on the importance of the crosstalk between cytokinin and other hormones, such as abscisic acid, jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development and stress adaptation. Finally, the impact of the current research in the biotechnological industry will be discussed.","lang":"eng"}],"ddc":["580"],"oa":1,"file":[{"file_name":"2013_FrontiersPlant_OBrien.pdf","relation":"main_file","content_type":"application/pdf","date_created":"2019-01-31T10:40:38Z","access_level":"open_access","file_id":"5903","date_updated":"2020-07-14T12:48:11Z","creator":"dernst","checksum":"fdc25ddd1bf9a99b99f662cdbafeddd4","file_size":953299}],"author":[{"last_name":"O'Brien","first_name":"José","full_name":"O'Brien, José"},{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"department":[{"_id":"EvBe"}],"oa_version":"Published Version","date_created":"2018-12-11T11:48:43Z","project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis","call_identifier":"FP7","grant_number":"207362"}],"file_date_updated":"2020-07-14T12:48:11Z","publication":"Frontiers in Plant Science","type":"journal_article","_id":"827","volume":4,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Cytokinin cross talking during biotic and abiotic stress responses","status":"public","article_number":"451","day":"19","scopus_import":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6821","date_updated":"2021-01-12T08:17:50Z","publisher":"Frontiers Research Foundation","month":"11","date_published":"2013-11-19T00:00:00Z"},{"day":"26","status":"public","article_number":"537","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":4,"title":"Systems approaches to study root architecture dynamics","file_date_updated":"2020-07-14T12:48:11Z","publication":"Frontiers in Plant Science","_id":"828","type":"journal_article","oa_version":"Published Version","date_created":"2018-12-11T11:48:43Z","project":[{"call_identifier":"FP7","grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"EvBe"}],"author":[{"orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela","last_name":"Cuesta","first_name":"Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T"},{"last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"date_published":"2013-12-26T00:00:00Z","month":"12","publist_id":"6820","date_updated":"2021-01-12T08:17:52Z","publisher":"Frontiers Research Foundation","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"language":[{"iso":"eng"}],"year":"2013","intvolume":" 4","has_accepted_license":"1","ec_funded":1,"quality_controlled":"1","doi":"10.3389/fpls.2013.00537","citation":{"ama":"Cuesta C, Wabnik KT, Benková E. Systems approaches to study root architecture dynamics. Frontiers in Plant Science. 2013;4. doi:10.3389/fpls.2013.00537","chicago":"Cuesta, Candela, Krzysztof T Wabnik, and Eva Benková. “Systems Approaches to Study Root Architecture Dynamics.” Frontiers in Plant Science. Frontiers Research Foundation, 2013. https://doi.org/10.3389/fpls.2013.00537.","short":"C. Cuesta, K.T. Wabnik, E. Benková, Frontiers in Plant Science 4 (2013).","apa":"Cuesta, C., Wabnik, K. T., & Benková, E. (2013). Systems approaches to study root architecture dynamics. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2013.00537","mla":"Cuesta, Candela, et al. “Systems Approaches to Study Root Architecture Dynamics.” Frontiers in Plant Science, vol. 4, 537, Frontiers Research Foundation, 2013, doi:10.3389/fpls.2013.00537.","ieee":"C. Cuesta, K. T. Wabnik, and E. Benková, “Systems approaches to study root architecture dynamics,” Frontiers in Plant Science, vol. 4. Frontiers Research Foundation, 2013.","ista":"Cuesta C, Wabnik KT, Benková E. 2013. Systems approaches to study root architecture dynamics. Frontiers in Plant Science. 4, 537."},"file":[{"creator":"dernst","checksum":"0185b3c4d7df9a94bd3ce5a66d213506","file_size":710835,"date_updated":"2020-07-14T12:48:11Z","access_level":"open_access","date_created":"2019-01-31T10:36:43Z","file_id":"5902","relation":"main_file","file_name":"2013_FrontiersPlant_Cuesta.pdf","content_type":"application/pdf"}],"abstract":[{"lang":"eng","text":"The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed."}],"ddc":["580"],"oa":1},{"author":[{"full_name":"Galbiati, Francesca","last_name":"Galbiati","first_name":"Francesca"},{"last_name":"Sinha Roy","first_name":"Dola","full_name":"Sinha Roy, Dola"},{"last_name":"Simonini","first_name":"Sara","full_name":"Simonini, Sara"},{"last_name":"Cucinotta","first_name":"Mara","full_name":"Cucinotta, Mara"},{"full_name":"Ceccato, Luca","first_name":"Luca","last_name":"Ceccato"},{"orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela","last_name":"Cuesta","first_name":"Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Šimášková, Mária","first_name":"Mária","last_name":"Šimášková"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"},{"full_name":"Kamiuchi, Yuri","first_name":"Yuri","last_name":"Kamiuchi"},{"full_name":"Aida, Mitsuhiro","first_name":"Mitsuhiro","last_name":"Aida"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"full_name":"Simon, Rüdiger","first_name":"Rüdiger","last_name":"Simon"},{"first_name":"Simona","last_name":"Masiero","full_name":"Masiero, Simona"},{"first_name":"Lucia","last_name":"Colombo","full_name":"Colombo, Lucia"}],"article_processing_charge":"No","_id":"830","issue":"3","type":"journal_article","publication":"The Plant journal for cell and molecular biology","date_created":"2018-12-11T11:48:44Z","oa_version":"None","status":"public","volume":76,"title":"An integrative model of the control of ovule primordia formation","day":"19","scopus_import":"1","publisher":"Wiley-Blackwell","date_updated":"2022-03-21T07:17:26Z","publist_id":"6818","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","month":"09","date_published":"2013-09-19T00:00:00Z","article_type":"original","acknowledgement":"The project and F.G. were supported by the CARIPLO Foundation (project 2009-2990) and COST (European Cooperation in Science and Technology) action HAPRECI (Harnessing Plant Reproduction for Crop Improvement). E.B. and C.C. were supported by the European Research Council through a ‘Starting Independent Research’ grant (ERC-2007-Stg-207362-HCPO). We thank A.P. MacCabe (Consejo Superior de Investigaciones Científicas, Valencia, Spain) for critical reading of the manuscript.","extern":"1","citation":{"ama":"Galbiati F, Sinha Roy D, Simonini S, et al. An integrative model of the control of ovule primordia formation. The Plant journal for cell and molecular biology. 2013;76(3):446-455. doi:10.1111/tpj.12309","short":"F. Galbiati, D. Sinha Roy, S. Simonini, M. Cucinotta, L. Ceccato, C. Cuesta, M. Šimášková, E. Benková, Y. Kamiuchi, M. Aida, D. Weijers, R. Simon, S. Masiero, L. Colombo, The Plant Journal for Cell and Molecular Biology 76 (2013) 446–455.","chicago":"Galbiati, Francesca, Dola Sinha Roy, Sara Simonini, Mara Cucinotta, Luca Ceccato, Candela Cuesta, Mária Šimášková, et al. “An Integrative Model of the Control of Ovule Primordia Formation.” The Plant Journal for Cell and Molecular Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/tpj.12309.","apa":"Galbiati, F., Sinha Roy, D., Simonini, S., Cucinotta, M., Ceccato, L., Cuesta, C., … Colombo, L. (2013). An integrative model of the control of ovule primordia formation. The Plant Journal for Cell and Molecular Biology. Wiley-Blackwell. https://doi.org/10.1111/tpj.12309","mla":"Galbiati, Francesca, et al. “An Integrative Model of the Control of Ovule Primordia Formation.” The Plant Journal for Cell and Molecular Biology, vol. 76, no. 3, Wiley-Blackwell, 2013, pp. 446–55, doi:10.1111/tpj.12309.","ista":"Galbiati F, Sinha Roy D, Simonini S, Cucinotta M, Ceccato L, Cuesta C, Šimášková M, Benková E, Kamiuchi Y, Aida M, Weijers D, Simon R, Masiero S, Colombo L. 2013. An integrative model of the control of ovule primordia formation. The Plant journal for cell and molecular biology. 76(3), 446–455.","ieee":"F. Galbiati et al., “An integrative model of the control of ovule primordia formation,” The Plant journal for cell and molecular biology, vol. 76, no. 3. Wiley-Blackwell, pp. 446–455, 2013."},"doi":"10.1111/tpj.12309","quality_controlled":"1","pmid":1,"intvolume":" 76","language":[{"iso":"eng"}],"year":"2013","external_id":{"pmid":["23941199"]},"page":"446 - 455","abstract":[{"lang":"eng","text":"Upon hormonal signaling, ovules develop as lateral organs from the placenta. Ovule numbers ultimately determine the number of seeds that develop, and thereby contribute to the final seed yield in crop plants. We demonstrate here that CUP-SHAPED COTYLEDON 1 (CUC1), CUC2 and AINTEGUMENTA (ANT) have additive effects on ovule primordia formation. We show that expression of the CUC1 and CUC2 genes is required to redundantly regulate expression of PINFORMED1 (PIN1), which in turn is required for ovule primordia formation. Furthermore, our results suggest that the auxin response factor MONOPTEROS (MP/ARF5) may directly bind ANT, CUC1 and CUC2 and promote their transcription. Based on our findings, we propose an integrative model to describe the molecular mechanisms of the early stages of ovule development."}]},{"publication":"Molecular Systems Biology","extern":1,"type":"journal_article","_id":"831","date_created":"2018-12-11T11:48:44Z","quality_controlled":0,"citation":{"ama":"Péret B, Middleton A, French A, et al. Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology. 2013;9. doi:10.1038/msb.2013.43","ista":"Péret B, Middleton A, French A, Larrieu A, Bishopp A, Njo M, Wells D, Porco S, Mellor N, Band L, Casimiro I, Kleine Vehn J, Vanneste S, Sairanen I, Mallet R, Sandberg G, Ljung K, Beeckman T, Benková E, Friml J, Kramer E, King J, De Smet I, Pridmore T, Owen M, Bennett M. 2013. Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology. 9.","ieee":"B. Péret et al., “Sequential induction of auxin efflux and influx carriers regulates lateral root emergence,” Molecular Systems Biology, vol. 9. Nature Publishing Group, 2013.","mla":"Péret, Benjamin, et al. “Sequential Induction of Auxin Efflux and Influx Carriers Regulates Lateral Root Emergence.” Molecular Systems Biology, vol. 9, Nature Publishing Group, 2013, doi:10.1038/msb.2013.43.","apa":"Péret, B., Middleton, A., French, A., Larrieu, A., Bishopp, A., Njo, M., … Bennett, M. (2013). Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology. Nature Publishing Group. https://doi.org/10.1038/msb.2013.43","chicago":"Péret, Benjamin, Alistair Middleton, Andrew French, Antoine Larrieu, Anthony Bishopp, Maria Njo, Darren Wells, et al. “Sequential Induction of Auxin Efflux and Influx Carriers Regulates Lateral Root Emergence.” Molecular Systems Biology. Nature Publishing Group, 2013. https://doi.org/10.1038/msb.2013.43.","short":"B. Péret, A. Middleton, A. French, A. Larrieu, A. Bishopp, M. Njo, D. Wells, S. Porco, N. Mellor, L. Band, I. Casimiro, J. Kleine Vehn, S. Vanneste, I. Sairanen, R. Mallet, G. Sandberg, K. Ljung, T. Beeckman, E. Benková, J. Friml, E. Kramer, J. King, I. De Smet, T. Pridmore, M. Owen, M. Bennett, Molecular Systems Biology 9 (2013)."},"doi":"10.1038/msb.2013.43","acknowledgement":"This work was supported by an FEBS Long‐Term Fellowship (BP), an Intra‐European Fellowship for Career Development under the 7th framework of the European Commission (IEF‐2008‐220506 to BP), an EMBO Long‐Term Fellowship (BP), an European Reintegration Grant under the 7th framework of the European Commission (ERG‐2010‐276662 to BP) and the Swedish Research Council (VR 621‐2010‐5720 to IS, GS and KL). AMM, APF, AL, LRB, SP, NM, DMW, MO, JRK and MJB acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC) and Engineering and Physical Sciences Research Council (EPSRC) funding to the Centre for Plant Integrative Biology (CPIB); BBSRC Professorial Research Fellowship funding to DMW and MJB; Belgian Scientific policy (BELSPO contract MARS) to TB and MJB. We thank Bert de Rybel for his help in Multisite Gateway cloning.","author":[{"full_name":"Péret, Benjamin","last_name":"Péret","first_name":"Benjamin"},{"full_name":"Middleton, Alistair M","first_name":"Alistair","last_name":"Middleton"},{"last_name":"French","first_name":"Andrew","full_name":"French, Andrew P"},{"last_name":"Larrieu","first_name":"Antoine","full_name":"Larrieu, Antoine"},{"full_name":"Bishopp, Anthony","first_name":"Anthony","last_name":"Bishopp"},{"first_name":"Maria","last_name":"Njo","full_name":"Njo, Maria"},{"full_name":"Wells, Darren M","first_name":"Darren","last_name":"Wells"},{"full_name":"Porco, Silvana","last_name":"Porco","first_name":"Silvana"},{"first_name":"Nathan","last_name":"Mellor","full_name":"Mellor, Nathan"},{"full_name":"Band, Leah R","last_name":"Band","first_name":"Leah"},{"last_name":"Casimiro","first_name":"Ilda","full_name":"Casimiro, Ilda"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine-Vehn, Jürgen"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"last_name":"Sairanen","first_name":"Ilkka","full_name":"Sairanen, Ilkka"},{"full_name":"Mallet, Romain","first_name":"Romain","last_name":"Mallet"},{"full_name":"Sandberg, Göran","last_name":"Sandberg","first_name":"Göran"},{"full_name":"Ljung, Karin","first_name":"Karin","last_name":"Ljung"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Eva Benková","orcid":"0000-0002-8510-9739"},{"full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eric","last_name":"Kramer","full_name":"Kramer, Eric"},{"last_name":"King","first_name":"John","full_name":"King, John R"},{"full_name":"De Smet, Ive","last_name":"De Smet","first_name":"Ive"},{"full_name":"Pridmore, Tony","first_name":"Tony","last_name":"Pridmore"},{"last_name":"Owen","first_name":"Markus","full_name":"Owen, Markus"},{"full_name":"Bennett, Malcolm J","last_name":"Bennett","first_name":"Malcolm"}],"day":"22","year":"2013","intvolume":" 9","status":"public","tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"volume":9,"title":"Sequential induction of auxin efflux and influx carriers regulates lateral root emergence","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","date_published":"2013-10-22T00:00:00Z","month":"10","abstract":[{"lang":"eng","text":"In Arabidopsis, lateral roots originate from pericycle cells deep within the primary root. New lateral root primordia (LRP) have to emerge through several overlaying tissues. Here, we report that auxin produced in new LRP is transported towards the outer tissues where it triggers cell separation by inducing both the auxin influx carrier LAX3 and cell-wall enzymes. LAX3 is expressed in just two cell files overlaying new LRP. To understand how this striking pattern of LAX3 expression is regulated, we developed a mathematical model that captures the network regulating its expression and auxin transport within realistic three-dimensional cell and tissue geometries. Our model revealed that, for the LAX3 spatial expression to be robust to natural variations in root tissue geometry, an efflux carrier is required--later identified to be PIN3. To prevent LAX3 from being transiently expressed in multiple cell files, PIN3 and LAX3 must be induced consecutively, which we later demonstrated to be the case. Our study exemplifies how mathematical models can be used to direct experiments to elucidate complex developmental processes."}],"publist_id":"6817","date_updated":"2021-01-12T08:18:03Z","publisher":"Nature Publishing Group","publication_status":"published"},{"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:26Z","publisher":"Springer Nature","keyword":["Spectroscopy","Biochemistry"],"abstract":[{"lang":"eng","text":"Solid-state NMR provides insight into protein motion over time scales ranging from picoseconds to seconds. While in solution state the methodology to measure protein dynamics is well established, there is currently no such consensus protocol for measuring dynamics in solids. In this article, we perform a detailed investigation of measurement protocols for fast motions, i.e. motions ranging from picoseconds to a few microseconds, which is the range covered by dipolar coupling and relaxation experiments. We perform a detailed theoretical investigation how dipolar couplings and relaxation data can provide information about amplitudes and time scales of local motion. We show that the measurement of dipolar couplings is crucial for obtaining accurate motional parameters, while systematic errors are found when only relaxation data are used. Based on this realization, we investigate how the REDOR experiment can provide such data in a very accurate manner. We identify that with accurate rf calibration, and explicit consideration of rf field inhomogeneities, one can obtain highly accurate absolute order parameters. We then perform joint model-free analyses of 6 relaxation data sets and dipolar couplings, based on previously existing, as well as new data sets on microcrystalline ubiquitin. We show that nanosecond motion can be detected primarily in loop regions, and compare solid-state data to solution-state relaxation and RDC analyses. The protocols investigated here will serve as a useful basis towards the establishment of a routine protocol for the characterization of ps–μs motions in proteins by solid-state NMR."}],"article_type":"original","date_published":"2013-10-09T00:00:00Z","month":"10","page":"263-280","volume":57,"title":"Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin","intvolume":" 57","status":"public","day":"09","year":"2013","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0925-2738","1573-5001"]},"author":[{"full_name":"Haller, Jens D.","first_name":"Jens D.","last_name":"Haller"},{"last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"}],"date_created":"2020-09-18T10:09:05Z","quality_controlled":"1","oa_version":"None","citation":{"ama":"Haller JD, Schanda P. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR. 2013;57(3):263-280. doi:10.1007/s10858-013-9787-x","ieee":"J. D. Haller and P. Schanda, “Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin,” Journal of Biomolecular NMR, vol. 57, no. 3. Springer Nature, pp. 263–280, 2013.","ista":"Haller JD, Schanda P. 2013. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR. 57(3), 263–280.","mla":"Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental Approaches and Application to Crystalline Ubiquitin.” Journal of Biomolecular NMR, vol. 57, no. 3, Springer Nature, 2013, pp. 263–80, doi:10.1007/s10858-013-9787-x.","apa":"Haller, J. D., & Schanda, P. (2013). Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-013-9787-x","chicago":"Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental Approaches and Application to Crystalline Ubiquitin.” Journal of Biomolecular NMR. Springer Nature, 2013. https://doi.org/10.1007/s10858-013-9787-x.","short":"J.D. Haller, P. Schanda, Journal of Biomolecular NMR 57 (2013) 263–280."},"doi":"10.1007/s10858-013-9787-x","extern":"1","publication":"Journal of Biomolecular NMR","article_processing_charge":"No","_id":"8461","type":"journal_article","issue":"3"},{"article_type":"original","month":"08","date_published":"2013-08-09T00:00:00Z","abstract":[{"text":"The transition of proteins from their soluble functional state to amyloid fibrils and aggregates is associated with the onset of several human diseases. Protein aggregation often requires some structural reshaping and the subsequent formation of intermolecular contacts. Therefore, the study of the conformation of excited protein states and their ability to form oligomers is of primary importance for understanding the molecular basis of amyloid fibril formation. Here, we investigated the oligomerization processes that occur along the folding of the amyloidogenic human protein β2-microglobulin. The combination of real-time two-dimensional NMR data with real-time small-angle X-ray scattering measurements allowed us to derive thermodynamic and kinetic information on protein oligomerization of different conformational states populated along the folding pathways. In particular, we could demonstrate that a long-lived folding intermediate (I-state) has a higher propensity to oligomerize compared to the native state. Our data agree well with a simple five-state kinetic model that involves only monomeric and dimeric species. The dimers have an elongated shape with the dimerization interface located at the apical side of β2-microglobulin close to Pro32, the residue that has a trans conformation in the I-state and a cis conformation in the native (N) state. Our experimental data suggest that partial unfolding in the apical half of the protein close to Pro32 leads to an excited state conformation with enhanced propensity for oligomerization. This excited state becomes more populated in the transient I-state due to the destabilization of the native conformation by the trans-Pro32 configuration.","lang":"eng"}],"keyword":["Molecular Biology"],"date_updated":"2022-08-25T14:56:24Z","publisher":"Elsevier","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","page":"2722-2736","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-2836"]},"day":"09","year":"2013","status":"public","intvolume":" 425","volume":425,"title":"Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure","publication":"Journal of Molecular Biology","extern":"1","_id":"8462","issue":"15","type":"journal_article","article_processing_charge":"No","oa_version":"None","date_created":"2020-09-18T10:09:12Z","quality_controlled":"1","citation":{"mla":"Rennella, E., et al. “Oligomeric States along the Folding Pathways of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” Journal of Molecular Biology, vol. 425, no. 15, Elsevier, 2013, pp. 2722–36, doi:10.1016/j.jmb.2013.04.028.","ista":"Rennella E, Cutuil T, Schanda P, Ayala I, Gabel F, Forge V, Corazza A, Esposito G, Brutscher B. 2013. Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal of Molecular Biology. 425(15), 2722–2736.","ieee":"E. Rennella et al., “Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure,” Journal of Molecular Biology, vol. 425, no. 15. Elsevier, pp. 2722–2736, 2013.","chicago":"Rennella, E., T. Cutuil, Paul Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza, G. Esposito, and B. Brutscher. “Oligomeric States along the Folding Pathways of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” Journal of Molecular Biology. Elsevier, 2013. https://doi.org/10.1016/j.jmb.2013.04.028.","short":"E. Rennella, T. Cutuil, P. Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza, G. Esposito, B. Brutscher, Journal of Molecular Biology 425 (2013) 2722–2736.","apa":"Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Gabel, F., Forge, V., … Brutscher, B. (2013). Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2013.04.028","ama":"Rennella E, Cutuil T, Schanda P, et al. Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal of Molecular Biology. 2013;425(15):2722-2736. doi:10.1016/j.jmb.2013.04.028"},"doi":"10.1016/j.jmb.2013.04.028","author":[{"full_name":"Rennella, E.","first_name":"E.","last_name":"Rennella"},{"last_name":"Cutuil","first_name":"T.","full_name":"Cutuil, T."},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda"},{"first_name":"I.","last_name":"Ayala","full_name":"Ayala, I."},{"last_name":"Gabel","first_name":"F.","full_name":"Gabel, F."},{"first_name":"V.","last_name":"Forge","full_name":"Forge, V."},{"full_name":"Corazza, A.","first_name":"A.","last_name":"Corazza"},{"full_name":"Esposito, G.","first_name":"G.","last_name":"Esposito"},{"full_name":"Brutscher, B.","first_name":"B.","last_name":"Brutscher"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"BioMed Central","publist_id":"6752","date_updated":"2021-01-12T08:21:25Z","abstract":[{"lang":"eng","text":"Background: Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in many birds. Feral pigeons (Columba livia) show two major melanin-based colorations: a red coloration due to pheomelanic pigment and a black coloration due to eumelanic pigment. Furthermore, within each color type, feral pigeons display continuous variation in the amount of melanin pigment present in the feathers, with individuals varying from pure white to a full dark melanic color. Coloration is highly heritable and it has been suggested that it is under natural or sexual selection, or both. Our objective was to investigate whether MC1R allelic variants are associated with plumage color in feral pigeons. Findings. We sequenced 888 bp of the coding sequence of MC1R among pigeons varying both in the type, eumelanin or pheomelanin, and the amount of melanin in their feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution but none of them were associated with a plumage type. It remains possible that non-synonymous substitutions that influence coloration are present in the short MC1R fragment that we did not sequence but this seems unlikely because we analyzed the entire functionally important region of the gene. Conclusions: Our results show that color differences among feral pigeons are probably not attributable to amino acid variation at the MC1R locus. Therefore, variation in regulatory regions of MC1R or variation in other genes may be responsible for the color polymorphism of feral pigeons."}],"date_published":"2013-01-01T00:00:00Z","month":"01","title":"Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R","volume":6,"status":"public","intvolume":" 6","day":"01","year":"2013","language":[{"iso":"eng"}],"author":[{"full_name":"Derelle, Romain","last_name":"Derelle","first_name":"Romain"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov"},{"last_name":"Arkhipov","first_name":"Vladimir","full_name":"Arkhipov, Vladimir"},{"full_name":"Corbel, Hélène","first_name":"Hélène","last_name":"Corbel"},{"first_name":"Adrien","last_name":"Frantz","full_name":"Frantz, Adrien"},{"full_name":"Gasparini, Julien","last_name":"Gasparini","first_name":"Julien"},{"full_name":"Jacquin, Lisa","last_name":"Jacquin","first_name":"Lisa"},{"first_name":"Gwenaël","last_name":"Jacob","full_name":"Jacob, Gwenaël"},{"full_name":"Thibault, Sophie","first_name":"Sophie","last_name":"Thibault"},{"full_name":"Baudry, Emmanuelle","last_name":"Baudry","first_name":"Emmanuelle"}],"acknowledgement":"Romain Derelle was supported by grant from Plan Nacional 004302 BFU2012-31329. Fyodor A Kondrashov was supported by grants HHMI (Howard Hughes Medical Institute) 003803 and EMBO 003691 EUI-EURYIP-2011-4320.","doi":"10.1186/1756-0500-6-310","citation":{"ama":"Derelle R, Kondrashov F, Arkhipov V, et al. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 2013;6(1). doi:10.1186/1756-0500-6-310","chicago":"Derelle, Romain, Fyodor Kondrashov, Vladimir Arkhipov, Hélène Corbel, Adrien Frantz, Julien Gasparini, Lisa Jacquin, Gwenaël Jacob, Sophie Thibault, and Emmanuelle Baudry. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” BMC Research Notes. BioMed Central, 2013. https://doi.org/10.1186/1756-0500-6-310.","short":"R. Derelle, F. Kondrashov, V. Arkhipov, H. Corbel, A. Frantz, J. Gasparini, L. Jacquin, G. Jacob, S. Thibault, E. Baudry, BMC Research Notes 6 (2013).","apa":"Derelle, R., Kondrashov, F., Arkhipov, V., Corbel, H., Frantz, A., Gasparini, J., … Baudry, E. (2013). Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. BioMed Central. https://doi.org/10.1186/1756-0500-6-310","mla":"Derelle, Romain, et al. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” BMC Research Notes, vol. 6, no. 1, BioMed Central, 2013, doi:10.1186/1756-0500-6-310.","ieee":"R. Derelle et al., “Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R,” BMC Research Notes, vol. 6, no. 1. BioMed Central, 2013.","ista":"Derelle R, Kondrashov F, Arkhipov V, Corbel H, Frantz A, Gasparini J, Jacquin L, Jacob G, Thibault S, Baudry E. 2013. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 6(1)."},"date_created":"2018-12-11T11:49:04Z","oa_version":"None","_id":"894","issue":"1","type":"journal_article","publication":"BMC Research Notes","extern":"1"},{"author":[{"first_name":"Michael","last_name":"Breen","full_name":"Breen, Michael S"},{"first_name":"Carsten","last_name":"Kemena","full_name":"Kemena, Carsten"},{"first_name":"Peter","last_name":"Vlasov","full_name":"Vlasov, Peter K"},{"last_name":"Notredame","first_name":"Cédric","full_name":"Notredame, Cédric"},{"last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694"}],"publication":"Nature","extern":1,"issue":"7451","_id":"899","type":"journal_article","quality_controlled":0,"date_created":"2018-12-11T11:49:05Z","citation":{"ama":"Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Breen et al. reply. Nature. 2013;497(7451):E2-E3. doi:10.1038/nature12220","mla":"Breen, Michael, et al. “Breen et Al. Reply.” Nature, vol. 497, no. 7451, Nature Publishing Group, 2013, pp. E2–3, doi:10.1038/nature12220.","ieee":"M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Breen et al. reply,” Nature, vol. 497, no. 7451. Nature Publishing Group, pp. E2–E3, 2013.","ista":"Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2013. Breen et al. reply. Nature. 497(7451), E2–E3.","short":"M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 497 (2013) E2–E3.","chicago":"Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor Kondrashov. “Breen et Al. Reply.” Nature. Nature Publishing Group, 2013. https://doi.org/10.1038/nature12220.","apa":"Breen, M., Kemena, C., Vlasov, P., Notredame, C., & Kondrashov, F. (2013). Breen et al. reply. Nature. Nature Publishing Group. https://doi.org/10.1038/nature12220"},"doi":"10.1038/nature12220","intvolume":" 497","status":"public","volume":497,"title":"Breen et al. reply","day":"30","year":"2013","page":"E2 - E3","date_updated":"2021-01-12T08:21:40Z","publist_id":"6747","publisher":"Nature Publishing Group","publication_status":"published","month":"05","date_published":"2013-05-30T00:00:00Z","abstract":[{"text":"Understanding fitness landscapes, a conceptual depiction of the genotype-to-phenotype relationship, is crucial to many areas of biology. Two aspects of fitness landscapes are the focus of contemporary studies of molecular evolution. First, the local shape of the fitness landscape defined by the contribution of individual alleles to fitness that is independent of all genetic interactions. Second, the global, multidimensional fitness landscape shape determined by how interactions between alleles at different loci change each other’s fitness impact, or epistasis. In explaining the high amino-acid usage (u), we focused on the global shape of the fitness landscape, ignoring the perturbations at individual sites.","lang":"eng"}]},{"extern":1,"publication":"Forktail","_id":"905","issue":"29","type":"journal_article","date_created":"2018-12-11T11:49:07Z","quality_controlled":0,"citation":{"ieee":"V. Arkhipov, T. Noah, S. Koschkar, and F. Kondrashov, “Birds of Mys Shmidta, north Chukotka, Russia,” Forktail, no. 29. Oriental Bird Club, pp. 25–30, 2013.","ista":"Arkhipov V, Noah T, Koschkar S, Kondrashov F. 2013. Birds of Mys Shmidta, north Chukotka, Russia. Forktail. (29), 25–30.","mla":"Arkhipov, Vladimir, et al. “Birds of Mys Shmidta, North Chukotka, Russia.” Forktail, no. 29, Oriental Bird Club, 2013, pp. 25–30.","apa":"Arkhipov, V., Noah, T., Koschkar, S., & Kondrashov, F. (2013). Birds of Mys Shmidta, north Chukotka, Russia. Forktail. Oriental Bird Club.","chicago":"Arkhipov, Vladimir, T Noah, Steffen Koschkar, and Fyodor Kondrashov. “Birds of Mys Shmidta, North Chukotka, Russia.” Forktail. Oriental Bird Club, 2013.","short":"V. Arkhipov, T. Noah, S. Koschkar, F. Kondrashov, Forktail (2013) 25–30.","ama":"Arkhipov V, Noah T, Koschkar S, Kondrashov F. Birds of Mys Shmidta, north Chukotka, Russia. Forktail. 2013;(29):25-30."},"acknowledgement":"We thank Natalya Kveten and Oksana Makarova, heads of administrations of Mys Shmidta and Ryrkaypiy for hospitality and for help with organising our excursions. Warm thanks too to Pavel Tomkovich for useful comments on local birds and ornithological literature. We are very grateful to The David and Lucile Packard Foundation for the support to Birds Russia’s Spoon-billed Sandpiper conservation programme in 2011 and to Evgeny Syroechkovsky Jr, the leader of the Spoon-billed Sandpiper conservation team in Russia.","author":[{"last_name":"Arkhipov","first_name":"Vladimir","full_name":"Arkhipov, Vladimir Y"},{"full_name":"Noah T","last_name":"Noah","first_name":"T"},{"last_name":"Koschkar","first_name":"Steffen","full_name":"Koschkar, Steffen"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694"}],"day":"01","year":"2013","status":"public","title":"Birds of Mys Shmidta, north Chukotka, Russia","main_file_link":[{"url":"http://orientalbirdclub.org/forktail29/","open_access":"1"}],"page":"25 - 30","month":"09","date_published":"2013-09-01T00:00:00Z","abstract":[{"lang":"eng","text":"A survey of avifauna was carried out in the Mys Shmidta area, north Chukotka, Russia from 8 June to 12 July 2011. A total of 90 species was recorded in the area, which together with literature data made a final list of 104 species. For several species this area is beyond the northern, north-eastern or north-western limits of their known distribution. We collected new data for 19 globally or locally threatened species. Tundra Swan Cygnus columbianus, Emperor Goose Anser canagica, American Golden Plover Pluvialis dominica, Western Sandpiper Calidris mauri, Semipalmated Sandpiper C. pusilla, Northern House Martin Delichon urbica and Barn Swallow Hirundo rustica were all confirmed to be breeding. Breeding of Brent Goose Branta bernicla nigricans, Spectacled Eider Somateria fischeri and Steller's Eider Polysticta stelleri was judged to be 'very likely'. There was no evidence for breeding of Ross's Gull Rhodostethia rosea despite several records. Two Eurasian Dotterels Eudromias morinellus were recorded displaying for the first time in the area, but the status of the species is unclear. The area is important for Snowy Owl Nyctea scandiaca, and as moulting grounds for Emperor Goose. Canada Goose Branta canadensis, Baikal Teal Anas formosa, Bar-tailed Godwit Limosa lapponica, Slaty-backed Gull Larus schistisagus, Thayer's Gull L. thayeri, Black-headed Gull L. ridibundus, White-tailed Eagle Haliaeetus albicilla, Steller's Sea Eagle H. pelagicus, Osprey Pandion haliaetus, Arctic Warbler Phylloscopus borealis and House Sparrow Passer domesticus are more likely to be rare vagrants or migrants. An observation of a Pine Siskin Carduelis pinus is the first record for Eurasia."}],"oa":1,"publist_id":"6741","date_updated":"2021-01-12T08:21:48Z","publisher":"Oriental Bird Club","publication_status":"published"},{"author":[{"orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A"},{"first_name":"S.","last_name":"Sacanna","full_name":"Sacanna, S."},{"full_name":"Steinberg, A. P.","last_name":"Steinberg","first_name":"A. P."},{"full_name":"Pine, D. J.","last_name":"Pine","first_name":"D. J."},{"last_name":"Chaikin","first_name":"P. M.","full_name":"Chaikin, P. M."}],"publication":"Science","article_processing_charge":"No","_id":"9055","type":"journal_article","issue":"6122","oa_version":"None","date_created":"2021-02-01T14:37:29Z","status":"public","title":"Living crystals of light-activated colloidal surfers","volume":339,"day":"22","scopus_import":"1","date_updated":"2022-08-25T14:57:43Z","publisher":"American Association for the Advancement of Science ","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_type":"original","month":"02","date_published":"2013-02-22T00:00:00Z","extern":"1","quality_controlled":"1","doi":"10.1126/science.1230020","citation":{"ama":"Palacci JA, Sacanna S, Steinberg AP, Pine DJ, Chaikin PM. Living crystals of light-activated colloidal surfers. Science. 2013;339(6122):936-940. doi:10.1126/science.1230020","ieee":"J. A. Palacci, S. Sacanna, A. P. Steinberg, D. J. Pine, and P. M. Chaikin, “Living crystals of light-activated colloidal surfers,” Science, vol. 339, no. 6122. American Association for the Advancement of Science , pp. 936–940, 2013.","ista":"Palacci JA, Sacanna S, Steinberg AP, Pine DJ, Chaikin PM. 2013. Living crystals of light-activated colloidal surfers. Science. 339(6122), 936–940.","mla":"Palacci, Jérémie A., et al. “Living Crystals of Light-Activated Colloidal Surfers.” Science, vol. 339, no. 6122, American Association for the Advancement of Science , 2013, pp. 936–40, doi:10.1126/science.1230020.","apa":"Palacci, J. A., Sacanna, S., Steinberg, A. P., Pine, D. J., & Chaikin, P. M. (2013). Living crystals of light-activated colloidal surfers. Science. American Association for the Advancement of Science . https://doi.org/10.1126/science.1230020","chicago":"Palacci, Jérémie A, S. Sacanna, A. P. Steinberg, D. J. Pine, and P. M. Chaikin. “Living Crystals of Light-Activated Colloidal Surfers.” Science. American Association for the Advancement of Science , 2013. https://doi.org/10.1126/science.1230020.","short":"J.A. Palacci, S. Sacanna, A.P. Steinberg, D.J. Pine, P.M. Chaikin, Science 339 (2013) 936–940."},"intvolume":" 339","pmid":1,"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"language":[{"iso":"eng"}],"year":"2013","external_id":{"pmid":["23371555"]},"page":"936-940","keyword":["Multidisciplinary"],"abstract":[{"text":"Spontaneous formation of colonies of bacteria or flocks of birds are examples of self-organization in active living matter. Here, we demonstrate a form of self-organization from nonequilibrium driving forces in a suspension of synthetic photoactivated colloidal particles. They lead to two-dimensional \"living crystals,\" which form, break, explode, and re-form elsewhere. The dynamic assembly results from a competition between self-propulsion of particles and an attractive interaction induced respectively by osmotic and phoretic effects and activated by light. We measured a transition from normal to giant-number fluctuations. Our experiments are quantitatively described by simple numerical simulations. We show that the existence of the living crystals is intrinsically related to the out-of-equilibrium collisions of the self-propelled particles.","lang":"eng"}]},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","publisher":"American Geophysical Union","date_updated":"2022-01-24T13:46:15Z","month":"11","date_published":"2013-11-07T00:00:00Z","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/2013JC009212"}],"title":"Internal tide generation by abyssal hills using analytical theory","volume":118,"status":"public","day":"07","author":[{"full_name":"Melet, Angélique","first_name":"Angélique","last_name":"Melet"},{"full_name":"Nikurashin, Maxim","first_name":"Maxim","last_name":"Nikurashin"},{"orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J"},{"first_name":"S.","last_name":"Falahat","full_name":"Falahat, S."},{"full_name":"Nycander, Jonas","first_name":"Jonas","last_name":"Nycander"},{"full_name":"Timko, Patrick G.","first_name":"Patrick G.","last_name":"Timko"},{"full_name":"Arbic, Brian K.","first_name":"Brian K.","last_name":"Arbic"},{"last_name":"Goff","first_name":"John A.","full_name":"Goff, John A."}],"oa_version":"Published Version","date_created":"2021-02-15T15:11:39Z","issue":"11","type":"journal_article","article_processing_charge":"No","_id":"9153","publication":"Journal of Geophysical Research: Oceans","oa":1,"abstract":[{"lang":"eng","text":"Internal tide driven mixing plays a key role in sustaining the deep ocean stratification and meridional overturning circulation. Internal tides can be generated by topographic horizontal scales ranging from hundreds of meters to tens of kilometers. State of the art topographic products barely resolve scales smaller than ∼10 km in the deep ocean. On these scales abyssal hills dominate ocean floor roughness. The impact of abyssal hill roughness on internal‐tide generation is evaluated in this study. The conversion of M2 barotropic to baroclinic tidal energy is calculated based on linear wave theory both in real and spectral space using the Shuttle Radar Topography Mission SRTM30_PLUS bathymetric product at 1/120° resolution with and without the addition of synthetic abyssal hill roughness. Internal tide generation by abyssal hills integrates to 0.1 TW globally or 0.03 TW when the energy flux is empirically corrected for supercritical slope (i.e., ∼10% of the energy flux due to larger topographic scales resolved in standard products in both cases). The abyssal hill driven energy conversion is dominated by mid‐ocean ridges, where abyssal hill roughness is large. Focusing on two regions located over the Mid‐Atlantic Ridge and the East Pacific Rise, it is shown that regionally linear theory predicts an increase of the energy flux due to abyssal hills of up to 100% or 60% when an empirical correction for supercritical slopes is attempted. Therefore, abyssal hills, unresolved in state of the art topographic products, can have a strong impact on internal tide generation, especially over mid‐ocean ridges."}],"page":"6303-6318","intvolume":" 118","year":"2013","publication_identifier":{"issn":["2169-9275"]},"language":[{"iso":"eng"}],"citation":{"chicago":"Melet, Angélique, Maxim Nikurashin, Caroline J Muller, S. Falahat, Jonas Nycander, Patrick G. Timko, Brian K. Arbic, and John A. Goff. “Internal Tide Generation by Abyssal Hills Using Analytical Theory.” Journal of Geophysical Research: Oceans. American Geophysical Union, 2013. https://doi.org/10.1002/2013jc009212.","short":"A. Melet, M. Nikurashin, C.J. Muller, S. Falahat, J. Nycander, P.G. Timko, B.K. Arbic, J.A. Goff, Journal of Geophysical Research: Oceans 118 (2013) 6303–6318.","apa":"Melet, A., Nikurashin, M., Muller, C. J., Falahat, S., Nycander, J., Timko, P. G., … Goff, J. A. (2013). Internal tide generation by abyssal hills using analytical theory. Journal of Geophysical Research: Oceans. American Geophysical Union. https://doi.org/10.1002/2013jc009212","mla":"Melet, Angélique, et al. “Internal Tide Generation by Abyssal Hills Using Analytical Theory.” Journal of Geophysical Research: Oceans, vol. 118, no. 11, American Geophysical Union, 2013, pp. 6303–18, doi:10.1002/2013jc009212.","ieee":"A. Melet et al., “Internal tide generation by abyssal hills using analytical theory,” Journal of Geophysical Research: Oceans, vol. 118, no. 11. American Geophysical Union, pp. 6303–6318, 2013.","ista":"Melet A, Nikurashin M, Muller CJ, Falahat S, Nycander J, Timko PG, Arbic BK, Goff JA. 2013. Internal tide generation by abyssal hills using analytical theory. Journal of Geophysical Research: Oceans. 118(11), 6303–6318.","ama":"Melet A, Nikurashin M, Muller CJ, et al. Internal tide generation by abyssal hills using analytical theory. Journal of Geophysical Research: Oceans. 2013;118(11):6303-6318. doi:10.1002/2013jc009212"},"doi":"10.1002/2013jc009212","quality_controlled":"1","extern":"1"},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0894-8755","1520-0442"]},"year":"2013","intvolume":" 26","extern":"1","quality_controlled":"1","doi":"10.1175/jcli-d-12-00655.1","citation":{"apa":"Muller, C. J. (2013). Impact of convective organization on the response of tropical precipitation extremes to warming. Journal of Climate. American Meteorological Society. https://doi.org/10.1175/jcli-d-12-00655.1","short":"C.J. Muller, Journal of Climate 26 (2013) 5028–5043.","chicago":"Muller, Caroline J. “Impact of Convective Organization on the Response of Tropical Precipitation Extremes to Warming.” Journal of Climate. American Meteorological Society, 2013. https://doi.org/10.1175/jcli-d-12-00655.1.","ieee":"C. J. Muller, “Impact of convective organization on the response of tropical precipitation extremes to warming,” Journal of Climate, vol. 26, no. 14. American Meteorological Society, pp. 5028–5043, 2013.","ista":"Muller CJ. 2013. Impact of convective organization on the response of tropical precipitation extremes to warming. Journal of Climate. 26(14), 5028–5043.","mla":"Muller, Caroline J. “Impact of Convective Organization on the Response of Tropical Precipitation Extremes to Warming.” Journal of Climate, vol. 26, no. 14, American Meteorological Society, 2013, pp. 5028–43, doi:10.1175/jcli-d-12-00655.1.","ama":"Muller CJ. Impact of convective organization on the response of tropical precipitation extremes to warming. Journal of Climate. 2013;26(14):5028-5043. doi:10.1175/jcli-d-12-00655.1"},"abstract":[{"lang":"eng","text":"In this study the response of tropical precipitation extremes to warming in organized convection is examined using a cloud-resolving model. Vertical shear is imposed to organize the convection into squall lines. Earlier studies show that in disorganized convection, the fractional increase of precipitation extremes is similar to that of surface water vapor, which is substantially smaller than the increase in column water vapor. It has been suggested that organized convection could lead to stronger amplifications.\r\nRegardless of the strength of the shear, amplifications of precipitation extremes in the cloud-resolving simulations are comparable to those of surface water vapor and are substantially less than increases in column water vapor. The results without shear and with critical shear, for which the squall lines are perpendicular to the shear, are surprisingly similar with a fractional rate of increase of precipitation extremes slightly smaller than that of surface water vapor. Interestingly, the dependence on shear is nonmonotonic, and stronger supercritical shear yields larger rates, close to or slightly larger than surface humidity.\r\nA scaling is used to evaluate the thermodynamic and dynamic contributions to precipitation extreme changes. To first order, they are dominated by the thermodynamic component, which has the same magnitude for all shears, close to the change in surface water vapor. The dynamic contribution plays a secondary role and tends to weaken extremes without shear and with critical shear, while it strengthens extremes with supercritical shear. These different dynamic contributions for different shears are due to different responses of convective mass fluxes in individual updrafts to warming."}],"keyword":["Atmospheric Science"],"oa":1,"page":"5028-5043","day":"15","status":"public","title":"Impact of convective organization on the response of tropical precipitation extremes to warming","volume":26,"publication":"Journal of Climate","_id":"9154","article_processing_charge":"No","type":"journal_article","issue":"14","oa_version":"Published Version","date_created":"2021-02-15T15:26:39Z","author":[{"orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller"}],"article_type":"original","date_published":"2013-07-15T00:00:00Z","month":"07","date_updated":"2022-01-24T13:46:41Z","publisher":"American Meteorological Society","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1175/JCLI-D-12-00655.1"}]},{"day":"30","status":"public","volume":135,"title":"Photoactivated colloidal dockers for cargo transportation","publication":"Journal of the American Chemical Society","_id":"9167","type":"journal_article","issue":"43","article_processing_charge":"No","date_created":"2021-02-18T14:31:26Z","oa_version":"Preprint","author":[{"orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A"},{"last_name":"Sacanna","first_name":"Stefano","full_name":"Sacanna, Stefano"},{"full_name":"Vatchinsky, Adrian","first_name":"Adrian","last_name":"Vatchinsky"},{"full_name":"Chaikin, Paul M.","first_name":"Paul M.","last_name":"Chaikin"},{"first_name":"David J.","last_name":"Pine","full_name":"Pine, David J."}],"article_type":"original","date_published":"2013-10-30T00:00:00Z","month":"10","date_updated":"2021-02-22T10:10:41Z","publisher":"American Chemical Society","publication_status":"published","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","main_file_link":[{"url":"https://arxiv.org/abs/1310.5724","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15205126"],"issn":["00027863"]},"year":"2013","arxiv":1,"intvolume":" 135","pmid":1,"extern":"1","quality_controlled":"1","citation":{"ama":"Palacci JA, Sacanna S, Vatchinsky A, Chaikin PM, Pine DJ. Photoactivated colloidal dockers for cargo transportation. Journal of the American Chemical Society. 2013;135(43):15978-15981. doi:10.1021/ja406090s","mla":"Palacci, Jérémie A., et al. “Photoactivated Colloidal Dockers for Cargo Transportation.” Journal of the American Chemical Society, vol. 135, no. 43, American Chemical Society, 2013, pp. 15978–81, doi:10.1021/ja406090s.","ista":"Palacci JA, Sacanna S, Vatchinsky A, Chaikin PM, Pine DJ. 2013. Photoactivated colloidal dockers for cargo transportation. Journal of the American Chemical Society. 135(43), 15978–15981.","ieee":"J. A. Palacci, S. Sacanna, A. Vatchinsky, P. M. Chaikin, and D. J. Pine, “Photoactivated colloidal dockers for cargo transportation,” Journal of the American Chemical Society, vol. 135, no. 43. American Chemical Society, pp. 15978–15981, 2013.","chicago":"Palacci, Jérémie A, Stefano Sacanna, Adrian Vatchinsky, Paul M. Chaikin, and David J. Pine. “Photoactivated Colloidal Dockers for Cargo Transportation.” Journal of the American Chemical Society. American Chemical Society, 2013. https://doi.org/10.1021/ja406090s.","short":"J.A. Palacci, S. Sacanna, A. Vatchinsky, P.M. Chaikin, D.J. Pine, Journal of the American Chemical Society 135 (2013) 15978–15981.","apa":"Palacci, J. A., Sacanna, S., Vatchinsky, A., Chaikin, P. M., & Pine, D. J. (2013). Photoactivated colloidal dockers for cargo transportation. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja406090s"},"doi":"10.1021/ja406090s","abstract":[{"text":"We introduce a self-propelled colloidal hematite docker that can be steered to a small particle cargo many times its size, dock, transport the cargo to a remote location, and then release it. The self-propulsion and docking are reversible and activated by visible light. The docker can be steered either by a weak uniform magnetic field or by nanoscale tracks in a textured substrate. The light-activated motion and docking originate from osmotic/phoretic particle transport in a concentration gradient of fuel, hydrogen peroxide, induced by the photocatalytic activity of the hematite. The docking mechanism is versatile and can be applied to various materials and shapes. The hematite dockers are simple single-component particles and are synthesized in bulk quantities. This system opens up new possibilities for designing complex micrometer-size factories as well as new biomimetic systems.","lang":"eng"}],"keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"oa":1,"external_id":{"pmid":["24131488"],"arxiv":["1310.5724"]},"page":"15978-15981"},{"volume":110,"title":"Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing","intvolume":" 110","status":"public","year":"2013","day":"12","language":[{"iso":"eng"}],"author":[{"full_name":"Basan, Markus","last_name":"Basan","first_name":"Markus"},{"first_name":"Jens","last_name":"Elgeti","full_name":"Elgeti, Jens"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo"},{"full_name":"Rappel, Wouter","last_name":"Rappel","first_name":"Wouter"},{"last_name":"Levine","first_name":"Herbert","full_name":"Levine, Herbert"}],"acknowledgement":"This work was supported by National Science Foundation (NSF) Grant DMS-1068869 and by the NSF Center for Theoretical Biological Physics (Grant NSF PHY-0822283).\r\nWe acknowledge useful discussions with Eshel Ben-Jacob and Assaf Zaritsky. ","date_created":"2018-12-11T11:49:12Z","oa_version":"None","citation":{"ama":"Basan M, Elgeti J, Hannezo EB, Rappel W, Levine H. Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing. PNAS. 2013;110(7):2452-2459. doi:10.1073/pnas.1219937110","ista":"Basan M, Elgeti J, Hannezo EB, Rappel W, Levine H. 2013. Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing. PNAS. 110(7), 2452–2459.","ieee":"M. Basan, J. Elgeti, E. B. Hannezo, W. Rappel, and H. Levine, “Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing,” PNAS, vol. 110, no. 7. National Academy of Sciences, pp. 2452–2459, 2013.","mla":"Basan, Markus, et al. “Alignment of Cellular Motility Forces with Tissue Flow as a Mechanism for Efficient Wound Healing.” PNAS, vol. 110, no. 7, National Academy of Sciences, 2013, pp. 2452–59, doi:10.1073/pnas.1219937110.","apa":"Basan, M., Elgeti, J., Hannezo, E. B., Rappel, W., & Levine, H. (2013). Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1219937110","short":"M. Basan, J. Elgeti, E.B. Hannezo, W. Rappel, H. Levine, PNAS 110 (2013) 2452–2459.","chicago":"Basan, Markus, Jens Elgeti, Edouard B Hannezo, Wouter Rappel, and Herbert Levine. “Alignment of Cellular Motility Forces with Tissue Flow as a Mechanism for Efficient Wound Healing.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1219937110."},"doi":"10.1073/pnas.1219937110","extern":"1","publication":"PNAS","_id":"921","type":"journal_article","issue":"7","article_processing_charge":"No","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:21:55Z","publist_id":"6518","publisher":"National Academy of Sciences","abstract":[{"lang":"eng","text":"Recent experiments have shown that spreading epithelial sheets exhibit a long-range coordination of motility forces that leads to a buildup of tension in the tissue, which may enhance cell division and the speed of wound healing. Furthermore, the edges of these epithelial sheets commonly show finger-like protrusions whereas the bulk often displays spontaneous swirls of motile cells. To explain these experimental observations, we propose a simple flocking-type mechanism, in which cells tend to align their motility forceswith their velocity. Implementing this idea in amechanical tissue simulation, the proposed model gives rise to efficient spreading and can explain the experimentally observed long-range alignment of motility forces in highly disordered patterns, as well as the buildup of tensile stress throughout the tissue. Our model also qualitatively reproduces the dependence of swirl size and swirl velocity on cell density reported in experiments and exhibits an undulation instability at the edge of the spreading tissue commonly observed in vivo. Finally, we study the dependence of colony spreading speed on important physical and biological parameters and derive simple scaling relations that show that coordination of motility forces leads to an improvement of the wound healing process for realistic tissue parameters."}],"date_published":"2013-02-12T00:00:00Z","month":"02","page":"2452 - 2459"},{"author":[{"full_name":"Ottakam Thotiyl, Muhammed M.","last_name":"Ottakam Thotiyl","first_name":"Muhammed M."},{"orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"first_name":"Zhangquan","last_name":"Peng","full_name":"Peng, Zhangquan"},{"full_name":"Chen, Yuhui","first_name":"Yuhui","last_name":"Chen"},{"full_name":"Liu, Zheng","last_name":"Liu","first_name":"Zheng"},{"full_name":"Bruce, Peter G.","first_name":"Peter G.","last_name":"Bruce"}],"extern":"1","publication":"Nature Materials","type":"journal_article","_id":"7306","article_processing_charge":"No","issue":"11","quality_controlled":"1","oa_version":"None","date_created":"2020-01-15T12:18:29Z","citation":{"ista":"Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. 2013. A stable cathode for the aprotic Li–O2 battery. Nature Materials. 12(11), 1050–1056.","ieee":"M. M. Ottakam Thotiyl, S. A. Freunberger, Z. Peng, Y. Chen, Z. Liu, and P. G. Bruce, “A stable cathode for the aprotic Li–O2 battery,” Nature Materials, vol. 12, no. 11. Springer Nature, pp. 1050–1056, 2013.","mla":"Ottakam Thotiyl, Muhammed M., et al. “A Stable Cathode for the Aprotic Li–O2 Battery.” Nature Materials, vol. 12, no. 11, Springer Nature, 2013, pp. 1050–56, doi:10.1038/nmat3737.","apa":"Ottakam Thotiyl, M. M., Freunberger, S. A., Peng, Z., Chen, Y., Liu, Z., & Bruce, P. G. (2013). A stable cathode for the aprotic Li–O2 battery. Nature Materials. Springer Nature. https://doi.org/10.1038/nmat3737","short":"M.M. Ottakam Thotiyl, S.A. Freunberger, Z. Peng, Y. Chen, Z. Liu, P.G. Bruce, Nature Materials 12 (2013) 1050–1056.","chicago":"Ottakam Thotiyl, Muhammed M., Stefan Alexander Freunberger, Zhangquan Peng, Yuhui Chen, Zheng Liu, and Peter G. Bruce. “A Stable Cathode for the Aprotic Li–O2 Battery.” Nature Materials. Springer Nature, 2013. https://doi.org/10.1038/nmat3737.","ama":"Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. A stable cathode for the aprotic Li–O2 battery. Nature Materials. 2013;12(11):1050-1056. doi:10.1038/nmat3737"},"doi":"10.1038/nmat3737","status":"public","intvolume":" 12","title":"A stable cathode for the aprotic Li–O2 battery","volume":12,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1476-1122","1476-4660"]},"day":"01","year":"2013","page":"1050-1056","date_updated":"2021-01-12T08:12:55Z","publisher":"Springer Nature","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","date_published":"2013-09-01T00:00:00Z","month":"09","abstract":[{"lang":"eng","text":"Rechargeable lithium–air (O2) batteries are receiving intense interest because their high theoretical specific energy exceeds that of lithium-ion batteries. If the Li–O2 battery is ever to succeed, highly reversible formation/decomposition of Li2O2 must take place at the cathode on cycling. However, carbon, used ubiquitously as the basis of the cathode, decomposes during Li2O2 oxidation on charge and actively promotes electrolyte decomposition on cycling. Replacing carbon with a nanoporous gold cathode, when in contact with a dimethyl sulphoxide-based electrolyte, does seem to demonstrate better stability. However, nanoporous gold is not a suitable cathode; its high mass destroys the key advantage of Li–O2 over Li ion (specific energy), it is too expensive and too difficult to fabricate. Identifying a suitable cathode material for the Li–O2 cell is one of the greatest challenges at present. Here we show that a TiC-based cathode reduces greatly side reactions (arising from the electrolyte and electrode degradation) compared with carbon and exhibits better reversible formation/decomposition of Li2O2 even than nanoporous gold (>98% capacity retention after 100 cycles, compared with 95% for nanoporous gold); it is also four times lighter, of lower cost and easier to fabricate. The stability may originate from the presence of TiO2 (along with some TiOC) on the surface of TiC. In contrast to carbon or nanoporous gold, TiC seems to represent a more viable, stable, cathode for aprotic Li–O2 cells."}]},{"page":"489-494","abstract":[{"text":"The non-aqueous Li–air (O2) battery is receiving intense interest because its theoretical specific energy exceeds that of Li-ion batteries. Recharging the Li–O2 battery depends on oxidizing solid lithium peroxide (Li2O2), which is formed on discharge within the porous cathode. However, transporting charge between Li2O2 particles and the solid electrode surface is at best very difficult and leads to voltage polarization on charging, even at modest rates. This is a significant problem facing the non-aqueous Li–O2 battery. Here we show that incorporation of a redox mediator, tetrathiafulvalene (TTF), enables recharging at rates that are impossible for the cell in the absence of the mediator. On charging, TTF is oxidized to TTF+ at the cathode surface; TTF+ in turn oxidizes the solid Li2O2, which results in the regeneration of TTF. The mediator acts as an electron–hole transfer agent that permits efficient oxidation of solid Li2O2. The cell with the mediator demonstrated 100 charge/discharge cycles.","lang":"eng"}],"month":"05","date_published":"2013-05-12T00:00:00Z","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Springer Nature","date_updated":"2021-01-12T08:12:56Z","citation":{"ama":"Chen Y, Freunberger SA, Peng Z, Fontaine O, Bruce PG. Charging a Li–O2 battery using a redox mediator. Nature Chemistry. 2013;5(6):489-494. doi:10.1038/nchem.1646","apa":"Chen, Y., Freunberger, S. A., Peng, Z., Fontaine, O., & Bruce, P. G. (2013). Charging a Li–O2 battery using a redox mediator. Nature Chemistry. Springer Nature. https://doi.org/10.1038/nchem.1646","short":"Y. Chen, S.A. Freunberger, Z. Peng, O. Fontaine, P.G. Bruce, Nature Chemistry 5 (2013) 489–494.","chicago":"Chen, Yuhui, Stefan Alexander Freunberger, Zhangquan Peng, Olivier Fontaine, and Peter G. Bruce. “Charging a Li–O2 Battery Using a Redox Mediator.” Nature Chemistry. Springer Nature, 2013. https://doi.org/10.1038/nchem.1646.","ieee":"Y. Chen, S. A. Freunberger, Z. Peng, O. Fontaine, and P. G. Bruce, “Charging a Li–O2 battery using a redox mediator,” Nature Chemistry, vol. 5, no. 6. Springer Nature, pp. 489–494, 2013.","ista":"Chen Y, Freunberger SA, Peng Z, Fontaine O, Bruce PG. 2013. Charging a Li–O2 battery using a redox mediator. Nature Chemistry. 5(6), 489–494.","mla":"Chen, Yuhui, et al. “Charging a Li–O2 Battery Using a Redox Mediator.” Nature Chemistry, vol. 5, no. 6, Springer Nature, 2013, pp. 489–94, doi:10.1038/nchem.1646."},"doi":"10.1038/nchem.1646","oa_version":"None","date_created":"2020-01-15T12:18:43Z","quality_controlled":"1","_id":"7307","type":"journal_article","issue":"6","article_processing_charge":"No","extern":"1","publication":"Nature Chemistry","author":[{"full_name":"Chen, Yuhui","first_name":"Yuhui","last_name":"Chen"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319"},{"full_name":"Peng, Zhangquan","first_name":"Zhangquan","last_name":"Peng"},{"last_name":"Fontaine","first_name":"Olivier","full_name":"Fontaine, Olivier"},{"first_name":"Peter G.","last_name":"Bruce","full_name":"Bruce, Peter G."}],"day":"12","year":"2013","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1755-4330","1755-4349"]},"volume":5,"title":"Charging a Li–O2 battery using a redox mediator","intvolume":" 5","status":"public"},{"day":"01","volume":45,"title":"Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development","status":"public","date_created":"2020-03-21T16:06:36Z","oa_version":"None","publication":"Acta Biochimica et Biophysica Sinica","issue":"7","_id":"7595","type":"journal_article","article_processing_charge":"No","author":[{"first_name":"Yong","last_name":"Tang","full_name":"Tang, Yong"},{"last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang"},{"full_name":"Xue, Hongwei","first_name":"Hongwei","last_name":"Xue"}],"article_type":"original","month":"07","date_published":"2013-07-01T00:00:00Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:14:23Z","publisher":"Oxford University Press","year":"2013","publication_identifier":{"issn":["1745-7270","1672-9145"]},"language":[{"iso":"eng"}],"intvolume":" 45","pmid":1,"quality_controlled":"1","citation":{"ieee":"Y. Tang, S. Tan, and H. Xue, “Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development,” Acta Biochimica et Biophysica Sinica, vol. 45, no. 7. Oxford University Press, pp. 549–560, 2013.","ista":"Tang Y, Tan S, Xue H. 2013. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica Sinica. 45(7), 549–560.","mla":"Tang, Yong, et al. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is Required for Seed Coat Development.” Acta Biochimica et Biophysica Sinica, vol. 45, no. 7, Oxford University Press, 2013, pp. 549–60, doi:10.1093/abbs/gmt039.","apa":"Tang, Y., Tan, S., & Xue, H. (2013). Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica Sinica. Oxford University Press. https://doi.org/10.1093/abbs/gmt039","chicago":"Tang, Yong, Shutang Tan, and Hongwei Xue. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is Required for Seed Coat Development.” Acta Biochimica et Biophysica Sinica. Oxford University Press, 2013. https://doi.org/10.1093/abbs/gmt039.","short":"Y. Tang, S. Tan, H. Xue, Acta Biochimica et Biophysica Sinica 45 (2013) 549–560.","ama":"Tang Y, Tan S, Xue H. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica Sinica. 2013;45(7):549-560. doi:10.1093/abbs/gmt039"},"doi":"10.1093/abbs/gmt039","extern":"1","abstract":[{"text":"Inositol 1,3,4-trisphosphate 5/6 kinase (ITPK) phosphorylates inositol 1,3,4-trisphosphate to form inositol 1,3,4,5-tetrakisphosphate and inositol 1,3,4,6-tetrakisphosphate which can be finally transferred to inositol hexaphosphate (IP6) and play important roles during plant growth and development. There are 4 putative ITPK members in Arabidopsis. Expression pattern analysis showed that ITPK2 is constitutively expressed in various tissues. A T-DNA knockout mutant of ITPK2 was identified and scanning electron microscopy (SEM) analysis showed that the epidermis structure of seed coat was irregularly formed in seeds of itpk2-1 mutant, resulting in the increased permeability of seed coat to tetrazolium salts. Further analysis by gas chromatography coupled with mass spectrometry of lipid polyester monomers in cell wall confirmed a dramatic decrease in composition of suberin and cutin, which relate to the permeability of seed coat and the formation of which is accompanied with seed coat development. These results indicate that ITPK2 plays an essential role in seed coat development and lipid polyester barrier formation.","lang":"eng"}],"page":"549-560","external_id":{"pmid":["23595027"]}},{"external_id":{"pmid":["23897926"]},"page":"2618-2632","abstract":[{"lang":"eng","text":"Casein kinase1 (CK1) plays crucial roles in regulating growth and development via phosphorylating various substrates throughout the eukaryote kingdom. Blue light is crucial for normal growth of both plants and animals, and blue light receptor cryptochrome2 (CRY2) undergoes blue light–dependent phosphorylation and degradation in planta. To study the function of plant CK1s, systematic genetic analysis showed that deficiency of two paralogous Arabidopsis thaliana CK1s, CK1.3 and CK1.4, caused shortened hypocotyls, especially under blue light, while overexpression of either CK1.3 or CK1.4 resulted in the insensitive response to blue light and delayed flowering under long-day conditions. CK1.3 or CK1.4 act dependently on CRY2, and overexpression of CK1.3 or CK1.4 significantly suppresses the hypersensitive response to blue light by CRY2 overexpression. Biochemical studies showed that CK1.3 and CK1.4 directly phosphorylate CRY2 at Ser-587 and Thr-603 in vitro and negatively regulate CRY2 stability in planta, which are stimulated by blue light, further confirming the crucial roles of CK1.3 and CK1.4 in blue light responses through phosphorylating CRY2. Interestingly, expression of CK1.3 and CK1.4 is stimulated by blue light and feedback regulated by CRY2-mediated signaling. These results provide direct evidence for CRY2 phosphorylation and informative clues on the mechanisms of CRY2-mediated light responses."}],"extern":"1","doi":"10.1105/tpc.113.114322","citation":{"ama":"Tan S, Dai C, Liu H-T, Xue H-W. Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. The Plant Cell. 2013;25(7):2618-2632. doi:10.1105/tpc.113.114322","mla":"Tan, Shutang, et al. “Arabidopsis Casein Kinase1 Proteins CK1.3 and CK1.4 Phosphorylate Cryptochrome2 to Regulate Blue Light Signaling.” The Plant Cell, vol. 25, no. 7, American Society of Plant Biologists, 2013, pp. 2618–32, doi:10.1105/tpc.113.114322.","ista":"Tan S, Dai C, Liu H-T, Xue H-W. 2013. Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. The Plant Cell. 25(7), 2618–2632.","ieee":"S. Tan, C. Dai, H.-T. Liu, and H.-W. Xue, “Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling,” The Plant Cell, vol. 25, no. 7. American Society of Plant Biologists, pp. 2618–2632, 2013.","short":"S. Tan, C. Dai, H.-T. Liu, H.-W. Xue, The Plant Cell 25 (2013) 2618–2632.","chicago":"Tan, Shutang, C. Dai, H.-T. Liu, and H.-W. Xue. “Arabidopsis Casein Kinase1 Proteins CK1.3 and CK1.4 Phosphorylate Cryptochrome2 to Regulate Blue Light Signaling.” The Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114322.","apa":"Tan, S., Dai, C., Liu, H.-T., & Xue, H.-W. (2013). Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114322"},"quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1040-4651","1532-298X"]},"year":"2013","pmid":1,"intvolume":" 25","date_published":"2013-08-26T00:00:00Z","month":"08","article_type":"original","publisher":"American Society of Plant Biologists","date_updated":"2021-01-12T08:14:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","issue":"7","type":"journal_article","_id":"7596","article_processing_charge":"No","publication":"The Plant Cell","date_created":"2020-03-21T16:06:55Z","oa_version":"None","author":[{"orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan"},{"first_name":"C.","last_name":"Dai","full_name":"Dai, C."},{"full_name":"Liu, H.-T.","first_name":"H.-T.","last_name":"Liu"},{"full_name":"Xue, H.-W.","first_name":"H.-W.","last_name":"Xue"}],"day":"26","status":"public","title":"Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling","volume":25},{"status":"public","title":"Randomized loose renaming in O(loglogn) time","language":[{"iso":"eng"}],"day":"01","year":"2013","acknowledgement":"Dan Alistarh - This author was supported by the SNF Postdoctoral Fellows Program, NSF grant CCF-1217921, DoE ASCR grant\r\nER26116/DE-SC0008923, and by grants from the Oracle\r\nand Intel corporations.\r\nJames Aspnes - Supported in part by NSF grant CCF-0916389.\r\nGeorge Giakkoupis - This work was funded in part by INRIA Associate Team\r\nRADCON, and ERC Starting Grant GOSSPLE 204742.\r\nPhilipp Woelfel - This research was undertaken, in part, thanks to funding\r\nfrom the Canada Research Chairs program and the HP Labs\r\nInnovation Research Program.","conference":{"name":"PODC: Principles of Distributed Computing"},"author":[{"last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"full_name":"Aspnes, James","first_name":"James","last_name":"Aspnes"},{"full_name":"Giakkoupis, George","first_name":"George","last_name":"Giakkoupis"},{"first_name":"Philipp","last_name":"Woelfel","full_name":"Woelfel, Philipp"}],"extern":"1","_id":"765","type":"conference","article_processing_charge":"No","oa_version":"None","date_created":"2018-12-11T11:48:23Z","doi":"10.1145/2484239.2484240","citation":{"mla":"Alistarh, Dan-Adrian, et al. Randomized Loose Renaming in O(Loglogn) Time. ACM, 2013, pp. 200–09, doi:10.1145/2484239.2484240.","ieee":"D.-A. Alistarh, J. Aspnes, G. Giakkoupis, and P. Woelfel, “Randomized loose renaming in O(loglogn) time,” presented at the PODC: Principles of Distributed Computing, 2013, pp. 200–209.","ista":"Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. 2013. Randomized loose renaming in O(loglogn) time. PODC: Principles of Distributed Computing, 200–209.","short":"D.-A. Alistarh, J. Aspnes, G. Giakkoupis, P. Woelfel, in:, ACM, 2013, pp. 200–209.","chicago":"Alistarh, Dan-Adrian, James Aspnes, George Giakkoupis, and Philipp Woelfel. “Randomized Loose Renaming in O(Loglogn) Time,” 200–209. ACM, 2013. https://doi.org/10.1145/2484239.2484240.","apa":"Alistarh, D.-A., Aspnes, J., Giakkoupis, G., & Woelfel, P. (2013). Randomized loose renaming in O(loglogn) time (pp. 200–209). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2484239.2484240","ama":"Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. Randomized loose renaming in O(loglogn) time. In: ACM; 2013:200-209. doi:10.1145/2484239.2484240"},"date_updated":"2023-02-23T13:13:14Z","publist_id":"6889","publisher":"ACM","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","date_published":"2013-01-01T00:00:00Z","abstract":[{"lang":"eng","text":"Renaming is a classic distributed coordination task in which a set of processes must pick distinct identifiers from a small namespace. In this paper, we consider the time complexity of this problem when the namespace is linear in the number of participants, a variant known as loose renaming. We give a non-adaptive algorithm with O(log log n) (individual) step complexity, where n is a known upper bound on contention, and an adaptive algorithm with step complexity O((log log k)2), where k is the actual contention in the execution. We also present a variant of the adaptive algorithm which requires O(k log log k) total process steps. All upper bounds hold with high probability against a strong adaptive adversary. We complement the algorithms with an ω(log log n) expected time lower bound on the complexity of randomized renaming using test-and-set operations and linear space. The result is based on a new coupling technique, and is the first to apply to non-adaptive randomized renaming. Since our algorithms use O(n) test-and-set objects, our results provide matching bounds on the cost of loose renaming in this setting."}],"page":"200 - 209"},{"issue":"15","_id":"7745","article_processing_charge":"No","type":"journal_article","extern":"1","publication":"Molecular Ecology","doi":"10.1111/mec.12375","citation":{"ama":"Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology. 2013;22(15):3963-3980. doi:10.1111/mec.12375","ista":"Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. 2013. Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology. 22(15), 3963–3980.","ieee":"M. R. Robinson, A. W. Santure, I. DeCauwer, B. C. Sheldon, and J. Slate, “Partitioning of genetic variation across the genome using multimarker methods in a wild bird population,” Molecular Ecology, vol. 22, no. 15. Wiley, pp. 3963–3980, 2013.","mla":"Robinson, Matthew Richard, et al. “Partitioning of Genetic Variation across the Genome Using Multimarker Methods in a Wild Bird Population.” Molecular Ecology, vol. 22, no. 15, Wiley, 2013, pp. 3963–80, doi:10.1111/mec.12375.","apa":"Robinson, M. R., Santure, A. W., DeCauwer, I., Sheldon, B. C., & Slate, J. (2013). Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.12375","chicago":"Robinson, Matthew Richard, Anna W. Santure, Isabelle DeCauwer, Ben C. Sheldon, and Jon Slate. “Partitioning of Genetic Variation across the Genome Using Multimarker Methods in a Wild Bird Population.” Molecular Ecology. Wiley, 2013. https://doi.org/10.1111/mec.12375.","short":"M.R. Robinson, A.W. Santure, I. DeCauwer, B.C. Sheldon, J. Slate, Molecular Ecology 22 (2013) 3963–3980."},"date_created":"2020-04-30T11:00:15Z","quality_controlled":"1","oa_version":"None","author":[{"orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"last_name":"Santure","first_name":"Anna W.","full_name":"Santure, Anna W."},{"full_name":"DeCauwer, Isabelle","first_name":"Isabelle","last_name":"DeCauwer"},{"full_name":"Sheldon, Ben C.","last_name":"Sheldon","first_name":"Ben C."},{"full_name":"Slate, Jon","last_name":"Slate","first_name":"Jon"}],"publication_identifier":{"issn":["0962-1083"]},"language":[{"iso":"eng"}],"day":"01","year":"2013","intvolume":" 22","status":"public","title":"Partitioning of genetic variation across the genome using multimarker methods in a wild bird population","volume":22,"page":"3963-3980","date_published":"2013-08-01T00:00:00Z","month":"08","article_type":"original","abstract":[{"text":"The underlying basis of genetic variation in quantitative traits, in terms of the number of causal variants and the size of their effects, is largely unknown in natural populations. The expectation is that complex quantitative trait variation is attributable to many, possibly interacting, causal variants, whose effects may depend upon the sex, age and the environment in which they are expressed. A recently developed methodology in animal breeding derives a value of relatedness among individuals from high‐density genomic marker data, to estimate additive genetic variance within livestock populations. Here, we adapt and test the effectiveness of these methods to partition genetic variation for complex traits across genomic regions within ecological study populations where individuals have varying degrees of relatedness. We then apply this approach for the first time to a natural population and demonstrate that genetic variation in wing length in the great tit (Parus major) reflects contributions from multiple genomic regions. We show that a polygenic additive mode of gene action best describes the patterns observed, and we find no evidence of dosage compensation for the sex chromosome. Our results suggest that most of the genomic regions that influence wing length have the same effects in both sexes. We found a limited amount of genetic variance in males that is attributed to regions that have no effects in females, which could facilitate the sexual dimorphism observed for this trait. Although this exploratory work focuses on one complex trait, the methodology is generally applicable to any trait for any laboratory or wild population, paving the way for investigating sex‐, age‐ and environment‐specific genetic effects and thus the underlying genetic architecture of phenotype in biological study systems.","lang":"eng"}],"publisher":"Wiley","date_updated":"2021-01-12T08:15:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published"}]