[{"publication_status":"published","doi":"10.1098/rsta.2017.0419","publication":"Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences","oa_version":"None","type":"journal_article","abstract":[{"text":"In this survey, we provide a concise introduction to convex billiards and describe some recent results, obtained by the authors and collaborators, on the classification of integrable billiards, namely the so-called Birkhoff conjecture.\r\n\r\nThis article is part of the theme issue ‘Finite dimensional integrable systems: new trends and methods’.","lang":"eng"}],"extern":"1","citation":{"chicago":"Kaloshin, Vadim, and Alfonso Sorrentino. “On the Integrability of Birkhoff Billiards.” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society, 2018. https://doi.org/10.1098/rsta.2017.0419.","short":"V. Kaloshin, A. Sorrentino, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 376 (2018).","ista":"Kaloshin V, Sorrentino A. 2018. On the integrability of Birkhoff billiards. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 376(2131), 20170419.","ieee":"V. Kaloshin and A. Sorrentino, “On the integrability of Birkhoff billiards,” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 376, no. 2131. The Royal Society, 2018.","ama":"Kaloshin V, Sorrentino A. On the integrability of Birkhoff billiards. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2018;376(2131). doi:10.1098/rsta.2017.0419","mla":"Kaloshin, Vadim, and Alfonso Sorrentino. “On the Integrability of Birkhoff Billiards.” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 376, no. 2131, 20170419, The Royal Society, 2018, doi:10.1098/rsta.2017.0419.","apa":"Kaloshin, V., & Sorrentino, A. (2018). On the integrability of Birkhoff billiards. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society. https://doi.org/10.1098/rsta.2017.0419"},"publication_identifier":{"issn":["1364-503X","1471-2962"]},"volume":376,"day":"28","status":"public","quality_controlled":"1","_id":"8419","date_created":"2020-09-17T10:42:01Z","article_processing_charge":"No","year":"2018","article_type":"original","language":[{"iso":"eng"}],"article_number":"20170419","publisher":"The Royal Society","month":"10","intvolume":" 376","date_published":"2018-10-28T00:00:00Z","issue":"2131","title":"On the integrability of Birkhoff billiards","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","last_name":"Kaloshin","orcid":"0000-0002-6051-2628"},{"last_name":"Sorrentino","first_name":"Alfonso","full_name":"Sorrentino, Alfonso"}],"date_updated":"2021-01-12T08:19:09Z","keyword":["General Engineering","General Physics and Astronomy","General Mathematics"]},{"year":"2018","page":"5214-5234","external_id":{"arxiv":["1706.07968"]},"date_updated":"2021-01-12T08:19:10Z","keyword":["Mathematical Physics","General Physics and Astronomy","Applied Mathematics","Statistical and Nonlinear Physics"],"issue":"11","oa":1,"month":"10","intvolume":" 31","date_published":"2018-10-15T00:00:00Z","oa_version":"Preprint","doi":"10.1088/1361-6544/aadc12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.07968"}],"publication":"Nonlinearity","date_created":"2020-09-17T10:42:09Z","status":"public","day":"15","volume":31,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","last_name":"Kaloshin","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim"},{"first_name":"Ke","last_name":"Zhang","full_name":"Zhang, Ke"}],"title":"Density of convex billiards with rational caustics","publisher":"IOP Publishing","publication_status":"published","_id":"8420","quality_controlled":"1","extern":"1","publication_identifier":{"issn":["0951-7715","1361-6544"]},"citation":{"chicago":"Kaloshin, Vadim, and Ke Zhang. “Density of Convex Billiards with Rational Caustics.” Nonlinearity. IOP Publishing, 2018. https://doi.org/10.1088/1361-6544/aadc12.","ama":"Kaloshin V, Zhang K. Density of convex billiards with rational caustics. Nonlinearity. 2018;31(11):5214-5234. doi:10.1088/1361-6544/aadc12","ista":"Kaloshin V, Zhang K. 2018. Density of convex billiards with rational caustics. Nonlinearity. 31(11), 5214–5234.","ieee":"V. Kaloshin and K. Zhang, “Density of convex billiards with rational caustics,” Nonlinearity, vol. 31, no. 11. IOP Publishing, pp. 5214–5234, 2018.","short":"V. Kaloshin, K. Zhang, Nonlinearity 31 (2018) 5214–5234.","mla":"Kaloshin, Vadim, and Ke Zhang. “Density of Convex Billiards with Rational Caustics.” Nonlinearity, vol. 31, no. 11, IOP Publishing, 2018, pp. 5214–34, doi:10.1088/1361-6544/aadc12.","apa":"Kaloshin, V., & Zhang, K. (2018). Density of convex billiards with rational caustics. Nonlinearity. IOP Publishing. https://doi.org/10.1088/1361-6544/aadc12"},"type":"journal_article","abstract":[{"text":"We show that in the space of all convex billiard boundaries, the set of boundaries with rational caustics is dense. More precisely, the set of billiard boundaries with caustics of rotation number 1/q is polynomially sense in the smooth case, and exponentially dense in the analytic case.","lang":"eng"}],"arxiv":1},{"publication_status":"published","quality_controlled":"1","_id":"8421","type":"journal_article","abstract":[{"lang":"eng","text":"The classical Birkhoff conjecture claims that the boundary of a strictly convex integrable billiard table is necessarily an ellipse (or a circle as a special case). In this article we prove a complete local version of this conjecture: a small integrable perturbation of an ellipse must be an ellipse. This extends and completes the result in Avila-De Simoi-Kaloshin, where nearly circular domains were considered. One of the crucial ideas in the proof is to extend action-angle coordinates for elliptic billiards into complex domains (with respect to the angle), and to thoroughly analyze the nature of their complex singularities. As an application, we are able to prove some spectral rigidity results for elliptic domains."}],"arxiv":1,"publication_identifier":{"issn":["0003-486X"]},"citation":{"mla":"Kaloshin, Vadim, and Alfonso Sorrentino. “On the Local Birkhoff Conjecture for Convex Billiards.” Annals of Mathematics, vol. 188, no. 1, Annals of Mathematics, Princeton U, 2018, pp. 315–80, doi:10.4007/annals.2018.188.1.6.","apa":"Kaloshin, V., & Sorrentino, A. (2018). On the local Birkhoff conjecture for convex billiards. Annals of Mathematics. Annals of Mathematics, Princeton U. https://doi.org/10.4007/annals.2018.188.1.6","chicago":"Kaloshin, Vadim, and Alfonso Sorrentino. “On the Local Birkhoff Conjecture for Convex Billiards.” Annals of Mathematics. Annals of Mathematics, Princeton U, 2018. https://doi.org/10.4007/annals.2018.188.1.6.","ieee":"V. Kaloshin and A. Sorrentino, “On the local Birkhoff conjecture for convex billiards,” Annals of Mathematics, vol. 188, no. 1. Annals of Mathematics, Princeton U, pp. 315–380, 2018.","short":"V. Kaloshin, A. Sorrentino, Annals of Mathematics 188 (2018) 315–380.","ista":"Kaloshin V, Sorrentino A. 2018. On the local Birkhoff conjecture for convex billiards. Annals of Mathematics. 188(1), 315–380.","ama":"Kaloshin V, Sorrentino A. On the local Birkhoff conjecture for convex billiards. Annals of Mathematics. 2018;188(1):315-380. doi:10.4007/annals.2018.188.1.6"},"extern":"1","article_type":"original","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"On the local Birkhoff conjecture for convex billiards","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Kaloshin","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","full_name":"Kaloshin, Vadim"},{"full_name":"Sorrentino, Alfonso","last_name":"Sorrentino","first_name":"Alfonso"}],"publisher":"Annals of Mathematics, Princeton U","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.09194"}],"doi":"10.4007/annals.2018.188.1.6","publication":"Annals of Mathematics","day":"01","status":"public","date_created":"2020-09-17T10:42:22Z","volume":188,"year":"2018","external_id":{"arxiv":["1612.09194"]},"page":"315-380","issue":"1","oa":1,"date_updated":"2021-01-12T08:19:10Z","keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"month":"07","intvolume":" 188","date_published":"2018-07-01T00:00:00Z"},{"article_processing_charge":"No","language":[{"iso":"eng"}],"article_type":"original","publisher":"Springer Nature","author":[{"last_name":"Huang","first_name":"Guan","full_name":"Huang, Guan"},{"orcid":"0000-0002-6051-2628","last_name":"Kaloshin","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim"},{"full_name":"Sorrentino, Alfonso","last_name":"Sorrentino","first_name":"Alfonso"}],"title":"Nearly circular domains which are integrable close to the boundary are ellipses","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publication_identifier":{"issn":["1016-443X","1420-8970"]},"citation":{"mla":"Huang, Guan, et al. “Nearly Circular Domains Which Are Integrable Close to the Boundary Are Ellipses.” Geometric and Functional Analysis, vol. 28, no. 2, Springer Nature, 2018, pp. 334–92, doi:10.1007/s00039-018-0440-4.","apa":"Huang, G., Kaloshin, V., & Sorrentino, A. (2018). Nearly circular domains which are integrable close to the boundary are ellipses. Geometric and Functional Analysis. Springer Nature. https://doi.org/10.1007/s00039-018-0440-4","chicago":"Huang, Guan, Vadim Kaloshin, and Alfonso Sorrentino. “Nearly Circular Domains Which Are Integrable Close to the Boundary Are Ellipses.” Geometric and Functional Analysis. Springer Nature, 2018. https://doi.org/10.1007/s00039-018-0440-4.","short":"G. Huang, V. Kaloshin, A. Sorrentino, Geometric and Functional Analysis 28 (2018) 334–392.","ista":"Huang G, Kaloshin V, Sorrentino A. 2018. Nearly circular domains which are integrable close to the boundary are ellipses. Geometric and Functional Analysis. 28(2), 334–392.","ieee":"G. Huang, V. Kaloshin, and A. Sorrentino, “Nearly circular domains which are integrable close to the boundary are ellipses,” Geometric and Functional Analysis, vol. 28, no. 2. Springer Nature, pp. 334–392, 2018.","ama":"Huang G, Kaloshin V, Sorrentino A. Nearly circular domains which are integrable close to the boundary are ellipses. Geometric and Functional Analysis. 2018;28(2):334-392. doi:10.1007/s00039-018-0440-4"},"extern":"1","abstract":[{"lang":"eng","text":"The Birkhoff conjecture says that the boundary of a strictly convex integrable billiard table is necessarily an ellipse. In this article, we consider a stronger notion of integrability, namely integrability close to the boundary, and prove a local version of this conjecture: a small perturbation of an ellipse of small eccentricity which preserves integrability near the boundary, is itself an ellipse. This extends the result in Avila et al. (Ann Math 184:527–558, ADK16), where integrability was assumed on a larger set. In particular, it shows that (local) integrability near the boundary implies global integrability. One of the crucial ideas in the proof consists in analyzing Taylor expansion of the corresponding action-angle coordinates with respect to the eccentricity parameter, deriving and studying higher order conditions for the preservation of integrable rational caustics."}],"arxiv":1,"type":"journal_article","_id":"8422","quality_controlled":"1","page":"334-392","external_id":{"arxiv":["1705.10601"]},"year":"2018","date_published":"2018-03-18T00:00:00Z","intvolume":" 28","month":"03","keyword":["Geometry and Topology","Analysis"],"date_updated":"2021-01-12T08:19:11Z","oa":1,"issue":"2","publication":"Geometric and Functional Analysis","doi":"10.1007/s00039-018-0440-4","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.10601"}],"oa_version":"Preprint","volume":28,"date_created":"2020-09-17T10:42:30Z","day":"18","status":"public"},{"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Lev","last_name":"Buhovsky","full_name":"Buhovsky, Lev"},{"full_name":"Kaloshin, Vadim","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","last_name":"Kaloshin"}],"title":"Nonisometric domains with the same Marvizi-Melrose invariants","article_processing_charge":"No","language":[{"iso":"eng"}],"article_type":"original","citation":{"mla":"Buhovsky, Lev, and Vadim Kaloshin. “Nonisometric Domains with the Same Marvizi-Melrose Invariants.” Regular and Chaotic Dynamics, vol. 23, Springer Nature, 2018, pp. 54–59, doi:10.1134/s1560354718010057.","apa":"Buhovsky, L., & Kaloshin, V. (2018). Nonisometric domains with the same Marvizi-Melrose invariants. Regular and Chaotic Dynamics. Springer Nature. https://doi.org/10.1134/s1560354718010057","chicago":"Buhovsky, Lev, and Vadim Kaloshin. “Nonisometric Domains with the Same Marvizi-Melrose Invariants.” Regular and Chaotic Dynamics. Springer Nature, 2018. https://doi.org/10.1134/s1560354718010057.","ista":"Buhovsky L, Kaloshin V. 2018. Nonisometric domains with the same Marvizi-Melrose invariants. Regular and Chaotic Dynamics. 23, 54–59.","short":"L. Buhovsky, V. Kaloshin, Regular and Chaotic Dynamics 23 (2018) 54–59.","ieee":"L. Buhovsky and V. Kaloshin, “Nonisometric domains with the same Marvizi-Melrose invariants,” Regular and Chaotic Dynamics, vol. 23. Springer Nature, pp. 54–59, 2018.","ama":"Buhovsky L, Kaloshin V. Nonisometric domains with the same Marvizi-Melrose invariants. Regular and Chaotic Dynamics. 2018;23:54-59. doi:10.1134/s1560354718010057"},"publication_identifier":{"issn":["1560-3547","1468-4845"]},"extern":"1","abstract":[{"lang":"eng","text":"For any strictly convex planar domain Ω ⊂ R2 with a C∞ boundary one can associate an infinite sequence of spectral invariants introduced by Marvizi–Merlose [5]. These invariants can generically be determined using the spectrum of the Dirichlet problem of the Laplace operator. A natural question asks if this collection is sufficient to determine Ω up to isometry. In this paper we give a counterexample, namely, we present two nonisometric domains Ω and Ω¯ with the same collection of Marvizi–Melrose invariants. Moreover, each domain has countably many periodic orbits {Sn}n≥1 (resp. {S¯n}n⩾1) of period going to infinity such that Sn and S¯n have the same period and perimeter for each n."}],"arxiv":1,"type":"journal_article","_id":"8426","quality_controlled":"1","publication_status":"published","date_published":"2018-02-05T00:00:00Z","intvolume":" 23","month":"02","date_updated":"2021-01-12T08:19:11Z","oa":1,"page":"54-59","external_id":{"arxiv":["1801.00952"]},"year":"2018","volume":23,"date_created":"2020-09-17T10:43:21Z","day":"05","status":"public","publication":"Regular and Chaotic Dynamics","doi":"10.1134/s1560354718010057","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1801.00952"}],"oa_version":"Preprint"},{"keyword":["General Biochemistry","Genetics and Molecular Biology"],"date_updated":"2021-01-12T08:19:15Z","title":"Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Weinhäupl","first_name":"Katharina","full_name":"Weinhäupl, Katharina"},{"full_name":"Lindau, Caroline","last_name":"Lindau","first_name":"Caroline"},{"full_name":"Hessel, Audrey","last_name":"Hessel","first_name":"Audrey"},{"last_name":"Wang","first_name":"Yong","full_name":"Wang, Yong"},{"full_name":"Schütze, Conny","first_name":"Conny","last_name":"Schütze"},{"first_name":"Tobias","last_name":"Jores","full_name":"Jores, Tobias"},{"last_name":"Melchionda","first_name":"Laura","full_name":"Melchionda, Laura"},{"last_name":"Schönfisch","first_name":"Birgit","full_name":"Schönfisch, Birgit"},{"first_name":"Hubert","last_name":"Kalbacher","full_name":"Kalbacher, Hubert"},{"first_name":"Beate","last_name":"Bersch","full_name":"Bersch, Beate"},{"last_name":"Rapaport","first_name":"Doron","full_name":"Rapaport, Doron"},{"first_name":"Martha","last_name":"Brennich","full_name":"Brennich, Martha"},{"full_name":"Lindorff-Larsen, Kresten","last_name":"Lindorff-Larsen","first_name":"Kresten"},{"full_name":"Wiedemann, Nils","last_name":"Wiedemann","first_name":"Nils"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"}],"issue":"5","date_published":"2018-11-15T00:00:00Z","month":"11","intvolume":" 175","publisher":"Elsevier","language":[{"iso":"eng"}],"article_type":"original","year":"2018","article_processing_charge":"No","page":"1365-1379.e25","date_created":"2020-09-18T10:04:39Z","_id":"8436","quality_controlled":"1","day":"15","status":"public","volume":175,"publication_identifier":{"issn":["0092-8674"]},"extern":"1","citation":{"chicago":"Weinhäupl, Katharina, Caroline Lindau, Audrey Hessel, Yong Wang, Conny Schütze, Tobias Jores, Laura Melchionda, et al. “Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space.” Cell. Elsevier, 2018. https://doi.org/10.1016/j.cell.2018.10.039.","short":"K. Weinhäupl, C. Lindau, A. Hessel, Y. Wang, C. Schütze, T. Jores, L. Melchionda, B. Schönfisch, H. Kalbacher, B. Bersch, D. Rapaport, M. Brennich, K. Lindorff-Larsen, N. Wiedemann, P. Schanda, Cell 175 (2018) 1365–1379.e25.","ista":"Weinhäupl K, Lindau C, Hessel A, Wang Y, Schütze C, Jores T, Melchionda L, Schönfisch B, Kalbacher H, Bersch B, Rapaport D, Brennich M, Lindorff-Larsen K, Wiedemann N, Schanda P. 2018. Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space. Cell. 175(5), 1365–1379.e25.","ieee":"K. Weinhäupl et al., “Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space,” Cell, vol. 175, no. 5. Elsevier, p. 1365–1379.e25, 2018.","ama":"Weinhäupl K, Lindau C, Hessel A, et al. Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space. Cell. 2018;175(5):1365-1379.e25. doi:10.1016/j.cell.2018.10.039","mla":"Weinhäupl, Katharina, et al. “Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space.” Cell, vol. 175, no. 5, Elsevier, 2018, p. 1365–1379.e25, doi:10.1016/j.cell.2018.10.039.","apa":"Weinhäupl, K., Lindau, C., Hessel, A., Wang, Y., Schütze, C., Jores, T., … Schanda, P. (2018). Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space. Cell. Elsevier. https://doi.org/10.1016/j.cell.2018.10.039"},"abstract":[{"text":"The exchange of metabolites between the mitochondrial matrix and the cytosol depends on β-barrel channels in the outer membrane and α-helical carrier proteins in the inner membrane. The essential translocase of the inner membrane (TIM) chaperones escort these proteins through the intermembrane space, but the structural and mechanistic details remain elusive. We have used an integrated structural biology approach to reveal the functional principle of TIM chaperones. Multiple clamp-like binding sites hold the mitochondrial membrane proteins in a translocation-competent elongated form, thus mimicking characteristics of co-translational membrane insertion. The bound preprotein undergoes conformational dynamics within the chaperone binding clefts, pointing to a multitude of dynamic local binding events. Mutations in these binding sites cause cell death or growth defects associated with impairment of carrier and β-barrel protein biogenesis. Our work reveals how a single mitochondrial “transfer-chaperone” system is able to guide α-helical and β-barrel membrane proteins in a “nascent chain-like” conformation through a ribosome-free compartment.","lang":"eng"}],"type":"journal_article","oa_version":"None","publication":"Cell","publication_status":"published","doi":"10.1016/j.cell.2018.10.039"},{"date_created":"2020-09-18T10:04:51Z","_id":"8437","day":"19","status":"public","quality_controlled":"1","volume":4,"citation":{"ieee":"G. Mas et al., “Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle,” Science Advances, vol. 4, no. 9. American Association for the Advancement of Science, 2018.","ista":"Mas G, Guan J-Y, Crublet E, Debled EC, Moriscot C, Gans P, Schoehn G, Macek P, Schanda P, Boisbouvier J. 2018. Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle. Science Advances. 4(9), eaau4196.","short":"G. Mas, J.-Y. Guan, E. Crublet, E.C. Debled, C. Moriscot, P. Gans, G. Schoehn, P. Macek, P. Schanda, J. Boisbouvier, Science Advances 4 (2018).","ama":"Mas G, Guan J-Y, Crublet E, et al. Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle. Science Advances. 2018;4(9). doi:10.1126/sciadv.aau4196","chicago":"Mas, Guillaume, Jia-Ying Guan, Elodie Crublet, Elisa Colas Debled, Christine Moriscot, Pierre Gans, Guy Schoehn, Pavel Macek, Paul Schanda, and Jerome Boisbouvier. “Structural Investigation of a Chaperonin in Action Reveals How Nucleotide Binding Regulates the Functional Cycle.” Science Advances. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/sciadv.aau4196.","apa":"Mas, G., Guan, J.-Y., Crublet, E., Debled, E. C., Moriscot, C., Gans, P., … Boisbouvier, J. (2018). Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aau4196","mla":"Mas, Guillaume, et al. “Structural Investigation of a Chaperonin in Action Reveals How Nucleotide Binding Regulates the Functional Cycle.” Science Advances, vol. 4, no. 9, eaau4196, American Association for the Advancement of Science, 2018, doi:10.1126/sciadv.aau4196."},"extern":"1","publication_identifier":{"issn":["2375-2548"]},"abstract":[{"lang":"eng","text":"Chaperonins are ubiquitous protein assemblies present in bacteria, eukaryota, and archaea, facilitating the folding of proteins, preventing protein aggregation, and thus participating in maintaining protein homeostasis in the cell. During their functional cycle, they bind unfolded client proteins inside their double ring structure and promote protein folding by closing the ring chamber in an adenosine 5′-triphosphate (ATP)–dependent manner. Although the static structures of fully open and closed forms of chaperonins were solved by x-ray crystallography or electron microscopy, elucidating the mechanisms of such ATP-driven molecular events requires studying the proteins at the structural level under working conditions. We introduce an approach that combines site-specific nuclear magnetic resonance observation of very large proteins, enabled by advanced isotope labeling methods, with an in situ ATP regeneration system. Using this method, we provide functional insight into the 1-MDa large hsp60 chaperonin while processing client proteins and reveal how nucleotide binding, hydrolysis, and release control switching between closed and open states. While the open conformation stabilizes the unfolded state of client proteins, the internalization of the client protein inside the chaperonin cavity speeds up its functional cycle. This approach opens new perspectives to study structures and mechanisms of various ATP-driven biological machineries in the heat of action."}],"type":"journal_article","oa_version":"None","publication":"Science Advances","doi":"10.1126/sciadv.aau4196","publication_status":"published","date_updated":"2022-08-26T09:11:06Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle","author":[{"last_name":"Mas","first_name":"Guillaume","full_name":"Mas, Guillaume"},{"last_name":"Guan","first_name":"Jia-Ying","full_name":"Guan, Jia-Ying"},{"full_name":"Crublet, Elodie","last_name":"Crublet","first_name":"Elodie"},{"full_name":"Debled, Elisa Colas","first_name":"Elisa Colas","last_name":"Debled"},{"full_name":"Moriscot, Christine","first_name":"Christine","last_name":"Moriscot"},{"full_name":"Gans, Pierre","first_name":"Pierre","last_name":"Gans"},{"first_name":"Guy","last_name":"Schoehn","full_name":"Schoehn, Guy"},{"last_name":"Macek","first_name":"Pavel","full_name":"Macek, Pavel"},{"full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda"},{"first_name":"Jerome","last_name":"Boisbouvier","full_name":"Boisbouvier, Jerome"}],"issue":"9","date_published":"2018-09-19T00:00:00Z","month":"09","intvolume":" 4","publisher":"American Association for the Advancement of Science","article_number":"eaau4196","language":[{"iso":"eng"}],"article_type":"original","year":"2018","article_processing_charge":"No"},{"article_processing_charge":"No","page":"745-747","article_type":"letter_note","year":"2018","language":[{"iso":"eng"}],"publisher":"Springer Nature","date_published":"2018-09-03T00:00:00Z","intvolume":" 25","month":"09","title":"Dynamics and interactions of AAC3 in DPC are not functionally relevant","author":[{"full_name":"Kurauskas, Vilius","last_name":"Kurauskas","first_name":"Vilius"},{"full_name":"Hessel, Audrey","last_name":"Hessel","first_name":"Audrey"},{"first_name":"François","last_name":"Dehez","full_name":"Dehez, François"},{"full_name":"Chipot, Christophe","first_name":"Christophe","last_name":"Chipot"},{"first_name":"Beate","last_name":"Bersch","full_name":"Bersch, Beate"},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"9","keyword":["Molecular Biology","Structural Biology"],"date_updated":"2021-01-12T08:19:16Z","publication":"Nature Structural & Molecular Biology","publication_status":"published","doi":"10.1038/s41594-018-0127-4","oa_version":"None","type":"journal_article","volume":25,"publication_identifier":{"issn":["1545-9993","1545-9985"]},"extern":"1","citation":{"ieee":"V. Kurauskas, A. Hessel, F. Dehez, C. Chipot, B. Bersch, and P. Schanda, “Dynamics and interactions of AAC3 in DPC are not functionally relevant,” Nature Structural & Molecular Biology, vol. 25, no. 9. Springer Nature, pp. 745–747, 2018.","ista":"Kurauskas V, Hessel A, Dehez F, Chipot C, Bersch B, Schanda P. 2018. Dynamics and interactions of AAC3 in DPC are not functionally relevant. Nature Structural & Molecular Biology. 25(9), 745–747.","short":"V. Kurauskas, A. Hessel, F. Dehez, C. Chipot, B. Bersch, P. Schanda, Nature Structural & Molecular Biology 25 (2018) 745–747.","ama":"Kurauskas V, Hessel A, Dehez F, Chipot C, Bersch B, Schanda P. Dynamics and interactions of AAC3 in DPC are not functionally relevant. Nature Structural & Molecular Biology. 2018;25(9):745-747. doi:10.1038/s41594-018-0127-4","chicago":"Kurauskas, Vilius, Audrey Hessel, François Dehez, Christophe Chipot, Beate Bersch, and Paul Schanda. “Dynamics and Interactions of AAC3 in DPC Are Not Functionally Relevant.” Nature Structural & Molecular Biology. Springer Nature, 2018. https://doi.org/10.1038/s41594-018-0127-4.","apa":"Kurauskas, V., Hessel, A., Dehez, F., Chipot, C., Bersch, B., & Schanda, P. (2018). Dynamics and interactions of AAC3 in DPC are not functionally relevant. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-018-0127-4","mla":"Kurauskas, Vilius, et al. “Dynamics and Interactions of AAC3 in DPC Are Not Functionally Relevant.” Nature Structural & Molecular Biology, vol. 25, no. 9, Springer Nature, 2018, pp. 745–47, doi:10.1038/s41594-018-0127-4."},"day":"03","quality_controlled":"1","status":"public","date_created":"2020-09-18T10:04:59Z","_id":"8438"},{"page":"2106-2113","article_processing_charge":"No","article_type":"original","year":"2018","language":[{"iso":"eng"}],"publisher":"American Chemical Society","date_published":"2018-07-02T00:00:00Z","month":"07","intvolume":" 13","author":[{"first_name":"Cedric","last_name":"Laguri","full_name":"Laguri, Cedric"},{"full_name":"Silipo, Alba","first_name":"Alba","last_name":"Silipo"},{"last_name":"Martorana","first_name":"Alessandra M.","full_name":"Martorana, Alessandra M."},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"},{"first_name":"Roberta","last_name":"Marchetti","full_name":"Marchetti, Roberta"},{"last_name":"Polissi","first_name":"Alessandra","full_name":"Polissi, Alessandra"},{"full_name":"Molinaro, Antonio","first_name":"Antonio","last_name":"Molinaro"},{"first_name":"Jean-Pierre","last_name":"Simorre","full_name":"Simorre, Jean-Pierre"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Solid state NMR studies of intact lipopolysaccharide endotoxin","issue":"8","keyword":["Molecular Medicine","Biochemistry","General Medicine"],"date_updated":"2021-01-12T08:19:16Z","publication":"ACS Chemical Biology","doi":"10.1021/acschembio.8b00271","publication_status":"published","oa_version":"None","abstract":[{"text":"Lipopolysaccharides (LPS) are complex glycolipids forming the outside layer of Gram-negative bacteria. Their hydrophobic and heterogeneous nature greatly hampers their structural study in an environment similar to the bacterial surface. We have studied LPS purified from E. coli and pathogenic P. aeruginosa with long O-antigen polysaccharides assembled in solution as vesicles or elongated micelles. Solid-state NMR with magic-angle spinning permitted the identification of NMR signals arising from regions with different flexibilities in the LPS, from the lipid components to the O-antigen polysaccharides. Atomic scale data on the LPS enabled the study of the interaction of gentamicin antibiotic bound to P. aeruginosa LPS, for which we could confirm that a specific oligosaccharide is involved in the antibiotic binding. The possibility to study LPS alone and bound to a ligand when it is assembled in membrane-like structures opens great prospects for the investigation of proteins and antibiotics that specifically target such an important molecule at the surface of Gram-negative bacteria.","lang":"eng"}],"type":"journal_article","volume":13,"citation":{"mla":"Laguri, Cedric, et al. “Solid State NMR Studies of Intact Lipopolysaccharide Endotoxin.” ACS Chemical Biology, vol. 13, no. 8, American Chemical Society, 2018, pp. 2106–13, doi:10.1021/acschembio.8b00271.","apa":"Laguri, C., Silipo, A., Martorana, A. M., Schanda, P., Marchetti, R., Polissi, A., … Simorre, J.-P. (2018). Solid state NMR studies of intact lipopolysaccharide endotoxin. ACS Chemical Biology. American Chemical Society. https://doi.org/10.1021/acschembio.8b00271","chicago":"Laguri, Cedric, Alba Silipo, Alessandra M. Martorana, Paul Schanda, Roberta Marchetti, Alessandra Polissi, Antonio Molinaro, and Jean-Pierre Simorre. “Solid State NMR Studies of Intact Lipopolysaccharide Endotoxin.” ACS Chemical Biology. American Chemical Society, 2018. https://doi.org/10.1021/acschembio.8b00271.","short":"C. Laguri, A. Silipo, A.M. Martorana, P. Schanda, R. Marchetti, A. Polissi, A. Molinaro, J.-P. Simorre, ACS Chemical Biology 13 (2018) 2106–2113.","ista":"Laguri C, Silipo A, Martorana AM, Schanda P, Marchetti R, Polissi A, Molinaro A, Simorre J-P. 2018. Solid state NMR studies of intact lipopolysaccharide endotoxin. ACS Chemical Biology. 13(8), 2106–2113.","ieee":"C. Laguri et al., “Solid state NMR studies of intact lipopolysaccharide endotoxin,” ACS Chemical Biology, vol. 13, no. 8. American Chemical Society, pp. 2106–2113, 2018.","ama":"Laguri C, Silipo A, Martorana AM, et al. Solid state NMR studies of intact lipopolysaccharide endotoxin. ACS Chemical Biology. 2018;13(8):2106-2113. doi:10.1021/acschembio.8b00271"},"publication_identifier":{"issn":["1554-8929","1554-8937"]},"extern":"1","quality_controlled":"1","day":"02","status":"public","_id":"8439","date_created":"2020-09-18T10:05:09Z"},{"abstract":[{"text":"Mycobacterium tuberculosis can remain dormant in the host, an ability that explains the failure of many current tuberculosis treatments. Recently, the natural products cyclomarin, ecumicin, and lassomycin have been shown to efficiently kill Mycobacterium tuberculosis persisters. Their target is the N-terminal domain of the hexameric AAA+ ATPase ClpC1, which recognizes, unfolds, and translocates protein substrates, such as proteins containing phosphorylated arginine residues, to the ClpP1P2 protease for degradation. Surprisingly, these antibiotics do not inhibit ClpC1 ATPase activity, and how they cause cell death is still unclear. Here, using NMR and small-angle X-ray scattering, we demonstrate that arginine-phosphate binding to the ClpC1 N-terminal domain induces millisecond dynamics. We show that these dynamics are caused by conformational changes and do not result from unfolding or oligomerization of this domain. Cyclomarin binding to this domain specifically blocked these N-terminal dynamics. On the basis of these results, we propose a mechanism of action involving cyclomarin-induced restriction of ClpC1 dynamics, which modulates the chaperone enzymatic activity leading eventually to cell death.","lang":"eng"}],"type":"journal_article","volume":293,"publication_identifier":{"issn":["0021-9258","1083-351X"]},"extern":"1","citation":{"mla":"Weinhäupl, Katharina, et al. “The Antibiotic Cyclomarin Blocks Arginine-Phosphate–Induced Millisecond Dynamics in the N-Terminal Domain of ClpC1 from Mycobacterium Tuberculosis.” Journal of Biological Chemistry, vol. 293, no. 22, American Society for Biochemistry & Molecular Biology, 2018, pp. 8379–93, doi:10.1074/jbc.ra118.002251.","apa":"Weinhäupl, K., Brennich, M., Kazmaier, U., Lelievre, J., Ballell, L., Goldberg, A., … Fraga, H. (2018). The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis. Journal of Biological Chemistry. American Society for Biochemistry & Molecular Biology. https://doi.org/10.1074/jbc.ra118.002251","chicago":"Weinhäupl, Katharina, Martha Brennich, Uli Kazmaier, Joel Lelievre, Lluis Ballell, Alfred Goldberg, Paul Schanda, and Hugo Fraga. “The Antibiotic Cyclomarin Blocks Arginine-Phosphate–Induced Millisecond Dynamics in the N-Terminal Domain of ClpC1 from Mycobacterium Tuberculosis.” Journal of Biological Chemistry. American Society for Biochemistry & Molecular Biology, 2018. https://doi.org/10.1074/jbc.ra118.002251.","short":"K. Weinhäupl, M. Brennich, U. Kazmaier, J. Lelievre, L. Ballell, A. Goldberg, P. Schanda, H. Fraga, Journal of Biological Chemistry 293 (2018) 8379–8393.","ista":"Weinhäupl K, Brennich M, Kazmaier U, Lelievre J, Ballell L, Goldberg A, Schanda P, Fraga H. 2018. The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis. Journal of Biological Chemistry. 293(22), 8379–8393.","ieee":"K. Weinhäupl et al., “The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis,” Journal of Biological Chemistry, vol. 293, no. 22. American Society for Biochemistry & Molecular Biology, pp. 8379–8393, 2018.","ama":"Weinhäupl K, Brennich M, Kazmaier U, et al. The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis. Journal of Biological Chemistry. 2018;293(22):8379-8393. doi:10.1074/jbc.ra118.002251"},"status":"public","quality_controlled":"1","day":"01","date_created":"2020-09-18T10:05:18Z","_id":"8440","publication":"Journal of Biological Chemistry","publication_status":"published","doi":"10.1074/jbc.ra118.002251","oa_version":"None","publisher":"American Society for Biochemistry & Molecular Biology","date_published":"2018-06-01T00:00:00Z","month":"06","intvolume":" 293","author":[{"last_name":"Weinhäupl","first_name":"Katharina","full_name":"Weinhäupl, Katharina"},{"first_name":"Martha","last_name":"Brennich","full_name":"Brennich, Martha"},{"full_name":"Kazmaier, Uli","last_name":"Kazmaier","first_name":"Uli"},{"last_name":"Lelievre","first_name":"Joel","full_name":"Lelievre, Joel"},{"full_name":"Ballell, Lluis","first_name":"Lluis","last_name":"Ballell"},{"full_name":"Goldberg, Alfred","last_name":"Goldberg","first_name":"Alfred"},{"full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda"},{"last_name":"Fraga","first_name":"Hugo","full_name":"Fraga, Hugo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis","issue":"22","keyword":["Cell Biology","Biochemistry","Molecular Biology"],"date_updated":"2021-01-12T08:19:17Z","article_processing_charge":"No","page":"8379-8393","article_type":"original","year":"2018","language":[{"iso":"eng"}]},{"oa_version":"Published Version","doi":"10.1007/s10858-018-0191-4","publication_status":"published","publication":"Journal of Biomolecular NMR","date_created":"2020-09-18T10:05:28Z","_id":"8441","day":"30","status":"public","quality_controlled":"1","extern":"1","citation":{"chicago":"Krushelnitsky, Alexey, Diego Gauto, Diana C. Rodriguez Camargo, Paul Schanda, and Kay Saalwächter. “Microsecond Motions Probed by Near-Rotary-Resonance R1ρ 15N MAS NMR Experiments: The Model Case of Protein Overall-Rocking in Crystals.” Journal of Biomolecular NMR. Springer Nature, 2018. https://doi.org/10.1007/s10858-018-0191-4.","ista":"Krushelnitsky A, Gauto D, Rodriguez Camargo DC, Schanda P, Saalwächter K. 2018. Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals. Journal of Biomolecular NMR. 71(1), 53–67.","short":"A. Krushelnitsky, D. Gauto, D.C. Rodriguez Camargo, P. Schanda, K. Saalwächter, Journal of Biomolecular NMR 71 (2018) 53–67.","ieee":"A. Krushelnitsky, D. Gauto, D. C. Rodriguez Camargo, P. Schanda, and K. Saalwächter, “Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals,” Journal of Biomolecular NMR, vol. 71, no. 1. Springer Nature, pp. 53–67, 2018.","ama":"Krushelnitsky A, Gauto D, Rodriguez Camargo DC, Schanda P, Saalwächter K. Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals. Journal of Biomolecular NMR. 2018;71(1):53-67. doi:10.1007/s10858-018-0191-4","mla":"Krushelnitsky, Alexey, et al. “Microsecond Motions Probed by Near-Rotary-Resonance R1ρ 15N MAS NMR Experiments: The Model Case of Protein Overall-Rocking in Crystals.” Journal of Biomolecular NMR, vol. 71, no. 1, Springer Nature, 2018, pp. 53–67, doi:10.1007/s10858-018-0191-4.","apa":"Krushelnitsky, A., Gauto, D., Rodriguez Camargo, D. C., Schanda, P., & Saalwächter, K. (2018). Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals. Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-018-0191-4"},"publication_identifier":{"issn":["0925-2738","1573-5001"]},"volume":71,"type":"journal_article","abstract":[{"text":"Solid-state near-rotary-resonance measurements of the spin–lattice relaxation rate in the rotating frame (R1ρ) is a powerful NMR technique for studying molecular dynamics in the microsecond time scale. The small difference between the spin-lock (SL) and magic-angle-spinning (MAS) frequencies allows sampling very slow motions, at the same time it brings up some methodological challenges. In this work, several issues affecting correct measurements and analysis of 15N R1ρ data are considered in detail. Among them are signal amplitude as a function of the difference between SL and MAS frequencies, “dead time” in the initial part of the relaxation decay caused by transient spin-dynamic oscillations, measurements under HORROR condition and proper treatment of the multi-exponential relaxation decays. The multiple 15N R1ρ measurements at different SL fields and temperatures have been conducted in 1D mode (i.e. without site-specific resolution) for a set of four different microcrystalline protein samples (GB1, SH3, MPD-ubiquitin and cubic-PEG-ubiquitin) to study the overall protein rocking in a crystal. While the amplitude of this motion varies very significantly, its correlation time for all four sample is practically the same, 30–50 μs. The amplitude of the rocking motion correlates with the packing density of a protein crystal. It has been suggested that the rocking motion is not diffusive but likely a jump-like dynamic process.","lang":"eng"}],"language":[{"iso":"eng"}],"year":"2018","article_type":"original","article_processing_charge":"No","page":"53-67","date_updated":"2021-01-12T08:19:17Z","issue":"1","author":[{"full_name":"Krushelnitsky, Alexey","first_name":"Alexey","last_name":"Krushelnitsky"},{"full_name":"Gauto, Diego","first_name":"Diego","last_name":"Gauto"},{"full_name":"Rodriguez Camargo, Diana C.","first_name":"Diana C.","last_name":"Rodriguez Camargo"},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606"},{"first_name":"Kay","last_name":"Saalwächter","full_name":"Saalwächter, Kay"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals","month":"05","intvolume":" 71","date_published":"2018-05-30T00:00:00Z","publisher":"Springer Nature"},{"intvolume":" 118","month":"02","date_published":"2018-02-28T00:00:00Z","publisher":"American Chemical Society","date_updated":"2021-01-12T08:19:18Z","keyword":["General Chemistry"],"issue":"7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Christophe","last_name":"Chipot","full_name":"Chipot, Christophe"},{"full_name":"Dehez, François","last_name":"Dehez","first_name":"François"},{"full_name":"Schnell, Jason R.","first_name":"Jason R.","last_name":"Schnell"},{"last_name":"Zitzmann","first_name":"Nicole","full_name":"Zitzmann, Nicole"},{"full_name":"Pebay-Peyroula, Eva","first_name":"Eva","last_name":"Pebay-Peyroula"},{"last_name":"Catoire","first_name":"Laurent J.","full_name":"Catoire, Laurent J."},{"full_name":"Miroux, Bruno","first_name":"Bruno","last_name":"Miroux"},{"first_name":"Edmund R. S.","last_name":"Kunji","full_name":"Kunji, Edmund R. S."},{"first_name":"Gianluigi","last_name":"Veglia","full_name":"Veglia, Gianluigi"},{"first_name":"Timothy A.","last_name":"Cross","full_name":"Cross, Timothy A."},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"title":"Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies","page":"3559-3607","article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2018","article_type":"original","publication_identifier":{"issn":["0009-2665","1520-6890"]},"citation":{"mla":"Chipot, Christophe, et al. “Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies.” Chemical Reviews, vol. 118, no. 7, American Chemical Society, 2018, pp. 3559–607, doi:10.1021/acs.chemrev.7b00570.","apa":"Chipot, C., Dehez, F., Schnell, J. R., Zitzmann, N., Pebay-Peyroula, E., Catoire, L. J., … Schanda, P. (2018). Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies. Chemical Reviews. American Chemical Society. https://doi.org/10.1021/acs.chemrev.7b00570","chicago":"Chipot, Christophe, François Dehez, Jason R. Schnell, Nicole Zitzmann, Eva Pebay-Peyroula, Laurent J. Catoire, Bruno Miroux, et al. “Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies.” Chemical Reviews. American Chemical Society, 2018. https://doi.org/10.1021/acs.chemrev.7b00570.","ama":"Chipot C, Dehez F, Schnell JR, et al. Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies. Chemical Reviews. 2018;118(7):3559-3607. doi:10.1021/acs.chemrev.7b00570","ieee":"C. Chipot et al., “Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies,” Chemical Reviews, vol. 118, no. 7. American Chemical Society, pp. 3559–3607, 2018.","short":"C. Chipot, F. Dehez, J.R. Schnell, N. Zitzmann, E. Pebay-Peyroula, L.J. Catoire, B. Miroux, E.R.S. Kunji, G. Veglia, T.A. Cross, P. Schanda, Chemical Reviews 118 (2018) 3559–3607.","ista":"Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ, Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. 2018. Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies. Chemical Reviews. 118(7), 3559–3607."},"extern":"1","volume":118,"type":"journal_article","abstract":[{"lang":"eng","text":"Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents."}],"_id":"8442","date_created":"2020-09-18T10:05:35Z","quality_controlled":"1","day":"28","status":"public","publication_status":"published","doi":"10.1021/acs.chemrev.7b00570","publication":"Chemical Reviews","oa_version":"None"},{"date_created":"2020-09-18T10:05:45Z","_id":"8443","day":"03","status":"public","quality_controlled":"1","citation":{"apa":"Kurauskas, V., Hessel, A., Ma, P., Lunetti, P., Weinhäupl, K., Imbert, L., … Schanda, P. (2018). How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.8b00269","mla":"Kurauskas, Vilius, et al. “How Detergent Impacts Membrane Proteins: Atomic-Level Views of Mitochondrial Carriers in Dodecylphosphocholine.” The Journal of Physical Chemistry Letters, vol. 9, no. 5, American Chemical Society, 2018, pp. 933–38, doi:10.1021/acs.jpclett.8b00269.","ama":"Kurauskas V, Hessel A, Ma P, et al. How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical Chemistry Letters. 2018;9(5):933-938. doi:10.1021/acs.jpclett.8b00269","ieee":"V. Kurauskas et al., “How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine,” The Journal of Physical Chemistry Letters, vol. 9, no. 5. American Chemical Society, pp. 933–938, 2018.","ista":"Kurauskas V, Hessel A, Ma P, Lunetti P, Weinhäupl K, Imbert L, Brutscher B, King MS, Sounier R, Dolce V, Kunji ERS, Capobianco L, Chipot C, Dehez F, Bersch B, Schanda P. 2018. How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical Chemistry Letters. 9(5), 933–938.","short":"V. Kurauskas, A. Hessel, P. Ma, P. Lunetti, K. Weinhäupl, L. Imbert, B. Brutscher, M.S. King, R. Sounier, V. Dolce, E.R.S. Kunji, L. Capobianco, C. Chipot, F. Dehez, B. Bersch, P. Schanda, The Journal of Physical Chemistry Letters 9 (2018) 933–938.","chicago":"Kurauskas, Vilius, Audrey Hessel, Peixiang Ma, Paola Lunetti, Katharina Weinhäupl, Lionel Imbert, Bernhard Brutscher, et al. “How Detergent Impacts Membrane Proteins: Atomic-Level Views of Mitochondrial Carriers in Dodecylphosphocholine.” The Journal of Physical Chemistry Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.jpclett.8b00269."},"publication_identifier":{"issn":["1948-7185"]},"extern":"1","volume":9,"type":"journal_article","abstract":[{"lang":"eng","text":"Characterizing the structure of membrane proteins (MPs) generally requires extraction from their native environment, most commonly with detergents. Yet, the physicochemical properties of detergent micelles and lipid bilayers differ markedly and could alter the structural organization of MPs, albeit without general rules. Dodecylphosphocholine (DPC) is the most widely used detergent for MP structure determination by NMR, but the physiological relevance of several prominent structures has been questioned, though indirectly, by other biophysical techniques, e.g., functional/thermostability assay (TSA) and molecular dynamics (MD) simulations. Here, we resolve unambiguously this controversy by probing the functional relevance of three different mitochondrial carriers (MCs) in DPC at the atomic level, using an exhaustive set of solution-NMR experiments, complemented by functional/TSA and MD data. Our results provide atomic-level insight into the structure, substrate interaction and dynamics of the detergent–membrane protein complexes and demonstrates cogently that, while high-resolution NMR signals can be obtained for MCs in DPC, they systematically correspond to nonfunctional states."}],"oa_version":"None","doi":"10.1021/acs.jpclett.8b00269","publication_status":"published","publication":"The Journal of Physical Chemistry Letters","date_updated":"2021-01-12T08:19:18Z","keyword":["General Materials Science"],"issue":"5","title":"How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Kurauskas","first_name":"Vilius","full_name":"Kurauskas, Vilius"},{"full_name":"Hessel, Audrey","last_name":"Hessel","first_name":"Audrey"},{"full_name":"Ma, Peixiang","last_name":"Ma","first_name":"Peixiang"},{"full_name":"Lunetti, Paola","last_name":"Lunetti","first_name":"Paola"},{"full_name":"Weinhäupl, Katharina","last_name":"Weinhäupl","first_name":"Katharina"},{"full_name":"Imbert, Lionel","first_name":"Lionel","last_name":"Imbert"},{"full_name":"Brutscher, Bernhard","first_name":"Bernhard","last_name":"Brutscher"},{"last_name":"King","first_name":"Martin S.","full_name":"King, Martin S."},{"full_name":"Sounier, Rémy","first_name":"Rémy","last_name":"Sounier"},{"last_name":"Dolce","first_name":"Vincenza","full_name":"Dolce, Vincenza"},{"full_name":"Kunji, Edmund R. S.","last_name":"Kunji","first_name":"Edmund R. S."},{"first_name":"Loredana","last_name":"Capobianco","full_name":"Capobianco, Loredana"},{"full_name":"Chipot, Christophe","first_name":"Christophe","last_name":"Chipot"},{"first_name":"François","last_name":"Dehez","full_name":"Dehez, François"},{"last_name":"Bersch","first_name":"Beate","full_name":"Bersch, Beate"},{"last_name":"Schanda","orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"}],"month":"02","intvolume":" 9","date_published":"2018-02-03T00:00:00Z","publisher":"American Chemical Society","language":[{"iso":"eng"}],"year":"2018","article_type":"original","article_processing_charge":"No","page":"933-938"},{"quality_controlled":"1","_id":"85","scopus_import":"1","abstract":[{"lang":"eng","text":"Concurrent accesses to shared data structures must be synchronized to avoid data races. Coarse-grained synchronization, which locks the entire data structure, is easy to implement but does not scale. Fine-grained synchronization can scale well, but can be hard to reason about. Hand-over-hand locking, in which operations are pipelined as they traverse the data structure, combines fine-grained synchronization with ease of use. However, the traditional implementation suffers from inherent overheads. This paper introduces snapshot-based synchronization (SBS), a novel hand-over-hand locking mechanism. SBS decouples the synchronization state from the data, significantly improving cache utilization. Further, it relies on guarantees provided by pipelining to minimize synchronization that requires cross-thread communication. Snapshot-based synchronization thus scales much better than traditional hand-over-hand locking, while maintaining the same ease of use."}],"file_date_updated":"2020-07-14T12:48:14Z","type":"conference","citation":{"chicago":"Gilad, Eran, Trevor A Brown, Mark Oskin, and Yoav Etsion. “Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking,” 11014:465–79. Springer, 2018. https://doi.org/10.1007/978-3-319-96983-1_33.","short":"E. Gilad, T.A. Brown, M. Oskin, Y. Etsion, in:, Springer, 2018, pp. 465–479.","ieee":"E. Gilad, T. A. Brown, M. Oskin, and Y. Etsion, “Snapshot based synchronization: A fast replacement for Hand-over-Hand locking,” presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy, 2018, vol. 11014, pp. 465–479.","ista":"Gilad E, Brown TA, Oskin M, Etsion Y. 2018. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. Euro-Par: European Conference on Parallel Processing, LNCS, vol. 11014, 465–479.","ama":"Gilad E, Brown TA, Oskin M, Etsion Y. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. In: Vol 11014. Springer; 2018:465-479. doi:10.1007/978-3-319-96983-1_33","mla":"Gilad, Eran, et al. Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking. Vol. 11014, Springer, 2018, pp. 465–79, doi:10.1007/978-3-319-96983-1_33.","apa":"Gilad, E., Brown, T. A., Oskin, M., & Etsion, Y. (2018). Snapshot based synchronization: A fast replacement for Hand-over-Hand locking (Vol. 11014, pp. 465–479). Presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy: Springer. https://doi.org/10.1007/978-3-319-96983-1_33"},"publication_identifier":{"issn":["03029743"]},"publication_status":"published","project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Snapshot based synchronization: A fast replacement for Hand-over-Hand locking","author":[{"first_name":"Eran","last_name":"Gilad","full_name":"Gilad, Eran"},{"full_name":"Brown, Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A","last_name":"Brown"},{"full_name":"Oskin, Mark","last_name":"Oskin","first_name":"Mark"},{"last_name":"Etsion","first_name":"Yoav","full_name":"Etsion, Yoav"}],"file":[{"file_id":"5954","content_type":"application/pdf","file_size":665372,"creator":"dernst","access_level":"open_access","checksum":"13a3f250be8878405e791b53c19722ad","relation":"main_file","file_name":"2018_Brown.pdf","date_updated":"2020-07-14T12:48:14Z","date_created":"2019-02-12T07:40:40Z"}],"publisher":"Springer","has_accepted_license":"1","language":[{"iso":"eng"}],"publist_id":"7969","department":[{"_id":"DaAl"}],"article_processing_charge":"No","day":"01","status":"public","ddc":["000"],"date_created":"2018-12-11T11:44:33Z","volume":11014,"oa_version":"Preprint","isi":1,"doi":"10.1007/978-3-319-96983-1_33","oa":1,"date_updated":"2023-09-18T09:32:36Z","acknowledgement":"Trevor Brown was supported in part by the ISF (grants 2005/17 & 1749/14) and by a NSERC post-doctoral fellowship.","date_published":"2018-08-01T00:00:00Z","alternative_title":["LNCS"],"month":"08","intvolume":" 11014","year":"2018","conference":{"end_date":"2018-08-31","start_date":"2018-08-27","name":"Euro-Par: European Conference on Parallel Processing","location":"Turin, Italy"},"external_id":{"isi":["000851042300031"]},"page":"465 - 479"},{"date_created":"2020-09-21T12:01:50Z","_id":"8547","status":"public","day":"13","citation":{"ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv, 10.1101/494088.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, BioRxiv (n.d.).","ieee":"A. Llorca et al., “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” bioRxiv. Cold Spring Harbor Laboratory.","ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. doi:10.1101/494088","chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/494088.","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou, E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/494088","mla":"Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/494088."},"abstract":[{"text":"The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex.","lang":"eng"}],"type":"preprint","ec_funded":1,"oa_version":"Preprint","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780"},{"name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","_id":"264E56E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02416"}],"publication":"bioRxiv","main_file_link":[{"url":"https://doi.org/10.1101/494088","open_access":"1"}],"doi":"10.1101/494088","publication_status":"submitted","date_updated":"2021-01-12T08:20:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Alfredo","last_name":"Llorca","full_name":"Llorca, Alfredo"},{"full_name":"Ciceri, Gabriele","first_name":"Gabriele","last_name":"Ciceri"},{"full_name":"Beattie, Robert J","first_name":"Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie","orcid":"0000-0002-8483-8753"},{"full_name":"Wong, Fong K.","first_name":"Fong K.","last_name":"Wong"},{"first_name":"Giovanni","last_name":"Diana","full_name":"Diana, Giovanni"},{"full_name":"Serafeimidou, Eleni","first_name":"Eleni","last_name":"Serafeimidou"},{"first_name":"Marian","last_name":"Fernández-Otero","full_name":"Fernández-Otero, Marian"},{"full_name":"Streicher, Carmen","last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Arnold","first_name":"Sebastian J.","full_name":"Arnold, Sebastian J."},{"first_name":"Martin","last_name":"Meyer","full_name":"Meyer, Martin"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon"},{"first_name":"Miguel","last_name":"Maravall","full_name":"Maravall, Miguel"},{"full_name":"Marín, Oscar","first_name":"Oscar","last_name":"Marín"}],"oa":1,"title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","date_published":"2018-12-13T00:00:00Z","month":"12","publisher":"Cold Spring Harbor Laboratory","acknowledgement":"We thank I. Andrew and S.E. Bae for excellent technical assistance, F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members of the Marín and Rico laboratories for stimulating discussions and ideas. Our research on this topic is supported by grants from the European Research Council (ERC-2017-AdG 787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M. L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the European Commission under the H2020 Programme.","language":[{"iso":"eng"}],"year":"2018","article_processing_charge":"No","department":[{"_id":"SiHi"}]},{"type":"book_chapter","file_date_updated":"2020-07-14T12:48:14Z","abstract":[{"lang":"eng","text":"Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms."}],"scopus_import":1,"citation":{"mla":"Chatterjee, Krishnendu, et al. “Computing Average Response Time.” Principles of Modeling, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018, pp. 143–61, doi:10.1007/978-3-319-95246-8_9.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2018). Computing average response time. In M. Lohstroh, P. Derler, & M. Sirjani (Eds.), Principles of Modeling (Vol. 10760, pp. 143–161). Springer. https://doi.org/10.1007/978-3-319-95246-8_9","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average Response Time.” In Principles of Modeling, edited by Marten Lohstroh, Patricia Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. https://doi.org/10.1007/978-3-319-95246-8_9.","ama":"Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh M, Derler P, Sirjani M, eds. Principles of Modeling. Vol 10760. Springer; 2018:143-161. doi:10.1007/978-3-319-95246-8_9","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,” in Principles of Modeling, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani, Eds. Springer, 2018, pp. 143–161.","ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161."},"quality_controlled":"1","editor":[{"first_name":"Marten","last_name":"Lohstroh","full_name":"Lohstroh, Marten"},{"first_name":"Patricia","last_name":"Derler","full_name":"Derler, Patricia"},{"last_name":"Sirjani","first_name":"Marjan","full_name":"Sirjani, Marjan"}],"_id":"86","publication_status":"published","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"},{"grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"publisher":"Springer","has_accepted_license":"1","file":[{"file_name":"2018_PrinciplesModeling_Chatterjee.pdf","date_created":"2019-11-19T08:22:18Z","date_updated":"2020-07-14T12:48:14Z","file_id":"7053","content_type":"application/pdf","creator":"dernst","file_size":516307,"checksum":"9995c6ce6957333baf616fc4f20be597","access_level":"open_access","relation":"main_file"}],"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan"}],"title":"Computing average response time","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7968","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"language":[{"iso":"eng"}],"volume":10760,"day":"20","status":"public","ddc":["000"],"date_created":"2018-12-11T11:44:33Z","doi":"10.1007/978-3-319-95246-8_9","publication":"Principles of Modeling","oa_version":"Submitted Version","ec_funded":1,"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.","month":"07","intvolume":" 10760","date_published":"2018-07-20T00:00:00Z","alternative_title":["LNCS"],"oa":1,"date_updated":"2021-01-12T08:20:14Z","page":"143 - 161","year":"2018"},{"doi":"10.1038/s41598-018-19947-1","publication":"Scientific Reports","isi":1,"oa_version":"Published Version","pmid":1,"volume":8,"day":"09","status":"public","ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-10-06T16:33:37Z","license":"https://creativecommons.org/licenses/by/4.0/","external_id":{"pmid":["29426833"],"isi":["000424630400037"]},"year":"2018","article_number":"2724","month":"02","intvolume":" 8","date_published":"2018-02-09T00:00:00Z","oa":1,"date_updated":"2023-09-19T15:04:49Z","keyword":["Multidisciplinary"],"publication_status":"published","type":"journal_article","file_date_updated":"2020-10-06T16:35:16Z","abstract":[{"lang":"eng","text":"The reversibly switchable fluorescent proteins (RSFPs) commonly used for RESOLFT nanoscopy have been developed from fluorescent proteins of the GFP superfamily. These proteins are bright, but exhibit several drawbacks such as relatively large size, oxygen-dependence, sensitivity to low pH, and limited switching speed. Therefore, RSFPs from other origins with improved properties need to be explored. Here, we report the development of two RSFPs based on the LOV domain of the photoreceptor protein YtvA from Bacillus subtilis. LOV domains obtain their fluorescence by association with the abundant cellular cofactor flavin mononucleotide (FMN). Under illumination with blue and ultraviolet light, they undergo a photocycle, making these proteins inherently photoswitchable. Our first improved variant, rsLOV1, can be used for RESOLFT imaging, whereas rsLOV2 proved useful for STED nanoscopy of living cells with a resolution of down to 50 nm. In addition to their smaller size compared to GFP-related proteins (17 kDa instead of 27 kDa) and their usability at low pH, rsLOV1 and rsLOV2 exhibit faster switching kinetics, switching on and off 3 times faster than rsEGFP2, the fastest-switching RSFP reported to date. Therefore, LOV-domain-based RSFPs have potential for applications where the switching speed of GFP-based proteins is limiting."}],"publication_identifier":{"issn":["2045-2322"]},"citation":{"ama":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. 2018;8. doi:10.1038/s41598-018-19947-1","ista":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. 2018. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. 8, 2724.","short":"C. Gregor, S.C. Sidenstein, M. Andresen, S.J. Sahl, J.G. Danzl, S.W. Hell, Scientific Reports 8 (2018).","ieee":"C. Gregor, S. C. Sidenstein, M. Andresen, S. J. Sahl, J. G. Danzl, and S. W. Hell, “Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA,” Scientific Reports, vol. 8. Springer Nature, 2018.","chicago":"Gregor, Carola, Sven C. Sidenstein, Martin Andresen, Steffen J. Sahl, Johann G Danzl, and Stefan W. Hell. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” Scientific Reports. Springer Nature, 2018. https://doi.org/10.1038/s41598-018-19947-1.","apa":"Gregor, C., Sidenstein, S. C., Andresen, M., Sahl, S. J., Danzl, J. G., & Hell, S. W. (2018). Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-018-19947-1","mla":"Gregor, Carola, et al. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” Scientific Reports, vol. 8, 2724, Springer Nature, 2018, doi:10.1038/s41598-018-19947-1."},"quality_controlled":"1","_id":"8618","department":[{"_id":"JoDa"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"Springer Nature","has_accepted_license":"1","file":[{"content_type":"application/pdf","file_id":"8619","file_size":2818077,"creator":"dernst","relation":"main_file","checksum":"e642080fcbde9584c63544f587c74f03","access_level":"open_access","success":1,"file_name":"2018_ScientificReports_Gregor.pdf","date_updated":"2020-10-06T16:35:16Z","date_created":"2020-10-06T16:35:16Z"}],"author":[{"full_name":"Gregor, Carola","last_name":"Gregor","first_name":"Carola"},{"last_name":"Sidenstein","first_name":"Sven C.","full_name":"Sidenstein, Sven C."},{"full_name":"Andresen, Martin","first_name":"Martin","last_name":"Andresen"},{"full_name":"Sahl, Steffen J.","first_name":"Steffen J.","last_name":"Sahl"},{"full_name":"Danzl, Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hell, Stefan W.","first_name":"Stefan W.","last_name":"Hell"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA"},{"intvolume":" 28","month":"10","date_published":"2018-10-01T00:00:00Z","issue":"5","oa":1,"date_updated":"2023-09-15T12:10:35Z","external_id":{"isi":["000442893500018"],"arxiv":["1705.02870"]},"page":"3215 - 3238","year":"2018","volume":28,"status":"public","day":"01","date_created":"2018-12-11T11:44:33Z","doi":"10.1214/18-AAP1389","main_file_link":[{"url":"https://arxiv.org/abs/1705.02870","open_access":"1"}],"publication":"Annals of Applied Probability","isi":1,"oa_version":"Preprint","related_material":{"record":[{"id":"6287","relation":"dissertation_contains","status":"public"}]},"publisher":"Institute of Mathematical Statistics","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics","author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"first_name":"Anton","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","last_name":"Nikitenko","orcid":"0000-0002-0659-3201","full_name":"Nikitenko, Anton"}],"publist_id":"7967","department":[{"_id":"HeEd"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","text":"Using the geodesic distance on the n-dimensional sphere, we study the expected radius function of the Delaunay mosaic of a random set of points. Specifically, we consider the partition of the mosaic into intervals of the radius function and determine the expected number of intervals whose radii are less than or equal to a given threshold. We find that the expectations are essentially the same as for the Poisson–Delaunay mosaic in n-dimensional Euclidean space. Assuming the points are not contained in a hemisphere, the Delaunay mosaic is isomorphic to the boundary complex of the convex hull in Rn+1, so we also get the expected number of faces of a random inscribed polytope. As proved in Antonelli et al. [Adv. in Appl. Probab. 9–12 (1977–1980)], an orthant section of the n-sphere is isometric to the standard n-simplex equipped with the Fisher information metric. It follows that the latter space has similar stochastic properties as the n-dimensional Euclidean space. Our results are therefore relevant in information geometry and in population genetics."}],"arxiv":1,"citation":{"ama":"Edelsbrunner H, Nikitenko A. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 2018;28(5):3215-3238. doi:10.1214/18-AAP1389","ieee":"H. Edelsbrunner and A. Nikitenko, “Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics,” Annals of Applied Probability, vol. 28, no. 5. Institute of Mathematical Statistics, pp. 3215–3238, 2018.","short":"H. Edelsbrunner, A. Nikitenko, Annals of Applied Probability 28 (2018) 3215–3238.","ista":"Edelsbrunner H, Nikitenko A. 2018. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 28(5), 3215–3238.","chicago":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied Probability. Institute of Mathematical Statistics, 2018. https://doi.org/10.1214/18-AAP1389.","apa":"Edelsbrunner, H., & Nikitenko, A. (2018). Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AAP1389","mla":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied Probability, vol. 28, no. 5, Institute of Mathematical Statistics, 2018, pp. 3215–38, doi:10.1214/18-AAP1389."},"quality_controlled":"1","_id":"87","publication_status":"published","project":[{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","call_identifier":"FWF"}]},{"alternative_title":["ISTA Thesis"],"date_published":"2018-07-01T00:00:00Z","month":"07","oa":1,"date_updated":"2023-09-07T12:43:10Z","page":"96","year":"2018","status":"public","day":"01","supervisor":[{"full_name":"Siekhaus, Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"date_created":"2018-12-11T11:44:08Z","doi":"10.15479/AT:ISTA:th1064","degree_awarded":"PhD","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","title":"Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ","author":[{"last_name":"Belyaeva","id":"47F080FE-F248-11E8-B48F-1D18A9856A87","first_name":"Vera","full_name":"Belyaeva, Vera"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6243","embargo_to":"open_access","file_size":102737483,"creator":"dernst","checksum":"d27b2465cb70d0c9678a0381b9b6ced1","access_level":"closed","relation":"source_file","file_name":"2018_Thesis_Belyaeva_source.docx","date_updated":"2020-07-14T12:48:14Z","date_created":"2019-04-08T14:13:12Z"},{"file_name":"2018_Thesis_Belyaeva.pdf","date_updated":"2021-02-11T11:17:16Z","date_created":"2019-04-08T14:14:08Z","file_size":88077843,"creator":"dernst","content_type":"application/pdf","file_id":"6244","access_level":"open_access","embargo":"2019-11-19","relation":"main_file","checksum":"a2939b61bde2de7b8ced77bbae0eaaed"}],"publist_id":"8047","department":[{"_id":"DaSi"}],"article_processing_charge":"No","pubrep_id":"1064","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Immune cells migrating to the sites of infection navigate through diverse tissue architectures and switch their migratory mechanisms upon demand. However, little is known about systemic regulators that could allow the acquisition of these mechanisms. We performed a genetic screen in Drosophila melanogaster to identify regulators of germband invasion by embryonic macrophages into the confined space between the ectoderm and mesoderm. We have found that bZIP circadian transcription factors (TFs) Kayak (dFos) and Vrille (dNFIL3) have opposite effects on macrophage germband infiltration: Kayak facilitated and Vrille inhibited it. These TFs are enriched in the macrophages during migration and genetically interact to control it. Kayak sets a less coordinated mode of migration of the macrophage group and increases the probability and length of Levy walks. Intriguingly, the motility of kayak mutant macrophages was also strongly affected during initial germband invasion but not along another less confined route. Inhibiting Rho1 signaling within the tail ectoderm partially rescued the Kayak mutant phenotype, strongly suggesting that migrating macrophages have to overcome a barrier imposed by the stiffness of the ectoderm. Also, Kayak appeared to be important for the maintenance of the round cell shape and the rear edge translocation of the macrophages invading the germband. Complementary to this, the cortical actin cytoskeleton of Kayak- deficient macrophages was strongly affected. RNA sequencing revealed the filamin Cheerio and tetraspanin TM4SF to be downstream of Kayak. Chromatin immunoprecipitation and immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Indeed, Cheerio, TM4SF and Diaphanous are required within macrophages for germband invasion, and expression of constitutively active Diaphanous in macrophages was able to rescue the kayak mutant phenotype. Moreover, Cher and Diaphanous are also reduced in the macrophages overexpressing Vrille. We hypothesize that Kayak, through its targets, increases actin polymerization and cortical tension in macrophages and thus allows extra force generation necessary for macrophage dissemination and migration through confined stiff tissues, while Vrille counterbalances it."}],"file_date_updated":"2021-02-11T11:17:16Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"citation":{"chicago":"Belyaeva, Vera. “Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1064.","short":"V. Belyaeva, Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo , Institute of Science and Technology Austria, 2018.","ieee":"V. Belyaeva, “Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ,” Institute of Science and Technology Austria, 2018.","ista":"Belyaeva V. 2018. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria.","ama":"Belyaeva V. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . 2018. doi:10.15479/AT:ISTA:th1064","mla":"Belyaeva, Vera. Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1064.","apa":"Belyaeva, V. (2018). Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1064"},"_id":"9","publication_status":"published"},{"oa":1,"date_updated":"2023-09-18T09:29:07Z","article_number":"e34465","date_published":"2018-06-13T00:00:00Z","intvolume":" 7","month":"06","year":"2018","external_id":{"isi":["000436227500001"]},"day":"13","status":"public","ddc":["571"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:44:57Z","volume":7,"ec_funded":1,"oa_version":"Published Version","isi":1,"related_material":{"record":[{"status":"public","relation":"research_data","id":"9838"}]},"publication":"eLife","doi":"10.7554/eLife.34465","author":[{"full_name":"Kaucka, Marketa","last_name":"Kaucka","first_name":"Marketa"},{"last_name":"Petersen","first_name":"Julian","full_name":"Petersen, Julian"},{"last_name":"Tesarova","first_name":"Marketa","full_name":"Tesarova, Marketa"},{"full_name":"Szarowska, Bara","last_name":"Szarowska","first_name":"Bara"},{"first_name":"Maria","last_name":"Kastriti","full_name":"Kastriti, Maria"},{"last_name":"Xie","first_name":"Meng","full_name":"Xie, Meng"},{"orcid":"0000-0003-4509-4998","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","full_name":"Kicheva, Anna"},{"full_name":"Annusver, Karl","last_name":"Annusver","first_name":"Karl"},{"full_name":"Kasper, Maria","first_name":"Maria","last_name":"Kasper"},{"full_name":"Symmons, Orsolya","first_name":"Orsolya","last_name":"Symmons"},{"last_name":"Pan","first_name":"Leslie","full_name":"Pan, Leslie"},{"full_name":"Spitz, Francois","first_name":"Francois","last_name":"Spitz"},{"full_name":"Kaiser, Jozef","first_name":"Jozef","last_name":"Kaiser"},{"full_name":"Hovorakova, Maria","first_name":"Maria","last_name":"Hovorakova"},{"full_name":"Zikmund, Tomas","last_name":"Zikmund","first_name":"Tomas"},{"last_name":"Sunadome","first_name":"Kazunori","full_name":"Sunadome, Kazunori"},{"full_name":"Matise, Michael P","last_name":"Matise","first_name":"Michael P"},{"full_name":"Wang, Hui","last_name":"Wang","first_name":"Hui"},{"last_name":"Marklund","first_name":"Ulrika","full_name":"Marklund, Ulrika"},{"last_name":"Abdo","first_name":"Hind","full_name":"Abdo, Hind"},{"first_name":"Patrik","last_name":"Ernfors","full_name":"Ernfors, Patrik"},{"full_name":"Maire, Pascal","last_name":"Maire","first_name":"Pascal"},{"last_name":"Wurmser","first_name":"Maud","full_name":"Wurmser, Maud"},{"full_name":"Chagin, Andrei S","first_name":"Andrei S","last_name":"Chagin"},{"full_name":"Fried, Kaj","last_name":"Fried","first_name":"Kaj"},{"full_name":"Adameyko, Igor","first_name":"Igor","last_name":"Adameyko"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","file":[{"date_updated":"2020-07-14T12:45:07Z","date_created":"2018-12-17T16:41:58Z","file_name":"2018_eLife_Kaucka.pdf","checksum":"da2378cdcf6b5461dcde194e4d608343","access_level":"open_access","relation":"main_file","file_size":9816484,"creator":"dernst","content_type":"application/pdf","file_id":"5727"}],"publisher":"eLife Sciences Publications","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"AnKi"}],"publist_id":"7759","article_processing_charge":"No","quality_controlled":"1","_id":"162","abstract":[{"lang":"eng","text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here, we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts."}],"scopus_import":"1","type":"journal_article","file_date_updated":"2020-07-14T12:45:07Z","citation":{"chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Kastriti, Meng Xie, Anna Kicheva, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.34465.","ieee":"M. Kaucka et al., “Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage,” eLife, vol. 7. eLife Sciences Publications, 2018.","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, ELife 7 (2018).","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti M, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 7, e34465.","ama":"Kaucka M, Petersen J, Tesarova M, et al. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 2018;7. doi:10.7554/eLife.34465","mla":"Kaucka, Marketa, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife, vol. 7, e34465, eLife Sciences Publications, 2018, doi:10.7554/eLife.34465.","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M., Xie, M., … Adameyko, I. (2018). Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.34465"},"publication_status":"published","project":[{"grant_number":"680037","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425"}]}]