[{"citation":{"apa":"Filipp, S., Göppl, M., Fink, J. M., Baur, M., Bianchetti, R., Steffen, L., &#38; Wallraff, A. (2011). Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.83.063827\">https://doi.org/10.1103/PhysRevA.83.063827</a>","ama":"Filipp S, Göppl M, Fink JM, et al. Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2011;83(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.83.063827\">10.1103/PhysRevA.83.063827</a>","mla":"Filipp, Stefan, et al. “Multimode Mediated Qubit-Qubit Coupling and Dark-State Symmetries in Circuit Quantum Electrodynamics.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 83, no. 6, American Physical Society, 2011, doi:<a href=\"https://doi.org/10.1103/PhysRevA.83.063827\">10.1103/PhysRevA.83.063827</a>.","ieee":"S. Filipp <i>et al.</i>, “Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics,” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 83, no. 6. American Physical Society, 2011.","short":"S. Filipp, M. Göppl, J.M. Fink, M. Baur, R. Bianchetti, L. Steffen, A. Wallraff, Physical Review A - Atomic, Molecular, and Optical Physics 83 (2011).","ista":"Filipp S, Göppl M, Fink JM, Baur M, Bianchetti R, Steffen L, Wallraff A. 2011. Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. 83(6).","chicago":"Filipp, Stefan, M Göppl, Johannes M Fink, Matthias Baur, R Bianchetti, L. Steffen, and Andreas Wallraff. “Multimode Mediated Qubit-Qubit Coupling and Dark-State Symmetries in Circuit Quantum Electrodynamics.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2011. <a href=\"https://doi.org/10.1103/PhysRevA.83.063827\">https://doi.org/10.1103/PhysRevA.83.063827</a>."},"volume":83,"year":"2011","month":"06","type":"journal_article","abstract":[{"lang":"eng","text":"Microwave cavities with high quality factors enable coherent coupling of distant quantum systems. Virtual photons lead to a transverse interaction between qubits when they are nonresonant with the cavity but resonant with each other. We experimentally investigate the inverse scaling of the interqubit coupling with the detuning from a cavity mode and its proportionality to the qubit-cavity interaction strength. We demonstrate that the enhanced coupling at higher frequencies is mediated by multiple higher-harmonic cavity modes. Moreover, we observe dark states of the coupled qubit-qubit system and analyze their relation to the symmetry of the applied driving field at different frequencies."}],"day":"22","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","title":"Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics","status":"public","date_updated":"2021-01-12T06:53:09Z","date_created":"2018-12-11T11:53:58Z","issue":"6","date_published":"2011-06-22T00:00:00Z","extern":1,"intvolume":"        83","_id":"1781","quality_controlled":0,"acknowledgement":"This work was supported by the Swiss National Science Foundation (SNF), the Austrian Science Foundation (FWF), and ETH Zurich","publist_id":"5335","doi":"10.1103/PhysRevA.83.063827","publisher":"American Physical Society","publication_status":"published","author":[{"first_name":"Stefan","last_name":"Filipp","full_name":"Filipp, Stefan"},{"last_name":"Göppl","first_name":"M","full_name":"Göppl, M"},{"first_name":"Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Johannes Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Baur","first_name":"Matthias","full_name":"Baur, Matthias P"},{"last_name":"Bianchetti","first_name":"R","full_name":"Bianchetti, R"},{"full_name":"Steffen, L. Kraig","last_name":"Steffen","first_name":"L."},{"first_name":"Andreas","last_name":"Wallraff","full_name":"Wallraff, Andreas"}]},{"publication_status":"published","oa":1,"author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Tamar Friedlander","last_name":"Friedlander","first_name":"Tamar"},{"full_name":"Brenner, Naama","first_name":"Naama","last_name":"Brenner"}],"doi":"10.3934/mbe.2011.8.515","publist_id":"5291","publisher":"Arizona State University","intvolume":"         8","extern":1,"_id":"1815","quality_controlled":0,"date_updated":"2021-01-12T06:53:23Z","status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1003.2791"}],"date_published":"2011-04-02T00:00:00Z","date_created":"2018-12-11T11:54:10Z","issue":"2","day":"02","abstract":[{"text":"Many membrane channels and receptors exhibit adaptive, or desensitized, response to a strong sustained input stimulus, often supported by protein activity-dependent inactivation. Adaptive response is thought to be related to various cellular functions such as homeostasis and enlargement of dynamic range by background compensation. Here we study the quantitative relation between adaptive response and background compensation within a modeling framework. We show that any particular type of adaptive response is neither sufficient nor necessary for adaptive enlargement of dynamic range. In particular a precise adaptive response, where system activity is maintained at a constant level at steady state, does not ensure a large dynamic range neither in input signal nor in system output. A general mechanism for input dynamic range enlargement can come about from the activity-dependent modulation of protein responsiveness by multiple biochemical modification, regardless of the type of adaptive response it induces. Therefore hierarchical biochemical processes such as methylation and phosphorylation are natural candidates to induce this property in signaling systems.","lang":"eng"}],"title":"Adaptive response and enlargement of dynamic range","publication":"Mathematical Biosciences and Engineering","page":"515 - 526","volume":8,"year":"2011","type":"journal_article","month":"04","citation":{"apa":"Friedlander, T., &#38; Brenner, N. (2011). Adaptive response and enlargement of dynamic range. <i>Mathematical Biosciences and Engineering</i>. Arizona State University. <a href=\"https://doi.org/10.3934/mbe.2011.8.515\">https://doi.org/10.3934/mbe.2011.8.515</a>","ama":"Friedlander T, Brenner N. Adaptive response and enlargement of dynamic range. <i>Mathematical Biosciences and Engineering</i>. 2011;8(2):515-526. doi:<a href=\"https://doi.org/10.3934/mbe.2011.8.515\">10.3934/mbe.2011.8.515</a>","mla":"Friedlander, Tamar, and Naama Brenner. “Adaptive Response and Enlargement of Dynamic Range.” <i>Mathematical Biosciences and Engineering</i>, vol. 8, no. 2, Arizona State University, 2011, pp. 515–26, doi:<a href=\"https://doi.org/10.3934/mbe.2011.8.515\">10.3934/mbe.2011.8.515</a>.","ieee":"T. Friedlander and N. Brenner, “Adaptive response and enlargement of dynamic range,” <i>Mathematical Biosciences and Engineering</i>, vol. 8, no. 2. Arizona State University, pp. 515–526, 2011.","short":"T. Friedlander, N. Brenner, Mathematical Biosciences and Engineering 8 (2011) 515–526.","ista":"Friedlander T, Brenner N. 2011. Adaptive response and enlargement of dynamic range. Mathematical Biosciences and Engineering. 8(2), 515–526.","chicago":"Friedlander, Tamar, and Naama Brenner. “Adaptive Response and Enlargement of Dynamic Range.” <i>Mathematical Biosciences and Engineering</i>. Arizona State University, 2011. <a href=\"https://doi.org/10.3934/mbe.2011.8.515\">https://doi.org/10.3934/mbe.2011.8.515</a>."}},{"day":"01","abstract":[{"lang":"eng","text":"The Levene model is the simplest mathematical model to describe the evolution of gene frequencies in spatially subdivided populations. It provides insight into how locally varying selection promotes a population’s genetic diversity. Despite its simplicity, interesting problems have remained unsolved even in the diallelic case. In this paper we answer an open problem by establishing that for two alleles at one locus and J demes, up to 2J−1 polymorphic equilibria may coexist. We first present a proof for the case of stable monomorphisms and then show that the result also holds for protected alleles. These findings allow us to prove that any odd number (up to 2J−1) of equilibria is possible, before we extend the proof to even numbers. We conclude with some numerical results and show that for J&gt;2, the proportion of parameter space affording this maximum is extremely small."}],"publication":"Theoretical Population Biology","title":"The number of equilibria in the diallelic Levene model with multiple demes","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","page":"97 - 101","status":"public","date_updated":"2021-01-12T06:53:42Z","date_published":"2011-05-01T00:00:00Z","issue":"3","date_created":"2018-12-11T11:54:25Z","citation":{"ama":"Novak S. The number of equilibria in the diallelic Levene model with multiple demes. <i>Theoretical Population Biology</i>. 2011;79(3):97-101. doi:<a href=\"https://doi.org/10.1016/j.tpb.2010.12.002\">10.1016/j.tpb.2010.12.002</a>","apa":"Novak, S. (2011). The number of equilibria in the diallelic Levene model with multiple demes. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.tpb.2010.12.002\">https://doi.org/10.1016/j.tpb.2010.12.002</a>","ieee":"S. Novak, “The number of equilibria in the diallelic Levene model with multiple demes,” <i>Theoretical Population Biology</i>, vol. 79, no. 3. Academic Press, pp. 97–101, 2011.","mla":"Novak, Sebastian. “The Number of Equilibria in the Diallelic Levene Model with Multiple Demes.” <i>Theoretical Population Biology</i>, vol. 79, no. 3, Academic Press, 2011, pp. 97–101, doi:<a href=\"https://doi.org/10.1016/j.tpb.2010.12.002\">10.1016/j.tpb.2010.12.002</a>.","short":"S. Novak, Theoretical Population Biology 79 (2011) 97–101.","ista":"Novak S. 2011. The number of equilibria in the diallelic Levene model with multiple demes. Theoretical Population Biology. 79(3), 97–101.","chicago":"Novak, Sebastian. “The Number of Equilibria in the Diallelic Levene Model with Multiple Demes.” <i>Theoretical Population Biology</i>. Academic Press, 2011. <a href=\"https://doi.org/10.1016/j.tpb.2010.12.002\">https://doi.org/10.1016/j.tpb.2010.12.002</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"year":"2011","volume":79,"type":"journal_article","month":"05","doi":"10.1016/j.tpb.2010.12.002","publist_id":"5236","publisher":"Academic Press","publication_status":"published","author":[{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Sebastian Novak","last_name":"Novak","first_name":"Sebastian"}],"intvolume":"        79","extern":1,"acknowledgement":"FWF 21305","_id":"1863","quality_controlled":0},{"acknowledgement":"This work was funded by the Medical Research Council.","quality_controlled":0,"_id":"1973","intvolume":"       476","extern":1,"publisher":"Nature Publishing Group","doi":"10.1038/nature10330","publist_id":"5110","author":[{"full_name":"Efremov, Rouslan G","last_name":"Efremov","first_name":"Rouslan"},{"last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Leonid Sazanov"}],"publication_status":"published","citation":{"apa":"Efremov, R., &#38; Sazanov, L. A. (2011). Structure of the membrane domain of respiratory complex i. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature10330\">https://doi.org/10.1038/nature10330</a>","ama":"Efremov R, Sazanov LA. Structure of the membrane domain of respiratory complex i. <i>Nature</i>. 2011;476(7361):414-421. doi:<a href=\"https://doi.org/10.1038/nature10330\">10.1038/nature10330</a>","mla":"Efremov, Rouslan, and Leonid A. Sazanov. “Structure of the Membrane Domain of Respiratory Complex I.” <i>Nature</i>, vol. 476, no. 7361, Nature Publishing Group, 2011, pp. 414–21, doi:<a href=\"https://doi.org/10.1038/nature10330\">10.1038/nature10330</a>.","ieee":"R. Efremov and L. A. Sazanov, “Structure of the membrane domain of respiratory complex i,” <i>Nature</i>, vol. 476, no. 7361. Nature Publishing Group, pp. 414–421, 2011.","short":"R. Efremov, L.A. Sazanov, Nature 476 (2011) 414–421.","ista":"Efremov R, Sazanov LA. 2011. Structure of the membrane domain of respiratory complex i. Nature. 476(7361), 414–421.","chicago":"Efremov, Rouslan, and Leonid A Sazanov. “Structure of the Membrane Domain of Respiratory Complex I.” <i>Nature</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/nature10330\">https://doi.org/10.1038/nature10330</a>."},"type":"journal_article","month":"08","volume":476,"year":"2011","publication":"Nature","title":"Structure of the membrane domain of respiratory complex i","page":"414 - 421","day":"25","abstract":[{"text":"Complex I is the first and largest enzyme of the respiratory chain, coupling electron transfer between NADH and ubiquinone to the translocation of four protons across the membrane. It has a central role in cellular energy production and has been implicated in many human neurodegenerative diseases. The L-shaped enzyme consists of hydrophilic and membrane domains. Previously, we determined the structure of the hydrophilic domain. Here we report the crystal structure of the Esherichia coli complex I membrane domain at 3.0 Ã. resolution. It includes six subunits, NuoL, NuoM, NuoN, NuoA, NuoJ and NuoK, with 55 transmembrane helices. The fold of the homologous antiporter-like subunits L, M and N is novel, with two inverted structural repeats of five transmembrane helices arranged, unusually, face-to-back. Each repeat includes a discontinuous transmembrane helix and forms half of a channel across the membrane. A network of conserved polar residues connects the two half-channels, completing the proton translocation pathway. Unexpectedly, lysines rather than carboxylate residues act as the main elements of the proton pump in these subunits. The fourth probable proton-translocation channel is at the interface of subunits N, K, J and A. The structure indicates that proton translocation in complex I, uniquely, involves coordinated conformational changes in six symmetrical structural elements.","lang":"eng"}],"date_published":"2011-08-25T00:00:00Z","date_created":"2018-12-11T11:54:59Z","issue":"7361","status":"public","date_updated":"2021-01-12T06:54:26Z"},{"citation":{"short":"R. Efremov, L.A. Sazanov, Current Opinion in Structural Biology 21 (2011) 532–540.","ieee":"R. Efremov and L. A. Sazanov, “Respiratory complex I: ‘steam engine’ of the cell?,” <i>Current Opinion in Structural Biology</i>, vol. 21, no. 4. Elsevier, pp. 532–540, 2011.","mla":"Efremov, Rouslan, and Leonid A. Sazanov. “Respiratory Complex I: ‘steam Engine’ of the Cell?” <i>Current Opinion in Structural Biology</i>, vol. 21, no. 4, Elsevier, 2011, pp. 532–40, doi:<a href=\"https://doi.org/10.1016/j.sbi.2011.07.002\">10.1016/j.sbi.2011.07.002</a>.","apa":"Efremov, R., &#38; Sazanov, L. A. (2011). Respiratory complex I: “steam engine” of the cell? <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2011.07.002\">https://doi.org/10.1016/j.sbi.2011.07.002</a>","ama":"Efremov R, Sazanov LA. Respiratory complex I: “steam engine” of the cell? <i>Current Opinion in Structural Biology</i>. 2011;21(4):532-540. doi:<a href=\"https://doi.org/10.1016/j.sbi.2011.07.002\">10.1016/j.sbi.2011.07.002</a>","chicago":"Efremov, Rouslan, and Leonid A Sazanov. “Respiratory Complex I: ‘steam Engine’ of the Cell?” <i>Current Opinion in Structural Biology</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.sbi.2011.07.002\">https://doi.org/10.1016/j.sbi.2011.07.002</a>.","ista":"Efremov R, Sazanov LA. 2011. Respiratory complex I: ‘steam engine’ of the cell? Current Opinion in Structural Biology. 21(4), 532–540."},"volume":21,"year":"2011","month":"08","type":"journal_article","abstract":[{"lang":"eng","text":"Complex I is the first enzyme of the respiratory chain and plays a central role in cellular energy production. It has been implicated in many human neurodegenerative diseases, as well as in ageing. One of the biggest membrane protein complexes, it is an L-shaped assembly consisting of hydrophilic and membrane domains. Previously, we have determined structures of the hydrophilic domain in several redox states. Last year was marked by fascinating breakthroughs in the understanding of the complete structure. We described the architecture of the membrane domain and of the entire bacterial complex I. X-ray analysis of the larger mitochondrial enzyme has also been published. The core subunits of the bacterial and mitochondrial enzymes have remarkably similar structures. The proposed mechanism of coupling between electron transfer and proton translocation involves long-range conformational changes, coordinated in part by a long α-helix, akin to the coupling rod of a steam engine."}],"day":"01","page":"532 - 540","title":"Respiratory complex I: 'steam engine' of the cell?","publication":"Current Opinion in Structural Biology","date_updated":"2021-01-12T06:54:27Z","status":"public","issue":"4","date_created":"2018-12-11T11:54:59Z","date_published":"2011-08-01T00:00:00Z","extern":1,"intvolume":"        21","quality_controlled":0,"_id":"1974","acknowledgement":"The work in authors’ laboratory was funded by the Medical Research Council.","publist_id":"5111","doi":"10.1016/j.sbi.2011.07.002","publisher":"Elsevier","publication_status":"published","author":[{"full_name":"Efremov, Rouslan G","first_name":"Rouslan","last_name":"Efremov"},{"first_name":"Leonid A","last_name":"Sazanov","full_name":"Leonid Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}]},{"acknowledgement":"This work was supported by the Medical Research Council. ","quality_controlled":0,"_id":"1975","intvolume":"       286","extern":1,"publisher":"American Society for Biochemistry and Molecular Biology","doi":"10.1074/jbc.M110.194993","publist_id":"5112","author":[{"full_name":"Yip, Chui Y","last_name":"Yip","first_name":"Chui"},{"last_name":"Harbour","first_name":"Michael","full_name":"Harbour, Michael E"},{"full_name":"Jayawardena, Kamburapola G","last_name":"Jayawardena","first_name":"Kamburapola"},{"full_name":"Fearnley, Ian M","last_name":"Fearnley","first_name":"Ian"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Leonid Sazanov","orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A"}],"publication_status":"published","citation":{"ista":"Yip C, Harbour M, Jayawardena K, Fearnley I, Sazanov LA. 2011. Evolution of respiratory complex I &#38;quot;Supernumerary&#38;quot; subunits are present in the α-proteobacterial enzyme. Journal of Biological Chemistry. 286(7), 5023–5033.","chicago":"Yip, Chui, Michael Harbour, Kamburapola Jayawardena, Ian Fearnley, and Leonid A Sazanov. “Evolution of Respiratory Complex I &#38;quot;Supernumerary&#38;quot; Subunits Are Present in the α-Proteobacterial Enzyme.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology, 2011. <a href=\"https://doi.org/10.1074/jbc.M110.194993\">https://doi.org/10.1074/jbc.M110.194993</a>.","apa":"Yip, C., Harbour, M., Jayawardena, K., Fearnley, I., &#38; Sazanov, L. A. (2011). Evolution of respiratory complex I &#38;quot;Supernumerary&#38;quot; subunits are present in the α-proteobacterial enzyme. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.M110.194993\">https://doi.org/10.1074/jbc.M110.194993</a>","ama":"Yip C, Harbour M, Jayawardena K, Fearnley I, Sazanov LA. Evolution of respiratory complex I &#38;quot;Supernumerary&#38;quot; subunits are present in the α-proteobacterial enzyme. <i>Journal of Biological Chemistry</i>. 2011;286(7):5023-5033. doi:<a href=\"https://doi.org/10.1074/jbc.M110.194993\">10.1074/jbc.M110.194993</a>","ieee":"C. Yip, M. Harbour, K. Jayawardena, I. Fearnley, and L. A. Sazanov, “Evolution of respiratory complex I &#38;quot;Supernumerary&#38;quot; subunits are present in the α-proteobacterial enzyme,” <i>Journal of Biological Chemistry</i>, vol. 286, no. 7. American Society for Biochemistry and Molecular Biology, pp. 5023–5033, 2011.","mla":"Yip, Chui, et al. “Evolution of Respiratory Complex I &#38;quot;Supernumerary&#38;quot; Subunits Are Present in the α-Proteobacterial Enzyme.” <i>Journal of Biological Chemistry</i>, vol. 286, no. 7, American Society for Biochemistry and Molecular Biology, 2011, pp. 5023–33, doi:<a href=\"https://doi.org/10.1074/jbc.M110.194993\">10.1074/jbc.M110.194993</a>.","short":"C. Yip, M. Harbour, K. Jayawardena, I. Fearnley, L.A. Sazanov, Journal of Biological Chemistry 286 (2011) 5023–5033."},"type":"journal_article","month":"02","volume":286,"year":"2011","title":"Evolution of respiratory complex I &quot;Supernumerary&quot; subunits are present in the α-proteobacterial enzyme","publication":"Journal of Biological Chemistry","page":"5023 - 5033","day":"18","abstract":[{"text":"Modern α-proteobacteria are thought to be closely related to the ancient symbiont of eukaryotes, an ancestor of mitochondria. Respiratory complex I from α-proteobacteria and mitochondria is well conserved at the level of the 14 &quot;core&quot; subunits, consistent with that notion. Mitochondrial complex I contains the core subunits, present in all species, and up to 31 &quot;supernumerary&quot; subunits, generally thought to have originated only within eukaryotic lineages. However, the full protein composition of an α-proteobacterial complex I has not been established previously. Here, we report the first purification and characterization of complex I from the α-proteobacterium Paracoccus denitrificans. Single particle electron microscopy shows that the complex has a well defined L-shape. Unexpectedly, in addition to the 14 core subunits, the enzyme also contains homologues of three supernumerary mitochondrial subunits as follows: B17.2, AQDQ/18, and 13 kDa (bovine nomenclature). This finding suggests that evolution of complex I via addition of supernumerary or &quot;accessory&quot; subunits started before the original endosymbiotic event that led to the creation of the eukaryotic cell. It also provides further confirmation that α-proteobacteria are the closest extant relatives of mitochondria.","lang":"eng"}],"date_published":"2011-02-18T00:00:00Z","date_created":"2018-12-11T11:55:00Z","issue":"7","date_updated":"2021-01-12T06:54:27Z","status":"public"},{"author":[{"first_name":"Martin","last_name":"Loose","full_name":"Martin Loose","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fischer Friedrich","first_name":"Elisabeth","full_name":"Fischer-Friedrich, Elisabeth"},{"first_name":"Christoph","last_name":"Herold","full_name":"Herold, Christoph"},{"last_name":"Kruse","first_name":"Karsten","full_name":"Kruse, Karsten"},{"first_name":"Petra","last_name":"Schwille","full_name":"Schwille, Petra "}],"publication_status":"published","publisher":"Nature Publishing Group","doi":"10.1038/nsmb.2037","publist_id":"5098","acknowledgement":"This work was also supported by the Max Planck Society (M.L., E.F.-F., P.S.).","_id":"1985","quality_controlled":0,"intvolume":"        18","extern":1,"date_published":"2011-05-01T00:00:00Z","issue":"5","date_created":"2018-12-11T11:55:03Z","status":"public","date_updated":"2021-01-12T06:54:31Z","publication":"Nature Structural and Molecular Biology","title":"Min protein patterns emerge from rapid rebinding and membrane interaction of MinE","page":"577 - 583","day":"01","abstract":[{"lang":"eng","text":"\n\nIn Escherichia coli, the pole-to-pole oscillation of the Min proteins directs septum formation to midcell, which is required for symmetric cell division. In vitro, protein waves emerge from the self-organization of MinD, a membrane-binding ATPase, and its activator MinE. For wave propagation, the proteins need to cycle through states of collective membrane binding and unbinding. Although MinD presumably undergoes cooperative membrane attachment, it is unclear how synchronous detachment is coordinated. We used confocal and single-molecule microscopy to elucidate the order of events during Min wave propagation. We propose that protein detachment at the rear of the wave, and the formation of the E-ring, are accomplished by two complementary processes: first, local accumulation of MinE due to rapid rebinding, leading to dynamic instability; and second, a structural change induced by membrane-interaction of MinE in an equimolar MinD-MinE (MinDE) complex, which supports the robustness of pattern formation."}],"type":"journal_article","month":"05","volume":18,"year":"2011","citation":{"short":"M. Loose, E. Fischer Friedrich, C. Herold, K. Kruse, P. Schwille, Nature Structural and Molecular Biology 18 (2011) 577–583.","ieee":"M. Loose, E. Fischer Friedrich, C. Herold, K. Kruse, and P. Schwille, “Min protein patterns emerge from rapid rebinding and membrane interaction of MinE,” <i>Nature Structural and Molecular Biology</i>, vol. 18, no. 5. Nature Publishing Group, pp. 577–583, 2011.","mla":"Loose, Martin, et al. “Min Protein Patterns Emerge from Rapid Rebinding and Membrane Interaction of MinE.” <i>Nature Structural and Molecular Biology</i>, vol. 18, no. 5, Nature Publishing Group, 2011, pp. 577–83, doi:<a href=\"https://doi.org/10.1038/nsmb.2037\">10.1038/nsmb.2037</a>.","apa":"Loose, M., Fischer Friedrich, E., Herold, C., Kruse, K., &#38; Schwille, P. (2011). Min protein patterns emerge from rapid rebinding and membrane interaction of MinE. <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nsmb.2037\">https://doi.org/10.1038/nsmb.2037</a>","ama":"Loose M, Fischer Friedrich E, Herold C, Kruse K, Schwille P. Min protein patterns emerge from rapid rebinding and membrane interaction of MinE. <i>Nature Structural and Molecular Biology</i>. 2011;18(5):577-583. doi:<a href=\"https://doi.org/10.1038/nsmb.2037\">10.1038/nsmb.2037</a>","chicago":"Loose, Martin, Elisabeth Fischer Friedrich, Christoph Herold, Karsten Kruse, and Petra Schwille. “Min Protein Patterns Emerge from Rapid Rebinding and Membrane Interaction of MinE.” <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/nsmb.2037\">https://doi.org/10.1038/nsmb.2037</a>.","ista":"Loose M, Fischer Friedrich E, Herold C, Kruse K, Schwille P. 2011. Min protein patterns emerge from rapid rebinding and membrane interaction of MinE. Nature Structural and Molecular Biology. 18(5), 577–583."}},{"date_created":"2018-12-11T11:55:04Z","issue":"1","date_published":"2011-06-09T00:00:00Z","status":"public","date_updated":"2021-01-12T06:54:31Z","page":"315 - 336","title":"Protein self-organization: Lessons from the min system","publication":"Annual Review of Biophysics","abstract":[{"text":"One of the most fundamental features of biological systems is probably their ability to self-organize in space and time on different scales. Despite many elaborate theoretical models of how molecular self-organization can come about, only a few experimental systems of biological origin have so far been rigorously described, due mostly to their inherent complexity. The most promising strategy of modern biophysics is thus to identify minimal biological systems showing self-organized emergent behavior. One of the best-understood examples of protein self-organization, which has recently been successfully reconstituted in vitro, is represented by the oscillations of the Min proteins in Escherichia coli. In this review, we summarize the current understanding of the mechanism of Min protein self-organization in vivo and in vitro. We discuss the potential of the Min oscillations to sense the geometry of the cell and suggest that spontaneous protein waves could be a general means of intracellular organization. We hypothesize that cooperative membrane binding and unbinding, e.g., as an energy-dependent switch, may act as an important regulatory mechanism for protein oscillations and pattern formation in the cell.","lang":"eng"}],"day":"09","month":"06","type":"journal_article","volume":40,"year":"2011","citation":{"ista":"Loose M, Kruse K, Schwille P. 2011. Protein self-organization: Lessons from the min system. Annual Review of Biophysics. 40(1), 315–336.","chicago":"Loose, Martin, Karsten Kruse, and Petra Schwille. “Protein Self-Organization: Lessons from the Min System.” <i>Annual Review of Biophysics</i>. Annual Reviews, 2011. <a href=\"https://doi.org/10.1146/annurev-biophys-042910-155332\">https://doi.org/10.1146/annurev-biophys-042910-155332</a>.","apa":"Loose, M., Kruse, K., &#38; Schwille, P. (2011). Protein self-organization: Lessons from the min system. <i>Annual Review of Biophysics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-biophys-042910-155332\">https://doi.org/10.1146/annurev-biophys-042910-155332</a>","ama":"Loose M, Kruse K, Schwille P. Protein self-organization: Lessons from the min system. <i>Annual Review of Biophysics</i>. 2011;40(1):315-336. doi:<a href=\"https://doi.org/10.1146/annurev-biophys-042910-155332\">10.1146/annurev-biophys-042910-155332</a>","short":"M. Loose, K. Kruse, P. Schwille, Annual Review of Biophysics 40 (2011) 315–336.","mla":"Loose, Martin, et al. “Protein Self-Organization: Lessons from the Min System.” <i>Annual Review of Biophysics</i>, vol. 40, no. 1, Annual Reviews, 2011, pp. 315–36, doi:<a href=\"https://doi.org/10.1146/annurev-biophys-042910-155332\">10.1146/annurev-biophys-042910-155332</a>.","ieee":"M. Loose, K. Kruse, and P. Schwille, “Protein self-organization: Lessons from the min system,” <i>Annual Review of Biophysics</i>, vol. 40, no. 1. Annual Reviews, pp. 315–336, 2011."},"author":[{"last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Martin Loose"},{"full_name":"Kruse, Karsten","first_name":"Karsten","last_name":"Kruse"},{"first_name":"Petra","last_name":"Schwille","full_name":"Schwille, Petra "}],"publication_status":"published","publisher":"Annual Reviews","publist_id":"5097","doi":"10.1146/annurev-biophys-042910-155332","quality_controlled":0,"_id":"1986","extern":1,"intvolume":"        40"},{"day":"12","page":"3952-3957","publication":"PNAS","status":"public","date_created":"2023-09-06T12:54:36Z","language":[{"iso":"eng"}],"month":"01","article_type":"original","external_id":{"pmid":["21325613"]},"oa":1,"intvolume":"       108","article_processing_charge":"No","quality_controlled":"1","abstract":[{"text":"Understanding the mechanism of protein folding requires a detailed knowledge of the structural properties of the barriers separating unfolded from native conformations. The S-peptide from ribonuclease S forms its α-helical structure only upon binding to the folded S-protein. We characterized the transition state for this binding-induced folding reaction at high resolution by determining the effect of site-specific backbone thioxylation and side-chain modifications on the kinetics and thermodynamics of the reaction, which allows us to monitor formation of backbone hydrogen bonds and side-chain interactions in the transition state. The experiments reveal that α-helical structure in the S-peptide is absent in the transition state of binding. Recognition between the unfolded S-peptide and the S-protein is mediated by loosely packed hydrophobic side-chain interactions in two well defined regions on the S-peptide. Close packing and helix formation occurs rapidly after binding. Introducing hydrophobic residues at positions outside the recognition region can drastically slow down association.","lang":"eng"}],"title":"Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction","date_updated":"2023-11-07T11:50:29Z","issue":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1012668108"}],"date_published":"2011-01-12T00:00:00Z","citation":{"ieee":"A. Bachmann, D. Wildemann, F. M. Praetorius, G. Fischer, and T. Kiefhaber, “Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction,” <i>PNAS</i>, vol. 108, no. 10. Proceedings of the National Academy of Sciences, pp. 3952–3957, 2011.","mla":"Bachmann, Annett, et al. “Mapping Backbone and Side-Chain Interactions in the Transition State of a Coupled Protein Folding and Binding Reaction.” <i>PNAS</i>, vol. 108, no. 10, Proceedings of the National Academy of Sciences, 2011, pp. 3952–57, doi:<a href=\"https://doi.org/10.1073/pnas.1012668108\">10.1073/pnas.1012668108</a>.","short":"A. Bachmann, D. Wildemann, F.M. Praetorius, G. Fischer, T. Kiefhaber, PNAS 108 (2011) 3952–3957.","ama":"Bachmann A, Wildemann D, Praetorius FM, Fischer G, Kiefhaber T. Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction. <i>PNAS</i>. 2011;108(10):3952-3957. doi:<a href=\"https://doi.org/10.1073/pnas.1012668108\">10.1073/pnas.1012668108</a>","apa":"Bachmann, A., Wildemann, D., Praetorius, F. M., Fischer, G., &#38; Kiefhaber, T. (2011). Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction. <i>PNAS</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1012668108\">https://doi.org/10.1073/pnas.1012668108</a>","chicago":"Bachmann, Annett, Dirk Wildemann, Florian M Praetorius, Gunter Fischer, and Thomas Kiefhaber. “Mapping Backbone and Side-Chain Interactions in the Transition State of a Coupled Protein Folding and Binding Reaction.” <i>PNAS</i>. Proceedings of the National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1012668108\">https://doi.org/10.1073/pnas.1012668108</a>.","ista":"Bachmann A, Wildemann D, Praetorius FM, Fischer G, Kiefhaber T. 2011. Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction. PNAS. 108(10), 3952–3957."},"oa_version":"Published Version","keyword":["Multidisciplinary"],"volume":108,"year":"2011","scopus_import":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"type":"journal_article","doi":"10.1073/pnas.1012668108","publisher":"Proceedings of the National Academy of Sciences","publication_status":"published","author":[{"full_name":"Bachmann, Annett","first_name":"Annett","last_name":"Bachmann"},{"full_name":"Wildemann, Dirk","first_name":"Dirk","last_name":"Wildemann"},{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M","last_name":"Praetorius","first_name":"Florian M"},{"full_name":"Fischer, Gunter","first_name":"Gunter","last_name":"Fischer"},{"first_name":"Thomas","last_name":"Kiefhaber","full_name":"Kiefhaber, Thomas"}],"extern":"1","_id":"14305","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1},{"day":"01","abstract":[{"text":"We propose a general conjecture for the mixed Hodge polynomial of the generic character varieties of representations of the fundamental group of a Riemann surface of genus g to GLn(C) with fixed generic semisimple conjugacy classes at k punctures. This conjecture generalizes the Cauchy identity for Macdonald polynomials and is a common generalization of two formulas that we prove in this paper. The first is a formula for the E-polynomial of these character varieties which we obtain using the character table of GLn(Fq). We use this formula to compute the Euler characteristic of character varieties. The second formula gives the Poincaré polynomial of certain associated quiver varieties which we obtain using the character table of gln(Fq). In the last main result we prove that the Poincaré polynomials of the quiver varieties equal certain multiplicities in the tensor product of irreducible characters of GLn(Fq). As a consequence we find a curious connection between Kac-Moody algebras associated with comet-shaped, and typically wild, quivers and the representation theory of GLn(Fq).","lang":"eng"}],"publication":"Duke Mathematical Journal","title":"Arithmetic harmonic analysis on character and quiver varieties","page":"323 - 400","status":"public","date_updated":"2021-01-12T06:50:56Z","main_file_link":[{"url":"http://arxiv.org/abs/0810.2076","open_access":"1"}],"date_published":"2011-01-01T00:00:00Z","issue":"2","date_created":"2018-12-11T11:52:11Z","citation":{"mla":"Hausel, Tamás, et al. “Arithmetic Harmonic Analysis on Character and Quiver Varieties.” <i>Duke Mathematical Journal</i>, vol. 160, no. 2, Duke University Press, 2011, pp. 323–400, doi:<a href=\"https://doi.org/10.1215/00127094-1444258\">10.1215/00127094-1444258</a>.","ieee":"T. Hausel, E. Letellier, and F. Rodríguez Villegas, “Arithmetic harmonic analysis on character and quiver varieties,” <i>Duke Mathematical Journal</i>, vol. 160, no. 2. Duke University Press, pp. 323–400, 2011.","short":"T. Hausel, E. Letellier, F. Rodríguez Villegas, Duke Mathematical Journal 160 (2011) 323–400.","apa":"Hausel, T., Letellier, E., &#38; Rodríguez Villegas, F. (2011). Arithmetic harmonic analysis on character and quiver varieties. <i>Duke Mathematical Journal</i>. Duke University Press. <a href=\"https://doi.org/10.1215/00127094-1444258\">https://doi.org/10.1215/00127094-1444258</a>","ama":"Hausel T, Letellier E, Rodríguez Villegas F. Arithmetic harmonic analysis on character and quiver varieties. <i>Duke Mathematical Journal</i>. 2011;160(2):323-400. doi:<a href=\"https://doi.org/10.1215/00127094-1444258\">10.1215/00127094-1444258</a>","chicago":"Hausel, Tamás, Emmanuel Letellier, and Fernando Rodríguez Villegas. “Arithmetic Harmonic Analysis on Character and Quiver Varieties.” <i>Duke Mathematical Journal</i>. Duke University Press, 2011. <a href=\"https://doi.org/10.1215/00127094-1444258\">https://doi.org/10.1215/00127094-1444258</a>.","ista":"Hausel T, Letellier E, Rodríguez Villegas F. 2011. Arithmetic harmonic analysis on character and quiver varieties. Duke Mathematical Journal. 160(2), 323–400."},"volume":160,"year":"2011","type":"journal_article","month":"01","doi":"10.1215/00127094-1444258","publist_id":"5728","publisher":"Duke University Press","author":[{"first_name":"Tamas","last_name":"Hausel","full_name":"Tamas Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Letellier","first_name":"Emmanuel","full_name":"Letellier, Emmanuel"},{"full_name":"Rodríguez Villegas, Fernando","first_name":"Fernando","last_name":"Rodríguez Villegas"}],"publication_status":"published","oa":1,"intvolume":"       160","extern":1,"acknowledgement":"Hausel’s work was supported by National Science Foundation grants DMS-0305505 and DMS-0604775, by an Alfred Sloan Fellowship, and by a Royal Society University Research Fellowship. Letellier’s work supported by Agence Nationale de la Recherche grant ANR-09-JCJC-0102-01.\nRodriguez-Villegas’s work supported by National Science Foundation grant DMS-0200605, by an FRA from the University of Texas at Austin, by EPSRC grant EP/G027110/1, by visiting fellowships at All Souls and Wadham Colleges in Oxford, and by a Research Scholarship from the Clay Mathematical Institute.","quality_controlled":0,"_id":"1467"},{"month":"02","publication_identifier":{"issn":["2664-1690"]},"type":"technical_report","year":"2011","pubrep_id":"23","oa_version":"Published Version","citation":{"ista":"Chatterjee K, Doyen L. 2011. Energy and mean-payoff parity Markov decision processes, IST Austria, 20p.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Energy and Mean-Payoff Parity Markov Decision Processes</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">https://doi.org/10.15479/AT:IST-2011-0001</a>.","ama":"Chatterjee K, Doyen L. <i>Energy and Mean-Payoff Parity Markov Decision Processes</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">10.15479/AT:IST-2011-0001</a>","apa":"Chatterjee, K., &#38; Doyen, L. (2011). <i>Energy and mean-payoff parity Markov decision processes</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">https://doi.org/10.15479/AT:IST-2011-0001</a>","short":"K. Chatterjee, L. Doyen, Energy and Mean-Payoff Parity Markov Decision Processes, IST Austria, 2011.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Energy and Mean-Payoff Parity Markov Decision Processes</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">10.15479/AT:IST-2011-0001</a>.","ieee":"K. Chatterjee and L. Doyen, <i>Energy and mean-payoff parity Markov decision processes</i>. IST Austria, 2011."},"language":[{"iso":"eng"}],"ddc":["000","005"],"date_created":"2018-12-12T11:39:02Z","date_published":"2011-02-16T00:00:00Z","date_updated":"2023-02-23T11:23:11Z","status":"public","page":"20","related_material":{"record":[{"id":"3345","relation":"later_version","status":"public"}]},"title":"Energy and mean-payoff parity Markov decision processes","abstract":[{"text":"We consider Markov Decision Processes (MDPs) with mean-payoff parity and energy parity objectives. In system design, the parity objective is used to encode ω-regular specifications, and the mean-payoff and energy objectives can be used to model quantitative resource constraints. The energy condition re- quires that the resource level never drops below 0, and the mean-payoff condi- tion requires that the limit-average value of the resource consumption is within a threshold. While these two (energy and mean-payoff) classical conditions are equivalent for two-player games, we show that they differ for MDPs. We show that the problem of deciding whether a state is almost-sure winning (i.e., winning with probability 1) in energy parity MDPs is in NP ∩ coNP, while for mean- payoff parity MDPs, the problem is solvable in polynomial time, improving a recent PSPACE bound.","lang":"eng"}],"day":"16","_id":"5387","file_date_updated":"2020-07-14T12:46:41Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"}],"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"IST Austria","file":[{"creator":"system","content_type":"application/pdf","file_size":329976,"access_level":"open_access","date_created":"2018-12-12T11:52:57Z","file_name":"IST-2011-0001_IST-2011-0001.pdf","file_id":"5458","date_updated":"2020-07-14T12:46:41Z","checksum":"824d6c70e6d3feb3e836b009e0b3cf73","relation":"main_file"}],"alternative_title":["IST Austria Technical Report"],"doi":"10.15479/AT:IST-2011-0001","has_accepted_license":"1"},{"author":[{"last_name":"Hosten","first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","full_name":"Onur Hosten"}],"publication_status":"published","doi":"10.1038/474170a","publist_id":"7224","publisher":"Nature Publishing Group","intvolume":"       474","extern":1,"_id":"580","quality_controlled":0,"date_updated":"2021-01-12T08:03:34Z","status":"public","date_published":"2011-06-08T00:00:00Z","date_created":"2018-12-11T11:47:18Z","issue":"7350","day":"08","title":"Quantum physics: How to catch a wave","publication":"Nature","page":"170 - 171","volume":474,"year":"2011","type":"journal_article","month":"06","citation":{"ista":"Hosten O. 2011. Quantum physics: How to catch a wave. Nature. 474(7350), 170–171.","chicago":"Hosten, Onur. “Quantum Physics: How to Catch a Wave.” <i>Nature</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/474170a\">https://doi.org/10.1038/474170a</a>.","apa":"Hosten, O. (2011). Quantum physics: How to catch a wave. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/474170a\">https://doi.org/10.1038/474170a</a>","ama":"Hosten O. Quantum physics: How to catch a wave. <i>Nature</i>. 2011;474(7350):170-171. doi:<a href=\"https://doi.org/10.1038/474170a\">10.1038/474170a</a>","mla":"Hosten, Onur. “Quantum Physics: How to Catch a Wave.” <i>Nature</i>, vol. 474, no. 7350, Nature Publishing Group, 2011, pp. 170–71, doi:<a href=\"https://doi.org/10.1038/474170a\">10.1038/474170a</a>.","ieee":"O. Hosten, “Quantum physics: How to catch a wave,” <i>Nature</i>, vol. 474, no. 7350. Nature Publishing Group, pp. 170–171, 2011.","short":"O. Hosten, Nature 474 (2011) 170–171."}},{"year":"2011","type":"conference","month":"01","citation":{"chicago":"Schmid, David, Shiraz Hazrat, Radhika Rangarajan, Onur Hosten, Stephan Quint, and Paul Kwiat. “Methods towards Achieving Precise Birefringent Focusing.” OSA, 2011. <a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">https://doi.org/10.1364/CLEO_AT.2011.JThB130</a>.","ista":"Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. 2011. Methods towards achieving precise birefringent focusing. QELS: Quantum Electronics and Laser Science, Optics InfoBase Conference Papers, .","mla":"Schmid, David, et al. <i>Methods towards Achieving Precise Birefringent Focusing</i>. OSA, 2011, doi:<a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">10.1364/CLEO_AT.2011.JThB130</a>.","ieee":"D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, and P. Kwiat, “Methods towards achieving precise birefringent focusing,” presented at the QELS: Quantum Electronics and Laser Science, 2011.","short":"D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, P. Kwiat, in:, OSA, 2011.","apa":"Schmid, D., Hazrat, S., Rangarajan, R., Hosten, O., Quint, S., &#38; Kwiat, P. (2011). Methods towards achieving precise birefringent focusing. Presented at the QELS: Quantum Electronics and Laser Science, OSA. <a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">https://doi.org/10.1364/CLEO_AT.2011.JThB130</a>","ama":"Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. Methods towards achieving precise birefringent focusing. In: OSA; 2011. doi:<a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">10.1364/CLEO_AT.2011.JThB130</a>"},"date_updated":"2021-01-12T08:03:44Z","status":"public","date_published":"2011-01-01T00:00:00Z","date_created":"2018-12-11T11:47:20Z","day":"01","abstract":[{"lang":"eng","text":"We present two independent schemes for the precise focusing of orthogonal polarizations of light at arbitrary relative locations. The first scheme uses a polarization Sagnac interferometer, the second a set of three birefringent elements.\n\n"}],"conference":{"name":"QELS: Quantum Electronics and Laser Science"},"title":"Methods towards achieving precise birefringent focusing","extern":1,"_id":"585","quality_controlled":0,"author":[{"full_name":"Schmid, David","last_name":"Schmid","first_name":"David"},{"first_name":"Shiraz","last_name":"Hazrat","full_name":"Hazrat, Shiraz"},{"full_name":"Rangarajan, Radhika","last_name":"Rangarajan","first_name":"Radhika"},{"full_name":"Onur Hosten","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur","last_name":"Hosten"},{"full_name":"Quint, Stephan","first_name":"Stephan","last_name":"Quint"},{"first_name":"Paul","last_name":"Kwiat","full_name":"Kwiat, Paul G"}],"publication_status":"published","doi":"10.1364/CLEO_AT.2011.JThB130","publist_id":"7220","alternative_title":["Optics InfoBase Conference Papers"],"publisher":"OSA"},{"status":"public","date_updated":"2021-01-12T08:05:05Z","date_published":"2011-08-04T00:00:00Z","date_created":"2018-12-11T11:47:20Z","issue":"6","day":"04","abstract":[{"lang":"eng","text":"We demonstrate a Raman laser using cold Rb87 atoms as the gain medium in a high-finesse optical cavity. We observe robust continuous wave lasing in the atypical regime where single atoms can considerably affect the cavity field. Consequently, we discover unusual lasing threshold behavior in the system causing jumps in lasing power, and propose a model to explain the effect. We also measure the intermode laser linewidth, and observe values as low as 80Hz. The tunable gain properties of this laser suggest multiple directions for future research."}],"publication":"Physical Review Letters","title":"Raman lasing with a cold atom gain medium in a high-finesse optical cavity","year":"2011","volume":107,"type":"journal_article","month":"08","citation":{"ieee":"G. Vrijsen, O. Hosten, J. Lee, S. Bernon, and M. Kasevich, “Raman lasing with a cold atom gain medium in a high-finesse optical cavity,” <i>Physical Review Letters</i>, vol. 107, no. 6. American Physical Society, 2011.","mla":"Vrijsen, Geert, et al. “Raman Lasing with a Cold Atom Gain Medium in a High-Finesse Optical Cavity.” <i>Physical Review Letters</i>, vol. 107, no. 6, American Physical Society, 2011, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">10.1103/PhysRevLett.107.063904</a>.","short":"G. Vrijsen, O. Hosten, J. Lee, S. Bernon, M. Kasevich, Physical Review Letters 107 (2011).","apa":"Vrijsen, G., Hosten, O., Lee, J., Bernon, S., &#38; Kasevich, M. (2011). Raman lasing with a cold atom gain medium in a high-finesse optical cavity. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">https://doi.org/10.1103/PhysRevLett.107.063904</a>","ama":"Vrijsen G, Hosten O, Lee J, Bernon S, Kasevich M. Raman lasing with a cold atom gain medium in a high-finesse optical cavity. <i>Physical Review Letters</i>. 2011;107(6). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">10.1103/PhysRevLett.107.063904</a>","chicago":"Vrijsen, Geert, Onur Hosten, Jongmin Lee, Simon Bernon, and Mark Kasevich. “Raman Lasing with a Cold Atom Gain Medium in a High-Finesse Optical Cavity.” <i>Physical Review Letters</i>. American Physical Society, 2011. <a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">https://doi.org/10.1103/PhysRevLett.107.063904</a>.","ista":"Vrijsen G, Hosten O, Lee J, Bernon S, Kasevich M. 2011. Raman lasing with a cold atom gain medium in a high-finesse optical cavity. Physical Review Letters. 107(6)."},"publication_status":"published","author":[{"full_name":"Vrijsen, Geert","first_name":"Geert","last_name":"Vrijsen"},{"last_name":"Hosten","first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","full_name":"Onur Hosten"},{"last_name":"Lee","first_name":"Jongmin","full_name":"Lee, Jongmin"},{"full_name":"Bernon, Simon","first_name":"Simon","last_name":"Bernon"},{"full_name":"Kasevich, Mark A","last_name":"Kasevich","first_name":"Mark"}],"doi":"10.1103/PhysRevLett.107.063904","publist_id":"7223","publisher":"American Physical Society","intvolume":"       107","extern":1,"quality_controlled":0,"_id":"586"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","_id":"597","intvolume":"         9","extern":"1","publication_status":"published","author":[{"full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","last_name":"Bernecky"},{"last_name":"Grob","first_name":"Patricia","full_name":"Grob, Patricia"},{"full_name":"Ebmeier, Christopher","last_name":"Ebmeier","first_name":"Christopher"},{"full_name":"Nogales, Eva","last_name":"Nogales","first_name":"Eva"},{"full_name":"Taatjes, Dylan","last_name":"Taatjes","first_name":"Dylan"}],"publisher":"Public Library of Science","doi":"10.1371/journal.pbio.1000603","publist_id":"7209","type":"journal_article","month":"03","volume":9,"year":"2011","citation":{"chicago":"Bernecky, Carrie, Patricia Grob, Christopher Ebmeier, Eva Nogales, and Dylan Taatjes. “Molecular Architecture of the Human Mediator-RNA Polymerase II-TFIIF Assembly.” <i>PLoS Biology</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pbio.1000603\">https://doi.org/10.1371/journal.pbio.1000603</a>.","ista":"Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. 2011. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biology. 9(3).","short":"C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, D. Taatjes, PLoS Biology 9 (2011).","mla":"Bernecky, Carrie, et al. “Molecular Architecture of the Human Mediator-RNA Polymerase II-TFIIF Assembly.” <i>PLoS Biology</i>, vol. 9, no. 3, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000603\">10.1371/journal.pbio.1000603</a>.","ieee":"C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, and D. Taatjes, “Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly,” <i>PLoS Biology</i>, vol. 9, no. 3. Public Library of Science, 2011.","ama":"Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. <i>PLoS Biology</i>. 2011;9(3). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000603\">10.1371/journal.pbio.1000603</a>","apa":"Bernecky, C., Grob, P., Ebmeier, C., Nogales, E., &#38; Taatjes, D. (2011). Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1000603\">https://doi.org/10.1371/journal.pbio.1000603</a>"},"oa_version":"None","language":[{"iso":"eng"}],"date_published":"2011-03-01T00:00:00Z","issue":"3","date_created":"2018-12-11T11:47:24Z","status":"public","date_updated":"2021-01-12T08:05:25Z","title":"Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly","publication":"PLoS Biology","day":"01","abstract":[{"text":"The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator-pol II interface is not well-characterized, whereas attempts to structurally define the Mediator-pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator-pol II-TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator-pol II-TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator-pol II-TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator-CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator-pol II complexes lacking TFIIF reveal that TFIIF plays a key role in stabilizing pol II orientation within the assembly.","lang":"eng"}]},{"language":[{"iso":"eng"}],"month":"12","publication":"Proceedings of the National Academy of Sciences","page":"20672-20677","day":"20","date_created":"2019-03-20T14:30:06Z","status":"public","quality_controlled":"1","intvolume":"       108","external_id":{"pmid":["22135454"]},"oa":1,"citation":{"ista":"Milward K, Busch KE, Murphy RJ, de Bono M, Olofsson B. 2011. Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 108(51), 20672–20677.","chicago":"Milward, K., K. E. Busch, R. J. Murphy, Mario de Bono, and B. Olofsson. “Neuronal and Molecular Substrates for Optimal Foraging in Caenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1106134109\">https://doi.org/10.1073/pnas.1106134109</a>.","ama":"Milward K, Busch KE, Murphy RJ, de Bono M, Olofsson B. Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. 2011;108(51):20672-20677. doi:<a href=\"https://doi.org/10.1073/pnas.1106134109\">10.1073/pnas.1106134109</a>","apa":"Milward, K., Busch, K. E., Murphy, R. J., de Bono, M., &#38; Olofsson, B. (2011). Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1106134109\">https://doi.org/10.1073/pnas.1106134109</a>","short":"K. Milward, K.E. Busch, R.J. Murphy, M. de Bono, B. Olofsson, Proceedings of the National Academy of Sciences 108 (2011) 20672–20677.","mla":"Milward, K., et al. “Neuronal and Molecular Substrates for Optimal Foraging in Caenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 51, National Academy of Sciences, 2011, pp. 20672–77, doi:<a href=\"https://doi.org/10.1073/pnas.1106134109\">10.1073/pnas.1106134109</a>.","ieee":"K. Milward, K. E. Busch, R. J. Murphy, M. de Bono, and B. Olofsson, “Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans,” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 51. National Academy of Sciences, pp. 20672–20677, 2011."},"oa_version":"Submitted Version","type":"journal_article","publication_identifier":{"issn":["0027-8424","1091-6490"]},"year":"2011","volume":108,"title":"Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans","abstract":[{"lang":"eng","text":"Variation in food quality and abundance requires animals to decide whether to stay on a poor food patch or leave in search of better food. An important question in behavioral ecology asks when is it optimal for an animal to leave a food patch it is depleting. Although optimal foraging is central to evolutionary success, the neural and molecular mechanisms underlying it are poorly understood. Here we investigate the neuronal basis for adaptive food-leaving behavior in response to resource depletion in Caenorhabditis elegans, and identify several of the signaling pathways involved. The ASE neurons, previously implicated in salt chemoattraction, promote food-leaving behavior via a cGMP pathway as food becomes limited. High ambient O2 promotes food-leaving via the O2-sensing neurons AQR, PQR, and URX. Ectopic activation of these neurons using channelrhodopsin is sufficient to induce high food-leaving behavior. In contrast, the neuropeptide receptor NPR-1, which regulates social behavior on food, acts in the ASE neurons, the nociceptive ASH neurons, and in the RMG interneuron to repress food-leaving. Finally, we show that neuroendocrine signaling by TGF-β/DAF-7 and neuronal insulin signaling are necessary for adaptive food-leaving behavior. We suggest that animals integrate information about their nutritional state with ambient oxygen and gustatory stimuli to formulate optimal foraging strategies."}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251049/"}],"date_published":"2011-12-20T00:00:00Z","issue":"51","date_updated":"2021-01-12T08:06:18Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6137","extern":"1","pmid":1,"publisher":"National Academy of Sciences","doi":"10.1073/pnas.1106134109","author":[{"last_name":"Milward","first_name":"K.","full_name":"Milward, K."},{"first_name":"K. E.","last_name":"Busch","full_name":"Busch, K. E."},{"full_name":"Murphy, R. J.","first_name":"R. J.","last_name":"Murphy"},{"last_name":"de Bono","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443"},{"last_name":"Olofsson","first_name":"B.","full_name":"Olofsson, B."}],"publication_status":"published"},{"oa":1,"file":[{"relation":"main_file","file_id":"6139","checksum":"547cffd123f4c508ae927c9244b8f92a","date_updated":"2020-07-14T12:47:20Z","file_size":2448332,"access_level":"open_access","date_created":"2019-03-20T15:06:32Z","file_name":"2011_Cell_Bretscher.pdf","creator":"kschuh","content_type":"application/pdf"}],"external_id":{"pmid":["21435556"]},"has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:20Z","quality_controlled":"1","intvolume":"        69","date_created":"2019-03-20T15:01:41Z","status":"public","publication":"Neuron","page":"1099-1113","day":"24","month":"03","tmp":{"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)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"publication_status":"published","author":[{"last_name":"Bretscher","first_name":"Andrew Jonathan","full_name":"Bretscher, Andrew Jonathan"},{"first_name":"Eiji","last_name":"Kodama-Namba","full_name":"Kodama-Namba, Eiji"},{"full_name":"Busch, Karl Emanuel","last_name":"Busch","first_name":"Karl Emanuel"},{"full_name":"Murphy, Robin Joseph","last_name":"Murphy","first_name":"Robin Joseph"},{"last_name":"Soltesz","first_name":"Zoltan","full_name":"Soltesz, Zoltan"},{"first_name":"Patrick","last_name":"Laurent","full_name":"Laurent, Patrick"},{"last_name":"de Bono","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario"}],"publisher":"Elsevier BV","doi":"10.1016/j.neuron.2011.02.023","pmid":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6138","extern":"1","date_published":"2011-03-24T00:00:00Z","ddc":["570"],"issue":"6","date_updated":"2021-01-12T08:06:18Z","title":"Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior","license":"https://creativecommons.org/licenses/by/4.0/","type":"journal_article","publication_identifier":{"issn":["0896-6273"]},"volume":69,"year":"2011","oa_version":"Published Version","citation":{"ista":"Bretscher AJ, Kodama-Namba E, Busch KE, Murphy RJ, Soltesz Z, Laurent P, de Bono M. 2011. Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior. Neuron. 69(6), 1099–1113.","chicago":"Bretscher, Andrew Jonathan, Eiji Kodama-Namba, Karl Emanuel Busch, Robin Joseph Murphy, Zoltan Soltesz, Patrick Laurent, and Mario de Bono. “Temperature, Oxygen, and Salt-Sensing Neurons in C. Elegans Are Carbon Dioxide Sensors That Control Avoidance Behavior.” <i>Neuron</i>. Elsevier BV, 2011. <a href=\"https://doi.org/10.1016/j.neuron.2011.02.023\">https://doi.org/10.1016/j.neuron.2011.02.023</a>.","ama":"Bretscher AJ, Kodama-Namba E, Busch KE, et al. Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior. <i>Neuron</i>. 2011;69(6):1099-1113. doi:<a href=\"https://doi.org/10.1016/j.neuron.2011.02.023\">10.1016/j.neuron.2011.02.023</a>","apa":"Bretscher, A. J., Kodama-Namba, E., Busch, K. E., Murphy, R. J., Soltesz, Z., Laurent, P., &#38; de Bono, M. (2011). Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior. <i>Neuron</i>. Elsevier BV. <a href=\"https://doi.org/10.1016/j.neuron.2011.02.023\">https://doi.org/10.1016/j.neuron.2011.02.023</a>","ieee":"A. J. Bretscher <i>et al.</i>, “Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior,” <i>Neuron</i>, vol. 69, no. 6. Elsevier BV, pp. 1099–1113, 2011.","mla":"Bretscher, Andrew Jonathan, et al. “Temperature, Oxygen, and Salt-Sensing Neurons in C. Elegans Are Carbon Dioxide Sensors That Control Avoidance Behavior.” <i>Neuron</i>, vol. 69, no. 6, Elsevier BV, 2011, pp. 1099–113, doi:<a href=\"https://doi.org/10.1016/j.neuron.2011.02.023\">10.1016/j.neuron.2011.02.023</a>.","short":"A.J. Bretscher, E. Kodama-Namba, K.E. Busch, R.J. Murphy, Z. Soltesz, P. Laurent, M. de Bono, Neuron 69 (2011) 1099–1113."}},{"intvolume":"         7","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:20Z","oa":1,"has_accepted_license":"1","file":[{"relation":"main_file","content_type":"application/pdf","creator":"kschuh","file_name":"2011_PLOS_Arellano-Carbajal.PDF","date_created":"2019-03-20T15:18:11Z","access_level":"open_access","file_size":5625063,"date_updated":"2020-07-14T12:47:20Z","checksum":"c609b2ce616d7dafbb617ec5d022f1ea","file_id":"6141"}],"external_id":{"pmid":["21437263"]},"month":"03","language":[{"iso":"eng"}],"tmp":{"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)","image":"/images/cc_by.png"},"status":"public","date_created":"2019-03-20T15:08:23Z","day":"17","publication":"PLoS Genetics","pmid":1,"extern":"1","_id":"6140","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Arellano-Carbajal, Fausto","first_name":"Fausto","last_name":"Arellano-Carbajal"},{"last_name":"Briseño-Roa","first_name":"Luis","full_name":"Briseño-Roa, Luis"},{"last_name":"Couto","first_name":"Africa","full_name":"Couto, Africa"},{"full_name":"Cheung, Benny H. H.","last_name":"Cheung","first_name":"Benny H. H."},{"full_name":"Labouesse, Michel","first_name":"Michel","last_name":"Labouesse"},{"last_name":"de Bono","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario"}],"publication_status":"published","doi":"10.1371/journal.pgen.1001341","publisher":"Public Library of Science","volume":7,"year":"2011","publication_identifier":{"issn":["1553-7404"]},"type":"journal_article","citation":{"short":"F. Arellano-Carbajal, L. Briseño-Roa, A. Couto, B.H.H. Cheung, M. Labouesse, M. de Bono, PLoS Genetics 7 (2011).","ieee":"F. Arellano-Carbajal, L. Briseño-Roa, A. Couto, B. H. H. Cheung, M. Labouesse, and M. de Bono, “Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability,” <i>PLoS Genetics</i>, vol. 7, no. 3. Public Library of Science, 2011.","mla":"Arellano-Carbajal, Fausto, et al. “Macoilin, a Conserved Nervous System–Specific ER Membrane Protein That Regulates Neuronal Excitability.” <i>PLoS Genetics</i>, vol. 7, no. 3, e1001341, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1001341\">10.1371/journal.pgen.1001341</a>.","apa":"Arellano-Carbajal, F., Briseño-Roa, L., Couto, A., Cheung, B. H. H., Labouesse, M., &#38; de Bono, M. (2011). Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1001341\">https://doi.org/10.1371/journal.pgen.1001341</a>","ama":"Arellano-Carbajal F, Briseño-Roa L, Couto A, Cheung BHH, Labouesse M, de Bono M. Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability. <i>PLoS Genetics</i>. 2011;7(3). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1001341\">10.1371/journal.pgen.1001341</a>","chicago":"Arellano-Carbajal, Fausto, Luis Briseño-Roa, Africa Couto, Benny H. H. Cheung, Michel Labouesse, and Mario de Bono. “Macoilin, a Conserved Nervous System–Specific ER Membrane Protein That Regulates Neuronal Excitability.” <i>PLoS Genetics</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pgen.1001341\">https://doi.org/10.1371/journal.pgen.1001341</a>.","ista":"Arellano-Carbajal F, Briseño-Roa L, Couto A, Cheung BHH, Labouesse M, de Bono M. 2011. Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability. PLoS Genetics. 7(3), e1001341."},"oa_version":"Published Version","date_updated":"2021-01-12T08:06:19Z","issue":"3","ddc":["570"],"date_published":"2011-03-17T00:00:00Z","abstract":[{"lang":"eng","text":"Genome sequence comparisons have highlighted many novel gene families that are conserved across animal phyla but whose biological function is unknown. Here, we functionally characterize a member of one such family, the macoilins. Macoilins are characterized by several highly conserved predicted transmembrane domains towards the N-terminus and by coiled-coil regions C-terminally. They are found throughout Eumetazoa but not in other organisms. Mutants for the single Caenorhabditis elegans macoilin, maco-1, exhibit a constellation of behavioral phenotypes, including defects in aggregation, O2 responses, and swimming. MACO-1 protein is expressed broadly and specifically in the nervous system and localizes to the rough endoplasmic reticulum; it is excluded from dendrites and axons. Apart from subtle synapse defects, nervous system development appears wild-type in maco-1 mutants. However, maco-1 animals are resistant to the cholinesterase inhibitor aldicarb and sensitive to levamisole, suggesting pre-synaptic defects. Using in vivo imaging, we show that macoilin is required to evoke Ca2+ transients, at least in some neurons: in maco-1 mutants the O2-sensing neuron PQR is unable to generate a Ca2+ response to a rise in O2. By genetically disrupting neurotransmission, we show that pre-synaptic input is not necessary for PQR to respond to O2, indicating that the response is mediated by cell-intrinsic sensory transduction and amplification. Disrupting the sodium leak channels NCA-1/NCA-2, or the N-,P/Q,R-type voltage-gated Ca2+ channels, also fails to disrupt Ca2+ responses in the PQR cell body to O2 stimuli. By contrast, mutations in egl-19, which encodes the only Caenorhabditis elegans L-type voltage-gated Ca2+ channel α1 subunit, recapitulate the Ca2+ response defect we see in maco-1 mutants, although we do not see defects in localization of EGL-19. Together, our data suggest that macoilin acts in the ER to regulate assembly or traffic of ion channels or ion channel regulators."}],"article_number":"e1001341","title":"Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability"},{"date_updated":"2021-01-12T08:06:58Z","status":"public","date_published":"2011-07-22T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://www.jbc.org/content/286/29/25675.full.pdf"}],"issue":"29","date_created":"2019-04-11T20:57:43Z","day":"22","abstract":[{"text":"Tumor necrosis factor-stimulated gene-6 (TSG-6) is a hyalu-ronan (HA)-binding protein that plays important roles ininflammation and ovulation. TSG-6-mediated cross-linking ofHA has been proposed as a functional mechanism (e.g.for regu-lating leukocyte adhesion), but direct evidence for cross-linkingis lacking, and we know very little about its impact on HA ultra-structure. Here we used films of polymeric and oligomeric HAchains, end-grafted to a solid support, and a combination ofsurface-sensitive biophysical techniques to quantify the bindingof TSG-6 into HA films and to correlate binding to morpholog-ical changes. We find that full-length TSG-6 binds with pro-nounced positive cooperativity and demonstrate that it cancross-link HA at physiologically relevant concentrations. Ourdata indicate that cooperative binding of full-length TSG-6arises from HA-induced protein oligomerization and that theTSG-6 oligomers act as cross-linkers. In contrast, the HA-bind-ing domain of TSG-6 (the Link module) alone binds withoutpositive cooperativity and weaker than the full-length protein.Both the Link module and full-length TSG-6 condensed andrigidified HA films, and the degree of condensation scaled withthe affinity between the TSG-6 constructs and HA. We proposethat condensation is the result of protein-mediated HA cross-linking. Our findings firmly establish that TSG-6 is a potent HAcross-linking agent and might hence have important implica-tions for the mechanistic understanding of the biological func-tion of TSG-6 (e.g.in inflammation).","lang":"eng"}],"publication":"Journal of Biological Chemistry","title":"The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers","page":"25675-25686","year":"2011","volume":286,"type":"journal_article","publication_identifier":{"issn":["0021-9258","1083-351X"]},"month":"07","language":[{"iso":"eng"}],"citation":{"chicago":"Baranova, Natalia S., Erik Nilebäck, F. Michael Haller, David C. Briggs, Sofia Svedhem, Anthony J. Day, and Ralf P. Richter. “The Inflammation-Associated Protein TSG-6 Cross-Links Hyaluronan via Hyaluronan-Induced TSG-6 Oligomers.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry &#38; Molecular Biology, 2011. <a href=\"https://doi.org/10.1074/jbc.m111.247395\">https://doi.org/10.1074/jbc.m111.247395</a>.","ista":"Baranova NS, Nilebäck E, Haller FM, Briggs DC, Svedhem S, Day AJ, Richter RP. 2011. The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers. Journal of Biological Chemistry. 286(29), 25675–25686.","ieee":"N. S. Baranova <i>et al.</i>, “The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers,” <i>Journal of Biological Chemistry</i>, vol. 286, no. 29. American Society for Biochemistry &#38; Molecular Biology, pp. 25675–25686, 2011.","mla":"Baranova, Natalia S., et al. “The Inflammation-Associated Protein TSG-6 Cross-Links Hyaluronan via Hyaluronan-Induced TSG-6 Oligomers.” <i>Journal of Biological Chemistry</i>, vol. 286, no. 29, American Society for Biochemistry &#38; Molecular Biology, 2011, pp. 25675–86, doi:<a href=\"https://doi.org/10.1074/jbc.m111.247395\">10.1074/jbc.m111.247395</a>.","short":"N.S. Baranova, E. Nilebäck, F.M. Haller, D.C. Briggs, S. Svedhem, A.J. Day, R.P. Richter, Journal of Biological Chemistry 286 (2011) 25675–25686.","ama":"Baranova NS, Nilebäck E, Haller FM, et al. The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers. <i>Journal of Biological Chemistry</i>. 2011;286(29):25675-25686. doi:<a href=\"https://doi.org/10.1074/jbc.m111.247395\">10.1074/jbc.m111.247395</a>","apa":"Baranova, N. S., Nilebäck, E., Haller, F. M., Briggs, D. C., Svedhem, S., Day, A. J., &#38; Richter, R. P. (2011). The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry &#38; Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.m111.247395\">https://doi.org/10.1074/jbc.m111.247395</a>"},"oa_version":"Published Version","publication_status":"published","oa":1,"author":[{"last_name":"Baranova","first_name":"Natalia","id":"38661662-F248-11E8-B48F-1D18A9856A87","full_name":"Baranova, Natalia","orcid":"0000-0002-3086-9124"},{"first_name":"Erik","last_name":"Nilebäck","full_name":"Nilebäck, Erik"},{"last_name":"Haller","first_name":"F. Michael","full_name":"Haller, F. Michael"},{"last_name":"Briggs","first_name":"David C.","full_name":"Briggs, David C."},{"last_name":"Svedhem","first_name":"Sofia","full_name":"Svedhem, Sofia"},{"full_name":"Day, Anthony J.","last_name":"Day","first_name":"Anthony J."},{"full_name":"Richter, Ralf P.","first_name":"Ralf P.","last_name":"Richter"}],"doi":"10.1074/jbc.m111.247395","publisher":"American Society for Biochemistry & Molecular Biology","intvolume":"       286","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6298","quality_controlled":"1"},{"publisher":"Elsevier","doi":"10.1016/j.bpj.2011.09.040","publication_status":"published","author":[{"first_name":"Heungwon","last_name":"Park","full_name":"Park, Heungwon"},{"full_name":"Oikonomou, Panos","last_name":"Oikonomou","first_name":"Panos"},{"first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Philippe","last_name":"Cluzel","full_name":"Cluzel, Philippe"}],"department":[{"_id":"CaGu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6496","pmid":1,"title":"Noise underlies switching behavior of the bacterial flagellum","abstract":[{"lang":"eng","text":"We report the switching behavior of the full bacterial flagellum system that includes the filament and the motor in wild-type Escherichia coli cells. In sorting the motor behavior by the clockwise bias, we find that the distributions of the clockwise (CW) and counterclockwise (CCW) intervals are either exponential or nonexponential with long tails. At low bias, CW intervals are exponentially distributed and CCW intervals exhibit long tails. At intermediate CW bias (0.5) both CW and CCW intervals are mainly exponentially distributed. A simple model suggests that these two distinct switching behaviors are governed by the presence of signaling noise within the chemotaxis network. Low noise yields exponentially distributed intervals, whereas large noise yields nonexponential behavior with long tails. These drastically different motor statistics may play a role in optimizing bacterial behavior for a wide range of environmental conditions."}],"date_published":"2011-11-16T00:00:00Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218319/","open_access":"1"}],"issue":"10","date_updated":"2021-04-16T11:54:49Z","citation":{"short":"H. Park, P. Oikonomou, C.C. Guet, P. Cluzel, Biophysical Journal 101 (2011) 2336–2340.","ieee":"H. Park, P. Oikonomou, C. C. Guet, and P. Cluzel, “Noise underlies switching behavior of the bacterial flagellum,” <i>Biophysical Journal</i>, vol. 101, no. 10. Elsevier, pp. 2336–2340, 2011.","mla":"Park, Heungwon, et al. “Noise Underlies Switching Behavior of the Bacterial Flagellum.” <i>Biophysical Journal</i>, vol. 101, no. 10, Elsevier, 2011, pp. 2336–40, doi:<a href=\"https://doi.org/10.1016/j.bpj.2011.09.040\">10.1016/j.bpj.2011.09.040</a>.","ama":"Park H, Oikonomou P, Guet CC, Cluzel P. Noise underlies switching behavior of the bacterial flagellum. <i>Biophysical Journal</i>. 2011;101(10):2336-2340. doi:<a href=\"https://doi.org/10.1016/j.bpj.2011.09.040\">10.1016/j.bpj.2011.09.040</a>","apa":"Park, H., Oikonomou, P., Guet, C. C., &#38; Cluzel, P. (2011). Noise underlies switching behavior of the bacterial flagellum. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2011.09.040\">https://doi.org/10.1016/j.bpj.2011.09.040</a>","chicago":"Park, Heungwon, Panos Oikonomou, Calin C Guet, and Philippe Cluzel. “Noise Underlies Switching Behavior of the Bacterial Flagellum.” <i>Biophysical Journal</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.bpj.2011.09.040\">https://doi.org/10.1016/j.bpj.2011.09.040</a>.","ista":"Park H, Oikonomou P, Guet CC, Cluzel P. 2011. Noise underlies switching behavior of the bacterial flagellum. Biophysical Journal. 101(10), 2336–2340."},"oa_version":"Published Version","type":"journal_article","publication_identifier":{"issn":["0006-3495"]},"scopus_import":"1","year":"2011","volume":101,"external_id":{"pmid":["22098731"]},"oa":1,"article_processing_charge":"No","quality_controlled":"1","intvolume":"       101","publication":"Biophysical Journal","page":"2336-2340","day":"16","date_created":"2019-05-28T11:54:29Z","status":"public","language":[{"iso":"eng"}],"month":"11"}]