--- _id: '1781' 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. acknowledgement: This work was supported by the Swiss National Science Foundation (SNF), the Austrian Science Foundation (FWF), and ETH Zurich author: - first_name: Stefan full_name: Filipp, Stefan last_name: Filipp - first_name: M full_name: Göppl, M last_name: Göppl - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Matthias full_name: Baur, Matthias P last_name: Baur - first_name: R full_name: Bianchetti, R last_name: Bianchetti - first_name: L. full_name: Steffen, L. Kraig last_name: Steffen - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff citation: ama: Filipp S, Göppl M, Fink JM, et al. Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. 2011;83(6). doi:10.1103/PhysRevA.83.063827 apa: Filipp, S., Göppl, M., Fink, J. M., 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. American Physical Society. https://doi.org/10.1103/PhysRevA.83.063827 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.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevA.83.063827. ieee: S. Filipp et al., “Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 83, no. 6. American Physical Society, 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). mla: Filipp, Stefan, et al. “Multimode Mediated Qubit-Qubit Coupling and Dark-State Symmetries in Circuit Quantum Electrodynamics.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 83, no. 6, American Physical Society, 2011, doi:10.1103/PhysRevA.83.063827. 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). date_created: 2018-12-11T11:53:58Z date_published: 2011-06-22T00:00:00Z date_updated: 2021-01-12T06:53:09Z day: '22' doi: 10.1103/PhysRevA.83.063827 extern: 1 intvolume: ' 83' issue: '6' month: '06' publication: Physical Review A - Atomic, Molecular, and Optical Physics publication_status: published publisher: American Physical Society publist_id: '5335' quality_controlled: 0 status: public title: Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics type: journal_article volume: 83 year: '2011' ... --- _id: '1780' abstract: - lang: eng text: Continuous variable entanglement between two modes of a radiation field is usually studied at optical frequencies. Here we demonstrate experiments that show the entanglement between microwave photons of different energy in a broadband squeezed beam. We use a Josephson parametric amplifier to generate the two-mode correlated state and detect all four quadrature components simultaneously in a two-channel heterodyne setup using amplitude detectors. Analyzing two-dimensional phase space histograms for all possible pairs of quadratures allows us to determine the full covariance matrix, which is in good agreement with the one expected for a two-mode squeezed state. acknowledgement: This work was supported by the European Research Council (ERC) through a Starting grant and by ETHZ. S. F. acknowledges the Austrian Science Foundation (FWF) for support author: - first_name: Christopher full_name: Eichler, Christopher last_name: Eichler - first_name: Deniz full_name: Bozyigit, Deniz last_name: Bozyigit - first_name: C full_name: Lang, C last_name: Lang - first_name: Matthias full_name: Baur, Matthias P last_name: Baur - first_name: L. full_name: Steffen, L. Kraig last_name: Steffen - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Stefan full_name: Filipp, Stefan last_name: Filipp - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff citation: ama: Eichler C, Bozyigit D, Lang C, et al. Observation of two-mode squeezing in the microwave frequency domain. Physical Review Letters. 2011;107(11). doi:10.1103/PhysRevLett.107.113601 apa: Eichler, C., Bozyigit, D., Lang, C., Baur, M., Steffen, L., Fink, J. M., … Wallraff, A. (2011). Observation of two-mode squeezing in the microwave frequency domain. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.107.113601 chicago: Eichler, Christopher, Deniz Bozyigit, C Lang, Matthias Baur, L. Steffen, Johannes M Fink, Stefan Filipp, and Andreas Wallraff. “Observation of Two-Mode Squeezing in the Microwave Frequency Domain.” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.113601. ieee: C. Eichler et al., “Observation of two-mode squeezing in the microwave frequency domain,” Physical Review Letters, vol. 107, no. 11. American Physical Society, 2011. ista: Eichler C, Bozyigit D, Lang C, Baur M, Steffen L, Fink JM, Filipp S, Wallraff A. 2011. Observation of two-mode squeezing in the microwave frequency domain. Physical Review Letters. 107(11). mla: Eichler, Christopher, et al. “Observation of Two-Mode Squeezing in the Microwave Frequency Domain.” Physical Review Letters, vol. 107, no. 11, American Physical Society, 2011, doi:10.1103/PhysRevLett.107.113601. short: C. Eichler, D. Bozyigit, C. Lang, M. Baur, L. Steffen, J.M. Fink, S. Filipp, A. Wallraff, Physical Review Letters 107 (2011). date_created: 2018-12-11T11:53:58Z date_published: 2011-09-06T00:00:00Z date_updated: 2021-01-12T06:53:09Z day: '06' doi: 10.1103/PhysRevLett.107.113601 extern: 1 intvolume: ' 107' issue: '11' month: '09' publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5334' quality_controlled: 0 status: public title: Observation of two-mode squeezing in the microwave frequency domain type: journal_article volume: 107 year: '2011' ... --- _id: '1815' abstract: - lang: eng 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. author: - first_name: Tamar full_name: Tamar Friedlander id: 36A5845C-F248-11E8-B48F-1D18A9856A87 last_name: Friedlander - first_name: Naama full_name: Brenner, Naama last_name: Brenner citation: ama: Friedlander T, Brenner N. Adaptive response and enlargement of dynamic range. Mathematical Biosciences and Engineering. 2011;8(2):515-526. doi:10.3934/mbe.2011.8.515 apa: Friedlander, T., & Brenner, N. (2011). Adaptive response and enlargement of dynamic range. Mathematical Biosciences and Engineering. Arizona State University. https://doi.org/10.3934/mbe.2011.8.515 chicago: Friedlander, Tamar, and Naama Brenner. “Adaptive Response and Enlargement of Dynamic Range.” Mathematical Biosciences and Engineering. Arizona State University, 2011. https://doi.org/10.3934/mbe.2011.8.515. ieee: T. Friedlander and N. Brenner, “Adaptive response and enlargement of dynamic range,” Mathematical Biosciences and Engineering, vol. 8, no. 2. Arizona State University, pp. 515–526, 2011. ista: Friedlander T, Brenner N. 2011. Adaptive response and enlargement of dynamic range. Mathematical Biosciences and Engineering. 8(2), 515–526. mla: Friedlander, Tamar, and Naama Brenner. “Adaptive Response and Enlargement of Dynamic Range.” Mathematical Biosciences and Engineering, vol. 8, no. 2, Arizona State University, 2011, pp. 515–26, doi:10.3934/mbe.2011.8.515. short: T. Friedlander, N. Brenner, Mathematical Biosciences and Engineering 8 (2011) 515–526. date_created: 2018-12-11T11:54:10Z date_published: 2011-04-02T00:00:00Z date_updated: 2021-01-12T06:53:23Z day: '02' doi: 10.3934/mbe.2011.8.515 extern: 1 intvolume: ' 8' issue: '2' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1003.2791 month: '04' oa: 1 page: 515 - 526 publication: Mathematical Biosciences and Engineering publication_status: published publisher: Arizona State University publist_id: '5291' quality_controlled: 0 status: public title: Adaptive response and enlargement of dynamic range type: journal_article volume: 8 year: '2011' ... --- _id: '1863' 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>2, the proportion of parameter space affording this maximum is extremely small. acknowledgement: FWF 21305 author: - first_name: Sebastian full_name: Sebastian Novak id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak citation: ama: Novak S. The number of equilibria in the diallelic Levene model with multiple demes. Theoretical Population Biology. 2011;79(3):97-101. doi:10.1016/j.tpb.2010.12.002 apa: Novak, S. (2011). The number of equilibria in the diallelic Levene model with multiple demes. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2010.12.002 chicago: Novak, Sebastian. “The Number of Equilibria in the Diallelic Levene Model with Multiple Demes.” Theoretical Population Biology. Academic Press, 2011. https://doi.org/10.1016/j.tpb.2010.12.002. ieee: S. Novak, “The number of equilibria in the diallelic Levene model with multiple demes,” Theoretical Population Biology, vol. 79, no. 3. Academic Press, pp. 97–101, 2011. ista: Novak S. 2011. The number of equilibria in the diallelic Levene model with multiple demes. Theoretical Population Biology. 79(3), 97–101. mla: Novak, Sebastian. “The Number of Equilibria in the Diallelic Levene Model with Multiple Demes.” Theoretical Population Biology, vol. 79, no. 3, Academic Press, 2011, pp. 97–101, doi:10.1016/j.tpb.2010.12.002. short: S. Novak, Theoretical Population Biology 79 (2011) 97–101. date_created: 2018-12-11T11:54:25Z date_published: 2011-05-01T00:00:00Z date_updated: 2021-01-12T06:53:42Z day: '01' doi: 10.1016/j.tpb.2010.12.002 extern: 1 intvolume: ' 79' issue: '3' month: '05' page: 97 - 101 publication: Theoretical Population Biology publication_status: published publisher: Academic Press publist_id: '5236' quality_controlled: 0 status: public title: The number of equilibria in the diallelic Levene model with multiple demes tmp: image: /images/cc_by_nc_nd.png 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) type: journal_article volume: 79 year: '2011' ... --- _id: '1975' abstract: - lang: eng 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 "core" subunits, consistent with that notion. Mitochondrial complex I contains the core subunits, present in all species, and up to 31 "supernumerary" 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 "accessory" 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.' acknowledgement: 'This work was supported by the Medical Research Council. ' author: - first_name: Chui full_name: Yip, Chui Y last_name: Yip - first_name: Michael full_name: Harbour, Michael E last_name: Harbour - first_name: Kamburapola full_name: Jayawardena, Kamburapola G last_name: Jayawardena - first_name: Ian full_name: Fearnley, Ian M last_name: Fearnley - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Yip C, Harbour M, Jayawardena K, Fearnley I, Sazanov LA. Evolution of respiratory complex I "Supernumerary" subunits are present in the α-proteobacterial enzyme. Journal of Biological Chemistry. 2011;286(7):5023-5033. doi:10.1074/jbc.M110.194993 apa: Yip, C., Harbour, M., Jayawardena, K., Fearnley, I., & Sazanov, L. A. (2011). Evolution of respiratory complex I "Supernumerary" subunits are present in the α-proteobacterial enzyme. Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M110.194993 chicago: Yip, Chui, Michael Harbour, Kamburapola Jayawardena, Ian Fearnley, and Leonid A Sazanov. “Evolution of Respiratory Complex I "Supernumerary" Subunits Are Present in the α-Proteobacterial Enzyme.” Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology, 2011. https://doi.org/10.1074/jbc.M110.194993. ieee: C. Yip, M. Harbour, K. Jayawardena, I. Fearnley, and L. A. Sazanov, “Evolution of respiratory complex I "Supernumerary" subunits are present in the α-proteobacterial enzyme,” Journal of Biological Chemistry, vol. 286, no. 7. American Society for Biochemistry and Molecular Biology, pp. 5023–5033, 2011. ista: Yip C, Harbour M, Jayawardena K, Fearnley I, Sazanov LA. 2011. Evolution of respiratory complex I "Supernumerary" subunits are present in the α-proteobacterial enzyme. Journal of Biological Chemistry. 286(7), 5023–5033. mla: Yip, Chui, et al. “Evolution of Respiratory Complex I "Supernumerary" Subunits Are Present in the α-Proteobacterial Enzyme.” Journal of Biological Chemistry, vol. 286, no. 7, American Society for Biochemistry and Molecular Biology, 2011, pp. 5023–33, doi:10.1074/jbc.M110.194993. short: C. Yip, M. Harbour, K. Jayawardena, I. Fearnley, L.A. Sazanov, Journal of Biological Chemistry 286 (2011) 5023–5033. date_created: 2018-12-11T11:55:00Z date_published: 2011-02-18T00:00:00Z date_updated: 2021-01-12T06:54:27Z day: '18' doi: 10.1074/jbc.M110.194993 extern: 1 intvolume: ' 286' issue: '7' month: '02' page: 5023 - 5033 publication: Journal of Biological Chemistry publication_status: published publisher: American Society for Biochemistry and Molecular Biology publist_id: '5112' quality_controlled: 0 status: public title: Evolution of respiratory complex I "Supernumerary" subunits are present in the α-proteobacterial enzyme type: journal_article volume: 286 year: '2011' ... --- _id: '1973' abstract: - lang: eng 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. acknowledgement: This work was funded by the Medical Research Council. author: - first_name: Rouslan full_name: Efremov, Rouslan G last_name: Efremov - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Efremov R, Sazanov LA. Structure of the membrane domain of respiratory complex i. Nature. 2011;476(7361):414-421. doi:10.1038/nature10330 apa: Efremov, R., & Sazanov, L. A. (2011). Structure of the membrane domain of respiratory complex i. Nature. Nature Publishing Group. https://doi.org/10.1038/nature10330 chicago: Efremov, Rouslan, and Leonid A Sazanov. “Structure of the Membrane Domain of Respiratory Complex I.” Nature. Nature Publishing Group, 2011. https://doi.org/10.1038/nature10330. ieee: R. Efremov and L. A. Sazanov, “Structure of the membrane domain of respiratory complex i,” Nature, vol. 476, no. 7361. Nature Publishing Group, pp. 414–421, 2011. ista: Efremov R, Sazanov LA. 2011. Structure of the membrane domain of respiratory complex i. Nature. 476(7361), 414–421. mla: Efremov, Rouslan, and Leonid A. Sazanov. “Structure of the Membrane Domain of Respiratory Complex I.” Nature, vol. 476, no. 7361, Nature Publishing Group, 2011, pp. 414–21, doi:10.1038/nature10330. short: R. Efremov, L.A. Sazanov, Nature 476 (2011) 414–421. date_created: 2018-12-11T11:54:59Z date_published: 2011-08-25T00:00:00Z date_updated: 2021-01-12T06:54:26Z day: '25' doi: 10.1038/nature10330 extern: 1 intvolume: ' 476' issue: '7361' month: '08' page: 414 - 421 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '5110' quality_controlled: 0 status: public title: Structure of the membrane domain of respiratory complex i type: journal_article volume: 476 year: '2011' ... --- _id: '1974' 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. acknowledgement: The work in authors’ laboratory was funded by the Medical Research Council. author: - first_name: Rouslan full_name: Efremov, Rouslan G last_name: Efremov - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: 'Efremov R, Sazanov LA. Respiratory complex I: “steam engine” of the cell? Current Opinion in Structural Biology. 2011;21(4):532-540. doi:10.1016/j.sbi.2011.07.002' apa: 'Efremov, R., & Sazanov, L. A. (2011). Respiratory complex I: “steam engine” of the cell? Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2011.07.002' chicago: 'Efremov, Rouslan, and Leonid A Sazanov. “Respiratory Complex I: ‘steam Engine’ of the Cell?” Current Opinion in Structural Biology. Elsevier, 2011. https://doi.org/10.1016/j.sbi.2011.07.002.' ieee: 'R. Efremov and L. A. Sazanov, “Respiratory complex I: ‘steam engine’ of the cell?,” Current Opinion in Structural Biology, vol. 21, no. 4. Elsevier, pp. 532–540, 2011.' ista: 'Efremov R, Sazanov LA. 2011. Respiratory complex I: ‘steam engine’ of the cell? Current Opinion in Structural Biology. 21(4), 532–540.' mla: 'Efremov, Rouslan, and Leonid A. Sazanov. “Respiratory Complex I: ‘steam Engine’ of the Cell?” Current Opinion in Structural Biology, vol. 21, no. 4, Elsevier, 2011, pp. 532–40, doi:10.1016/j.sbi.2011.07.002.' short: R. Efremov, L.A. Sazanov, Current Opinion in Structural Biology 21 (2011) 532–540. date_created: 2018-12-11T11:54:59Z date_published: 2011-08-01T00:00:00Z date_updated: 2021-01-12T06:54:27Z day: '01' doi: 10.1016/j.sbi.2011.07.002 extern: 1 intvolume: ' 21' issue: '4' month: '08' page: 532 - 540 publication: Current Opinion in Structural Biology publication_status: published publisher: Elsevier publist_id: '5111' quality_controlled: 0 status: public title: 'Respiratory complex I: ''steam engine'' of the cell?' type: journal_article volume: 21 year: '2011' ... --- _id: '1985' abstract: - lang: eng text: |2- In 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. acknowledgement: This work was also supported by the Max Planck Society (M.L., E.F.-F., P.S.). author: - first_name: Martin full_name: Martin Loose id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Elisabeth full_name: Fischer-Friedrich, Elisabeth last_name: Fischer Friedrich - first_name: Christoph full_name: Herold, Christoph last_name: Herold - first_name: Karsten full_name: Kruse, Karsten last_name: Kruse - first_name: Petra full_name: 'Schwille, Petra ' last_name: Schwille citation: ama: Loose M, Fischer Friedrich E, Herold C, Kruse K, Schwille P. Min protein patterns emerge from rapid rebinding and membrane interaction of MinE. Nature Structural and Molecular Biology. 2011;18(5):577-583. doi:10.1038/nsmb.2037 apa: 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. Nature Publishing Group. https://doi.org/10.1038/nsmb.2037 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.” Nature Structural and Molecular Biology. Nature Publishing Group, 2011. https://doi.org/10.1038/nsmb.2037. 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,” Nature Structural and Molecular Biology, vol. 18, no. 5. Nature Publishing Group, pp. 577–583, 2011. 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. mla: Loose, Martin, et al. “Min Protein Patterns Emerge from Rapid Rebinding and Membrane Interaction of MinE.” Nature Structural and Molecular Biology, vol. 18, no. 5, Nature Publishing Group, 2011, pp. 577–83, doi:10.1038/nsmb.2037. short: M. Loose, E. Fischer Friedrich, C. Herold, K. Kruse, P. Schwille, Nature Structural and Molecular Biology 18 (2011) 577–583. date_created: 2018-12-11T11:55:03Z date_published: 2011-05-01T00:00:00Z date_updated: 2021-01-12T06:54:31Z day: '01' doi: 10.1038/nsmb.2037 extern: 1 intvolume: ' 18' issue: '5' month: '05' page: 577 - 583 publication: Nature Structural and Molecular Biology publication_status: published publisher: Nature Publishing Group publist_id: '5098' quality_controlled: 0 status: public title: Min protein patterns emerge from rapid rebinding and membrane interaction of MinE type: journal_article volume: 18 year: '2011' ... --- _id: '1986' abstract: - lang: eng 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. author: - first_name: Martin full_name: Martin Loose id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Karsten full_name: Kruse, Karsten last_name: Kruse - first_name: Petra full_name: 'Schwille, Petra ' last_name: Schwille citation: ama: 'Loose M, Kruse K, Schwille P. Protein self-organization: Lessons from the min system. Annual Review of Biophysics. 2011;40(1):315-336. doi:10.1146/annurev-biophys-042910-155332' apa: 'Loose, M., Kruse, K., & Schwille, P. (2011). Protein self-organization: Lessons from the min system. Annual Review of Biophysics. Annual Reviews. https://doi.org/10.1146/annurev-biophys-042910-155332' chicago: 'Loose, Martin, Karsten Kruse, and Petra Schwille. “Protein Self-Organization: Lessons from the Min System.” Annual Review of Biophysics. Annual Reviews, 2011. https://doi.org/10.1146/annurev-biophys-042910-155332.' ieee: 'M. Loose, K. Kruse, and P. Schwille, “Protein self-organization: Lessons from the min system,” Annual Review of Biophysics, vol. 40, no. 1. Annual Reviews, pp. 315–336, 2011.' ista: 'Loose M, Kruse K, Schwille P. 2011. Protein self-organization: Lessons from the min system. Annual Review of Biophysics. 40(1), 315–336.' mla: 'Loose, Martin, et al. “Protein Self-Organization: Lessons from the Min System.” Annual Review of Biophysics, vol. 40, no. 1, Annual Reviews, 2011, pp. 315–36, doi:10.1146/annurev-biophys-042910-155332.' short: M. Loose, K. Kruse, P. Schwille, Annual Review of Biophysics 40 (2011) 315–336. date_created: 2018-12-11T11:55:04Z date_published: 2011-06-09T00:00:00Z date_updated: 2021-01-12T06:54:31Z day: '09' doi: 10.1146/annurev-biophys-042910-155332 extern: 1 intvolume: ' 40' issue: '1' month: '06' page: 315 - 336 publication: Annual Review of Biophysics publication_status: published publisher: Annual Reviews publist_id: '5097' quality_controlled: 0 status: public title: 'Protein self-organization: Lessons from the min system' type: journal_article volume: 40 year: '2011' ... --- _id: '2072' abstract: - lang: eng text: Many species have morphologically and genetically differentiated sex chromosomes, such as the XY pair of mammals. Y chromosomes are often highly degenerated and carry few functional genes, so that XY males have only one copy of most Xlinked genes (whereas females have two). As a result, chromosome-wide mechanisms of dosage compensation, such as the mammalian X-inactivation, often evolve to reestablish expression balance. A similar phenomenon is expected in femaleheterogametic species, where ZW females should suffer from imbalances due to W-chromosome degeneration. However, no global dosage compensation mechanisms have been detected in the two independent ZW systems that have been studied systematically (birds and silkworm), leading to the suggestion that lack of global dosage compensation may be a general feature of female-heterogametic species. However, analyses of other independently evolved ZW systems are required to test if this is the case. In this study, we use published genomic and expression data to test for the presence of global dosage compensation in Schistosoma mansoni, a trematode parasite that causes schistosomiasis in humans. We find that Z-linked expression is reduced relative to autosomal expression in females but not males, consistent with incomplete or localized dosage compensation. This gives further support to the theory that female-heterogametic species may not require global mechanisms of dosage compensation. author: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Doris full_name: Bachtrog, Doris last_name: Bachtrog citation: ama: Vicoso B, Bachtrog D. Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite. Genome Biology and Evolution. 2011;3(1):230-235. doi:10.1093/gbe/evr010 apa: Vicoso, B., & Bachtrog, D. (2011). Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evr010 chicago: Vicoso, Beatriz, and Doris Bachtrog. “Lack of Global Dosage Compensation in Schistosoma Mansoni, a Female-Heterogametic Parasite.” Genome Biology and Evolution. Oxford University Press, 2011. https://doi.org/10.1093/gbe/evr010. ieee: B. Vicoso and D. Bachtrog, “Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite,” Genome Biology and Evolution, vol. 3, no. 1. Oxford University Press, pp. 230–235, 2011. ista: Vicoso B, Bachtrog D. 2011. Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite. Genome Biology and Evolution. 3(1), 230–235. mla: Vicoso, Beatriz, and Doris Bachtrog. “Lack of Global Dosage Compensation in Schistosoma Mansoni, a Female-Heterogametic Parasite.” Genome Biology and Evolution, vol. 3, no. 1, Oxford University Press, 2011, pp. 230–35, doi:10.1093/gbe/evr010. short: B. Vicoso, D. Bachtrog, Genome Biology and Evolution 3 (2011) 230–235. date_created: 2018-12-11T11:55:33Z date_published: 2011-02-11T00:00:00Z date_updated: 2021-01-12T06:55:08Z day: '11' ddc: - '570' doi: 10.1093/gbe/evr010 extern: '1' file: - access_level: open_access checksum: 7855c134436e4f6a13d63b6606d7e8dd content_type: application/pdf creator: dernst date_created: 2019-05-10T07:41:28Z date_updated: 2020-07-14T12:45:27Z file_id: '6395' file_name: 2011_GBE_Vicoso.pdf file_size: 212547 relation: main_file file_date_updated: 2020-07-14T12:45:27Z has_accepted_license: '1' intvolume: ' 3' issue: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 230 - 235 publication: Genome Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '4966' quality_controlled: '1' status: public title: Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2011' ...