[{"publication":"Biophysical Journal","page":"2311-2315","date_created":"2020-09-18T10:05:54Z","doi":"10.1016/j.bpj.2017.09.019","publication_status":"published","date_published":"2017-12-05T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"None","type":"journal_article","article_type":"original","article_processing_charge":"No","volume":113,"intvolume":"       113","citation":{"chicago":"Dehez, François, Paul Schanda, Martin S. King, Edmund R.S. Kunji, and Christophe Chipot. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-Native Affinity.” <i>Biophysical Journal</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.bpj.2017.09.019\">https://doi.org/10.1016/j.bpj.2017.09.019</a>.","ista":"Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. 2017. Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity. Biophysical Journal. 113(11), 2311–2315.","apa":"Dehez, F., Schanda, P., King, M. S., Kunji, E. R. S., &#38; Chipot, C. (2017). Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2017.09.019\">https://doi.org/10.1016/j.bpj.2017.09.019</a>","mla":"Dehez, François, et al. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-Native Affinity.” <i>Biophysical Journal</i>, vol. 113, no. 11, Elsevier, 2017, pp. 2311–15, doi:<a href=\"https://doi.org/10.1016/j.bpj.2017.09.019\">10.1016/j.bpj.2017.09.019</a>.","ieee":"F. Dehez, P. Schanda, M. S. King, E. R. S. Kunji, and C. Chipot, “Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity,” <i>Biophysical Journal</i>, vol. 113, no. 11. Elsevier, pp. 2311–2315, 2017.","ama":"Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity. <i>Biophysical Journal</i>. 2017;113(11):2311-2315. doi:<a href=\"https://doi.org/10.1016/j.bpj.2017.09.019\">10.1016/j.bpj.2017.09.019</a>","short":"F. Dehez, P. Schanda, M.S. King, E.R.S. Kunji, C. Chipot, Biophysical Journal 113 (2017) 2311–2315."},"quality_controlled":"1","keyword":["Biophysics"],"year":"2017","extern":"1","day":"05","issue":"11","abstract":[{"lang":"eng","text":"Biophysical investigation of membrane proteins generally requires their extraction from native sources using detergents, a step that can lead, possibly irreversibly, to protein denaturation. The propensity of dodecylphosphocholine (DPC), a detergent widely utilized in NMR studies of membrane proteins, to distort their structure has been the subject of much controversy. It has been recently proposed that the binding specificity of the yeast mitochondrial ADP/ATP carrier (yAAC3) toward cardiolipins is preserved in DPC, thereby suggesting that DPC is a suitable environment in which to study membrane proteins. In this communication, we used all-atom molecular dynamics simulations to investigate the specific binding of cardiolipins to yAAC3. Our data demonstrate that the interaction interface observed in a native-like environment differs markedly from that inferred from an NMR investigation in DPC, implying that in this detergent, the protein structure is distorted. We further investigated yAAC3 solubilized in DPC and in the milder dodecylmaltoside with thermal-shift assays. The loss of thermal transition observed in DPC confirms that the protein is no longer properly folded in this environment."}],"date_updated":"2021-01-12T08:19:18Z","_id":"8444","author":[{"last_name":"Dehez","first_name":"François","full_name":"Dehez, François"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","orcid":"0000-0002-9350-7606","first_name":"Paul","full_name":"Schanda, Paul"},{"first_name":"Martin S.","last_name":"King","full_name":"King, Martin S."},{"last_name":"Kunji","first_name":"Edmund R.S.","full_name":"Kunji, Edmund R.S."},{"full_name":"Chipot, Christophe","first_name":"Christophe","last_name":"Chipot"}],"publication_identifier":{"issn":["0006-3495"]},"title":"Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Elsevier","month":"12"},{"publication_identifier":{"issn":["2041-1723"]},"title":"Slow conformational exchange and overall rocking motion in ubiquitin protein crystals","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","status":"public","month":"07","year":"2017","extern":"1","day":"27","abstract":[{"lang":"eng","text":"Proteins perform their functions in solution but their structures are most frequently studied inside crystals. Here we probe how the crystal packing alters microsecond dynamics, using solid-state NMR measurements and multi-microsecond MD simulations of different crystal forms of ubiquitin. In particular, near-rotary-resonance relaxation dispersion (NERRD) experiments probe angular backbone motion, while Bloch–McConnell relaxation dispersion data report on fluctuations of the local electronic environment. These experiments and simulations reveal that the packing of the protein can significantly alter the thermodynamics and kinetics of local conformational exchange. Moreover, we report small-amplitude reorientational motion of protein molecules in the crystal lattice with an ~3–5° amplitude on a tens-of-microseconds time scale in one of the crystals, but not in others. An intriguing possibility arises that overall motion is to some extent coupled to local dynamics. Our study highlights the importance of considering the packing when analyzing dynamics of crystalline proteins."}],"date_updated":"2021-01-12T08:19:19Z","_id":"8445","author":[{"full_name":"Kurauskas, Vilius","last_name":"Kurauskas","first_name":"Vilius"},{"first_name":"Sergei A.","last_name":"Izmailov","full_name":"Izmailov, Sergei A."},{"first_name":"Olga N.","last_name":"Rogacheva","full_name":"Rogacheva, Olga N."},{"full_name":"Hessel, Audrey","last_name":"Hessel","first_name":"Audrey"},{"first_name":"Isabel","last_name":"Ayala","full_name":"Ayala, Isabel"},{"full_name":"Woodhouse, Joyce","last_name":"Woodhouse","first_name":"Joyce"},{"last_name":"Shilova","first_name":"Anastasya","full_name":"Shilova, Anastasya"},{"first_name":"Yi","last_name":"Xue","full_name":"Xue, Yi"},{"last_name":"Yuwen","first_name":"Tairan","full_name":"Yuwen, Tairan"},{"full_name":"Coquelle, Nicolas","first_name":"Nicolas","last_name":"Coquelle"},{"first_name":"Jacques-Philippe","last_name":"Colletier","full_name":"Colletier, Jacques-Philippe"},{"full_name":"Skrynnikov, Nikolai R.","first_name":"Nikolai R.","last_name":"Skrynnikov"},{"last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"}],"article_number":"145","article_processing_charge":"No","article_type":"original","intvolume":"         8","volume":8,"quality_controlled":"1","citation":{"ieee":"V. Kurauskas <i>et al.</i>, “Slow conformational exchange and overall rocking motion in ubiquitin protein crystals,” <i>Nature Communications</i>, vol. 8. Springer Nature, 2017.","ama":"Kurauskas V, Izmailov SA, Rogacheva ON, et al. Slow conformational exchange and overall rocking motion in ubiquitin protein crystals. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/s41467-017-00165-8\">10.1038/s41467-017-00165-8</a>","short":"V. Kurauskas, S.A. Izmailov, O.N. Rogacheva, A. Hessel, I. Ayala, J. Woodhouse, A. Shilova, Y. Xue, T. Yuwen, N. Coquelle, J.-P. Colletier, N.R. Skrynnikov, P. Schanda, Nature Communications 8 (2017).","apa":"Kurauskas, V., Izmailov, S. A., Rogacheva, O. N., Hessel, A., Ayala, I., Woodhouse, J., … Schanda, P. (2017). Slow conformational exchange and overall rocking motion in ubiquitin protein crystals. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-017-00165-8\">https://doi.org/10.1038/s41467-017-00165-8</a>","mla":"Kurauskas, Vilius, et al. “Slow Conformational Exchange and Overall Rocking Motion in Ubiquitin Protein Crystals.” <i>Nature Communications</i>, vol. 8, 145, Springer Nature, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-00165-8\">10.1038/s41467-017-00165-8</a>.","ista":"Kurauskas V, Izmailov SA, Rogacheva ON, Hessel A, Ayala I, Woodhouse J, Shilova A, Xue Y, Yuwen T, Coquelle N, Colletier J-P, Skrynnikov NR, Schanda P. 2017. Slow conformational exchange and overall rocking motion in ubiquitin protein crystals. Nature Communications. 8, 145.","chicago":"Kurauskas, Vilius, Sergei A. Izmailov, Olga N. Rogacheva, Audrey Hessel, Isabel Ayala, Joyce Woodhouse, Anastasya Shilova, et al. “Slow Conformational Exchange and Overall Rocking Motion in Ubiquitin Protein Crystals.” <i>Nature Communications</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/s41467-017-00165-8\">https://doi.org/10.1038/s41467-017-00165-8</a>."},"publication":"Nature Communications","date_created":"2020-09-18T10:06:01Z","doi":"10.1038/s41467-017-00165-8","publication_status":"published","date_published":"2017-07-27T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"Published Version","type":"journal_article"},{"publication_status":"published","doi":"10.1002/cphc.201700572","page":"2697-2703","date_created":"2020-09-18T10:06:09Z","publication":"ChemPhysChem","oa_version":"None","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2017-08-09T00:00:00Z","article_type":"original","article_processing_charge":"No","keyword":["Physical and Theoretical Chemistry","Atomic and Molecular Physics","and Optics"],"citation":{"short":"H. Fraga, C. Arnaud, D.F. Gauto, M. Audin, V. Kurauskas, P. Macek, C. Krichel, J. Guan, J. Boisbouvier, R. Sprangers, C. Breyton, P. Schanda, ChemPhysChem 18 (2017) 2697–2703.","ama":"Fraga H, Arnaud C, Gauto DF, et al. Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins. <i>ChemPhysChem</i>. 2017;18(19):2697-2703. doi:<a href=\"https://doi.org/10.1002/cphc.201700572\">10.1002/cphc.201700572</a>","ieee":"H. Fraga <i>et al.</i>, “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins,” <i>ChemPhysChem</i>, vol. 18, no. 19. Wiley, pp. 2697–2703, 2017.","apa":"Fraga, H., Arnaud, C., Gauto, D. F., Audin, M., Kurauskas, V., Macek, P., … Schanda, P. (2017). Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins. <i>ChemPhysChem</i>. Wiley. <a href=\"https://doi.org/10.1002/cphc.201700572\">https://doi.org/10.1002/cphc.201700572</a>","mla":"Fraga, Hugo, et al. “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D Correlation Experiments for Resonance Assignment of Large Proteins.” <i>ChemPhysChem</i>, vol. 18, no. 19, Wiley, 2017, pp. 2697–703, doi:<a href=\"https://doi.org/10.1002/cphc.201700572\">10.1002/cphc.201700572</a>.","ista":"Fraga H, Arnaud C, Gauto DF, Audin M, Kurauskas V, Macek P, Krichel C, Guan J, Boisbouvier J, Sprangers R, Breyton C, Schanda P. 2017. Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins. ChemPhysChem. 18(19), 2697–2703.","chicago":"Fraga, Hugo, Charles‐Adrien Arnaud, Diego F. Gauto, Maxime Audin, Vilius Kurauskas, Pavel Macek, Carsten Krichel, et al. “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D Correlation Experiments for Resonance Assignment of Large Proteins.” <i>ChemPhysChem</i>. Wiley, 2017. <a href=\"https://doi.org/10.1002/cphc.201700572\">https://doi.org/10.1002/cphc.201700572</a>."},"intvolume":"        18","quality_controlled":"1","volume":18,"date_updated":"2021-01-12T08:19:19Z","abstract":[{"text":"Solid‐state NMR spectroscopy can provide insight into protein structure and dynamics at the atomic level without inherent protein size limitations. However, a major hurdle to studying large proteins by solid‐state NMR spectroscopy is related to spectral complexity and resonance overlap, which increase with molecular weight and severely hamper the assignment process. Here the use of two sets of experiments is shown to expand the tool kit of 1H‐detected assignment approaches, which correlate a given amide pair either to the two adjacent CO–CA pairs (4D hCOCANH/hCOCAcoNH), or to the amide 1H of the neighboring residue (3D HcocaNH/HcacoNH, which can be extended to 5D). The experiments are based on efficient coherence transfers between backbone atoms using INEPT transfers between carbons and cross‐polarization for heteronuclear transfers. The utility of these experiments is exemplified with application to assemblies of deuterated, fully amide‐protonated proteins from approximately 20 to 60 kDa monomer, at magic‐angle spinning (MAS) frequencies from approximately 40 to 55 kHz. These experiments will also be applicable to protonated proteins at higher MAS frequencies. The resonance assignment of a domain within the 50.4 kDa bacteriophage T5 tube protein pb6 is reported, and this is compared to NMR assignments of the isolated domain in solution. This comparison reveals contacts of this domain to the core of the polymeric tail tube assembly.","lang":"eng"}],"issue":"19","day":"09","year":"2017","extern":"1","author":[{"full_name":"Fraga, Hugo","last_name":"Fraga","first_name":"Hugo"},{"first_name":"Charles‐Adrien","last_name":"Arnaud","full_name":"Arnaud, Charles‐Adrien"},{"full_name":"Gauto, Diego F.","last_name":"Gauto","first_name":"Diego F."},{"last_name":"Audin","first_name":"Maxime","full_name":"Audin, Maxime"},{"full_name":"Kurauskas, Vilius","first_name":"Vilius","last_name":"Kurauskas"},{"full_name":"Macek, Pavel","last_name":"Macek","first_name":"Pavel"},{"last_name":"Krichel","first_name":"Carsten","full_name":"Krichel, Carsten"},{"last_name":"Guan","first_name":"Jia‐Ying","full_name":"Guan, Jia‐Ying"},{"full_name":"Boisbouvier, Jerome","last_name":"Boisbouvier","first_name":"Jerome"},{"first_name":"Remco","last_name":"Sprangers","full_name":"Sprangers, Remco"},{"first_name":"Cécile","last_name":"Breyton","full_name":"Breyton, Cécile"},{"last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"}],"_id":"8446","status":"public","publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins","publication_identifier":{"issn":["1439-4235","1439-7641"]},"month":"08"},{"keyword":["Nuclear and High Energy Physics","Instrumentation","General Chemistry","Radiation"],"citation":{"ama":"Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals. <i>Solid State Nuclear Magnetic Resonance</i>. 2017;87(10):86-95. doi:<a href=\"https://doi.org/10.1016/j.ssnmr.2017.04.002\">10.1016/j.ssnmr.2017.04.002</a>","ieee":"D. F. Gauto, A. Hessel, P. Rovó, V. Kurauskas, R. Linser, and P. Schanda, “Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals,” <i>Solid State Nuclear Magnetic Resonance</i>, vol. 87, no. 10. Elsevier, pp. 86–95, 2017.","short":"D.F. Gauto, A. Hessel, P. Rovó, V. Kurauskas, R. Linser, P. Schanda, Solid State Nuclear Magnetic Resonance 87 (2017) 86–95.","chicago":"Gauto, Diego F., Audrey Hessel, Petra Rovó, Vilius Kurauskas, Rasmus Linser, and Paul Schanda. “Protein Conformational Dynamics Studied by 15N and 1HR1ρ Relaxation Dispersion: Application to Wild-Type and G53A Ubiquitin Crystals.” <i>Solid State Nuclear Magnetic Resonance</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ssnmr.2017.04.002\">https://doi.org/10.1016/j.ssnmr.2017.04.002</a>.","ista":"Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. 2017. Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals. Solid State Nuclear Magnetic Resonance. 87(10), 86–95.","mla":"Gauto, Diego F., et al. “Protein Conformational Dynamics Studied by 15N and 1HR1ρ Relaxation Dispersion: Application to Wild-Type and G53A Ubiquitin Crystals.” <i>Solid State Nuclear Magnetic Resonance</i>, vol. 87, no. 10, Elsevier, 2017, pp. 86–95, doi:<a href=\"https://doi.org/10.1016/j.ssnmr.2017.04.002\">10.1016/j.ssnmr.2017.04.002</a>.","apa":"Gauto, D. F., Hessel, A., Rovó, P., Kurauskas, V., Linser, R., &#38; Schanda, P. (2017). Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals. <i>Solid State Nuclear Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ssnmr.2017.04.002\">https://doi.org/10.1016/j.ssnmr.2017.04.002</a>"},"volume":87,"intvolume":"        87","quality_controlled":"1","article_processing_charge":"No","article_type":"original","oa_version":"None","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2017-10-01T00:00:00Z","publication_status":"published","doi":"10.1016/j.ssnmr.2017.04.002","page":"86-95","date_created":"2020-09-18T10:06:18Z","publication":"Solid State Nuclear Magnetic Resonance","month":"10","publisher":"Elsevier","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals","publication_identifier":{"issn":["0926-2040"]},"author":[{"full_name":"Gauto, Diego F.","first_name":"Diego F.","last_name":"Gauto"},{"full_name":"Hessel, Audrey","last_name":"Hessel","first_name":"Audrey"},{"last_name":"Rovó","first_name":"Petra","full_name":"Rovó, Petra"},{"full_name":"Kurauskas, Vilius","first_name":"Vilius","last_name":"Kurauskas"},{"last_name":"Linser","first_name":"Rasmus","full_name":"Linser, Rasmus"},{"full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul"}],"_id":"8447","date_updated":"2021-01-12T08:19:20Z","abstract":[{"lang":"eng","text":"Solid-state NMR spectroscopy can provide site-resolved information about protein dynamics over many time scales. Here we combine protein deuteration, fast magic-angle spinning (~45–60 kHz) and proton detection to study dynamics of ubiquitin in microcrystals, and in particular a mutant in a region that undergoes microsecond motions in a β-turn region in the wild-type protein. We use 15N R1ρ relaxation measurements as a function of the radio-frequency (RF) field strength, i.e. relaxation dispersion, to probe how the G53A mutation alters these dynamics. We report a population-inversion of conformational states: the conformation that in the wild-type protein is populated only sparsely becomes the predominant state. We furthermore explore the potential to use amide-1H R1ρ relaxation to obtain insight into dynamics. We show that while quantitative interpretation of 1H relaxation remains beyond reach under the experimental conditions, due to coherent contributions to decay, one may extract qualitative information about flexibility."}],"issue":"10","day":"01","extern":"1","year":"2017"},{"doi":"10.1016/j.jmr.2017.05.016","publication_status":"published","publication":"Journal of Magnetic Resonance","date_created":"2020-09-18T10:06:27Z","page":"125-129","type":"journal_article","oa_version":"None","date_published":"2017-08-01T00:00:00Z","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","volume":281,"quality_controlled":"1","intvolume":"       281","citation":{"short":"R. Franco, A. Favier, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 281 (2017) 125–129.","ieee":"R. Franco, A. Favier, P. Schanda, and B. Brutscher, “Optimized fast mixing device for real-time NMR applications,” <i>Journal of Magnetic Resonance</i>, vol. 281, no. 8. Elsevier, pp. 125–129, 2017.","ama":"Franco R, Favier A, Schanda P, Brutscher B. Optimized fast mixing device for real-time NMR applications. <i>Journal of Magnetic Resonance</i>. 2017;281(8):125-129. doi:<a href=\"https://doi.org/10.1016/j.jmr.2017.05.016\">10.1016/j.jmr.2017.05.016</a>","chicago":"Franco, Rémi, Adrien Favier, Paul Schanda, and Bernhard Brutscher. “Optimized Fast Mixing Device for Real-Time NMR Applications.” <i>Journal of Magnetic Resonance</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.jmr.2017.05.016\">https://doi.org/10.1016/j.jmr.2017.05.016</a>.","apa":"Franco, R., Favier, A., Schanda, P., &#38; Brutscher, B. (2017). Optimized fast mixing device for real-time NMR applications. <i>Journal of Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmr.2017.05.016\">https://doi.org/10.1016/j.jmr.2017.05.016</a>","mla":"Franco, Rémi, et al. “Optimized Fast Mixing Device for Real-Time NMR Applications.” <i>Journal of Magnetic Resonance</i>, vol. 281, no. 8, Elsevier, 2017, pp. 125–29, doi:<a href=\"https://doi.org/10.1016/j.jmr.2017.05.016\">10.1016/j.jmr.2017.05.016</a>.","ista":"Franco R, Favier A, Schanda P, Brutscher B. 2017. Optimized fast mixing device for real-time NMR applications. Journal of Magnetic Resonance. 281(8), 125–129."},"keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"],"abstract":[{"lang":"eng","text":"We present an improved fast mixing device based on the rapid mixing of two solutions inside the NMR probe, as originally proposed by Hore and coworkers (J. Am. Chem. Soc. 125 (2003) 12484–12492). Such a device is important for off-equilibrium studies of molecular kinetics by multidimensional real-time NMR spectrsocopy. The novelty of this device is that it allows removing the injector from the NMR detection volume after mixing, and thus provides good magnetic field homogeneity independently of the initial sample volume placed in the NMR probe. The apparatus is simple to build, inexpensive, and can be used without any hardware modification on any type of liquid-state NMR spectrometer. We demonstrate the performance of our fast mixing device in terms of improved magnetic field homogeneity, and show an application to the study of protein folding and the structural characterization of transiently populated folding intermediates."}],"issue":"8","date_updated":"2021-01-12T08:19:20Z","extern":"1","year":"2017","day":"01","author":[{"full_name":"Franco, Rémi","last_name":"Franco","first_name":"Rémi"},{"full_name":"Favier, Adrien","first_name":"Adrien","last_name":"Favier"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"},{"last_name":"Brutscher","first_name":"Bernhard","full_name":"Brutscher, Bernhard"}],"_id":"8448","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","status":"public","publication_identifier":{"issn":["1090-7807"]},"title":"Optimized fast mixing device for real-time NMR applications","month":"08"},{"month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Oxford University Press","publication_identifier":{"issn":["0305-1048","1362-4962"]},"title":"RNA binding and chaperone activity of the E.coli cold-shock protein CspA","author":[{"first_name":"Enrico","last_name":"Rennella","full_name":"Rennella, Enrico"},{"full_name":"Sára, Tomáš","first_name":"Tomáš","last_name":"Sára"},{"full_name":"Juen, Michael","first_name":"Michael","last_name":"Juen"},{"full_name":"Wunderlich, Christoph","last_name":"Wunderlich","first_name":"Christoph"},{"last_name":"Imbert","first_name":"Lionel","full_name":"Imbert, Lionel"},{"last_name":"Solyom","first_name":"Zsofia","full_name":"Solyom, Zsofia"},{"last_name":"Favier","first_name":"Adrien","full_name":"Favier, Adrien"},{"full_name":"Ayala, Isabel","last_name":"Ayala","first_name":"Isabel"},{"last_name":"Weinhäupl","first_name":"Katharina","full_name":"Weinhäupl, Katharina"},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","orcid":"0000-0002-9350-7606","first_name":"Paul"},{"first_name":"Robert","last_name":"Konrat","full_name":"Konrat, Robert"},{"first_name":"Christoph","last_name":"Kreutz","full_name":"Kreutz, Christoph"},{"full_name":"Brutscher, Bernhard","first_name":"Bernhard","last_name":"Brutscher"}],"_id":"8449","issue":"7","abstract":[{"text":"Ensuring the correct folding of RNA molecules in the cell is of major importance for a large variety of biological functions. Therefore, chaperone proteins that assist RNA in adopting their functionally active states are abundant in all living organisms. An important feature of RNA chaperone proteins is that they do not require an external energy source to perform their activity, and that they interact transiently and non-specifically with their RNA targets. So far, little is known about the mechanistic details of the RNA chaperone activity of these proteins. Prominent examples of RNA chaperones are bacterial cold shock proteins (Csp) that have been reported to bind single-stranded RNA and DNA. Here, we have used advanced NMR spectroscopy techniques to investigate at atomic resolution the RNA-melting activity of CspA, the major cold shock protein of Escherichia coli, upon binding to different RNA hairpins. Real-time NMR provides detailed information on the folding kinetics and folding pathways. Finally, comparison of wild-type CspA with single-point mutants and small peptides yields insights into the complementary roles of aromatic and positively charged amino-acid side chains for the RNA chaperone activity of the protein.","lang":"eng"}],"date_updated":"2021-01-12T08:19:20Z","extern":"1","year":"2017","day":"20","volume":45,"citation":{"ieee":"E. Rennella <i>et al.</i>, “RNA binding and chaperone activity of the E.coli cold-shock protein CspA,” <i>Nucleic Acids Research</i>, vol. 45, no. 7. Oxford University Press, pp. 4255–4268, 2017.","ama":"Rennella E, Sára T, Juen M, et al. RNA binding and chaperone activity of the E.coli cold-shock protein CspA. <i>Nucleic Acids Research</i>. 2017;45(7):4255-4268. doi:<a href=\"https://doi.org/10.1093/nar/gkx044\">10.1093/nar/gkx044</a>","short":"E. Rennella, T. Sára, M. Juen, C. Wunderlich, L. Imbert, Z. Solyom, A. Favier, I. Ayala, K. Weinhäupl, P. Schanda, R. Konrat, C. Kreutz, B. Brutscher, Nucleic Acids Research 45 (2017) 4255–4268.","chicago":"Rennella, Enrico, Tomáš Sára, Michael Juen, Christoph Wunderlich, Lionel Imbert, Zsofia Solyom, Adrien Favier, et al. “RNA Binding and Chaperone Activity of the E.Coli Cold-Shock Protein CspA.” <i>Nucleic Acids Research</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/nar/gkx044\">https://doi.org/10.1093/nar/gkx044</a>.","mla":"Rennella, Enrico, et al. “RNA Binding and Chaperone Activity of the E.Coli Cold-Shock Protein CspA.” <i>Nucleic Acids Research</i>, vol. 45, no. 7, Oxford University Press, 2017, pp. 4255–68, doi:<a href=\"https://doi.org/10.1093/nar/gkx044\">10.1093/nar/gkx044</a>.","apa":"Rennella, E., Sára, T., Juen, M., Wunderlich, C., Imbert, L., Solyom, Z., … Brutscher, B. (2017). RNA binding and chaperone activity of the E.coli cold-shock protein CspA. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkx044\">https://doi.org/10.1093/nar/gkx044</a>","ista":"Rennella E, Sára T, Juen M, Wunderlich C, Imbert L, Solyom Z, Favier A, Ayala I, Weinhäupl K, Schanda P, Konrat R, Kreutz C, Brutscher B. 2017. RNA binding and chaperone activity of the E.coli cold-shock protein CspA. Nucleic Acids Research. 45(7), 4255–4268."},"intvolume":"        45","quality_controlled":"1","article_processing_charge":"No","article_type":"original","oa_version":"None","type":"journal_article","date_published":"2017-04-20T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1093/nar/gkx044","publication_status":"published","publication":"Nucleic Acids Research","date_created":"2020-09-18T10:06:34Z","page":"4255-4268"},{"abstract":[{"text":"Methyl groups are very useful probes of structure, dynamics, and interactions in protein NMR spectroscopy. In particular, methyl-directed experiments provide high sensitivity even in very large proteins, such as membrane proteins in a membrane-mimicking environment. In this chapter, we discuss the approach for labeling methyl groups in E. coli-based protein expression, as exemplified with the mitochondrial carrier GGC.","lang":"eng"}],"date_updated":"2022-08-26T09:14:20Z","extern":"1","year":"2017","day":"29","author":[{"full_name":"Kurauskas, Vilius","first_name":"Vilius","last_name":"Kurauskas"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda"},{"full_name":"Sounier, Remy","last_name":"Sounier","first_name":"Remy"}],"_id":"8450","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Springer Nature","publication_identifier":{"issn":["1064-3745","1940-6029"],"isbn":["9781493971497","9781493971510"]},"title":"Methyl-specific isotope labeling strategies for NMR studies of membrane proteins","alternative_title":["Methods in Molecular Biology"],"month":"07","doi":"10.1007/978-1-4939-7151-0_6","publication_status":"published","publication":"Membrane protein structure and function characterization","date_created":"2020-09-18T10:06:44Z","page":"109-123","type":"book_chapter","oa_version":"None","date_published":"2017-07-29T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"No","quality_controlled":"1","citation":{"apa":"Kurauskas, V., Schanda, P., &#38; Sounier, R. (2017). Methyl-specific isotope labeling strategies for NMR studies of membrane proteins. In <i>Membrane protein structure and function characterization</i> (Vol. 1635, pp. 109–123). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4939-7151-0_6\">https://doi.org/10.1007/978-1-4939-7151-0_6</a>","mla":"Kurauskas, Vilius, et al. “Methyl-Specific Isotope Labeling Strategies for NMR Studies of Membrane Proteins.” <i>Membrane Protein Structure and Function Characterization</i>, vol. 1635, Springer Nature, 2017, pp. 109–23, doi:<a href=\"https://doi.org/10.1007/978-1-4939-7151-0_6\">10.1007/978-1-4939-7151-0_6</a>.","ista":"Kurauskas V, Schanda P, Sounier R. 2017.Methyl-specific isotope labeling strategies for NMR studies of membrane proteins. In: Membrane protein structure and function characterization. Methods in Molecular Biology, vol. 1635, 109–123.","chicago":"Kurauskas, Vilius, Paul Schanda, and Remy Sounier. “Methyl-Specific Isotope Labeling Strategies for NMR Studies of Membrane Proteins.” In <i>Membrane Protein Structure and Function Characterization</i>, 1635:109–23. Springer Nature, 2017. <a href=\"https://doi.org/10.1007/978-1-4939-7151-0_6\">https://doi.org/10.1007/978-1-4939-7151-0_6</a>.","ieee":"V. Kurauskas, P. Schanda, and R. Sounier, “Methyl-specific isotope labeling strategies for NMR studies of membrane proteins,” in <i>Membrane protein structure and function characterization</i>, vol. 1635, Springer Nature, 2017, pp. 109–123.","ama":"Kurauskas V, Schanda P, Sounier R. Methyl-specific isotope labeling strategies for NMR studies of membrane proteins. In: <i>Membrane Protein Structure and Function Characterization</i>. Vol 1635. Springer Nature; 2017:109-123. doi:<a href=\"https://doi.org/10.1007/978-1-4939-7151-0_6\">10.1007/978-1-4939-7151-0_6</a>","short":"V. Kurauskas, P. Schanda, R. Sounier, in:, Membrane Protein Structure and Function Characterization, Springer Nature, 2017, pp. 109–123."},"intvolume":"      1635","volume":1635},{"_id":"8451","author":[{"last_name":"Bersch","first_name":"Beate","full_name":"Bersch, Beate"},{"full_name":"Dörr, Jonas M.","last_name":"Dörr","first_name":"Jonas M."},{"full_name":"Hessel, Audrey","first_name":"Audrey","last_name":"Hessel"},{"full_name":"Killian, J. Antoinette","first_name":"J. Antoinette","last_name":"Killian"},{"full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606"}],"day":"27","extern":"1","year":"2017","date_updated":"2021-01-12T08:19:22Z","abstract":[{"text":"The structure, dynamics, and function of membrane proteins are intimately linked to the properties of the membrane environment in which the proteins are embedded. For structural and biophysical characterization, membrane proteins generally need to be extracted from the membrane and reconstituted in a suitable membrane‐mimicking environment. Ensuring functional and structural integrity in these environments is often a major concern. The styrene/maleic acid co‐polymer has recently been shown to be able to extract lipid/membrane protein patches directly from native membranes to form nanosize discoidal proteolipid particles, also referred to as native nanodiscs. In this work, we show that high‐resolution solid‐state NMR spectra can be obtained from an integral membrane protein in native nanodiscs, as exemplified by the 2×34 kDa bacterial cation diffusion facilitator CzcD.","lang":"eng"}],"issue":"9","month":"01","title":"Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs","publication_identifier":{"issn":["1433-7851"]},"status":"public","publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_published":"2017-01-27T00:00:00Z","oa_version":"None","type":"journal_article","date_created":"2020-09-18T10:06:50Z","page":"2508-2512","publication":"Angewandte Chemie International Edition","publication_status":"published","doi":"10.1002/anie.201610441","citation":{"chicago":"Bersch, Beate, Jonas M. Dörr, Audrey Hessel, J. Antoinette Killian, and Paul Schanda. “Proton-Detected Solid-State NMR Spectroscopy of a Zinc Diffusion Facilitator Protein in Native Nanodiscs.” <i>Angewandte Chemie International Edition</i>. Wiley, 2017. <a href=\"https://doi.org/10.1002/anie.201610441\">https://doi.org/10.1002/anie.201610441</a>.","ista":"Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. 2017. Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs. Angewandte Chemie International Edition. 56(9), 2508–2512.","mla":"Bersch, Beate, et al. “Proton-Detected Solid-State NMR Spectroscopy of a Zinc Diffusion Facilitator Protein in Native Nanodiscs.” <i>Angewandte Chemie International Edition</i>, vol. 56, no. 9, Wiley, 2017, pp. 2508–12, doi:<a href=\"https://doi.org/10.1002/anie.201610441\">10.1002/anie.201610441</a>.","apa":"Bersch, B., Dörr, J. M., Hessel, A., Killian, J. A., &#38; Schanda, P. (2017). Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201610441\">https://doi.org/10.1002/anie.201610441</a>","short":"B. Bersch, J.M. Dörr, A. Hessel, J.A. Killian, P. Schanda, Angewandte Chemie International Edition 56 (2017) 2508–2512.","ieee":"B. Bersch, J. M. Dörr, A. Hessel, J. A. Killian, and P. Schanda, “Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs,” <i>Angewandte Chemie International Edition</i>, vol. 56, no. 9. Wiley, pp. 2508–2512, 2017.","ama":"Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs. <i>Angewandte Chemie International Edition</i>. 2017;56(9):2508-2512. doi:<a href=\"https://doi.org/10.1002/anie.201610441\">10.1002/anie.201610441</a>"},"quality_controlled":"1","intvolume":"        56","volume":56,"article_processing_charge":"No","article_type":"original"},{"_id":"169","author":[{"last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D"},{"first_name":"Vinay","last_name":"Kumaraswamy","full_name":"Kumaraswamy, Vinay"},{"full_name":"Steiner, Rapael","last_name":"Steiner","first_name":"Rapael"}],"extern":"1","year":"2017","day":"19","arxiv":1,"abstract":[{"lang":"eng","text":"We show that a twisted variant of Linnik’s conjecture on sums of Kloosterman sums leads to an optimal covering exponent for S3."}],"date_updated":"2021-01-12T06:52:32Z","month":"06","oa":1,"title":"Twisted Linnik implies optimal covering exponent for S3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","status":"public","date_published":"2017-06-19T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"None","type":"journal_article","publication":"International Mathematics Research Notices","date_created":"2018-12-11T11:44:59Z","doi":"10.1093/imrn/rnx116","publication_status":"published","quality_controlled":"1","citation":{"ieee":"T. D. Browning, V. Kumaraswamy, and R. Steiner, “Twisted Linnik implies optimal covering exponent for S3,” <i>International Mathematics Research Notices</i>. Oxford University Press, 2017.","ama":"Browning TD, Kumaraswamy V, Steiner R. Twisted Linnik implies optimal covering exponent for S3. <i>International Mathematics Research Notices</i>. 2017. doi:<a href=\"https://doi.org/10.1093/imrn/rnx116\">10.1093/imrn/rnx116</a>","short":"T.D. Browning, V. Kumaraswamy, R. Steiner, International Mathematics Research Notices (2017).","apa":"Browning, T. D., Kumaraswamy, V., &#38; Steiner, R. (2017). Twisted Linnik implies optimal covering exponent for S3. <i>International Mathematics Research Notices</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/imrn/rnx116\">https://doi.org/10.1093/imrn/rnx116</a>","ista":"Browning TD, Kumaraswamy V, Steiner R. 2017. Twisted Linnik implies optimal covering exponent for S3. International Mathematics Research Notices.","mla":"Browning, Timothy D., et al. “Twisted Linnik Implies Optimal Covering Exponent for S3.” <i>International Mathematics Research Notices</i>, Oxford University Press, 2017, doi:<a href=\"https://doi.org/10.1093/imrn/rnx116\">10.1093/imrn/rnx116</a>.","chicago":"Browning, Timothy D, Vinay Kumaraswamy, and Rapael Steiner. “Twisted Linnik Implies Optimal Covering Exponent for S3.” <i>International Mathematics Research Notices</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/imrn/rnx116\">https://doi.org/10.1093/imrn/rnx116</a>."},"external_id":{"arxiv":["1609.06097"]},"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.06097"}],"publist_id":"7752"},{"external_id":{"arxiv":["1509.07744"]},"quality_controlled":"1","citation":{"ieee":"T. D. Browning and D. Schindler, “Strong approximation and a conjecture of Harpaz and Wittenberg,” <i>International Mathematics Research Notices</i>. Oxford University Press, 2017.","ama":"Browning TD, Schindler D. Strong approximation and a conjecture of Harpaz and Wittenberg. <i>International Mathematics Research Notices</i>. 2017. doi:<a href=\"https://doi.org/10.1093/imrn/rnx252\">10.1093/imrn/rnx252</a>","short":"T.D. Browning, D. Schindler, International Mathematics Research Notices (2017).","mla":"Browning, Timothy D., and Damaris Schindler. “Strong Approximation and a Conjecture of Harpaz and Wittenberg.” <i>International Mathematics Research Notices</i>, Oxford University Press, 2017, doi:<a href=\"https://doi.org/10.1093/imrn/rnx252\">10.1093/imrn/rnx252</a>.","apa":"Browning, T. D., &#38; Schindler, D. (2017). Strong approximation and a conjecture of Harpaz and Wittenberg. <i>International Mathematics Research Notices</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/imrn/rnx252\">https://doi.org/10.1093/imrn/rnx252</a>","ista":"Browning TD, Schindler D. 2017. Strong approximation and a conjecture of Harpaz and Wittenberg. International Mathematics Research Notices.","chicago":"Browning, Timothy D, and Damaris Schindler. “Strong Approximation and a Conjecture of Harpaz and Wittenberg.” <i>International Mathematics Research Notices</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/imrn/rnx252\">https://doi.org/10.1093/imrn/rnx252</a>."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1509.07744"}],"publist_id":"7749","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2017-10-30T00:00:00Z","type":"journal_article","oa_version":"None","date_created":"2018-12-11T11:45:00Z","publication":"International Mathematics Research Notices","publication_status":"published","doi":"10.1093/imrn/rnx252","month":"10","title":"Strong approximation and a conjecture of Harpaz and Wittenberg","oa":1,"status":"public","publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"172","author":[{"last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D"},{"full_name":"Schindler, Damaris","last_name":"Schindler","first_name":"Damaris"}],"day":"30","extern":"1","year":"2017","date_updated":"2021-01-12T06:52:45Z","arxiv":1,"abstract":[{"text":"We study strong approximation for some algebraic varieties over ℚ which are defined using norm forms. This allows us to confirm a special case of a conjecture due to Harpaz and Wittenberg.","lang":"eng"}]},{"publication_status":"published","doi":"10.1111/sjos.12251","date_published":"2017-06-01T00:00:00Z","oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.1242"}],"citation":{"short":"A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian Journal of Statistics 44 (2017) 285–306.","ieee":"A. Martin Del Campo Sanchez, S. A. Cepeda Humerez, and C. Uhler, “Exact goodness-of-fit testing for the Ising model,” <i>Scandinavian Journal of Statistics</i>, vol. 44, no. 2. Wiley-Blackwell, pp. 285–306, 2017.","ama":"Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. Exact goodness-of-fit testing for the Ising model. <i>Scandinavian Journal of Statistics</i>. 2017;44(2):285-306. doi:<a href=\"https://doi.org/10.1111/sjos.12251\">10.1111/sjos.12251</a>","mla":"Martin Del Campo Sanchez, Abraham, et al. “Exact Goodness-of-Fit Testing for the Ising Model.” <i>Scandinavian Journal of Statistics</i>, vol. 44, no. 2, Wiley-Blackwell, 2017, pp. 285–306, doi:<a href=\"https://doi.org/10.1111/sjos.12251\">10.1111/sjos.12251</a>.","ista":"Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. 2017. Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. 44(2), 285–306.","apa":"Martin Del Campo Sanchez, A., Cepeda Humerez, S. A., &#38; Uhler, C. (2017). Exact goodness-of-fit testing for the Ising model. <i>Scandinavian Journal of Statistics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/sjos.12251\">https://doi.org/10.1111/sjos.12251</a>","chicago":"Martin Del Campo Sanchez, Abraham, Sarah A Cepeda Humerez, and Caroline Uhler. “Exact Goodness-of-Fit Testing for the Ising Model.” <i>Scandinavian Journal of Statistics</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/sjos.12251\">https://doi.org/10.1111/sjos.12251</a>."},"intvolume":"        44","year":"2017","date_updated":"2023-09-19T15:13:27Z","issue":"2","abstract":[{"text":"The Ising model is one of the simplest and most famous models of interacting systems. It was originally proposed to model ferromagnetic interactions in statistical physics and is now widely used to model spatial processes in many areas such as ecology, sociology, and genetics, usually without testing its goodness-of-fit. Here, we propose an exact goodness-of-fit test for the finite-lattice Ising model. The theory of Markov bases has been developed in algebraic statistics for exact goodness-of-fit testing using a Monte Carlo approach. However, this beautiful theory has fallen short of its promise for applications, because finding a Markov basis is usually computationally intractable. We develop a Monte Carlo method for exact goodness-of-fit testing for the Ising model which avoids computing a Markov basis and also leads to a better connectivity of the Markov chain and hence to a faster convergence. We show how this method can be applied to analyze the spatial organization of receptors on the cell membrane.","lang":"eng"}],"arxiv":1,"_id":"2016","oa":1,"publication_identifier":{"issn":["03036898"]},"status":"public","month":"06","date_created":"2018-12-11T11:55:13Z","page":"285 - 306","publication":"Scandinavian Journal of Statistics","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"type":"journal_article","publist_id":"5060","article_processing_charge":"No","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6473"}]},"external_id":{"arxiv":["1410.1242"],"isi":["000400985000001"]},"volume":44,"quality_controlled":"1","day":"01","isi":1,"author":[{"full_name":"Martin Del Campo Sanchez, Abraham","first_name":"Abraham","last_name":"Martin Del Campo Sanchez"},{"full_name":"Cepeda Humerez, Sarah A","first_name":"Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","last_name":"Cepeda Humerez"},{"full_name":"Uhler, Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","first_name":"Caroline","orcid":"0000-0002-7008-0216"}],"title":"Exact goodness-of-fit testing for the Ising model","publisher":"Wiley-Blackwell","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"month":"10","status":"public","publication_identifier":{"issn":["2663-337X"]},"oa":1,"_id":"202","date_updated":"2023-09-15T12:04:56Z","abstract":[{"lang":"eng","text":"Restriction-modification (RM) represents the simplest and possibly the most widespread mechanism of self/non-self discrimination in nature. In order to provide bacteria with immunity against bacteriophages and other parasitic genetic elements, RM systems rely on a balance between two enzymes: the restriction enzyme, which cleaves non-self DNA at specific restriction sites, and the modification enzyme, which tags the host’s DNA as self and thus protects it from cleavage. In this thesis, I use population and single-cell level experiments in combination with mathematical modeling to study different aspects of the interplay between RM systems, bacteria and bacteriophages. First, I analyze how mutations in phage restriction sites affect the probability of phage escape – an inherently stochastic process, during which phages accidently get modified instead of restricted. Next, I use single-cell experiments to show that RM systems can, with a low probability, attack the genome of their bacterial host and that this primitive form of autoimmunity leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally, I investigate the nature of interactions between bacteria, RM systems and temperate bacteriophages to find that, as a consequence of phage escape and its impact on population dynamics, RM systems can promote acquisition of symbiotic bacteriophages, rather than limit it. The results presented here uncover new fundamental biological properties of RM systems and highlight their importance in the ecology and evolution of bacteria, bacteriophages and their interactions."}],"year":"2017","citation":{"ista":"Pleska M. 2017. Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria.","apa":"Pleska, M. (2017). <i>Biology of restriction-modification systems at the single-cell and population level</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">https://doi.org/10.15479/AT:ISTA:th_916</a>","mla":"Pleska, Maros. <i>Biology of Restriction-Modification Systems at the Single-Cell and Population Level</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">10.15479/AT:ISTA:th_916</a>.","chicago":"Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell and Population Level.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">https://doi.org/10.15479/AT:ISTA:th_916</a>.","ama":"Pleska M. Biology of restriction-modification systems at the single-cell and population level. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">10.15479/AT:ISTA:th_916</a>","ieee":"M. Pleska, “Biology of restriction-modification systems at the single-cell and population level,” Institute of Science and Technology Austria, 2017.","short":"M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell and Population Level, Institute of Science and Technology Austria, 2017."},"file_date_updated":"2020-07-14T12:45:24Z","ddc":["576","579"],"oa_version":"Published Version","date_published":"2017-10-01T00:00:00Z","publication_status":"published","doi":"10.15479/AT:ISTA:th_916","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"supervisor":[{"full_name":"Guet, Calin C","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet"}],"publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Biology of restriction-modification systems at the single-cell and population level","project":[{"name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)","grant_number":"24210","_id":"251D65D8-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Pleska, Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","last_name":"Pleska","first_name":"Maros","orcid":"0000-0001-7460-7479"}],"file":[{"access_level":"open_access","creator":"system","checksum":"33cfb59674e91f82e3738396d3fb3776","file_id":"4710","date_created":"2018-12-12T10:08:48Z","file_name":"IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf","date_updated":"2020-07-14T12:45:24Z","file_size":18569590,"content_type":"application/pdf","relation":"main_file"},{"file_size":2801649,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","date_created":"2019-04-05T08:33:14Z","date_updated":"2020-07-14T12:45:24Z","file_name":"2017_Pleska_Maros_Thesis.docx","access_level":"closed","file_id":"6204","creator":"dernst","checksum":"dcc239968decb233e7f98cf1083d8c26"}],"acknowledgement":"During my PhD studies, I received help from many people, all of which unfortunately cannot be listed here. I thank them deeply and hope that I never made them regret their kindness.\r\nI would like to express my deepest gratitude to Călin Guet, who went far beyond his responsibilities as an advisor and was to me also a great mentor and a friend. Călin never questioned my potential or lacked compassion and I cannot thank him enough for cultivating in me an independent scientist. I was amazed by his ability to recognize the most fascinating scientific problems in objects of study that others would find mundane. I hope I adopted at least a fraction of this ability.\r\nI will be forever grateful to Bruce Levin for all his support and especially for giving me the best possible example of how one can practice excellent science with humor and style. Working with Bruce was a true privilege.\r\nI thank Jonathan Bollback and Gašper Tkačik for serving in my PhD committee and the Austrian Academy of Science for funding my PhD research via the DOC fellowship.\r\nI thank all our lab members: Tobias Bergmiller for his guidance, especially in the first years of my research, and for being a good friend throughout; Remy Chait for staying in the lab at unreasonable hours and for the good laughs at bad jokes we shared; Anna Staron for supportively listening to my whines whenever I had to run a gel; Magdalena Steinrück for her pioneering work in the lab; Kathrin Tomasek for keeping the entropic forces in check and for her FACS virtuosity; Isabella Tomanek for always being nice to me, no matter how much bench space I took from her.\r\nI thank all my collaborators: Reiko Okura and Yuichi Wakamoto for performing and analyzing the microfluidic experiments; Long Qian and Edo Kussell for their bioinformatics analysis; Dominik Refardt for the λ kan phage; Moritz for his help with the mathematical modeling. I thank Fabienne Jesse for her tireless editorial work on all our manuscripts.\r\nFinally, I would like to thank my family and especially my wife Edita, who sacrificed a lot so that I can pursue my goals and dreams.\r\n","day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1243"},{"relation":"part_of_dissertation","status":"public","id":"561"},{"status":"public","relation":"part_of_dissertation","id":"457"}]},"publist_id":"7711","pubrep_id":"916","article_processing_charge":"No","type":"dissertation","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"}],"has_accepted_license":"1","page":"126","date_created":"2018-12-11T11:45:10Z"},{"year":"2017","abstract":[{"text":"We report a direct-numerical-simulation study of the Taylor-Couette flow in the quasi-Keplerian regime at shear Reynolds numbers up to (105). Quasi-Keplerian rotating flow has been investigated for decades as a simplified model system to study the origin of turbulence in accretion disks that is not fully understood. The flow in this study is axially periodic and thus the experimental end-wall effects on the stability of the flow are avoided. Using optimal linear perturbations as initial conditions, our simulations find no sustained turbulence: the strong initial perturbations distort the velocity profile and trigger turbulence that eventually decays.","lang":"eng"}],"issue":"4","date_updated":"2021-01-12T08:08:15Z","_id":"662","article_number":"044107","oa":1,"publication_identifier":{"issn":["10706631"]},"status":"public","month":"04","doi":"10.1063/1.4981525","publication_status":"published","date_published":"2017-04-01T00:00:00Z","oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1703.01714","open_access":"1"}],"scopus_import":1,"citation":{"chicago":"Shi, Liang, Björn Hof, Markus Rampp, and Marc Avila. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” <i>Physics of Fluids</i>. American Institute of Physics, 2017. <a href=\"https://doi.org/10.1063/1.4981525\">https://doi.org/10.1063/1.4981525</a>.","mla":"Shi, Liang, et al. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” <i>Physics of Fluids</i>, vol. 29, no. 4, 044107, American Institute of Physics, 2017, doi:<a href=\"https://doi.org/10.1063/1.4981525\">10.1063/1.4981525</a>.","apa":"Shi, L., Hof, B., Rampp, M., &#38; Avila, M. (2017). Hydrodynamic turbulence in quasi Keplerian rotating flows. <i>Physics of Fluids</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4981525\">https://doi.org/10.1063/1.4981525</a>","ista":"Shi L, Hof B, Rampp M, Avila M. 2017. Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. 29(4), 044107.","short":"L. Shi, B. Hof, M. Rampp, M. Avila, Physics of Fluids 29 (2017).","ama":"Shi L, Hof B, Rampp M, Avila M. Hydrodynamic turbulence in quasi Keplerian rotating flows. <i>Physics of Fluids</i>. 2017;29(4). doi:<a href=\"https://doi.org/10.1063/1.4981525\">10.1063/1.4981525</a>","ieee":"L. Shi, B. Hof, M. Rampp, and M. Avila, “Hydrodynamic turbulence in quasi Keplerian rotating flows,” <i>Physics of Fluids</i>, vol. 29, no. 4. American Institute of Physics, 2017."},"intvolume":"        29","day":"01","author":[{"full_name":"Shi, Liang","last_name":"Shi","first_name":"Liang"},{"full_name":"Hof, Björn","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"},{"full_name":"Rampp, Markus","last_name":"Rampp","first_name":"Markus"},{"full_name":"Avila, Marc","last_name":"Avila","first_name":"Marc"}],"project":[{"_id":"2511D90C-B435-11E9-9278-68D0E5697425","grant_number":"SFB 963  TP A8","name":"Astrophysical instability of currents and turbulences"}],"title":"Hydrodynamic turbulence in quasi Keplerian rotating flows","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"American Institute of Physics","publication":"Physics of Fluids","date_created":"2018-12-11T11:47:47Z","department":[{"_id":"BjHo"}],"language":[{"iso":"eng"}],"type":"journal_article","publist_id":"7072","quality_controlled":"1","volume":29},{"_id":"663","year":"2017","date_updated":"2021-01-12T08:08:17Z","abstract":[{"lang":"eng","text":"In this paper, we propose an approach to automatically compute invariant clusters for nonlinear semialgebraic hybrid systems. An invariant cluster for an ordinary differential equation (ODE) is a multivariate polynomial invariant g(u→, x→) = 0, parametric in u→, which can yield an infinite number of concrete invariants by assigning different values to u→ so that every trajectory of the system can be overapproximated precisely by the intersection of a group of concrete invariants. For semialgebraic systems, which involve ODEs with multivariate polynomial right-hand sides, given a template multivariate polynomial g(u→, x→), an invariant cluster can be obtained by first computing the remainder of the Lie derivative of g(u→, x→) divided by g(u→, x→) and then solving the system of polynomial equations obtained from the coefficients of the remainder. Based on invariant clusters and sum-of-squares (SOS) programming, we present a new method for the safety verification of hybrid systems. Experiments on nonlinear benchmark systems from biology and control theory show that our approach is efficient. "}],"month":"04","publication_identifier":{"isbn":["978-145034590-3"]},"oa":1,"status":"public","date_published":"2017-04-01T00:00:00Z","oa_version":"Submitted Version","publication_status":"published","conference":{"name":"HSCC: Hybrid Systems Computation and Control ","start_date":"2017-04-18","location":"Pittsburgh, PA, United States","end_date":"2017-04-20"},"doi":"10.1145/3049797.3049814","citation":{"ama":"Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. Safety verification of nonlinear hybrid systems based on invariant clusters. In: <i>Proceedings of the 20th International Conference on Hybrid Systems</i>. ACM; 2017:163-172. doi:<a href=\"https://doi.org/10.1145/3049797.3049814\">10.1145/3049797.3049814</a>","ieee":"H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, and T. A. Henzinger, “Safety verification of nonlinear hybrid systems based on invariant clusters,” in <i>Proceedings of the 20th International Conference on Hybrid Systems</i>, Pittsburgh, PA, United States, 2017, pp. 163–172.","short":"H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, T.A. Henzinger, in:, Proceedings of the 20th International Conference on Hybrid Systems, ACM, 2017, pp. 163–172.","chicago":"Kong, Hui, Sergiy Bogomolov, Christian Schilling, Yu Jiang, and Thomas A Henzinger. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant Clusters.” In <i>Proceedings of the 20th International Conference on Hybrid Systems</i>, 163–72. ACM, 2017. <a href=\"https://doi.org/10.1145/3049797.3049814\">https://doi.org/10.1145/3049797.3049814</a>.","mla":"Kong, Hui, et al. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant Clusters.” <i>Proceedings of the 20th International Conference on Hybrid Systems</i>, ACM, 2017, pp. 163–72, doi:<a href=\"https://doi.org/10.1145/3049797.3049814\">10.1145/3049797.3049814</a>.","ista":"Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. 2017. Safety verification of nonlinear hybrid systems based on invariant clusters. Proceedings of the 20th International Conference on Hybrid Systems. HSCC: Hybrid Systems Computation and Control , 163–172.","apa":"Kong, H., Bogomolov, S., Schilling, C., Jiang, Y., &#38; Henzinger, T. A. (2017). Safety verification of nonlinear hybrid systems based on invariant clusters. In <i>Proceedings of the 20th International Conference on Hybrid Systems</i> (pp. 163–172). Pittsburgh, PA, United States: ACM. <a href=\"https://doi.org/10.1145/3049797.3049814\">https://doi.org/10.1145/3049797.3049814</a>"},"ddc":["000"],"file_date_updated":"2020-07-14T12:47:34Z","scopus_import":1,"file":[{"creator":"system","file_id":"4873","checksum":"b7667434cbf5b5f0ade3bea1dbe5bf63","access_level":"open_access","date_updated":"2020-07-14T12:47:34Z","file_name":"IST-2017-817-v1+1_p163-kong.pdf","date_created":"2018-12-12T10:11:20Z","relation":"main_file","content_type":"application/pdf","file_size":1650530}],"author":[{"id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","last_name":"Kong","first_name":"Hui","orcid":"0000-0002-3066-6941","full_name":"Kong, Hui"},{"full_name":"Bogomolov, Sergiy","first_name":"Sergiy","orcid":"0000-0002-0686-0365","last_name":"Bogomolov"},{"last_name":"Schilling","first_name":"Christian","full_name":"Schilling, Christian"},{"first_name":"Yu","last_name":"Jiang","full_name":"Jiang, Yu"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"}],"day":"01","title":"Safety verification of nonlinear hybrid systems based on invariant clusters","publisher":"ACM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"type":"conference","date_created":"2018-12-11T11:47:47Z","page":"163 - 172","publication":"Proceedings of the 20th International Conference on Hybrid Systems","has_accepted_license":"1","quality_controlled":"1","publist_id":"7067","pubrep_id":"817"},{"year":"2017","day":"18","issue":"4","abstract":[{"lang":"eng","text":"Immune cells communicate using cytokine signals, but the quantitative rules of this communication aren't clear. In this issue of Immunity, Oyler-Yaniv et al. (2017) suggest that the distribution of a cytokine within a lymphatic organ is primarily governed by the local density of cells consuming it."}],"date_updated":"2024-03-25T23:30:05Z","_id":"664","author":[{"id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","last_name":"Assen","orcid":"0000-0003-3470-6119","first_name":"Frank P","full_name":"Assen, Frank P"},{"full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["10747613"]},"title":"The dynamic cytokine niche","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Cell Press","month":"04","publication":"Immunity","page":"519 - 520","date_created":"2018-12-11T11:47:47Z","doi":"10.1016/j.immuni.2017.04.006","publication_status":"published","department":[{"_id":"MiSi"}],"date_published":"2017-04-18T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"None","type":"journal_article","publist_id":"7065","scopus_import":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6947"}]},"volume":46,"citation":{"chicago":"Assen, Frank P, and Michael K Sixt. “The Dynamic Cytokine Niche.” <i>Immunity</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.immuni.2017.04.006\">https://doi.org/10.1016/j.immuni.2017.04.006</a>.","apa":"Assen, F. P., &#38; Sixt, M. K. (2017). The dynamic cytokine niche. <i>Immunity</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.immuni.2017.04.006\">https://doi.org/10.1016/j.immuni.2017.04.006</a>","mla":"Assen, Frank P., and Michael K. Sixt. “The Dynamic Cytokine Niche.” <i>Immunity</i>, vol. 46, no. 4, Cell Press, 2017, pp. 519–20, doi:<a href=\"https://doi.org/10.1016/j.immuni.2017.04.006\">10.1016/j.immuni.2017.04.006</a>.","ista":"Assen FP, Sixt MK. 2017. The dynamic cytokine niche. Immunity. 46(4), 519–520.","short":"F.P. Assen, M.K. Sixt, Immunity 46 (2017) 519–520.","ama":"Assen FP, Sixt MK. The dynamic cytokine niche. <i>Immunity</i>. 2017;46(4):519-520. doi:<a href=\"https://doi.org/10.1016/j.immuni.2017.04.006\">10.1016/j.immuni.2017.04.006</a>","ieee":"F. P. Assen and M. K. Sixt, “The dynamic cytokine niche,” <i>Immunity</i>, vol. 46, no. 4. Cell Press, pp. 519–520, 2017."},"intvolume":"        46","quality_controlled":"1"},{"date_created":"2018-12-11T11:47:48Z","page":"311 - 315","publication":"Science","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"Bio"}],"publist_id":"7064","article_type":"original","article_processing_charge":"No","quality_controlled":"1","volume":356,"related_material":{"record":[{"status":"public","relation":"popular_science","id":"5560"}]},"day":"21","project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"author":[{"first_name":"Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias"},{"first_name":"Anna M","orcid":"0000-0003-2912-6769","id":"2B8A40DA-F248-11E8-B48F-1D18A9856A87","last_name":"Andersson","full_name":"Andersson, Anna M"},{"full_name":"Tomasek, Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","first_name":"Kathrin","orcid":"0000-0003-3768-877X"},{"first_name":"Enrique","last_name":"Balleza","full_name":"Balleza, Enrique"},{"first_name":"Daniel","last_name":"Kiviet","full_name":"Kiviet, Daniel"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper","full_name":"Tkacik, Gasper"},{"full_name":"Guet, Calin C","first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"publisher":"American Association for the Advancement of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity","publication_status":"published","doi":"10.1126/science.aaf4762","oa_version":"None","date_published":"2017-04-21T00:00:00Z","scopus_import":1,"intvolume":"       356","citation":{"chicago":"Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” <i>Science</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/science.aaf4762\">https://doi.org/10.1126/science.aaf4762</a>.","apa":"Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aaf4762\">https://doi.org/10.1126/science.aaf4762</a>","mla":"Bergmiller, Tobias, et al. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” <i>Science</i>, vol. 356, no. 6335, American Association for the Advancement of Science, 2017, pp. 311–15, doi:<a href=\"https://doi.org/10.1126/science.aaf4762\">10.1126/science.aaf4762</a>.","ista":"Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik G, Guet CC. 2017. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 356(6335), 311–315.","short":"T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, Science 356 (2017) 311–315.","ieee":"T. Bergmiller <i>et al.</i>, “Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity,” <i>Science</i>, vol. 356, no. 6335. American Association for the Advancement of Science, pp. 311–315, 2017.","ama":"Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. <i>Science</i>. 2017;356(6335):311-315. doi:<a href=\"https://doi.org/10.1126/science.aaf4762\">10.1126/science.aaf4762</a>"},"date_updated":"2024-02-21T13:49:00Z","issue":"6335","abstract":[{"text":"The molecular mechanisms underlying phenotypic variation in isogenic bacterial populations remain poorly understood.We report that AcrAB-TolC, the main multidrug efflux pump of Escherichia coli, exhibits a strong partitioning bias for old cell poles by a segregation mechanism that is mediated by ternary AcrAB-TolC complex formation. Mother cells inheriting old poles are phenotypically distinct and display increased drug efflux activity relative to daughters. Consequently, we find systematic and long-lived growth differences between mother and daughter cells in the presence of subinhibitory drug concentrations. A simple model for biased partitioning predicts a population structure of long-lived and highly heterogeneous phenotypes. This straightforward mechanism of generating sustained growth rate differences at subinhibitory antibiotic concentrations has implications for understanding the emergence of multidrug resistance in bacteria.","lang":"eng"}],"year":"2017","_id":"665","status":"public","publication_identifier":{"issn":["00368075"]},"month":"04"},{"type":"journal_article","department":[{"_id":"ToBo"},{"_id":"GaTk"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Cell Systems","page":"393 - 403","date_created":"2018-12-11T11:47:48Z","quality_controlled":"1","volume":4,"related_material":{"record":[{"id":"818","status":"public","relation":"dissertation_contains"}]},"pubrep_id":"901","article_processing_charge":"Yes (in subscription journal)","publist_id":"7061","author":[{"first_name":"Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87","last_name":"Mitosch","full_name":"Mitosch, Karin"},{"last_name":"Rieckh","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","full_name":"Rieckh, Georg"},{"first_name":"Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","full_name":"Bollenbach, Tobias"}],"project":[{"call_identifier":"FP7","name":"Optimality principles in responses to antibiotics","grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"},{"name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22"},{"grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth"}],"file":[{"date_created":"2018-12-12T10:13:54Z","date_updated":"2020-07-14T12:47:35Z","file_name":"IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf","access_level":"open_access","creator":"system","checksum":"04ff20011c3d9a601c514aa999a5fe1a","file_id":"5041","file_size":2438660,"content_type":"application/pdf","relation":"main_file"}],"day":"26","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Cell Press","title":"Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment","oa_version":"Published Version","date_published":"2017-04-26T00:00:00Z","doi":"10.1016/j.cels.2017.03.001","publication_status":"published","citation":{"ista":"Mitosch K, Rieckh G, Bollenbach MT. 2017. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 4(4), 393–403.","mla":"Mitosch, Karin, et al. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” <i>Cell Systems</i>, vol. 4, no. 4, Cell Press, 2017, pp. 393–403, doi:<a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">10.1016/j.cels.2017.03.001</a>.","apa":"Mitosch, K., Rieckh, G., &#38; Bollenbach, M. T. (2017). Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. <i>Cell Systems</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">https://doi.org/10.1016/j.cels.2017.03.001</a>","chicago":"Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” <i>Cell Systems</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">https://doi.org/10.1016/j.cels.2017.03.001</a>.","ama":"Mitosch K, Rieckh G, Bollenbach MT. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. <i>Cell Systems</i>. 2017;4(4):393-403. doi:<a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">10.1016/j.cels.2017.03.001</a>","ieee":"K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment,” <i>Cell Systems</i>, vol. 4, no. 4. Cell Press, pp. 393–403, 2017.","short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403."},"intvolume":"         4","scopus_import":1,"file_date_updated":"2020-07-14T12:47:35Z","ddc":["576","610"],"_id":"666","issue":"4","abstract":[{"text":"Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to “cross-protect” bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors.","lang":"eng"}],"date_updated":"2023-09-07T12:00:25Z","year":"2017","month":"04","ec_funded":1,"status":"public","publication_identifier":{"issn":["24054712"]},"oa":1},{"date_published":"2017-04-26T00:00:00Z","department":[{"_id":"GaNo"}],"language":[{"iso":"eng"}],"type":"journal_article","oa_version":"None","publication":"Science Translational Medicine","date_created":"2018-12-11T11:47:48Z","doi":"10.1126/scitranslmed.aan2786","publication_status":"published","citation":{"ama":"Novarino G. The antisocial side of antibiotics. <i>Science Translational Medicine</i>. 2017;9(387). doi:<a href=\"https://doi.org/10.1126/scitranslmed.aan2786\">10.1126/scitranslmed.aan2786</a>","ieee":"G. Novarino, “The antisocial side of antibiotics,” <i>Science Translational Medicine</i>, vol. 9, no. 387. American Association for the Advancement of Science, 2017.","short":"G. Novarino, Science Translational Medicine 9 (2017).","apa":"Novarino, G. (2017). The antisocial side of antibiotics. <i>Science Translational Medicine</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scitranslmed.aan2786\">https://doi.org/10.1126/scitranslmed.aan2786</a>","ista":"Novarino G. 2017. The antisocial side of antibiotics. Science Translational Medicine. 9(387), 2786.","mla":"Novarino, Gaia. “The Antisocial Side of Antibiotics.” <i>Science Translational Medicine</i>, vol. 9, no. 387, 2786, American Association for the Advancement of Science, 2017, doi:<a href=\"https://doi.org/10.1126/scitranslmed.aan2786\">10.1126/scitranslmed.aan2786</a>.","chicago":"Novarino, Gaia. “The Antisocial Side of Antibiotics.” <i>Science Translational Medicine</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/scitranslmed.aan2786\">https://doi.org/10.1126/scitranslmed.aan2786</a>."},"volume":9,"intvolume":"         9","quality_controlled":"1","scopus_import":1,"publist_id":"7060","_id":"667","author":[{"full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia"}],"article_number":"2786","year":"2017","day":"26","abstract":[{"lang":"eng","text":"Perinatal exposure to penicillin may result in longlasting gut and behavioral changes."}],"issue":"387","date_updated":"2021-01-12T08:08:30Z","month":"04","publication_identifier":{"issn":["19466234"]},"title":"The antisocial side of antibiotics","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"American Association for the Advancement of Science","status":"public"},{"conference":{"end_date":"2017-12-08","location":"Singapore, Singapore","start_date":"2017-12-04","name":"GLOBECOM: Global Communications Conference"},"publication_status":"published","doi":"10.1109/glocom.2017.8254940","date_created":"2019-07-24T13:55:25Z","page":"1-7","publication":"2017 IEEE Global Communications Conference","type":"conference","oa_version":"Preprint","language":[{"iso":"eng"}],"date_published":"2017-12-01T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1705.05497","open_access":"1"}],"external_id":{"arxiv":["1705.05497"]},"citation":{"chicago":"Hashemi, Seyyed Ali, Marco Mondelli, Hamed Hassani, Ruediger Urbanke, and Warren Gross. “Partitioned List Decoding of Polar Codes: Analysis and Improvement of Finite Length Performance.” In <i>2017 IEEE Global Communications Conference</i>, 1–7. IEEE, 2017. <a href=\"https://doi.org/10.1109/glocom.2017.8254940\">https://doi.org/10.1109/glocom.2017.8254940</a>.","apa":"Hashemi, S. A., Mondelli, M., Hassani, H., Urbanke, R., &#38; Gross, W. (2017). Partitioned list decoding of polar codes: Analysis and improvement of finite length performance. In <i>2017 IEEE Global Communications Conference</i> (pp. 1–7). Singapore, Singapore: IEEE. <a href=\"https://doi.org/10.1109/glocom.2017.8254940\">https://doi.org/10.1109/glocom.2017.8254940</a>","ista":"Hashemi SA, Mondelli M, Hassani H, Urbanke R, Gross W. 2017. Partitioned list decoding of polar codes: Analysis and improvement of finite length performance. 2017 IEEE Global Communications Conference. GLOBECOM: Global Communications Conference, 1–7.","mla":"Hashemi, Seyyed Ali, et al. “Partitioned List Decoding of Polar Codes: Analysis and Improvement of Finite Length Performance.” <i>2017 IEEE Global Communications Conference</i>, IEEE, 2017, pp. 1–7, doi:<a href=\"https://doi.org/10.1109/glocom.2017.8254940\">10.1109/glocom.2017.8254940</a>.","ama":"Hashemi SA, Mondelli M, Hassani H, Urbanke R, Gross W. Partitioned list decoding of polar codes: Analysis and improvement of finite length performance. In: <i>2017 IEEE Global Communications Conference</i>. IEEE; 2017:1-7. doi:<a href=\"https://doi.org/10.1109/glocom.2017.8254940\">10.1109/glocom.2017.8254940</a>","ieee":"S. A. Hashemi, M. Mondelli, H. Hassani, R. Urbanke, and W. Gross, “Partitioned list decoding of polar codes: Analysis and improvement of finite length performance,” in <i>2017 IEEE Global Communications Conference</i>, Singapore, Singapore, 2017, pp. 1–7.","short":"S.A. Hashemi, M. Mondelli, H. Hassani, R. Urbanke, W. Gross, in:, 2017 IEEE Global Communications Conference, IEEE, 2017, pp. 1–7."},"quality_controlled":"1","date_updated":"2021-01-12T08:08:34Z","arxiv":1,"abstract":[{"text":"Polar codes represent one of the major recent breakthroughs in coding theory and, because of their attractive features, they have been selected for the incoming 5G standard. As such, a lot of attention has been devoted to the development of decoding algorithms with good error performance and efficient hardware implementation. One of the leading candidates in this regard is represented by successive-cancellation list (SCL) decoding. However, its hardware implementation requires a large amount of memory. Recently, a partitioned SCL (PSCL) decoder has been proposed to significantly reduce the memory consumption [1]. In this paper, we examine the paradigm of PSCL decoding from both theoretical and practical standpoints: (i) by changing the construction of the code, we are able to improve the performance at no additional computational, latency or memory cost, (ii) we present an optimal scheme to allocate cyclic redundancy checks (CRCs), and (iii) we provide an upper bound on the list size that allows MAP performance.","lang":"eng"}],"day":"01","extern":"1","year":"2017","author":[{"first_name":"Seyyed Ali","last_name":"Hashemi","full_name":"Hashemi, Seyyed Ali"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","orcid":"0000-0002-3242-7020","first_name":"Marco","full_name":"Mondelli, Marco"},{"full_name":"Hassani, Hamed","first_name":"Hamed","last_name":"Hassani"},{"full_name":"Urbanke, Ruediger","first_name":"Ruediger","last_name":"Urbanke"},{"full_name":"Gross, Warren","first_name":"Warren","last_name":"Gross"}],"_id":"6679","status":"public","publisher":"IEEE","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Partitioned list decoding of polar codes: Analysis and improvement of finite length performance","oa":1,"month":"12"},{"volume":292,"quality_controlled":"1","publist_id":"7059","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"MiSi"}],"type":"journal_article","date_created":"2018-12-11T11:47:49Z","page":"7258 - 7273","publication":"Journal of Biological Chemistry","has_accepted_license":"1","title":"Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion","publisher":"American Society for Biochemistry and Molecular Biology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":5647880,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6971","creator":"dernst","checksum":"d488162874326a4bb056065fa549dc4a","date_created":"2019-10-24T15:25:42Z","file_name":"2017_JBC_Horsthemke.pdf","date_updated":"2020-07-14T12:47:37Z"}],"author":[{"full_name":"Horsthemke, Markus","last_name":"Horsthemke","first_name":"Markus"},{"first_name":"Anne","last_name":"Bachg","full_name":"Bachg, Anne"},{"last_name":"Groll","first_name":"Katharina","full_name":"Groll, Katharina"},{"first_name":"Sven","last_name":"Moyzio","full_name":"Moyzio, Sven"},{"full_name":"Müther, Barbara","last_name":"Müther","first_name":"Barbara"},{"full_name":"Hemkemeyer, Sandra","last_name":"Hemkemeyer","first_name":"Sandra"},{"full_name":"Wedlich Söldner, Roland","first_name":"Roland","last_name":"Wedlich Söldner"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K"},{"first_name":"Sebastian","last_name":"Tacke","full_name":"Tacke, Sebastian"},{"first_name":"Martin","last_name":"Bähler","full_name":"Bähler, Martin"},{"last_name":"Hanley","first_name":"Peter","full_name":"Hanley, Peter"}],"day":"28","intvolume":"       292","citation":{"chicago":"Horsthemke, Markus, Anne Bachg, Katharina Groll, Sven Moyzio, Barbara Müther, Sandra Hemkemeyer, Roland Wedlich Söldner, et al. “Multiple Roles of Filopodial Dynamics in Particle Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10 Deletion.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology, 2017. <a href=\"https://doi.org/10.1074/jbc.M116.766923\">https://doi.org/10.1074/jbc.M116.766923</a>.","ista":"Horsthemke M, Bachg A, Groll K, Moyzio S, Müther B, Hemkemeyer S, Wedlich Söldner R, Sixt MK, Tacke S, Bähler M, Hanley P. 2017. Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. 292(17), 7258–7273.","apa":"Horsthemke, M., Bachg, A., Groll, K., Moyzio, S., Müther, B., Hemkemeyer, S., … Hanley, P. (2017). Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.M116.766923\">https://doi.org/10.1074/jbc.M116.766923</a>","mla":"Horsthemke, Markus, et al. “Multiple Roles of Filopodial Dynamics in Particle Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10 Deletion.” <i>Journal of Biological Chemistry</i>, vol. 292, no. 17, American Society for Biochemistry and Molecular Biology, 2017, pp. 7258–73, doi:<a href=\"https://doi.org/10.1074/jbc.M116.766923\">10.1074/jbc.M116.766923</a>.","short":"M. Horsthemke, A. Bachg, K. Groll, S. Moyzio, B. Müther, S. Hemkemeyer, R. Wedlich Söldner, M.K. Sixt, S. Tacke, M. Bähler, P. Hanley, Journal of Biological Chemistry 292 (2017) 7258–7273.","ama":"Horsthemke M, Bachg A, Groll K, et al. Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. <i>Journal of Biological Chemistry</i>. 2017;292(17):7258-7273. doi:<a href=\"https://doi.org/10.1074/jbc.M116.766923\">10.1074/jbc.M116.766923</a>","ieee":"M. Horsthemke <i>et al.</i>, “Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion,” <i>Journal of Biological Chemistry</i>, vol. 292, no. 17. American Society for Biochemistry and Molecular Biology, pp. 7258–7273, 2017."},"ddc":["570"],"scopus_import":1,"file_date_updated":"2020-07-14T12:47:37Z","date_published":"2017-04-28T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1074/jbc.M116.766923","month":"04","oa":1,"publication_identifier":{"issn":["00219258"]},"status":"public","_id":"668","year":"2017","date_updated":"2021-01-12T08:08:34Z","issue":"17","abstract":[{"lang":"eng","text":"Macrophage filopodia, finger-like membrane protrusions, were first implicated in phagocytosis more than 100 years ago, but little is still known about the involvement of these actin-dependent structures in particle clearance. Using spinning disk confocal microscopy to image filopodial dynamics in mouse resident Lifeact-EGFP macrophages, we show that filopodia, or filopodia-like structures, support pathogen clearance by multiple means. Filopodia supported the phagocytic uptake of bacterial (Escherichia coli) particles by (i) capturing along the filopodial shaft and surfing toward the cell body, the most common mode of capture; (ii) capturing via the tip followed by retraction; (iii) combinations of surfing and retraction; or (iv) sweeping actions. In addition, filopodia supported the uptake of zymosan (Saccharomyces cerevisiae) particles by (i) providing fixation, (ii) capturing at the tip and filopodia-guided actin anterograde flow with phagocytic cup formation, and (iii) the rapid growth of new protrusions. To explore the role of filopodia-inducing Cdc42, we generated myeloid-restricted Cdc42 knock-out mice. Cdc42-deficient macrophages exhibited rapid phagocytic cup kinetics, but reduced particle clearance, which could be explained by the marked rounded-up morphology of these cells. Macrophages lacking Myo10, thought to act downstream of Cdc42, had normal morphology, motility, and phagocytic cup formation, but displayed markedly reduced filopodia formation. In conclusion, live-cell imaging revealed multiple mechanisms involving macrophage filopodia in particle capture and engulfment. Cdc42 is not critical for filopodia or phagocytic cup formation, but plays a key role in driving macrophage lamellipodial spreading."}]}]