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  • Carbon sequestration
  • Entropy
  • Molecular biophysics
  • Nature Publishing Group (NPG)  (6)
  • American Physical Society  (1)
  • Annual Reviews  (1)
  • American Chemical Society
  • 2010-2014  (5)
  • 2005-2009  (3)
  • 1980-1984
  • 1970-1974
  • 1930-1934
Collection
Keywords
Publisher
Years
  • 2010-2014  (5)
  • 2005-2009  (3)
  • 1980-1984
  • 1970-1974
  • 1930-1934
Year
  • 1
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    Role of carbon cycle observations and knowledge in carbon management (2005)
    Annual Reviews
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © Annual Reviews, 2003. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Environment and Resources 28 (2003): 521-558, doi:10.1146/annurev.energy.28.011503.163443.
    Description: Agriculture and industrial development have led to inadvertent changes in the natural carbon cycle. As a consequence, concentrations of carbon dioxide and other greenhouse gases have increased in the atmosphere and may lead to changes in climate. The current challenge facing society is to develop options for future management of the carbon cycle. A variety of approaches has been suggested: direct reduction of emissions, deliberate manipulation of the natural carbon cycle to enhance sequestration, and capture and isolation of carbon from fossil fuel use. Policy development to date has laid out some of the general principles to which carbon management should adhere. These are summarized as: how much carbon is stored, by what means, and for how long. To successfully manage carbon for climate purposes requires increased understanding of carbon cycle dynamics and improvement in the scientific capabilities available for measurement as well as for policy needs. The specific needs for scientific information to underpin carbon cycle management decisions are not yet broadly known. A stronger dialogue between decision makers and scientists must be developed to foster improved application of scientific knowledge to decisions. This review focuses on the current knowledge of the carbon cycle, carbon measurement capabilities (with an emphasis on the continental scale) and the relevance of carbon cycle science to carbon sequestration goals.
    Description: The National Center for Atmospheric Research is supported by the National Science Foundation.
    Keywords: Carbon sequestration ; Measurement techniques ; Climate ; Kyoto protocol
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: 406392 bytes
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  • 2
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    Entropy-driven formation of a chiral liquid-crystalline phase of helical filaments (2006)
    American Physical Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2006. This article is posted here by permission of American Physical Society for personal use, not for redistribution. The definitive version was published in Physical Review Letters 96 (2006): 018305, doi:10.1103/PhysRevLett.96.018305.
    Description: We study the liquid-crystalline phase behavior of a concentrated suspension of helical flagella isolated from Salmonella typhimurium. Flagella are prepared with different polymorphic states, some of which have a pronounced helical character while others assume a rodlike shape. We show that the static phase behavior and dynamics of chiral helices are very different when compared to simpler achiral hard rods. With increasing concentration, helical flagella undergo an entropy-driven first order phase transition to a liquid-crystalline state having a novel chiral symmetry.
    Description: M. S. and R. O. are supported by NIH Grant No. EB002583.
    Keywords: Entropy ; Molecular biophysics ; Liquid crystal phase transformations ; Symmetry ; Chirality
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
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    Sleep and sensorimotor integration during early vocal learning in a songbird (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-12-17
    Description: Behavioural studies widely implicate sleep in memory consolidation in the learning of a broad range of behaviours. During sleep, brain regions are reactivated, and specific patterns of neural activity are replayed, consistent with patterns observed in previous waking behaviour. Birdsong learning is a paradigmatic model system for skill learning. Song development in juvenile zebra finches (Taeniopygia guttata) is characterized by sleep-dependent circadian fluctuations in singing behaviour, with immediate post-sleep deterioration in song structure followed by recovery later in the day. In sleeping adult birds, spontaneous bursting activity of forebrain premotor neurons in the robust nucleus of the arcopallium (RA) carries information about daytime singing. Here we show that, in juvenile zebra finches, playback during the day of an adult 'tutor' song induced profound and tutor-song-specific changes in bursting activity of RA neurons during the following night of sleep. The night-time neuronal changes preceded tutor-song-induced changes in singing, first observed the following day. Interruption of auditory feedback greatly reduced sleep bursting and prevented the tutor-song-specific neuronal remodelling. Thus, night-time neuronal activity is shaped by the interaction of the song model (sensory template) and auditory feedback, with changes in night-time activity preceding the onset of practice associated with vocal learning. We hypothesize that night-time bursting induces adaptive changes in premotor networks during sleep as part of vocal learning. By this hypothesis, adaptive changes driven by replay of sensory information at night and by evaluation of sensory feedback during the day interact to produce the complex circadian patterns seen early in vocal development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651989/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651989/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shank, Sylvan S -- Margoliash, Daniel -- R01 MH059831/MH/NIMH NIH HHS/ -- R01 MH059831-09/MH/NIMH NIH HHS/ -- England -- Nature. 2009 Mar 5;458(7234):73-7. doi: 10.1038/nature07615. Epub 2008 Dec 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Psychology, University of Chicago, Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19079238" target="_blank"〉PubMed〈/a〉
    Keywords: Acoustic Stimulation ; Action Potentials ; Animals ; Circadian Rhythm/physiology ; Darkness ; Entropy ; Feedback, Physiological ; Female ; Finches/*physiology ; Learning/*physiology ; Male ; Mental Recall/physiology ; *Models, Neurological ; Neurons/physiology ; Prosencephalon/cytology/*physiology ; Sleep/*physiology ; Vocalization, Animal/*physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Fundamental limits on the suppression of molecular fluctuations (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-09-11
    Description: Negative feedback is common in biological processes and can increase a system's stability to internal and external perturbations. But at the molecular level, control loops always involve signalling steps with finite rates for random births and deaths of individual molecules. Here we show, by developing mathematical tools that merge control and information theory with physical chemistry, that seemingly mild constraints on these rates place severe limits on the ability to suppress molecular fluctuations. Specifically, the minimum standard deviation in abundances decreases with the quartic root of the number of signalling events, making it extremely expensive to increase accuracy. Our results are formulated in terms of experimental observables, and existing data show that cells use brute force when noise suppression is essential; for example, regulatory genes are transcribed tens of thousands of times per cell cycle. The theory challenges conventional beliefs about biochemical accuracy and presents an approach to the rigorous analysis of poorly characterized biological systems.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996232/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996232/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lestas, Ioannis -- Vinnicombe, Glenn -- Paulsson, Johan -- BB/C008073/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- GM068763-06/GM/NIGMS NIH HHS/ -- GM081563-02/GM/NIGMS NIH HHS/ -- R01 GM081563/GM/NIGMS NIH HHS/ -- R01 GM081563-02/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Sep 9;467(7312):174-8. doi: 10.1038/nature09333.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20829788" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Cell Physiological Phenomena ; Entropy ; *Feedback ; Gene Expression Regulation ; *Models, Biological ; *Signal Transduction ; Systems Biology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
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    Sparse coding and high-order correlations in fine-scale cortical networks (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-07-06
    Description: Connectivity in the cortex is organized at multiple scales, suggesting that scale-dependent correlated activity is particularly important for understanding the behaviour of sensory cortices and their function in stimulus encoding. We analysed the scale-dependent structure of cortical interactions by using maximum entropy models to characterize multiple-tetrode recordings from primary visual cortex of anaesthetized macaque monkeys (Macaca mulatta). We compared the properties of firing patterns among local clusters of neurons (〈300 microm apart) with those of neurons separated by larger distances (600-2,500 microm). Here we report that local firing patterns are distinctive: whereas multi-neuronal firing patterns at larger distances can be predicted by pairwise interactions, patterns within local clusters often show evidence of high-order correlations. Surprisingly, these local correlations are flexible and rapidly reorganized by visual input. Although they modestly reduce the amount of information that a cluster conveys, they also modify the format of this information, creating sparser codes by increasing the periods of total quiescence, and concentrating information into briefer periods of common activity. These results imply a hierarchical organization of neuronal correlations: simple pairwise correlations link neurons over scales of tens to hundreds of minicolumns, but on the scale of a few minicolumns, ensembles of neurons form complex subnetworks whose moment-to-moment effective connectivity is dynamically reorganized by the stimulus.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912961/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912961/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ohiorhenuan, Ifije E -- Mechler, Ferenc -- Purpura, Keith P -- Schmid, Anita M -- Hu, Qin -- Victor, Jonathan D -- EY09314/EY/NEI NIH HHS/ -- EY19454/EY/NEI NIH HHS/ -- F31 EY019454-01/EY/NEI NIH HHS/ -- GM07739/GM/NIGMS NIH HHS/ -- R01 EY009314/EY/NEI NIH HHS/ -- R01 EY009314-16/EY/NEI NIH HHS/ -- T32 GM007739/GM/NIGMS NIH HHS/ -- T32 GM007739-32/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Jul 29;466(7306):617-21. doi: 10.1038/nature09178. Epub 2010 Jul 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurology and Neuroscience, Weill Cornell Medical College, New York, New York 10065, USA. ifo2001@med.cornell.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20601940" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Entropy ; Macaca mulatta/*physiology ; Models, Neurological ; Nerve Net/*cytology/*physiology ; Neurons/*physiology ; Photic Stimulation ; Visual Cortex/*cytology/*physiology ; Visual Perception/physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
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    Permanent El Nino during the Pliocene warm period not supported by coral evidence (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-03-11
    Description: The El Nino/Southern Oscillation (ENSO) system during the Pliocene warm period (PWP; 3-5 million years ago) may have existed in a permanent El Nino state with a sharply reduced zonal sea surface temperature (SST) gradient in the equatorial Pacific Ocean. This suggests that during the PWP, when global mean temperatures and atmospheric carbon dioxide concentrations were similar to those projected for near-term climate change, ENSO variability--and related global climate teleconnections-could have been radically different from that today. Yet, owing to a lack of observational evidence on seasonal and interannual SST variability from crucial low-latitude sites, this fundamental climate characteristic of the PWP remains controversial. Here we show that permanent El Nino conditions did not exist during the PWP. Our spectral analysis of the delta(18)O SST and salinity proxy, extracted from two 35-year, monthly resolved PWP Porites corals in the Philippines, reveals variability that is similar to present ENSO variation. Although our fossil corals cannot be directly compared with modern ENSO records, two lines of evidence suggest that Philippine corals are appropriate ENSO proxies. First, delta(18)O anomalies from a nearby live Porites coral are correlated with modern records of ENSO variability. Second, negative-delta(18)O events in the fossil corals closely resemble the decreases in delta(18)O seen in the live coral during El Nino events. Prior research advocating a permanent El Nino state may have been limited by the coarse resolution of many SST proxies, whereas our coral-based analysis identifies climate variability at the temporal scale required to resolve ENSO structure firmly.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Watanabe, Tsuyoshi -- Suzuki, Atsushi -- Minobe, Shoshiro -- Kawashima, Tatsunori -- Kameo, Koji -- Minoshima, Kayo -- Aguilar, Yolanda M -- Wani, Ryoji -- Kawahata, Hodaka -- Sowa, Kohki -- Nagai, Takaya -- Kase, Tomoki -- England -- Nature. 2011 Mar 10;471(7337):209-11. doi: 10.1038/nature09777.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan. nabe@mail.sci.hokudai.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21390128" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Anthozoa/metabolism ; Atmosphere ; *Climate ; El Nino-Southern Oscillation/*history ; Entropy ; Fossils ; History, Ancient ; Oxygen Isotopes ; Pacific Ocean ; Philippines ; Salinity ; Seasons ; Seawater/analysis ; *Temperature ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
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    A chain mechanism for flagellum growth (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-11-12
    Description: Bacteria swim by means of long flagella extending from the cell surface. These are assembled from thousands of protein subunits translocated across the cell membrane by an export machinery at the base of each flagellum. Unfolded subunits then transit through a narrow channel at the core of the growing flagellum to the tip, where they crystallize into the nascent structure. As the flagellum lengthens outside the cell, the rate of flagellum growth does not change. The mystery is how subunit transit is maintained at a constant rate without a discernible energy source in the channel of the external flagellum. We present evidence for a simple physical mechanism for flagellum growth that harnesses the entropic force of the unfolded subunits themselves. We show that a subunit docked at the export machinery can be captured by a free subunit through head-to-tail linkage of juxtaposed amino (N)- and carboxy (C)-terminal helices. We propose that sequential rounds of linkage would generate a multisubunit chain that pulls successive subunits into and through the channel to the flagellum tip, and by isolating filaments growing on bacterial cells we reveal the predicted chain of head-to-tail linked subunits in the transit channel of flagella. Thermodynamic analysis confirms that links in the subunit chain can withstand the pulling force generated by rounds of subunit crystallization at the flagellum tip, and polymer theory predicts that as the N terminus of each unfolded subunit crystallizes, the entropic force at the subunit C terminus would increase, rapidly overcoming the threshold required to pull the next subunit from the export machinery. This pulling force would adjust automatically over the increasing length of the growing flagellum, maintaining a constant rate of subunit delivery to the tip.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3864836/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3864836/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Evans, Lewis D B -- Poulter, Simon -- Terentjev, Eugene M -- Hughes, Colin -- Fraser, Gillian M -- 082895/Wellcome Trust/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2013 Dec 12;504(7479):287-90. doi: 10.1038/nature12682. Epub 2013 Nov 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK. ; Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 OHE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24213633" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallization ; Entropy ; Flagella/*chemistry/*metabolism ; Intrinsically Disordered Proteins/chemistry/metabolism/secretion ; Protein Folding ; Protein Subunits/*chemistry/*metabolism/secretion ; Protein Transport ; Salmonella typhimurium/*cytology
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
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    Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG (2014)
    Nature Publishing Group (NPG)
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    Publication Date: 2014-09-16
    Description: Curli are functional amyloid fibres that constitute the major protein component of the extracellular matrix in pellicle biofilms formed by Bacteroidetes and Proteobacteria (predominantly of the alpha and gamma classes). They provide a fitness advantage in pathogenic strains and induce a strong pro-inflammatory response during bacteraemia. Curli formation requires a dedicated protein secretion machinery comprising the outer membrane lipoprotein CsgG and two soluble accessory proteins, CsgE and CsgF. Here we report the X-ray structure of Escherichia coli CsgG in a non-lipidated, soluble form as well as in its native membrane-extracted conformation. CsgG forms an oligomeric transport complex composed of nine anticodon-binding-domain-like units that give rise to a 36-stranded beta-barrel that traverses the bilayer and is connected to a cage-like vestibule in the periplasm. The transmembrane and periplasmic domains are separated by a 0.9-nm channel constriction composed of three stacked concentric phenylalanine, asparagine and tyrosine rings that may guide the extended polypeptide substrate through the secretion pore. The specificity factor CsgE forms a nonameric adaptor that binds and closes off the periplasmic face of the secretion channel, creating a 24,000 A(3) pre-constriction chamber. Our structural, functional and electrophysiological analyses imply that CsgG is an ungated, non-selective protein secretion channel that is expected to employ a diffusion-based, entropy-driven transport mechanism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4268158/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4268158/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goyal, Parveen -- Krasteva, Petya V -- Van Gerven, Nani -- Gubellini, Francesca -- Van den Broeck, Imke -- Troupiotis-Tsailaki, Anastassia -- Jonckheere, Wim -- Pehau-Arnaudet, Gerard -- Pinkner, Jerome S -- Chapman, Matthew R -- Hultgren, Scott J -- Howorka, Stefan -- Fronzes, Remi -- Remaut, Han -- R01 A1073847/PHS HHS/ -- R01 AI048689/AI/NIAID NIH HHS/ -- R01 AI073847/AI/NIAID NIH HHS/ -- R01 AI099099/AI/NIAID NIH HHS/ -- R56 AI073847/AI/NIAID NIH HHS/ -- England -- Nature. 2014 Dec 11;516(7530):250-3. doi: 10.1038/nature13768. Epub 2014 Sep 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium [2] Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. ; 1] Unite G5 Biologie structurale de la secretion bacterienne, Institut Pasteur, 25-28 rue du Docteur Roux, 75015 Paris, France [2] UMR 3528, CNRS, Institut Pasteur, 25-28 rue du Docteur Roux, 75015 Paris, France. ; Structure et Fonction des Membranes Biologiques (SFMB), Universite Libre de Bruxelles, 1050 Brussels, Belgium. ; UMR 3528, CNRS, Institut Pasteur, 25-28 rue du Docteur Roux, 75015 Paris, France. ; Department of Molecular Microbiology and Microbial Pathogenesis, Washington University in Saint Louis School of Medicine, St Louis, Missouri 63110-1010, USA. ; Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109-1048, USA. ; Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London WC1H 0AJ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25219853" target="_blank"〉PubMed〈/a〉
    Keywords: Amyloid/*secretion ; Biofilms ; Cell Membrane ; Crystallography, X-Ray ; Diffusion ; Entropy ; Escherichia coli/*chemistry ; Escherichia coli Proteins/*chemistry/*metabolism ; Lipoproteins/*chemistry/*metabolism ; Membrane Transport Proteins/metabolism ; Models, Biological ; Models, Molecular ; Periplasm/metabolism ; Protein Conformation ; Protein Transport
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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