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The proteome landscape of the kingdoms of life 期刊论文
NATURE, 2020
作者:  Arzi, Anat;  Rozenkrantz, Liron;  Gorodisky, Lior;  Rozenkrantz, Danit;  Holtzman, Yael;  Ravia, Aharon;  Bekinschtein, Tristan A.;  Galperin, Tatyana;  Krimchansky, Ben-Zion;  Cohen, Gal;  Oksamitni, Anna;  Aidinoff, Elena;  Sacher, Yaron;  Sobel, Noam
收藏  |  浏览/下载:14/0  |  提交时间:2020/07/03

Proteins carry out the vast majority of functions in all biological domains, but for technological reasons their large-scale investigation has lagged behind the study of genomes. Since the first essentially complete eukaryotic proteome was reported(1), advances in mass-spectrometry-based proteomics(2)have enabled increasingly comprehensive identification and quantification of the human proteome(3-6). However, there have been few comparisons across species(7,8), in stark contrast with genomics initiatives(9). Here we use an advanced proteomics workflow-in which the peptide separation step is performed by a microstructured and extremely reproducible chromatographic system-for the in-depth study of 100 taxonomically diverse organisms. With two million peptide and 340,000 stringent protein identifications obtained in a standardized manner, we double the number of proteins with solid experimental evidence known to the scientific community. The data also provide a large-scale case study for sequence-based machine learning, as we demonstrate by experimentally confirming the predicted properties of peptides fromBacteroides uniformis. Our results offer a comparative view of the functional organization of organisms across the entire evolutionary range. A remarkably high fraction of the total proteome mass in all kingdoms is dedicated to protein homeostasis and folding, highlighting the biological challenge of maintaining protein structure in all branches of life. Likewise, a universally high fraction is involved in supplying energy resources, although these pathways range from photosynthesis through iron sulfur metabolism to carbohydrate metabolism. Generally, however, proteins and proteomes are remarkably diverse between organisms, and they can readily be explored and functionally compared at www.proteomesoflife.org.


  
Potential benefits and challenges of the relationship between social movements and the commons in the city of Barcelona 期刊论文
ECOLOGICAL ECONOMICS, 2020, 174
作者:  Pera, Marina
收藏  |  浏览/下载:2/0  |  提交时间:2020/05/13
Urban commons  Urban movements  Local government  Case study  
Structural transitions in influenza haemagglutinin at membrane fusion pH 期刊论文
NATURE, 2020, 583 (7814) : 150-+
作者:  Wei, Kevin;  Korsunsky, Ilya;  Marshall, Jennifer L.;  Gao, Anqi;  Watts, Gerald F. M.;  Major, Triin;  Croft, Adam P.;  Watts, Jordan;  Blazar, Philip E.;  Lange, Jeffrey K.;  Thornhill, Thomas S.;  Filer, Andrew;  Raza, Karim;  Donlin, Laura T.;  Siebel, Christian W.
收藏  |  浏览/下载:20/0  |  提交时间:2020/07/03

Cryo-electron microscopy studies of the influenza haemagglutinin glycoprotein at the low pH of host endosomes reveals structural intermediates, offering a dynamic view of how the protein mediates membrane fusion.


Infection by enveloped viruses involves fusion of their lipid envelopes with cellular membranes to release the viral genome into cells. For HIV, Ebola, influenza and numerous other viruses, envelope glycoproteins bind the infecting virion to cell-surface receptors and mediate membrane fusion. In the case of influenza, the receptor-binding glycoprotein is the haemagglutinin (HA), and following receptor-mediated uptake of the bound virus by endocytosis(1), it is the HA that mediates fusion of the virus envelope with the membrane of the endosome(2). Each subunit of the trimeric HA consists of two disulfide-linked polypeptides, HA1 and HA2. The larger, virus-membrane-distal, HA1 mediates receptor binding  the smaller, membrane-proximal, HA2 anchors HA in the envelope and contains the fusion peptide, a region that is directly involved in membrane interaction(3). The low pH of endosomes activates fusion by facilitating irreversible conformational changes in the glycoprotein. The structures of the initial HA at neutral pH and the final HA at fusion pH have been investigated by electron microscopy(4,5) and X-ray crystallography(6-8). Here, to further study the process of fusion, we incubate HA for different times at pH 5.0 and directly image structural changes using single-particle cryo-electron microscopy. We describe three distinct, previously undescribed forms of HA, most notably a 150 angstrom-long triple-helical coil of HA2, which may bridge between the viral and endosomal membranes. Comparison of these structures reveals concerted conformational rearrangements through which the HA mediates membrane fusion.


  
Simulation of Hubbard model physics in WSe2/WS2 moire superlattices 期刊论文
NATURE, 2020, 579 (7799) : 353-+
作者:  Stein, Reed M.;  Kang, Hye Jin;  McCorvy, John D.;  Glatfelter, Grant C.;  Jones, Anthony J.;  Che, Tao;  Slocum, Samuel;  Huang, Xi-Ping;  Savych, Olena;  Moroz, Yurii S.;  Stauch, Benjamin;  Johansson, Linda C.;  Cherezov, Vadim;  Kenakin, Terry;  Irwin, John J.;  Shoichet, Brian K.;  Roth, Bryan L.;  Dubocovich, Margarita L.
收藏  |  浏览/下载:8/0  |  提交时间:2020/07/03

Study of WSe2/WS2 moire superlattices reveals the phase diagram of the triangular-lattice Hubbard model, including a Mott insulating state at half-filling and a possible magnetic quantum phase transition near 0.6 filling.


The Hubbard model, formulated by physicist John Hubbard in the 1960s(1), is a simple theoretical model of interacting quantum particles in a lattice. The model is thought to capture the essential physics of high-temperature superconductors, magnetic insulators and other complex quantum many-body ground states(2,3). Although the Hubbard model provides a greatly simplified representation of most real materials, it is nevertheless difficult to solve accurately except in the one-dimensional case(2,3). Therefore, the physical realization of the Hubbard model in two or three dimensions, which can act as an analogue quantum simulator (that is, it can mimic the model and simulate its phase diagram and dynamics(4,5)), has a vital role in solving the strong-correlation puzzle, namely, revealing the physics of a large number of strongly interacting quantum particles. Here we obtain the phase diagram of the two-dimensional triangular-lattice Hubbard model by studying angle-aligned WSe2/WS2 bilayers, which form moire superlattices(6) because of the difference between the lattice constants of the two materials. We probe the charge and magnetic properties of the system by measuring the dependence of its optical response on an out-of-plane magnetic field and on the gate-tuned carrier density. At half-filling of the first hole moire superlattice band, we observe a Mott insulating state with antiferromagnetic Curie-Weiss behaviour, as expected for a Hubbard model in the strong-interaction regime(2,3,7-9). Above half-filling, our experiment suggests a possible quantum phase transition from an antiferromagnetic to a weak ferromagnetic state at filling factors near 0.6. Our results establish a new solid-state platform based on moire superlattices that can be used to simulate problems in strong-correlation physics that are described by triangular-lattice Hubbard models.


  
Probabilistic Assessment of Flood Hazard due to Levee Breaches Using Fragility Functions 期刊论文
WATER RESOURCES RESEARCH, 2019
作者:  D&;  39;Oria, M.
收藏  |  浏览/下载:2/0  |  提交时间:2020/02/16
Flood hazard assessment  Probabilistic method  Levee breaches  Fragility functions  Piping  Case study  
Compensating balancing demand by spatial load migration - The case of geographically distributed data centers 期刊论文
ENERGY POLICY, 2019, 132: 1130-1142
作者:  Thimmel, Markus;  Fridgen, Gilbert;  Keller, Robert;  Roevekamp, Patrick
收藏  |  浏览/下载:19/0  |  提交时间:2019/11/27
Distributed data centers  Spatial load migration  Balancing power compensation  Economic potential  Simulation-based case study  Demand response  
How Subordinate Financialization Shapes Urban Development: The Rise and Fall of Warsaw's Slu(z) over dotewiec Business District 期刊论文
INTERNATIONAL JOURNAL OF URBAN AND REGIONAL RESEARCH, 2019, 43 (4) : 666-684
作者:  Budenbender, Mirjam;  Aalbers, Manuel B.
收藏  |  浏览/下载:21/0  |  提交时间:2019/11/27
financialization  real estate developers  post-socialism  semi-periphery  business district  Warsaw  Poland  case study research  neighbourhood change  globalization  
Wind energy and local communities: A manufacturer's efforts to gain acceptance 期刊论文
ENERGY POLICY, 2018, 121: 314-324
作者:  Landeta-Manzano, Benat;  Arana-Landin, German;  Calvo, Pilar M.;  Heras-Saizarbitoria, Inaki
收藏  |  浏览/下载:1/0  |  提交时间:2019/04/09
Wind energy  Renewable energy  Social acceptance  Community acceptance  Original Equipment Manufacturer  Case study  
Sharing electricity storage at the community level: An empirical analysis of potential business models and barriers 期刊论文
ENERGY POLICY, 2018, 118: 492-503
作者:  Mueller, Simon C.;  Welpe, Isabel M.
收藏  |  浏览/下载:4/0  |  提交时间:2019/04/09
Distributed electricity storage  Sharing economy  Business model  Increase of self-consumption  Community energy  Cross-case study  
Learning to live with social-ecological complexity: An interpretive analysis of learning in 11 UNESCO Biosphere Reserves 期刊论文
GLOBAL ENVIRONMENTAL CHANGE-HUMAN AND POLICY DIMENSIONS, 2018, 50: 75-87
作者:  Schultz, Lisen;  39;Armengol, Laia
收藏  |  浏览/下载:7/0  |  提交时间:2019/04/09
Comparative case study  Qualitative  Bridging organizations  Sustainability science  Multi-level governance  Science-policy interface