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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:13/0  |  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.


  
Synchrotron infrared spectroscopic evidence of the probable transition to metal hydrogen 期刊论文
NATURE, 2020, 577 (7792) : 631-+
作者:  Zhuang, Zhe;  Yu, Jin-Quan
收藏  |  浏览/下载:25/0  |  提交时间:2020/07/03

Hydrogen has been an essential element in the development of atomic, molecular and condensed matter physics(1). It is predicted that hydrogen should have a metal state(2)  however, understanding the properties of dense hydrogen has been more complex than originally thought, because under extreme conditions the electrons and protons are strongly coupled to each other and ultimately must both be treated as quantum particles(3,4). Therefore, how and when molecular solid hydrogen may transform into a metal is an open question. Although the quest for metal hydrogen has pushed major developments in modern experimental high-pressure physics, the various claims of its observation remain unconfirmed(5-7). Here a discontinuous change of the direct bandgap of hydrogen, from 0.6 electronvolts to below 0.1 electronvolts, is observed near 425 gigapascals. This result is most probably associated with the formation of the metallic state because the nucleus zero-point energy is larger than this lowest bandgap value. Pressures above 400 gigapascals are achieved with the recently developed toroidal diamond anvil cell(8), and the structural changes and electronic properties of dense solid hydrogen at 80 kelvin are probed using synchrotron infrared absorption spectroscopy. The continuous downward shifts of the vibron wavenumber and the direct bandgap with increased pressure point to the stability of phase-III hydrogen up to 425 gigapascals. The present data suggest that metallization of hydrogen proceeds within the molecular solid, in good agreement with previous calculations that capture many-body electronic correlations(9).


  
Mechanical regulation of glycolysis via cytoskeleton architecture 期刊论文
NATURE, 2020, 578 (7796) : 621-+
作者:  Faivre, Emily J.;  McDaniel, Keith F.;  Albert, Daniel H.;  Mantena, Srinivasa R.;  Plotnik, Joshua P.;  Wilcox, Denise;  Zhang, Lu;  Bui, Mai H.;  Sheppard, George S.;  Wang, Le;  Sehgal, Vasudha;  Lin, Xiaoyu;  Huang, Xiaoli;  Lu, Xin;  Uziel, Tamar;  Hessler, Paul;  Lam, Lloyd T.;  Bellin, Richard J.;  Mehta, Gaurav;  Fidanze, Steve;  Pratt, John K.;  Liu, Dachun;  Hasvold, Lisa A.;  Sun, Chaohong;  Panchal, Sanjay C.;  Nicolette, John J.;  Fossey, Stacey L.;  Park, Chang H.;  Longenecker, Kenton;  Bigelow, Lance;  Torrent, Maricel;  Rosenberg, Saul H.;  Kati, Warren M.;  Shen, Yu
收藏  |  浏览/下载:15/0  |  提交时间:2020/07/03

The mechanics of the cellular microenvironment continuously modulates cell functions such as growth, survival, apoptosis, differentiation and morphogenesis via cytoskeletal remodelling and actomyosin contractility(1-3). Although all of these processes consume energy(4,5), it is unknown whether and how cells adapt their metabolic activity to variable mechanical cues. Here we report that the transfer of human bronchial epithelial cells from stiff to soft substrates causes a downregulation of glycolysis via proteasomal degradation of the rate-limiting metabolic enzyme phosphofructokinase (PFK). PFK degradation is triggered by the disassembly of stress fibres, which releases the PFK-targeting E3 ubiquitin ligase tripartite motif (TRIM)-containing protein 21 (TRIM21). Transformed non-small-cell lung cancer cells, which maintain high glycolytic rates regardless of changing environmental mechanics, retain PFK expression by downregulating TRIM21, and by sequestering residual TRIM21 on a stress-fibre subset that is insensitive to substrate stiffness. Our data reveal a mechanism by which glycolysis responds to architectural features of the actomyosin cytoskeleton, thus coupling cell metabolism to the mechanical properties of the surrounding tissue. These processes enable normal cells to tune energy production in variable microenvironments, whereas the resistance of the cytoskeleton in response to mechanical cues enables the persistence of high glycolytic rates in cancer cells despite constant alterations of the tumour tissue.


Glycolysis in normal epithelial cells responds to microenvironmental mechanics via the modulation of actin bundles that sequester the phosphofructokinase-targeting ubiquitin ligase TRIM21, a process superseded by persistent actin bundles in cancer cells.


  
Classification with a disordered dopantatom network in silicon 期刊论文
NATURE, 2020, 577 (7790) : 341-+
作者:  Vagnozzi, Ronald J.;  Maillet, Marjorie;  Sargent, Michelle A.;  Khalil, Hadi;  Johansen, Anne Katrine Z.;  Schwanekamp, Jennifer A.;  York, Allen J.;  Huang, Vincent;  Nahrendorf, Matthias;  Sadayappan, Sakthivel;  Molkentin, Jeffery D.
收藏  |  浏览/下载:23/0  |  提交时间:2020/07/03

Classification is an important task at which both biological and artificial neural networks excel(1,2). In machine learning, nonlinear projection into a high-dimensional feature space can make data linearly separable(3,4), simplifying the classification of complex features. Such nonlinear projections are computationally expensive in conventional computers. A promising approach is to exploit physical materials systems that perform this nonlinear projection intrinsically, because of their high computational density(5), inherent parallelism and energy efficiency(6,7). However, existing approaches either rely on the systems'  time dynamics, which requires sequential data processing and therefore hinders parallel computation(5,6,8), or employ large materials systems that are difficult to scale up(7). Here we use a parallel, nanoscale approach inspired by filters in the brain(1) and artificial neural networks(2) to perform nonlinear classification and feature extraction. We exploit the nonlinearity of hopping conduction(9-11) through an electrically tunable network of boron dopant atoms in silicon, reconfiguring the network through artificial evolution to realize different computational functions. We first solve the canonical two-input binary classification problem, realizing all Boolean logic gates(12) up to room temperature, demonstrating nonlinear classification with the nanomaterial system. We then evolve our dopant network to realize feature filters(2) that can perform four-input binary classification on the Modified National Institute of Standards and Technology handwritten digit database. Implementation of our material-based filters substantially improves the classification accuracy over that of a linear classifier directly applied to the original data(13). Our results establish a paradigm of silicon-based electronics for smallfootprint and energy-efficient computation(14).


  
Demonstration of cooling by the Muon Ionization Cooling Experiment 期刊论文
NATURE, 2020, 578 (7793) : 53-+
作者:  Zheng, Wen;  Zhao, Wenjing;  Wu, Meng;  Song, Xinyang;  Caro, Florence;  Sun, Ximei;  Gazzaniga, Francesca;  Stefanetti, Giuseppe;  Oh, Sungwhan;  Mekalanos, John J.;  Kasper, Dennis L.
收藏  |  浏览/下载:10/0  |  提交时间:2020/07/03

The use of accelerated beams of electrons, protons or ions has furthered the development of nearly every scientific discipline. However, high-energy muon beams of equivalent quality have not yet been delivered. Muon beams can be created through the decay of pions produced by the interaction of a proton beam with a target. Such '  tertiary'  beams have much lower brightness than those created by accelerating electrons, protons or ions. High-brightness muon beams comparable to those produced by state-of-the-art electron, proton and ion accelerators could facilitate the study of lepton-antilepton collisions at extremely high energies and provide well characterized neutrino beams(1-6). Such muon beams could be realized using ionization cooling, which has been proposed to increase muon-beam brightness(7,8). Here we report the realization of ionization cooling, which was confirmed by the observation of an increased number of low-amplitude muons after passage of the muon beam through an absorber, as well as an increase in the corresponding phase-space density. The simulated performance of the ionization cooling system is consistent with the measured data, validating designs of the ionization cooling channel in which the cooling process is repeated to produce a substantial cooling effect(9-11). The results presented here are an important step towards achieving the muon-beam quality required to search for phenomena at energy scales beyond the reach of the Large Hadron Collider at a facility of equivalent or reduced wfootprint(6).


  
Assimilating GRACE Into a Land Surface Model in the Presence of an Irrigation-Induced Groundwater Trend 期刊论文
WATER RESOURCES RESEARCH, 2019, 55 (12) : 11274-11294
作者:  Nie, Wanshu;  Zaitchik, Benjamin F.;  Rodell, Matthew;  Kumar, Sujay V.;  Arsenault, Kristi R.;  Li, Bailing;  Getirana, Augusto
收藏  |  浏览/下载:16/0  |  提交时间:2020/02/16
GRACE TWS  data assimilation  irrigation  groundwater withdrawal  water and energy fluxes  High Plains Aquifer  
Ensemble Streamflow Forecasting Using an Energy Balance Snowmelt Model Coupled to a Distributed Hydrologic Model with Assimilation of Snow and Streamflow Observations 期刊论文
WATER RESOURCES RESEARCH, 2019, 55 (12) : 10813-10838
作者:  Gichamo, Tseganeh Z.;  Tarboton, David G.
收藏  |  浏览/下载:12/0  |  提交时间:2020/02/16
ensemble streamflow forecast  Utah Energy Balance (UEB) snowmelt model  Research Distributed Hydrologic Model (RDHM)  data assimilation  ensemble Kalman filter (EnKF)  particle filter (PF)  
Sustainability efficiency assessment of the electricity mix of the 28 EU member countries combining data envelopment analysis and optimized projections 期刊论文
ENERGY POLICY, 2019, 134
作者:  Zurano-Cervello, Patricia;  Pozo, Carlos;  Maria Mateo-Sanz, Josep;  Jimenez, Laureano;  Guillen-Gosalbez, Gonzalo
收藏  |  浏览/下载:8/0  |  提交时间:2020/02/17
Sustainability  Data envelopment analysis (DEA)  Electricity mix  Eco-efficiency  Optimization  Energy systems  
Policy implications for achieving the carbon emission reduction target by 2030 in Japan-Analysis based on a bilevel equilibrium model 期刊论文
ENERGY POLICY, 2019, 134
作者:  Xu, Zhongwen;  Yao, Liming;  Liu, Qiaoling;  Long, Yin
收藏  |  浏览/下载:8/0  |  提交时间:2020/02/17
Carbon emission quotas  Zero sum gains-data envelopment analysis  Particle swarm optimization method  Biobjective bilevel equilibrium model  Regional energy policy  
Spectral Signature of the Biosphere: NISTAR Finds It in Our Solar System From the Lagrangian L-1 Point 期刊论文
GEOPHYSICAL RESEARCH LETTERS, 2019
作者:  Carlson, Barbara;  Lacis, Andrew;  Colose, Christopher;  Marshak, Alexander;  Su, Wenying;  Lorentz, Steven
收藏  |  浏览/下载:7/0  |  提交时间:2019/11/27
global energy budget  satellite data  remote sensing  climate model validation  diurnal cycle  exoplanet studies