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A reference map of the human binary protein interactome 期刊论文
NATURE, 2020, 580 (7803) : 402-+
作者:  Fan, Chen;  Sukomon, Nattakan;  Flood, Emelie;  Rheinberger, Jan;  Allen, Toby W.;  Nimigean, Crina M.
收藏  |  浏览/下载:16/0  |  提交时间:2020/07/03

Global insights into cellular organization and genome function require comprehensive understanding of the interactome networks that mediate genotype-phenotype relationships(1,2). Here we present a human '  all-by-all'  reference interactome map of human binary protein interactions, or '  HuRI'  . With approximately 53,000 protein-protein interactions, HuRI has approximately four times as many such interactions as there are high-quality curated interactions from small-scale studies. The integration of HuRI with genome(3), transcriptome(4) and proteome(5) data enables cellular function to be studied within most physiological or pathological cellular contexts. We demonstrate the utility of HuRI in identifying the specific subcellular roles of protein-protein interactions. Inferred tissue-specific networks reveal general principles for the formation of cellular context-specific functions and elucidate potential molecular mechanisms that might underlie tissue-specific phenotypes of Mendelian diseases. HuRI is a systematic proteome-wide reference that links genomic variation to phenotypic outcomes.


  
Tracking of marine predators to protect Southern Ocean ecosystems 期刊论文
NATURE, 2020
作者:  Kim, Eugene;  Kerssemakers, Jacob;  Shaltiel, Indra A.;  Haering, Christian H.;  Dekker, Cees
收藏  |  浏览/下载:37/0  |  提交时间:2020/07/03

Tracking data from 17 marine predator species in the Southern Ocean are used to identify Areas of Ecological Significance, the protection of which could help to mitigate increasing pressures on Southern Ocean ecosystems.


Southern Ocean ecosystems are under pressure from resource exploitation and climate change(1,2). Mitigation requires the identification and protection of Areas of Ecological Significance (AESs), which have so far not been determined at the ocean-basin scale. Here, using assemblage-level tracking of marine predators, we identify AESs for this globally important region and assess current threats and protection levels. Integration of more than 4,000 tracks from 17 bird and mammal species reveals AESs around sub-Antarctic islands in the Atlantic and Indian Oceans and over the Antarctic continental shelf. Fishing pressure is disproportionately concentrated inside AESs, and climate change over the next century is predicted to impose pressure on these areas, particularly around the Antarctic continent. At present, 7.1% of the ocean south of 40 degrees S is under formal protection, including 29% of the total AESs. The establishment and regular revision of networks of protection that encompass AESs are needed to provide long-term mitigation of growing pressures on Southern Ocean ecosystems.


  
Dynamic Processes of CO2 Storage in the Field: 1. Multiscale and Multipath Channeling of CO2 Flow in the Hierarchical Fluvial Reservoir at Cranfield, Mississippi 期刊论文
WATER RESOURCES RESEARCH, 2020, 56 (2)
作者:  Zhou, Quanlin;  Yang, Xianjin;  Zhang, Rui;  Hosseini, Seyyed A.;  Ajo-Franklin, Jonathan B.;  Freifeld, Barry M.;  Daley, Thomas M.;  Hovorka, Susan D.
收藏  |  浏览/下载:17/0  |  提交时间:2020/07/02
CO2 storage  channelized flow  field monitoring  data integration  natural heterogeneity  joint inversion  
Targeting of temperate phages drives loss of type I CRISPR-Cas systems 期刊论文
NATURE, 2020, 578 (7793) : 149-+
作者:  Xiang, Lifeng;  Yin, Yu;  Zheng, Yun;  Ma, Yanping;  Li, Yonggang;  Zhao, Zhigang;  Guo, Junqiang;  Ai, Zongyong;  Niu, Yuyu;  Duan, Kui;  He, Jingjing;  Ren, Shuchao;  Wu, Dan;  Bai, Yun;  Shang, Zhouchun;  Dai, Xi;  Ji, Weizhi;  Li, Tianqing
收藏  |  浏览/下载:80/0  |  提交时间:2020/07/03

On infection of their host, temperate viruses that infect bacteria (bacteriophages  hereafter referred to as phages) enter either a lytic or a lysogenic cycle. The former results in lysis of bacterial cells and phage release (resulting in horizontal transmission), whereas lysogeny is characterized by the integration of the phage into the host genome, and dormancy (resulting in vertical transmission)(1). Previous co-culture experiments using bacteria and mutants of temperate phages that are locked in the lytic cycle have shown that CRISPR-Cas systems can efficiently eliminate the invading phages(2,3). Here we show that, when challenged with wild-type temperate phages (which can become lysogenic), type I CRISPR-Cas immune systems cannot eliminate the phages from the bacterial population. Furthermore, our data suggest that, in this context, CRISPR-Cas immune systems are maladaptive to the host, owing to the severe immunopathological effects that are brought about by imperfect matching of spacers to the integrated phage sequences (prophages). These fitness costs drive the loss of CRISPR-Cas from bacterial populations, unless the phage carries anti-CRISPR (acr) genes that suppress the immune system of the host. Using bioinformatics, we show that this imperfect targeting is likely to occur frequently in nature. These findings help to explain the patchy distribution of CRISPR-Cas immune systems within and between bacterial species, and highlight the strong selective benefits of phage-encoded acr genes for both the phage and the host under these circumstances.


CRISPR-Cas systems cannot eliminate temperate bacteriophages from bacterial populations and-in this context-the systems impose immunopathological costs on the host, creating selective pressures that may explain their patchy distribution in bacteria.


  
Reduced carbon use efficiency and increased microbial turnover with soil warming 期刊论文
GLOBAL CHANGE BIOLOGY, 2019, 25 (3) : 900-910
作者:  Li, Jianwei;  Wang, Gangsheng;  Mayes, Melanie A.;  Allison, Steven D.;  Frey, Serita D.;  Shi, Zheng;  Hu, Xiao-Ming;  Luo, Yiqi;  Melillo, Jerry M.
收藏  |  浏览/下载:25/0  |  提交时间:2019/04/09
carbon use efficiency (CUE)  data-model integration  Harvard forest  microbial biomass turnover (rB)  soil warming  temperature sensitivity  
Integration of cloud top heights retrieved from FY-2 meteorological satellite, radiosonde, and ground-based millimeter wavelength cloud radar observations 期刊论文
ATMOSPHERIC RESEARCH, 2018, 214: 284-295
作者:  Wang, Yu;  Wang, Chunheng;  Shi, Cunzhao;  Xiao, Baihua
收藏  |  浏览/下载:11/0  |  提交时间:2019/04/09
Cloud top height  Bayesian decision theory  Data integration  Satellite observation  Radiosonde observation  Radar observation  
Forecasting future recruitment success for Atlantic cod in the warming and acidifying Barents Sea 期刊论文
GLOBAL CHANGE BIOLOGY, 2018, 24 (1) : 526-535
作者:  Koenigstein, Stefan;  Dahlke, Flemming T.;  Stiasny, Martina H.;  Storch, Daniela;  Clemmesen, Catriona;  Poertner, Hans-Otto
收藏  |  浏览/下载:17/0  |  提交时间:2019/04/09
early life stage survival  environmental drivers  experimental data integration  fish recruitment  Gadus morhua  ocean acidification  ocean warming  
Informing climate models with rapid chamber measurements of forest carbon uptake 期刊论文
GLOBAL CHANGE BIOLOGY, 2017, 23 (5)
作者:  Metcalfe, Daniel B.;  Ricciuto, Daniel;  Palmroth, Sari;  Campbell, Catherine;  Hurry, Vaughan;  Mao, Jiafu;  Keel, Sonja G.;  Linder, Sune;  Shi, Xiaoying;  Nsholm, Torgny;  Ohlsson, Klas E. A.;  Blackburn, M.;  Thornton, Peter E.;  Oren, Ram
收藏  |  浏览/下载:21/0  |  提交时间:2019/04/09
boreal forest  earth system model  model-data integration  nutrient limitation  photosynthetic downregulation  Pinus sylvestris  
Big Ship Data: Using vessel measurements to improve estimates of temperature and wind speed on the Great Lakes 期刊论文
WATER RESOURCES RESEARCH, 2017, 53 (5)
作者:  Fries, Kevin;  Kerkez, Branko
收藏  |  浏览/下载:12/0  |  提交时间:2019/04/09
data integration  Gaussian process regression