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The arms race between bacteria and their phage foes 期刊论文
NATURE, 2020, 577 (7790) : 327-336
作者:  Hirschey, Matthew
收藏  |  浏览/下载:20/0  |  提交时间:2020/07/03

Bacteria are under immense evolutionary pressure from their viral invaders-bacteriophages. Bacteria have evolved numerous immune mechanisms, both innate and adaptive, to cope with this pressure. The discovery and exploitation of CRISPR-Cas systems have stimulated a resurgence in the identification and characterization of anti-phage mechanisms. Bacteriophages use an extensive battery of counter-defence strategies to co-exist in the presence of these diverse phage defence mechanisms. Understanding the dynamics of the interactions between these microorganisms has implications for phage-based therapies, microbial ecology and evolution, and the development of new biotechnological tools. Here we review the spectrum of anti-phage systems and highlight their evasion by bacteriophages.


  
Internal state dynamics shape brainwide activity and foraging behaviour 期刊论文
NATURE, 2020, 577 (7789) : 239-+
作者:  Marques, Joao C.;  Li, Meng;  Schaak, Diane;  Robson, Drew N.;  Li, Jennifer M.
收藏  |  浏览/下载:6/0  |  提交时间:2020/07/03

The brain has persistent internal states that can modulate every aspect of an animal'  s mental experience(1-4). In complex tasks such as foraging, the internal state is dynamic(5-8). Caenorhabditis elegans alternate between local search and global dispersal(5). Rodents and primates exhibit trade-offs between exploitation and exploration(6,7). However, fundamental questions remain about how persistent states are maintained in the brain, which upstream networks drive state transitions and how state-encoding neurons exert neuromodulatory effects on sensory perception and decision-making to govern appropriate behaviour. Here, using tracking microscopy to monitor whole-brain neuronal activity at cellular resolution in freely moving zebrafish larvae(9), we show that zebrafish spontaneously alternate between two persistent internal states during foraging for live prey (Paramecia). In the exploitation state, the animal inhibits locomotion and promotes hunting, generating small, localized trajectories. In the exploration state, the animal promotes locomotion and suppresses hunting, generating long-ranging trajectories that enhance spatial dispersion. We uncover a dorsal raphe subpopulation with persistent activity that robustly encodes the exploitation state. The exploitation-state-encoding neurons, together with a multimodal trigger network that is associated with state transitions, form a stochastically activated nonlinear dynamical system. The activity of this oscillatory network correlates with a global retuning of sensorimotor transformations during foraging that leads to marked changes in both the motivation to hunt for prey and the accuracy of motor sequences during hunting. This work reveals an important hidden variable that shapes the temporal structure of motivation and decision-making.


  
Accurate compound-specific C-14 dating of archaeological pottery vessels 期刊论文
NATURE, 2020, 580 (7804) : 506-+
作者:  Yin, Yafei;  Lu, J. Yuyang;  Zhang, Xuechun;  Shao, Wen;  Xu, Yanhui;  Li, Pan;  Hong, Yantao;  Cui, Li;  Shan, Ge;  Tian, Bin;  Zhang, Qiangfeng Cliff;  Shen, Xiaohua
收藏  |  浏览/下载:21/0  |  提交时间:2020/05/13

Pottery is one of the most commonly recovered artefacts from archaeological sites. Despite more than a century of relative dating based on typology and seriation(1), accurate dating of pottery using the radiocarbon dating method has proven extremely challenging owing to the limited survival of organic temper and unreliability of visible residues(2-4). Here we report a method to directly date archaeological pottery based on accelerator mass spectrometry analysis of C-14 in absorbed food residues using palmitic (C-16:0) and stearic (C-18:0) fatty acids purified by preparative gas chromatography(5-8). We present accurate compound-specific radiocarbon determinations of lipids extracted from pottery vessels, which were rigorously evaluated by comparison with dendrochronological dates(9,10) and inclusion in site and regional chronologies that contained previously determined radiocarbon dates on other materials(11-15). Notably, the compound-specific dates from each of the C-16:0 and C-18:0 fatty acids in pottery vessels provide an internal quality control of the results(6) and are entirely compatible with dates for other commonly dated materials. Accurate radiocarbon dating of pottery vessels can reveal: (1) the period of use of pottery  (2) the antiquity of organic residues, including when specific foodstuffs were exploited  (3) the chronology of sites in the absence of traditionally datable materials  and (4) direct verification of pottery typochronologies. Here we used the method to date the exploitation of dairy and carcass products in Neolithic vessels from Britain, Anatolia, central and western Europe, and Saharan Africa.


Using lipid residues absorbed in potsherds, the ages of pottery from various archaeological sites are determined and validated using sites for which the dates are well known from other methods.


  
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:20/0  |  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.


  
The rate of environmental fluctuations shapes ecological dynamics in a two-species microbial system 期刊论文
ECOLOGY LETTERS, 2019, 22 (5) : 838-846
作者:  Rodriguez-Verdugo, Alejandra;  Vulin, Clement;  Ackermann, Martin
收藏  |  浏览/下载:5/0  |  提交时间:2019/11/26
Acinetobacter johnsonii  cross-feeding  exploitation  mathematical modelling  population dynamics  Pseudomonas putida  rate of environmental change  resource competition  species interactions  synthetic communities  
A Novel Approach to Model Earth Fissure Caused by Extensive Aquifer Exploitation and its Application to the Wuxi Case, China 期刊论文
WATER RESOURCES RESEARCH, 2018, 54 (3) : 2249-2269
作者:  Ye, Shujun;  Franceschini, Andrea;  Zhang, Yan;  Janna, Carlo;  Gong, Xulong;  Yu, Jun;  Teatini, Pietro
收藏  |  浏览/下载:7/0  |  提交时间:2019/04/09
earth fissure  numerical modeling  extensive aquifer exploitation  application  Wuxi case  China  
Local residents' risk perceptions in response to shale gas exploitation: Evidence from China 期刊论文
ENERGY POLICY, 2018, 113: 123-134
作者:  Yu, Chin-Hsien;  Huang, Shih-Kai;  Qin, Ping;  Chen, Xiaolan
收藏  |  浏览/下载:4/0  |  提交时间:2019/04/09
Risk perception  Benefit perception  Shale gas exploitation  Environmental awareness  China  
Impacts of 25 years of groundwater extraction on subsidence in the Mekong delta, Vietnam 期刊论文
ENVIRONMENTAL RESEARCH LETTERS, 2017, 12 (6)
作者:  Minderhoud, P. S. J.;  Erkens, G.;  Pham, V. H.;  Bui, V. T.;  Erban, L.;  Kooi, H.;  Stouthamer, E.
收藏  |  浏览/下载:5/0  |  提交时间:2019/04/09
Delta subsidence  sea-level rise  groundwater exploitation  modelling  iMOD  
Fishing degrades size structure of coral reef fish communities 期刊论文
GLOBAL CHANGE BIOLOGY, 2017, 23 (3)
作者:  Robinson, James P. W.;  Williams, Ivor D.;  Edwards, Andrew M.;  McPherson, Jana;  Yeager, Lauren;  Vigliola, Laurent;  Brainard, Russell E.;  Baum, Julia K.
收藏  |  浏览/下载:12/0  |  提交时间:2019/04/09
body size  community structure  coral reef fish  exploitation  fisheries  macroecology  overfishing  size spectra  size-based approaches  
GALAXY: A new hybrid MOEA for the optimal design of Water Distribution Systems 期刊论文
WATER RESOURCES RESEARCH, 2017, 53 (3)
作者:  Wang, Q.;  Savic, D. A.;  Kapelan, Z.
收藏  |  浏览/下载:8/0  |  提交时间:2019/04/09
hybrid algorithm  exploration and exploitation  multiobjective design  Water Distribution System