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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.


  
Check for publication integrity before misconduct 期刊论文
NATURE, 2020, 577 (7789) : 167-169
作者:  Grey, Andrew;  Bolland, Mark J.;  Avenell, Alison;  Klein, Andrew A.;  Gunsalus, C. K.
收藏  |  浏览/下载:5/0  |  提交时间:2020/07/03
Where I work Andrew Digby 期刊论文
NATURE, 2020, 580 (7804) : 556-556
作者:  Archard, David;  Dabrock, Peter;  Delfraissy, Jean-Francois
收藏  |  浏览/下载:5/0  |  提交时间:2020/07/03

Andrew Digby works to protect the kakapo, a critically endangered and charismatic New Zealand species of parrot.


Andrew Digby works to protect the kakapo, a critically endangered and charismatic New Zealand species of parrot.


  
Climate: managing deep uncertainty 期刊论文
NATURE, 2020, 580 (7804) : 456-456
作者:  Johansson, Michael A.;  Saderi, Daniela
收藏  |  浏览/下载:4/0  |  提交时间:2020/07/03
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:19/0  |  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.


  
Preindustrial (CH4)-C-14 indicates greater anthropogenic fossil CH4 emissions 期刊论文
NATURE, 2020, 578 (7795) : 409-+
作者:  Keener, Megan;  Hunt, Camden;  Carroll, Timothy G.;  Kampel, Vladimir;  Dobrovetsky, Roman;  Hayton, Trevor W.;  Menard, Gabriel
收藏  |  浏览/下载:25/0  |  提交时间:2020/05/13

Atmospheric methane (CH4) is a potent greenhouse gas, and its mole fraction has more than doubled since the preindustrial era(1). Fossil fuel extraction and use are among the largest anthropogenic sources of CH4 emissions, but the precise magnitude of these contributions is a subject of debate(2,3). Carbon-14 in CH4 ((CH4)-C-14) can be used to distinguish between fossil (C-14-free) CH4 emissions and contemporaneous biogenic sources  however, poorly constrained direct (CH4)-C-14 emissions from nuclear reactors have complicated this approach since the middle of the 20th century(4,5). Moreover, the partitioning of total fossil CH4 emissions (presently 172 to 195 teragrams CH4 per year)(2,3) between anthropogenic and natural geological sources (such as seeps and mud volcanoes) is under debate  emission inventories suggest that the latter account for about 40 to 60 teragrams CH4 per year(6,7). Geological emissions were less than 15.4 teragrams CH4 per year at the end of the Pleistocene, about 11,600 years ago(8), but that period is an imperfect analogue for present-day emissions owing to the large terrestrial ice sheet cover, lower sea level and extensive permafrost. Here we use preindustrial-era ice core (CH4)-C-14 measurements to show that natural geological CH4 emissions to the atmosphere were about 1.6 teragrams CH4 per year, with a maximum of 5.4 teragrams CH4 per year (95 per cent confidence limit)-an order of magnitude lower than the currently used estimates. This result indicates that anthropogenic fossil CH4 emissions are underestimated by about 38 to 58 teragrams CH4 per year, or about 25 to 40 per cent of recent estimates. Our record highlights the human impact on the atmosphere and climate, provides a firm target for inventories of the global CH4 budget, and will help to inform strategies for targeted emission reductions(9,10).


Isotopic evidence from ice cores indicates that preindustrial-era geological methane emissions were lower than previously thought, suggesting that present-day emissions of methane from fossil fuels are underestimated.


  
Oceanic forcing of penultimate deglacial and last interglacial sea-level rise 期刊论文
NATURE, 2020, 577 (7792) : 660-+
作者:  Rizal, Yan;  Westaway, Kira E.;  Zaim, Yahdi;  van den Bergh, Gerrit D.;  Bettis, E. Arthur, III;  Morwood, Michael J.;  Huffman, O. Frank;  Grun, Rainer;  Joannes-Boyau, Renaud;  Bailey, Richard M.;  Sidarto;  Westaway, Michael C.;  Kurniawan, Iwan;  Moore, Mark W.;  Storey, Michael;  Aziz, Fachroel;  Suminto;  Zhao, Jian-xin;  Aswan;  Sipola, Maija E.;  Larick, Roy;  Zonneveld, John-Paul;  Scott, Robert;  Putt, Shelby;  Ciochon, Russell L.
收藏  |  浏览/下载:21/0  |  提交时间:2020/05/13

Sea-level histories during the two most recent deglacial-interglacial intervals show substantial differences(1-3) despite both periods undergoing similar changes in global mean temperature(4,5) and forcing from greenhouse gases(6). Although the last interglaciation (LIG) experienced stronger boreal summer insolation forcing than the present interglaciation(7), understanding why LIG global mean sea level may have been six to nine metres higher than today has proven particularly challenging(2). Extensive areas of polar ice sheets were grounded below sea level during both glacial and interglacial periods, with grounding lines and fringing ice shelves extending onto continental shelves(8). This suggests that oceanic forcing by subsurface warming may also have contributed to ice-sheet loss(9-12) analogous to ongoing changes in the Antarctic(13,14) and Greenland(15) ice sheets. Such forcing would have been especially effective during glacial periods, when the Atlantic Meridional Overturning Circulation (AMOC) experienced large variations on millennial timescales(16), with a reduction of the AMOC causing subsurface warming throughout much of the Atlantic basin(9,12,17). Here we show that greater subsurface warming induced by the longer period of reduced AMOC during the penultimate deglaciation can explain the more-rapid sea-level rise compared with the last deglaciation. This greater forcing also contributed to excess loss from the Greenland and Antarctic ice sheets during the LIG, causing global mean sea level to rise at least four metres above modern levels. When accounting for the combined influences of penultimate and LIG deglaciation on glacial isostatic adjustment, this excess loss of polar ice during the LIG can explain much of the relative sea level recorded by fossil coral reefs and speleothems at intermediate- and far-field sites.


  
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:31/0  |  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.


  
Double counting and the Paris Agreement rulebook 期刊论文
SCIENCE, 2019, 366 (6462) : 180-183
作者:  Schneider, Lambert;  Duan, Maosheng;  Stavins, Robert;  Kizzier, Kelley;  Broekhoff, Derik;  Jotzo, Frank;  Winkler, Harald;  Lazarus, Michael;  Howard, Andrew;  Hood, Christina
收藏  |  浏览/下载:8/0  |  提交时间:2019/11/27
Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility 期刊论文
SCIENCE, 2019, 365 (6460) : 1417-+
作者:  Patsopoulos, Nikolas A.;  39;Inca, Renata;  39;Alfonso, Sandra
收藏  |  浏览/下载:4/0  |  提交时间:2019/11/27