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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
Very regular high-frequency pulsation modes in young intermediate-mass stars 期刊论文
NATURE, 2020, 581 (7807) : 147-+
作者:  Zhao, Chuangqi;  Zhang, Pengchao;  Zhou, Jiajia;  Qi, Shuanhu;  Yamauchi, Yoshihiro;  Shi, Ruirui;  Fang, Ruochen;  Ishida, Yasuhiro;  Wang, Shutao;  Tomsia, Antoni P.;  Jiang, Lei;  Liu, Mingjie
收藏  |  浏览/下载:10/0  |  提交时间:2020/07/03

Asteroseismology probes the internal structures of stars by using their natural pulsation frequencies(1). It relies on identifying sequences of pulsation modes that can be compared with theoretical models, which has been done successfully for many classes of pulsators, including low-mass solar-type stars(2), red giants(3), high-mass stars(4) and white dwarfs(5). However, a large group of pulsating stars of intermediate mass-the so-called delta Scuti stars-have rich pulsation spectra for which systematic mode identification has not hitherto been possible(6,7). This arises because only a seemingly random subset of possible modes are excited and because rapid rotation tends to spoil regular patterns(8-10). Here we report the detection of remarkably regular sequences of high-frequency pulsation modes in 60 intermediate-mass main-sequence stars, which enables definitive mode identification. The space motions of some of these stars indicate that they are members of known associations of young stars, as confirmed by modelling of their pulsation spectra.


The pulsation spectra of intermediate-mass stars (so-called delta Scuti stars) have been challenging to analyse, but new observations of 60 such stars reveal remarkably regular sequences of high-frequency pulsation modes.


  
Origin of complexity in haemoglobin evolution 期刊论文
NATURE, 2020
作者:  Cheema, Suraj S.;  Kwon, Daewoong;  Shanker, Nirmaan;  dos Reis, Roberto;  Hsu, Shang-Lin;  Xiao, Jun;  Zhang, Haigang;  Wagner, Ryan;  Datar, Adhiraj;  McCarter, Margaret R.;  Serrao, Claudy R.;  Yadav, Ajay K.;  Karbasian, Golnaz;  Hsu, Cheng-Hsiang;  Tan, Ava J.;  Wang, Li-Chen;  Thakare, Vishal;  Zhang, Xiang;  Mehta, Apurva;  Karapetrova, Evguenia;  Chopdekar, Rajesh, V;  Shafer, Padraic;  Arenholz, Elke;  Hu, Chenming;  Proksch, Roger;  Ramesh, Ramamoorthy;  Ciston, Jim;  Salahuddin, Sayeef
收藏  |  浏览/下载:50/0  |  提交时间:2020/07/03

Most proteins associate into multimeric complexes with specific architectures(1,2), which often have functional properties such as cooperative ligand binding or allosteric regulation(3). No detailed knowledge is available about how any multimer and its functions arose during evolution. Here we use ancestral protein reconstruction and biophysical assays to elucidate the origins of vertebrate haemoglobin, a heterotetramer of paralogous alpha- and beta-subunits that mediates respiratory oxygen transport and exchange by cooperatively binding oxygen with moderate affinity. We show that modern haemoglobin evolved from an ancient monomer and characterize the historical '  missing link'  through which the modern tetramer evolved-a noncooperative homodimer with high oxygen affinity that existed before the gene duplication that generated distinct alpha- and beta-subunits. Reintroducing just two post-duplication historical substitutions into the ancestral protein is sufficient to cause strong tetramerization by creating favourable contacts with more ancient residues on the opposing subunit. These surface substitutions markedly reduce oxygen affinity and even confer cooperativity, because an ancient linkage between the oxygen binding site and the multimerization interface was already an intrinsic feature of the protein'  s structure. Our findings establish that evolution can produce new complex molecular structures and functions via simple genetic mechanisms that recruit existing biophysical features into higher-level architectures.


Experimental analysis of reconstructed ancestral globins reveals that haemoglobin'  s complex tetrameric structure and oxygen-binding functions evolved by simple genetic and biophysical mechanisms.


  
Global conservation of species' niches 期刊论文
NATURE, 2020, 580 (7802) : 232-+
作者:  Guo, Xiaoyan;  Aviles, Giovanni;  Liu, Yi;  Tian, Ruilin;  Unger, Bret A.;  Lin, Yu-Hsiu T.;  Wiita, Arun P.;  Xu, Ke;  Correia, M. Almira;  Kampmann, Martin
收藏  |  浏览/下载:29/0  |  提交时间:2020/07/03

Environmental change is rapidly accelerating, and many species will need to adapt to survive(1). Ensuring that protected areas cover populations across a broad range of environmental conditions could safeguard the processes that lead to such adaptations(1-3). However, international conservation policies have largely neglected these considerations when setting targets for the expansion of protected areas(4). Here we show that-of 19,937 vertebrate species globally(5-8)-the representation of environmental conditions across their habitats in protected areas (hereafter, niche representation) is inadequate for 4,836 (93.1%) amphibian, 8,653 (89.5%) bird and 4,608 (90.9%) terrestrial mammal species. Expanding existing protected areas to cover these gaps would encompass 33.8% of the total land surface-exceeding the current target of 17% that has been adopted by governments. Priority locations for expanding the system of protected areas to improve niche representation occur in global biodiversity hotspots(9), including Colombia, Papua New Guinea, South Africa and southwest China, as well as across most of the major land masses of the Earth. Conversely, we also show that planning for the expansion of protected areas without explicitly considering environmental conditions would marginally reduce the land area required to 30.7%, but that this would lead to inadequate niche representation for 7,798 (39.1%) species. As the governments of the world prepare to renegotiate global conservation targets, policymakers have the opportunity to help to maintain the adaptive potential of species by considering niche representation within protected areas(1,2).


Protected areas would need to expand to 33.8% of the total land surface to adequately represent environmental conditions across the habitats of amphibians, birds and terrestrial mammals, far exceeding the current 17% target.


  
CORONAVIRUS DIARIES: A NEW WORLD OF WORK 期刊论文
NATURE, 2020, 581 (7807) : 225-227
作者:  Maxmen, Amy
收藏  |  浏览/下载:9/0  |  提交时间:2020/07/03

John Tregoning gets to grips with a new world of work.


John Tregoning gets to grips with a new world of work.


  
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.


  
Electrically pumped topological laser with valley edge modes 期刊论文
NATURE, 2020, 578 (7794) : 246-+
作者:  Erickson, Peter;  van Asselt, Harro;  Koplow, Doug;  Lazarus, Michael;  Newell, Peter;  Oreskes, Naomi;  Supran, Geoffrey
收藏  |  浏览/下载:46/0  |  提交时间:2020/07/03

Quantum cascade lasers are compact, electrically pumped light sources in the technologically important mid-infrared and terahertz region of the electromagnetic spectrum(1,2). Recently, the concept of topology(3) has been expanded from condensed matter physics into photonics(4), giving rise to a new type of lasing(5-8) using topologically protected photonic modes that can efficiently bypass corners and defects(4). Previous demonstrations of topological lasers have required an external laser source for optical pumping and have operated in the conventional optical frequency regime(5-8). Here we demonstrate an electrically pumped terahertz quantum cascade laser based on topologically protected valley edge states(9-11). Unlike topological lasers that rely on large-scale features to impart topological protection, our compact design makes use of the valley degree of freedom in photonic crystals(10,11), analogous to two-dimensional gapped valleytronic materials(12). Lasing with regularly spaced emission peaks occurs in a sharp-cornered triangular cavity, even if perturbations are introduced into the underlying structure, owing to the existence of topologically protected valley edge states that circulate around the cavity without experiencing localization. We probe the properties of the topological lasing modes by adding different outcouplers to the topological cavity. The laser based on valley edge states may open routes to the practical use of topological protection in electrically driven laser sources.


  
A simple dynamic model explains the diversity of island birds worldwide 期刊论文
NATURE, 2020
作者:  Li, Junxue;  Wilson, C. Blake;  Cheng, Ran;  Lohmann, Mark;  Kavand, Marzieh;  Yuan, Wei;  Aldosary, Mohammed;  Agladze, Nikolay;  Wei, Peng;  Sherwin, Mark S.;  Shi, Jing
收藏  |  浏览/下载:13/0  |  提交时间:2020/07/03

Colonization, speciation and extinction are dynamic processes that influence global patterns of species richness(1-6). Island biogeography theory predicts that the contribution of these processes to the accumulation of species diversity depends on the area and isolation of the island(7,8). Notably, there has been no robust global test of this prediction for islands where speciation cannot be ignored(9), because neither the appropriate data nor the analytical tools have been available. Here we address both deficiencies to reveal, for island birds, the empirical shape of the general relationships that determine how colonization, extinction and speciation rates co-vary with the area and isolation of islands. We compiled a global molecular phylogenetic dataset of birds on islands, based on the terrestrial avifaunas of 41 oceanic archipelagos worldwide (including 596 avian taxa), and applied a new analysis method to estimate the sensitivity of island-specific rates of colonization, speciation and extinction to island features (area and isolation). Our model predicts-with high explanatory power-several global relationships. We found a decline in colonization with isolation, a decline in extinction with area and an increase in speciation with area and isolation. Combining the theoretical foundations of island biogeography(7,8) with the temporal information contained in molecular phylogenies(10) proves a powerful approach to reveal the fundamental relationships that govern variation in biodiversity across the planet.


Using a global molecular phylogenetic dataset of birds on islands, the sensitivity of island-specific rates of colonization, speciation and extinction to island features (area and isolation) is estimated.


  
The repertoire of mutational signatures in human cancer 期刊论文
NATURE, 2020, 578 (7793) : 94-+
作者:  Ciurlo, Anna;  39;Neil, Kelly Kosmo
收藏  |  浏览/下载:7/0  |  提交时间:2020/07/03

Somatic mutations in cancer genomes are caused by multiple mutational processes, each of which generates a characteristic mutational signature(1). Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium(2) of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we characterized mutational signatures using 84,729,690 somatic mutations from 4,645 whole-genome and 19,184 exome sequences that encompass most types of cancer. We identified 49 single-base-substitution, 11 doublet-base-substitution, 4 clustered-base-substitution and 17 small insertion-and-deletion signatures. The substantial size of our dataset, compared with previous analyses(3-15), enabled the discovery of new signatures, the separation of overlapping signatures and the decomposition of signatures into components that may represent associated-but distinct-DNA damage, repair and/or replication mechanisms. By estimating the contribution of each signature to the mutational catalogues of individual cancer genomes, we revealed associations of signatures to exogenous or endogenous exposures, as well as to defective DNA-maintenance processes. However, many signatures are of unknown cause. This analysis provides a systematic perspective on the repertoire of mutational processes that contribute to the development of human cancer.