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Global status and conservation potential of reef sharks 期刊论文
Nature, 2020
作者:  M. Aaron MacNeil;  Demian D. Chapman;  Michelle Heupel;  Colin A. Simpfendorfer;  Michael Heithaus;  Mark Meekan;  Euan Harvey;  Jordan Goetze;  Jeremy Kiszka;  Mark E. Bond;  Leanne M. Currey-Randall;  Conrad W. Speed;  C. Samantha Sherman;  Matthew J. Rees;  Vinay Udyawer;  Kathryn I. Flowers;  Gina Clementi;  Jasmine Valentin-Albanese;  Taylor Gorham;  M. Shiham Adam;  Khadeeja Ali;  Fabiá;  n Pina-Amargó;  s;  Jorge A. Angulo-Valdé;  s;  Jacob Asher;  Laura Garcí;  a Barcia;  Océ;  ane Beaufort;  Cecilie Benjamin;  Anthony T. F. Bernard;  Michael L. Berumen;  Stacy Bierwagen;  Erika Bonnema;  Rosalind M. K. Bown;  Darcey Bradley;  Edd Brooks;  J. Jed Brown;  Dayne Buddo;  Patrick Burke;  Camila Cá;  ceres;  Diego Cardeñ;  osa;  Jeffrey C. Carrier;  Jennifer E. Caselle;  Venkatesh Charloo;  Thomas Claverie;  Eric Clua;  Jesse E. M. Cochran;  Neil Cook;  Jessica Cramp;  Brooke D’;  Alberto;  Martin de Graaf;  Mareike Dornhege;  Andy Estep;  Lanya Fanovich;  Naomi F. Farabough;  Daniel Fernando;  Anna L. Flam;  Camilla Floros;  Virginia Fourqurean;  Ricardo Garla;  Kirk Gastrich;  Lachlan George;  Rory Graham;  Tristan Guttridge;  Royale S. Hardenstine;  Stephen Heck;  Aaron C. Henderson;  Heidi Hertler;  Robert Hueter;  Mohini Johnson;  Stacy Jupiter;  Devanshi Kasana;  Steven T. Kessel;  Benedict Kiilu;  Taratu Kirata;  Baraka Kuguru;  Fabian Kyne;  Tim Langlois;  Elodie J. I. Lé;  ;  e;  Steve Lindfield;  Andrea Luna-Acosta;  Jade Maggs;  B. Mabel Manjaji-Matsumoto;  Andrea Marshall;  Philip Matich;  Erin McCombs;  Dianne McLean;  Llewelyn Meggs;  Stephen Moore;  Sushmita Mukherji;  Ryan Murray;  Muslimin Kaimuddin;  Stephen J. Newman;  Josep Nogué;  s;  Clay Obota;  Owen O’;  Shea;  Kennedy Osuka;  Yannis P. Papastamatiou;  Nishan Perera;  Bradley Peterson;  Alessandro Ponzo;  Andhika Prasetyo;  L. M. Sjamsul Quamar;  Jessica Quinlan;  Alexei Ruiz-Abierno;  Enric Sala;  Melita Samoilys;  Michelle Schä;  rer-Umpierre;  Audrey Schlaff;  Nikola Simpson;  Adam N. H. Smith;  Lauren Sparks;  Akshay Tanna;  Rubé;  n Torres;  Michael J. Travers;  Maurits van Zinnicq Bergmann;  Laurent Vigliola;  Juney Ward;  Alexandra M. Watts;  Colin Wen;  Elizabeth Whitman;  Aaron J. Wirsing;  Aljoscha Wothke;  Esteban Zarza-Gonzâ;  lez;  Joshua E. Cinner
收藏  |  浏览/下载:17/0  |  提交时间:2020/08/09
Future changes in the trading of virtual water 期刊论文
NATURE COMMUNICATIONS, 2020, 11 (1)
作者:  Graham, Neal T.;  Hejazi, Mohamad, I;  Kim, Son H.;  Davies, Evan G. R.;  Edmonds, James A.;  Miralles-Wilhelm, Fernando
收藏  |  浏览/下载:15/0  |  提交时间:2020/08/09
Representing the function and sensitivity of coastal interfaces in Earth system models 期刊论文
NATURE COMMUNICATIONS, 2020, 11 (1)
作者:  Ward, Nicholas D.;  Megonigal, J. Patrick;  Bond-Lamberty, Ben;  Bailey, Vanessa L.;  Butman, David;  Canuel, Elizabeth A.;  Diefenderfer, Heida;  Ganju, Neil K.;  Goni, Miguel A.;  Graham, Emily B.;  Hopkinson, Charles S.;  Khangaonkar, Tarang;  Langley, J. Adam;  McDowell, Nate G.;  Myers-Pigg, Allison N.;  Neumann, Rebecca B.;  Osburn, Christopher L.;  Price, Rene M.;  Rowland, Joel;  Sengupta, Aditi;  Simard, Marc;  Thornton, Peter E.;  Tzortziou, Maria;  Vargas, Rodrigo;  Weisenhorn, Pamela B.;  Windham-Myers, Lisamarie
收藏  |  浏览/下载:13/0  |  提交时间:2020/05/20
Phosphorus-limited conditions in the early Neoproterozoic ocean maintained low levels of atmospheric oxygen 期刊论文
NATURE GEOSCIENCE, 2020, 13 (4) : 296-+
作者:  Guilbaud, Romain;  Poulton, Simon W.;  Thompson, Jennifer;  Husband, Kathryn F.;  Zhu, Maoyan;  Zhou, Ying;  Shields, Graham A.;  Lenton, Timothy M.
收藏  |  浏览/下载:7/0  |  提交时间:2020/05/13
Ocean acidification does not impair the behaviour of coral reef fishes 期刊论文
NATURE, 2020, 577 (7790) : 370-+
作者:  Clark, Timothy D.;  Raby, Graham D.;  Roche, Dominique G.;  Binning, Sandra A.;  Speers-Roesch, Ben;  Jutfelt, Fredrik;  Sundin, Josefin
收藏  |  浏览/下载:10/0  |  提交时间:2020/07/03

The partial pressure of CO2 in the oceans has increased rapidly over the past century, driving ocean acidification and raising concern for the stability of marine ecosystems(1-3). Coral reef fishes are predicted to be especially susceptible to end-of-century ocean acidification on the basis of several high-profile papers(4,5) that have reported profound behavioural and sensory impairments-for example, complete attraction to the chemical cues of predators under conditions of ocean acidification. Here, we comprehensively and transparently show that-in contrast to previous studies-end-of-century ocean acidification levels have negligible effects on important behaviours of coral reef fishes, such as the avoidance of chemical cues from predators, fish activity levels and behavioural lateralization (left-right turning preference). Using data simulations, we additionally show that the large effect sizes and small within-group variances that have been reported in several previous studies are highly improbable. Together, our findings indicate that the reported effects of ocean acidification on the behaviour of coral reef fishes are not reproducible, suggesting that behavioural perturbations will not be a major consequence for coral reef fishes in high CO2 oceans.


  
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes 期刊论文
NATURE, 2020, 578 (7793) : 102-+
作者:  Clark, Timothy D.;  Raby, Graham D.;  Roche, Dominique G.;  Binning, Sandra A.;  Speers-Roesch, Ben;  Jutfelt, Fredrik;  Sundin, Josefin
收藏  |  浏览/下载:15/0  |  提交时间:2020/07/03

The discovery of drivers of cancer has traditionally focused on protein-coding genes(1-4). Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium(5) of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers(6,7), raise doubts about others and identify novel candidates, including point mutations in the 5'  region of TP53, in the 3'  untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.


  
Electron Bernstein waves driven by electron crescents near the electron diffusion region 期刊论文
NATURE COMMUNICATIONS, 2020, 11 (1)
作者:  Li, W. Y.;  Graham, D. B.;  Khotyaintsev, Yu. V.;  Vaivads, A.;  Andre, M.;  Min, K.;  Liu, K.;  Tang, B. B.;  Wang, C.;  Fujimoto, K.;  Norgren, C.;  Toledo-Redondo, S.;  Lindqvist, P. -A.;  Ergun, R. E.;  Torbert, R. B.;  Rager, A. C.;  Dorelli, J. C.;  Gershman, D. J.;  Giles, B. L.;  Lavraud, B.;  Plaschke, F.;  Magnes, W.;  Le Contel, O.;  Russell, C. T.;  Burch, J. L.
收藏  |  浏览/下载:19/0  |  提交时间:2020/05/13
An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity 期刊论文
NATURE, 2020, 577 (7791) : 572-+
作者:  Athukoralage, Januka S.;  McMahon, Stephen A.;  Zhang, Changyi;  Grueschow, Sabine;  Graham, Shirley;  Krupovic, Mart;  Whitaker, Rachel J.;  Gloster, Tracey M.;  White, Malcolm F.
收藏  |  浏览/下载:5/0  |  提交时间:2020/07/03

The CRISPR system in bacteria and archaea provides adaptive immunity against mobile genetic elements. Type III CRISPR systems detect viral RNA, resulting in the activation of two regions of the Cas10 protein: an HD nuclease domain (which degrades viral DNA)(1,2) and a cyclase domain (which synthesizes cyclic oligoadenylates from ATP)(3-5). Cyclic oligoadenylates in turn activate defence enzymes with a CRISPR-associated Rossmann fold domain(6), sculpting a powerful antiviral response(7-10) that can drive viruses to extinction(7,8). Cyclic nucleotides are increasingly implicated in host-pathogen interactions(11-13). Here we identify a new family of viral anti-CRISPR (Acr) enzymes that rapidly degrade cyclic tetra-adenylate (cA(4)). The viral ring nuclease AcrIII-1 is widely distributed in archaeal and bacterial viruses and in proviruses. The enzyme uses a previously unknown fold to bind cA(4) specifically, and a conserved active site to rapidly cleave this signalling molecule, allowing viruses to neutralize the type III CRISPR defence system. The AcrIII-1 family has a broad host range, as it targets cA(4) signalling molecules rather than specific CRISPR effector proteins. Our findings highlight the crucial role of cyclic nucleotide signalling in the conflict between viruses and their hosts.


Bacteria and archaea use cyclic oligoadenylate molecules as part of the CRISPR system for antiviral defence  here, a family of viral enzymes that rapidly degrades cyclic oligoadenylates is identified and biochemically and structurally described.


  
Zucchini consensus motifs determine the mechanism of pre-piRNA production 期刊论文
NATURE, 2020, 578 (7794) : 311-+
作者:  Clark, Timothy D.;  Raby, Graham D.;  Roche, Dominique G.;  Binning, Sandra A.;  Speers-Roesch, Ben;  Jutfelt, Fredrik;  Sundin, Josefin
收藏  |  浏览/下载:14/0  |  提交时间:2020/07/03

PIWI-interacting RNAs (piRNAs) of between approximately 24 and 31 nucleotides in length guide PIWI proteins to silence transposons in animal gonads, thereby ensuring fertility(1). In the biogenesis of piRNAs, PIWI proteins are first loaded with 5 '  -monophosphorylated RNA fragments called pre-pre-piRNAs, which then undergo endonucleolytic cleavage to produce pre-piRNAs(1,2). Subsequently, the 3 '  -ends of pre-piRNAs are trimmed by the exonuclease Trimmer (PNLDC1 in mouse)(3-6) and 2 '  -O-methylated by the methyltransferase Hen1 (HENMT1 in mouse)(7-9), generating mature piRNAs. It is assumed that the endonuclease Zucchini (MitoPLD in mouse) is a major enzyme catalysing the cleavage of pre-pre-piRNAs into pre-piRNAs(10-13). However, direct evidence for this model is lacking, and how pre-piRNAs are generated remains unclear. Here, to analyse pre-piRNA production, we established a Trimmer-knockout silkworm cell line and derived a cell-free system that faithfully recapitulates Zucchini-mediated cleavage of PIWI-loaded pre-pre-piRNAs. We found that pre-piRNAs are generated by parallel Zucchini-dependent and -independent mechanisms. Cleavage by Zucchini occurs at previously unrecognized consensus motifs on pre-pre-piRNAs, requires the RNA helicase Armitage, and is accompanied by 2 '  -O-methylation of pre-piRNAs. By contrast, slicing of pre-pre-piRNAs with weak Zucchini motifs is achieved by downstream complementary piRNAs, producing pre-piRNAs without 2 '  -O-methylation. Regardless of the endonucleolytic mechanism, pre-piRNAs are matured by Trimmer and Hen1. Our findings highlight multiplexed processing of piRNA precursors that supports robust and flexible piRNA biogenesis.


A silkworm model recapitulates key steps of Zucchini-mediated cleavage of pre-pre-piRNA and provides insights into Zucchini-mediated and -independent pathways that generate pre-piRNAs, which converge to a common piRNA maturation step.


  
AQP5 enriches for stem cells and cancer origins in the distal stomach 期刊论文
NATURE, 2020, 578 (7795) : 437-+
作者:  Athukoralage, Januka S.;  McMahon, Stephen A.;  Zhang, Changyi;  Grueschow, Sabine;  Graham, Shirley;  Krupovic, Mart;  Whitaker, Rachel J.;  Gloster, Tracey M.;  White, Malcolm F.
收藏  |  浏览/下载:17/0  |  提交时间:2020/07/03

LGR5 marks resident adult epithelial stem cells at the gland base in the mouse pyloric stomach(1), but the identity of the equivalent human stem cell population remains unknown owing to a lack of surface markers that facilitate its prospective isolation and validation. In mouse models of intestinal cancer, LGR5(+) intestinal stem cells are major sources of cancer following hyperactivation of the WNT pathway(2). However, the contribution of pyloric LGR5(+) stem cells to gastric cancer following dysregulation of the WNT pathway-a frequent event in gastric cancer in humans(3)-is unknown. Here we use comparative profiling of LGR5(+) stem cell populations along the mouse gastrointestinal tract to identify, and then functionally validate, the membrane protein AQP5 as a marker that enriches for mouse and human adult pyloric stem cells. We show that stem cells within the AQP5(+) compartment are a source of WNT-driven, invasive gastric cancer in vivo, using newly generated Aqp5-creERT2 mouse models. Additionally, tumour-resident AQP5(+) cells can selectively initiate organoid growth in vitro, which indicates that this population contains potential cancer stem cells. In humans, AQP5 is frequently expressed in primary intestinal and diffuse subtypes of gastric cancer (and in metastases of these subtypes), and often displays altered cellular localization compared with healthy tissue. These newly identified markers and mouse models will be an invaluable resource for deciphering the early formation of gastric cancer, and for isolating and characterizing human-stomach stem cells as a prerequisite for harnessing the regenerative-medicine potential of these cells in the clinic.


AQP5 is identified as a marker for pyloric stem cells in humans and mice, and stem cells in the AQP5(+) compartment are shown to be a source of invasive gastric cancer in mouse models.