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Not all driver mutations are equal 期刊论文
NATURE, 2020, 580 (7805) : 595-596
作者:  Legendre, Lucas J.;  Rubilar-Rogers, David;  Musser, Grace M.;  Davis, Sarah N.;  Otero, Rodrigo A.;  Vargas, Alexander O.;  Clarke, Julia A.
收藏  |  浏览/下载:12/0  |  提交时间:2020/07/03

A study of cancer-associated mutations in normal endometrial glands of the uterus has now been performed using whole-genome sequencing. The analysis sheds light on the early changes that lead to invasive disease.


  
Revealing enigmatic mucus structures in the deep sea using DeepPIV 期刊论文
NATURE, 2020, 583 (7814) : 78-+
作者:  Nguyen, Ngoc Uyen Nhi;  Canseco, Diana C.;  Xiao, Feng;  Nakada, Yuji;  Li, Shujuan;  Lam, Nicholas T.;  Muralidhar, Shalini A.;  Savla, Jainy J.;  Hill, Joseph A.;  Le, Victor;  Zidan, Kareem A.;  El-Feky, Hamed W.;  Wang, Zhaoning;  Ahmed, Mahmoud Salama;  Hubbi, Maimon E.;  Menendez-Montes, Ivan
收藏  |  浏览/下载:13/0  |  提交时间:2020/06/09

Advanced deep-sea imaging tools yield insights into the structure and function of mucus filtration houses built by midwater giant larvaceans.


Many animals build complex structures to aid in their survival, but very few are built exclusively from materials that animals create (1,2). In the midwaters of the ocean, mucoid structures are readily secreted by numerous animals, and serve many vital functions(3,4). However, little is known about these mucoid structures owing to the challenges of observing them in the deep sea. Among these mucoid forms, the '  houses'  of larvaceans are marvels of nature(5), and in the ocean twilight zone giant larvaceans secrete and build mucus filtering structures that can reach diameters of more than 1 m(6). Here we describe in situ laser-imaging technology(7) that reconstructs three-dimensional models of mucus forms. The models provide high-resolution views of giant larvacean houses and elucidate the role that house structure has in food capture and predator avoidance. Now that tools exist to study mucus structures found throughout the ocean, we can shed light on some of nature'  s most complex forms.


  
International evaluation of an AI system for breast cancer screening 期刊论文
NATURE, 2020, 577 (7788) : 89-+
作者:  McKinney, Scott Mayer;  Sieniek, Marcin;  Godbole, Varun;  Godwin, Jonathan;  Antropova, Natasha;  Ashrafian, Hutan;  Back, Trevor;  Chesus, Mary;  Corrado, Greg C.;  Darzi, Ara;  Etemadi, Mozziyar;  Garcia-Vicente, Florencia;  Gilbert, Fiona J.;  Halling-Brown, Mark;  Hassabis, Demis;  Jansen, Sunny;  Karthikesalingam, Alan;  Kelly, Christopher J.;  King, Dominic;  Ledsam, Joseph R.;  Melnick, David;  Mostofi, Hormuz;  Peng, Lily;  Reicher, Joshua Jay;  Romera-Paredes, Bernardino;  Sidebottom, Richard;  Suleyman, Mustafa;  Tse, Daniel;  Young, Kenneth C.;  De Fauw, Jeffrey;  Shetty, Shravya
收藏  |  浏览/下载:15/0  |  提交时间:2020/07/03

Screening mammography aims to identify breast cancer at earlier stages of the disease, when treatment can be more successful(1). Despite the existence of screening programmes worldwide, the interpretation of mammograms is affected by high rates of false positives and false negatives(2). Here we present an artificial intelligence (AI) system that is capable of surpassing human experts in breast cancer prediction. To assess its performance in the clinical setting, we curated a large representative dataset from the UK and a large enriched dataset from the USA. We show an absolute reduction of 5.7% and 1.2% (USA and UK) in false positives and 9.4% and 2.7% in false negatives. We provide evidence of the ability of the system to generalize from the UK to the USA. In an independent study of six radiologists, the AI system outperformed all of the human readers: the area under the receiver operating characteristic curve (AUC-ROC) for the AI system was greater than the AUC-ROC for the average radiologist by an absolute margin of 11.5%. We ran a simulation in which the AI system participated in the double-reading process that is used in the UK, and found that the AI system maintained non-inferior performance and reduced the workload of the second reader by 88%. This robust assessment of the AI system paves the way for clinical trials to improve the accuracy and efficiency of breast cancer screening.


  
Coupling delay controls synchronized oscillation in the segmentation clock 期刊论文
NATURE, 2020
作者:  Yoshioka-Kobayashi, Kumiko;  Matsumiya, Marina;  Niino, Yusuke;  Isomura, Akihiro;  Kori, Hiroshi;  Miyawaki, Atsushi;  Kageyama, Ryoichiro
收藏  |  浏览/下载:7/0  |  提交时间:2020/07/03

Individual cellular activities fluctuate but are constantly coordinated at the population level via cell-cell coupling. A notable example is the somite segmentation clock, in which the expression of clock genes (such as Hes7) oscillates in synchrony between the cells that comprise the presomitic mesoderm (PSM)(1,2). This synchronization depends on the Notch signalling pathway  inhibiting this pathway desynchronizes oscillations, leading to somite fusion(3-7). However, how Notch signalling regulates the synchronicity of HES7 oscillations is unknown. Here we establish a live-imaging system using a new fluorescent reporter (Achilles), which we fuse with HES7 to monitor synchronous oscillations in HES7 expression in the mouse PSM at a single-cell resolution. Wild-type cells can rapidly correct for phase fluctuations in HES7 oscillations, whereas the absence of the Notch modulator gene lunatic fringe (Lfng) leads to a loss of synchrony between PSM cells. Furthermore, HES7 oscillations are severely dampened in individual cells of Lfng-null PSM. However, when Lfng-null PSM cells were completely dissociated, the amplitude and periodicity of HES7 oscillations were almost normal, which suggests that LFNG is involved mostly in cell-cell coupling. Mixed cultures of control and Lfng-null PSM cells, and an optogenetic Notch signalling reporter assay, revealed that LFNG delays the signal-sending process of intercellular Notch signalling transmission. These results-together with mathematical modelling-raised the possibility that Lfng-null PSM cells shorten the coupling delay, thereby approaching a condition known as the oscillation or amplitude death of coupled oscillators(8). Indeed, a small compound that lengthens the coupling delay partially rescues the amplitude and synchrony of HES7 oscillations in Lfng-null PSM cells. Our study reveals a delay control mechanism of the oscillatory networks involved in somite segmentation, and indicates that intercellular coupling with the correct delay is essential for synchronized oscillation.


Monitoring cells of the mouse presomitic mesoderm using the Achilles reporter fused to HES7 sheds light on the mechanisms that underpin synchronous oscillations in the expression of clock genes between neighbouring cells.


  
Single-chain heteropolymers transport protons selectively and rapidly 期刊论文
NATURE, 2020, 577 (7789) : 216-+
作者:  Jiang, Tao;  Hall, Aaron;  Eres, Marco;  Hemmatian, Zahra;  Qiao, Baofu;  Zhou, Yun;  Ruan, Zhiyuan;  Couse, Andrew D.;  Heller, William T.;  Huang, Haiyan;  de la Cruz, Monica Olvera;  Rolandi, Marco;  Xu, Ting
收藏  |  浏览/下载:9/0  |  提交时间:2020/07/03

Precise protein sequencing and folding are believed to generate the structure and chemical diversity of natural channels(1,2), both of which are essential to synthetically achieve proton transport performance comparable to that seen in natural systems. Geometrically defined channels have been fabricated using peptides, DNAs, carbon nanotubes, sequence-defined polymers and organic frameworks(3-13). However, none of these channels rivals the performance observed in their natural counterparts. Here we show that without forming an atomically structured channel, four-monomer-based random heteropolymers (RHPs)(14) can mimic membrane proteins and exhibit selective proton transport across lipid bilayers at a rate similar to those of natural proton channels. Statistical control over the monomer distribution in an RHP leads to segmental heterogeneity in hydrophobicity, which facilitates the insertion of single RHPs into the lipid bilayers. It also results in bilayer-spanning segments containing polar monomers that promote the formation of hydrogen-bonded chains(15,16) for proton transport. Our study demonstrates the importance of the adaptability that is enabled by statistical similarity among RHP chains and of the modularity provided by the chemical diversity of monomers, to achieve uniform behaviour in heterogeneous systems. Our results also validate statistical randomness as an unexplored approach to realize protein-like behaviour at the single-polymer-chain level in a predictable manner.


  
Rapid non-uniform adaptation to conformation-specific KRAS(G12C) inhibition 期刊论文
NATURE, 2020, 577 (7790) : 421-+
作者:  Xue, Jenny Y.;  Zhao, Yulei;  Aronowitz, Jordan;  Mai, Trang T.;  Vides, Alberto;  Qeriqi, Besnik;  Kim, Dongsung;  Li, Chuanchuan;  de Stanchina, Elisa;  Mazutis, Linas;  Risso, Davide;  Lito, Piro
收藏  |  浏览/下载:13/0  |  提交时间:2020/07/03

KRAS GTPases are activated in one-third of cancers, and KRAS(G12C) is one of the most common activating alterations in lung adenocarcinoma(1,2). KRAS(G12C) inhibitors(3,4) are in phase-I clinical trials and early data show partial responses in nearly half of patients with lung cancer. How cancer cells bypass inhibition to prevent maximal response to therapy is not understood. Because KRAS(G12C) cycles between an active and inactive conformation(4-6), and the inhibitors bind only to the latter, we tested whether isogenic cell populations respond in a non-uniform manner by studying the effect of treatment at a single-cell resolution. Here we report that, shortly after treatment, some cancer cells are sequestered in a quiescent state with low KRAS activity, whereas others bypass this effect to resume proliferation. This rapid divergent response occurs because some quiescent cells produce new KRAS(G12C) in response to suppressed mitogen-activated protein kinase output. New KRAS(G12C) is maintained in its active, drug-insensitive state by epidermal growth factor receptor and aurora kinase signalling. Cells without these adaptive changes-or cells in which these changes are pharmacologically inhibited-remain sensitive to drug treatment, because new KRAS(G12C) is either not available or exists in its inactive, drug-sensitive state. The direct targeting of KRAS oncoproteins has been a longstanding objective in precision oncology. Our study uncovers a flexible non-uniform fitness mechanism that enables groups of cells within a population to rapidly bypass the effect of treatment. This adaptive process must be overcome if we are to achieve complete and durable responses in the clinic.


  
A sensory appendage protein protects malaria vectors from pyrethroids 期刊论文
NATURE, 2020, 577 (7790) : 376-+
作者:  Coyle, Diane
收藏  |  浏览/下载:32/0  |  提交时间:2020/07/03

Pyrethroid-impregnated bed nets have driven considerable reductions in malaria-associated morbidity and mortality in Africa since the beginning of the century(1). The intense selection pressure exerted by bed nets has precipitated widespread and escalating resistance to pyrethroids in African Anopheles populations, threatening to reverse the gains that been made by malaria control(2). Here we show that expression of a sensory appendage protein (SAP2), which is enriched in the legs, confers pyrethroid resistance to Anopheles gambiae. Expression of SAP2 is increased in insecticide-resistant populations and is further induced after the mosquito comes into contact with pyrethroids. SAP2 silencing fully restores mortality of the mosquitoes, whereas SAP2 overexpression results in increased resistance, probably owing to high-affinity binding of SAP2 to pyrethroid insecticides. Mining of genome sequence data reveals a selective sweep near the SAP2 locus in the mosquito populations of three West African countries (Cameroon, Guinea and Burkina Faso) with the observed increase in haplotype-associated single-nucleotide polymorphisms mirroring the increasing resistance of mosquitoes to pyrethroids reported in Burkina Faso. Our study identifies a previously undescribed mechanism of insecticide resistance that is likely to be highly relevant to malaria control efforts.


  
Lagrangian-based Simulations of Hypervelocity Impact Experiments on Mars Regolith Proxy 期刊论文
GEOPHYSICAL RESEARCH LETTERS, 2020, 47 (13)
作者:  Froment, M.;  Rougier, E.;  Larmat, C.;  Lei, Z.;  Euser, B.;  Kedar, S.;  Richardson, J. E.;  Kawamura, T.;  Lognonne, P.
收藏  |  浏览/下载:13/0  |  提交时间:2020/05/25
Parametric study  Lagrangian numerical model  Shock wave  granular media  Mars regolith  Impact  
Spectroscopic confirmation of a mature galaxy cluster at a redshift of 2 期刊论文
NATURE, 2020, 577 (7788) : 39-+
作者:  Willis, J. P.;  Canning, R. E. A.;  Noordeh, E. S.;  Allen, S. W.;  King, A. L.;  Mantz, A.;  Morris, R. G.;  Stanford, S. A.;  Brammer, G.
收藏  |  浏览/下载:12/0  |  提交时间:2020/07/03

Galaxy clusters are the most massive virialized structures in the Universe and are formed through the gravitational accretion of matter over cosmic time(1). The discovery(2) of an evolved galaxy cluster at redshift z = 2, corresponding to a look-back time of 10.4 billion years, provides an opportunity to study its properties. The galaxy cluster XLSSC 122 was originally detected as a faint, extended X-ray source in the XMM Large Scale Structure survey and was revealed to be coincident with a compact over-density of galaxies(2) with photometric redshifts of 1.9 +/- 0.2. Subsequent observations3 at millimetre wavelengths detected a Sunyaev-Zel'  dovich decrement along the line of sight to XLSSC 122, thus confirming the existence of hot intracluster gas, while deep imaging spectroscopy from the European Space Agency'  s X-ray Multi-Mirror Mission (XMM-Newton) revealed(4) an extended, X-ray-bright gaseous atmosphere with a virial temperature of 60 million Kelvin, enriched with metals to the same extent as are local clusters. Here we report optical spectroscopic observations of XLSSC 122 and identify 37 member galaxies at a mean redshift of 1.98, corresponding to a look-back time of 10.4 billion years. We use photometry to determine a mean, dust-free stellar age of 2.98 billion years, indicating that star formation commenced in these galaxies at a mean redshift of 12, when the Universe was only 370 million years old. The full range of inferred formation redshifts, including the effects of dust, covers the interval from 7 to 13. These observations confirm that XLSSC 122 is a remarkably mature galaxy cluster with both evolved stellar populations in the member galaxies and a hot, metal-rich gas composing the intracluster medium.


  
The proteome landscape of the kingdoms of life 期刊论文
NATURE, 2020
作者:  Arzi, Anat;  Rozenkrantz, Liron;  Gorodisky, Lior;  Rozenkrantz, Danit;  Holtzman, Yael;  Ravia, Aharon;  Bekinschtein, Tristan A.;  Galperin, Tatyana;  Krimchansky, Ben-Zion;  Cohen, Gal;  Oksamitni, Anna;  Aidinoff, Elena;  Sacher, Yaron;  Sobel, Noam
收藏  |  浏览/下载:14/0  |  提交时间:2020/07/03

Proteins carry out the vast majority of functions in all biological domains, but for technological reasons their large-scale investigation has lagged behind the study of genomes. Since the first essentially complete eukaryotic proteome was reported(1), advances in mass-spectrometry-based proteomics(2)have enabled increasingly comprehensive identification and quantification of the human proteome(3-6). However, there have been few comparisons across species(7,8), in stark contrast with genomics initiatives(9). Here we use an advanced proteomics workflow-in which the peptide separation step is performed by a microstructured and extremely reproducible chromatographic system-for the in-depth study of 100 taxonomically diverse organisms. With two million peptide and 340,000 stringent protein identifications obtained in a standardized manner, we double the number of proteins with solid experimental evidence known to the scientific community. The data also provide a large-scale case study for sequence-based machine learning, as we demonstrate by experimentally confirming the predicted properties of peptides fromBacteroides uniformis. Our results offer a comparative view of the functional organization of organisms across the entire evolutionary range. A remarkably high fraction of the total proteome mass in all kingdoms is dedicated to protein homeostasis and folding, highlighting the biological challenge of maintaining protein structure in all branches of life. Likewise, a universally high fraction is involved in supplying energy resources, although these pathways range from photosynthesis through iron sulfur metabolism to carbohydrate metabolism. Generally, however, proteins and proteomes are remarkably diverse between organisms, and they can readily be explored and functionally compared at www.proteomesoflife.org.