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Frequent mutations that converge on the NFKBIZ pathway in ulcerative colitis 期刊论文
NATURE, 2020, 577 (7789) : 260-+
作者:  Kakiuchi, Nobuyuki;  Yoshida, Kenichi;  Uchino, Motoi;  Kihara, Takako;  Akaki, Kotaro;  Inoue, Yoshikage;  Kawada, Kenji;  Nagayama, Satoshi;  Yokoyama, Akira;  Yamamoto, Shuji;  Matsuura, Minoru;  Horimatsu, Takahiro;  Hirano, Tomonori;  Goto, Norihiro;  Takeuchi, Yasuhide;  Ochi, Yotaro;  Shiozawa, Yusuke;  Kogure, Yasunori;  Watatani, Yosaku;  Fujii, Yoichi;  Kim, Soo Ki;  Kon, Ayana;  Kataoka, Keisuke;  Yoshizato, Tetsuichi;  Nakagawa, Masahiro M.;  Yoda, Akinori;  Nanya, Yasuhito;  Makishima, Hideki;  Shiraishi, Yuichi;  Chiba, Kenichi;  Tanaka, Hiroko;  Sanada, Masashi;  Sugihara, Eiji;  Sato, Taka-aki;  Maruyama, Takashi;  Miyoshi, Hiroyuki;  Taketo, Makoto Mark;  Oishi, Jun;  Inagaki, Ryosaku;  Ueda, Yutaka;  Okamoto, Shinya;  Okajima, Hideaki;  Sakai, Yoshiharu;  Sakurai, Takaki;  Haga, Hironori;  Hirota, Seiichi;  Ikeuchi, Hiroki;  Nakase, Hiroshi;  Marusawa, Hiroyuki;  Chiba, Tsutomu;  Takeuchi, Osamu;  Miyano, Satoru;  Seno, Hiroshi;  Ogawa, Seishi
收藏  |  浏览/下载:80/0  |  提交时间:2020/07/03

Chronic inflammation is accompanied by recurring cycles of tissue destruction and repair and is associated with an increased risk of cancer(1-3). However, how such cycles affect the clonal composition of tissues, particularly in terms of cancer development, remains unknown. Here we show that in patients with ulcerative colitis, the inflamed intestine undergoes widespread remodelling by pervasive clones, many of which are positively selected by acquiring mutations that commonly involve the NFKBIZ, TRAF3IP2, ZC3H12A, PIGR and HNRNPF genes and are implicated in the downregulation of IL-17 and other pro-inflammatory signals. Mutational profiles vary substantially between colitis-associated cancer and non-dysplastic tissues in ulcerative colitis, which indicates that there are distinct mechanisms of positive selection in both tissues. In particular, mutations in NFKBIZ are highly prevalent in the epithelium of patients with ulcerative colitis but rarely found in both sporadic and colitis-associated cancer, indicating that NFKBIZ-mutant cells are selected against during colorectal carcinogenesis. In further support of this negative selection, we found that tumour formation was significantly attenuated in Nfkbiz-mutant mice and cell competition was compromised by disruption of NFKBIZ in human colorectal cancer cells. Our results highlight common and discrete mechanisms of clonal selection in inflammatory tissues, which reveal unexpected cancer vulnerabilities that could potentially be exploited for therapeutics in colorectal cancer.


  
Patterns and trends of Northern Hemisphere snow mass from 1980 to 2018 期刊论文
NATURE, 2020, 581 (7808) : 294-+
作者:  Ibrahim, Nizar;  Maganuco, Simone;  Dal Sasso, Cristiano;  Fabbri, Matteo;  Auditore, Marco;  Bindellini, Gabriele;  Martill, David M.;  Zouhri, Samir;  Mattarelli, Diego A.;  Unwin, David M.;  Wiemann, Jasmina;  Bonadonna, Davide;  Amane, Ayoub;  Jakubczak, Juliana;  Joger, Ulrich;  Lauder, George V.;  Pierce, Stephanie E.
收藏  |  浏览/下载:18/0  |  提交时间:2020/05/25

Warming surface temperatures have driven a substantial reduction in the extent and duration of Northern Hemisphere snow cover(1-3). These changes in snow cover affect Earth'  s climate system via the surface energy budget, and influence freshwater resources across a large proportion of the Northern Hemisphere(4-6). In contrast to snow extent, reliable quantitative knowledge on seasonal snow mass and its trend is lacking(7-9). Here we use the new GlobSnow 3.0 dataset to show that the 1980-2018 annual maximum snow mass in the Northern Hemisphere was, on average, 3,062 +/- 35 billion tonnes (gigatonnes). Our quantification is for March (the month that most closely corresponds to peak snow mass), covers non-alpine regions above 40 degrees N and, crucially, includes a bias correction based on in-field snow observations. We compare our GlobSnow 3.0 estimates with three independent estimates of snow mass, each with and without the bias correction. Across the four datasets, the bias correction decreased the range from 2,433-3,380 gigatonnes (mean 2,867) to 2,846-3,062 gigatonnes (mean 2,938)-a reduction in uncertainty from 33% to 7.4%. On the basis of our bias-corrected GlobSnow 3.0 estimates, we find different continental trends over the 39-year satellite record. For example, snow mass decreased by 46 gigatonnes per decade across North America but had a negligible trend across Eurasia  both continents exhibit high regional variability. Our results enable a better estimation of the role of seasonal snow mass in Earth'  s energy, water and carbon budgets.


Applying a bias correction to a state-of-the-art dataset covering non-alpine regions of the Northern Hemisphere and to three other datasets yields a more constrained quantification of snow mass in March from 1980 to 2018.


  
Mapping the twist-angle disorder and Landau levels in magic-angle graphene 期刊论文
NATURE, 2020, 581 (7806) : 47-+
作者:  Luck, Katja;  39;Amata, Cassandra
收藏  |  浏览/下载:11/0  |  提交时间:2020/07/03

The recently discovered flat electronic bands and strongly correlated and superconducting phases in magic-angle twisted bilayer graphene (MATBG)(1,2) crucially depend on the interlayer twist angle, theta. Although control of the global theta with a precision of about 0.1 degrees has been demonstrated(1-7), little information is available on the distribution of the local twist angles. Here we use a nanoscale on-tip scanning superconducting quantum interference device (SQUID-on-tip)(8) to obtain tomographic images of the Landau levels in the quantum Hall state(9) and to map the local theta variations in hexagonal boron nitride (hBN)-encapsulated MATBG devices with relative precision better than 0.002 degrees and a spatial resolution of a few moire periods. We find a correlation between the degree of theta disorder and the quality of the MATBG transport characteristics and show that even state-of-the-art devices-which exhibit correlated states, Landau fans and superconductivity-display considerable local variation in theta of up to 0.1 degrees, exhibiting substantial gradients and networks of jumps, and may contain areas with no local MATBG behaviour. We observe that the correlated states in MATBG are particularly fragile with respect to the twist-angle disorder. We also show that the gradients of theta generate large gate-tunable in-plane electric fields, unscreened even in the metallic regions, which profoundly alter the quantum Hall state by forming edge channels in the bulk of the sample and may affect the phase diagram of the correlated and superconducting states. We thus establish the importance of theta disorder as an unconventional type of disorder enabling the use of twist-angle gradients for bandstructure engineering, for realization of correlated phenomena and for gate-tunable built-in planar electric fields for device applications.


SQUID-on-tip tomographic imaging of Landau levels in magic-angle graphene provides nanoscale maps of local twist-angle disorder and shows that its properties are fundamentally different from common types of disorder.


  
Preparation of cyclohexene isotopologues and stereoisotopomers from benzene 期刊论文
NATURE, 2020, 581 (7808) : 288-+
作者:  Shimazaki, Yuya;  Schwartz, Ido;  Watanabe, Kenji;  Taniguchi, Takashi;  Kroner, Martin;  Imamoglu, Atac
收藏  |  浏览/下载:12/0  |  提交时间:2020/07/03

The hydrogen isotopes deuterium (D) and tritium (T) have become essential tools in chemistry, biology and medicine(1). Beyond their widespread use in spectroscopy, mass spectrometry and mechanistic and pharmacokinetic studies, there has been considerable interest in incorporating deuterium into drug molecules(1). Deutetrabenazine, a deuterated drug that is promising for the treatment of Huntington'  s disease(2), was recently approved by the United States'  Food and Drug Administration. The deuterium kinetic isotope effect, which compares the rate of a chemical reaction for a compound with that for its deuterated counterpart, can be substantial(1,3,4). The strategic replacement of hydrogen with deuterium can affect both the rate of metabolism and the distribution of metabolites for a compound(5), improving the efficacy and safety of a drug. The pharmacokinetics of a deuterated compound depends on the location(s) of deuterium. Although methods are available for deuterium incorporation at both early and late stages of the synthesis of a drug(6,7), these processes are often unselective and the stereoisotopic purity can be difficult to measure(7,8). Here we describe the preparation of stereoselectively deuterated building blocks for pharmaceutical research. As a proof of concept, we demonstrate a four-step conversion of benzene to cyclohexene with varying degrees of deuterium incorporation, via binding to a tungsten complex. Using different combinations of deuterated and proteated acid and hydride reagents, the deuterated positions on the cyclohexene ring can be controlled precisely. In total, 52 unique stereoisotopomers of cyclohexene are available, in the form of ten different isotopologues. This concept can be extended to prepare discrete stereoisotopomers of functionalized cyclohexenes. Such systematic methods for the preparation of pharmacologically active compounds as discrete stereoisotopomers could improve the pharmacological and toxicological properties of drugs and provide mechanistic information related to their distribution and metabolism in the body.


Cyclohexene isotopologues and stereoisotopomers with varying degrees of deuteration are formed by binding a tungsten complex to benzene, which facilitates the selective incorporation of deuterium into any position on the ring.


  
A lower X-gate in TASK channels traps inhibitors within the vestibule 期刊论文
NATURE, 2020
作者:  Chen, Tao;  Nomura, Kinya;  Wang, Xiaolin;  Sohrabi, Reza;  Xu, Jin;  Yao, Lingya;  Paasch, Bradley C.;  Ma, Li;  Kremer, James;  Cheng, Yuti;  Zhang, Li;  Wang, Nian;  Wang, Ertao;  Xin, Xiu-Fang;  He, Sheng Yang
收藏  |  浏览/下载:41/0  |  提交时间:2020/07/03

TWIK-related acid-sensitive potassium (TASK) channels-members of the two pore domain potassium (K-2P) channel family-are found in neurons(1), cardiomyocytes(2-4) and vascular smooth muscle cells(5), where they are involved in the regulation of heart rate(6), pulmonary artery tone(5,7), sleep/wake cycles(8) and responses to volatile anaesthetics(8-11). K-2P channels regulate the resting membrane potential, providing background K+ currents controlled by numerous physiological stimuli(12-15). Unlike other K-2P channels, TASK channels are able to bind inhibitors with high affinity, exceptional selectivity and very slow compound washout rates. As such, these channels are attractive drug targets, and TASK-1 inhibitors are currently in clinical trials for obstructive sleep apnoea and atrial fibrillation(16). In general, potassium channels have an intramembrane vestibule with a selectivity filter situated above and a gate with four parallel helices located below  however, the K-2P channels studied so far all lack a lower gate. Here we present the X-ray crystal structure of TASK-1, and show that it contains a lower gate-which we designate as an '  X-gate'  -created by interaction of the two crossed C-terminal M4 transmembrane helices at the vestibule entrance. This structure is formed by six residues ((VLRFMT248)-V-243) that are essential for responses to volatile anaesthetics(10), neurotransmitters(13) and G-protein-coupled receptors(13). Mutations within the X-gate and the surrounding regions markedly affect both the channel-open probability and the activation of the channel by anaesthetics. Structures of TASK-1 bound to two high-affinity inhibitors show that both compounds bind below the selectivity filter and are trapped in the vestibule by the X-gate, which explains their exceptionally low washout rates. The presence of the X-gate in TASK channels explains many aspects of their physiological and pharmacological behaviour, which will be beneficial for the future development and optimization of TASK modulators for the treatment of heart, lung and sleep disorders.


The X-ray crystal structure of the potassium channel TASK-1 reveals the presence of an X-gate, which traps small-molecule inhibitors in the intramembrane vestibule and explains their low washout rates from the channel.


  
Sialylation of immunoglobulin E is a determinant of allergic pathogenicity 期刊论文
NATURE, 2020, 582 (7811) : 265-+
作者:  Abdul-Masih, Michael;  Banyard, Gareth;  Bodensteiner, Julia;  Bordier, Emma;  Bowman, Dominic M.;  Dsilva, Karan;  Fabry, Matthias;  Hawcroft, Calum;  Mahy, Laurent;  Marchant, Pablo;  Raskin, Gert;  Reggiani, Maddalena;  Shenar, Tomer;  Tkachenko, Andrew;  Van Winckel, Hans;  Vermeylen, Lore;  Sana, Hugues
收藏  |  浏览/下载:17/0  |  提交时间:2020/07/03

A specific type of glycosylation-sialylation-is more common on immunoglobulin E from individuals with a peanut allergys than from non-atopic people, suggesting that it has a role in regulating anaphylaxis.


Approximately one-third of the world'  s population suffers from allergies(1). Exposure to allergens crosslinks immunoglobulin E (IgE) antibodies that are bound to mast cells and basophils, triggering the release of inflammatory mediators, including histamine(2). Although IgE is absolutely required for allergies, it is not understood why total and allergen-specific IgE concentrations do not reproducibly correlate with allergic disease(3-5). It is well-established that glycosylation of IgG dictates its effector function and has disease-specific patterns. However, whether IgE glycans differ in disease states or affect biological activity is completely unknown(6). Here we perform an unbiased examination of glycosylation patterns of total IgE from individuals with a peanut allergy and from non-atopic individuals without allergies. Our analysis reveals an increase in sialic acid content on total IgE from individuals with a peanut allergy compared with non-atopic individuals. Removal of sialic acid from IgE attenuates effector-cell degranulation and anaphylaxis in several functional models of allergic disease. Therapeutic interventions-including removing sialic acid from cell-bound IgE with a neuraminidase enzyme targeted towards the IgE receptor Fc epsilon RI, and administering asialylated IgE-markedly reduce anaphylaxis. Together, these results establish IgE glycosylation, and specifically sialylation, as an important regulator of allergic disease.


  
Performance-limiting nanoscale trap clusters at grain junctions in halide perovskites 期刊论文
NATURE, 2020, 580 (7803) : 360-+
作者:  van den Brink, Susanne C.;  Alemany, Anna;  van Batenburg, Vincent;  Moris, Naomi;  Blotenburg, Marloes;  Vivie, Judith;  Baillie-Johnson, Peter;  Nichols, Jennifer;  Sonnen, Katharina F.;  Arias, Alfonso;  van Oudenaarden, Alexander
收藏  |  浏览/下载:27/0  |  提交时间:2020/07/03

Halide perovskite materials have promising performance characteristics for low-cost optoelectronic applications. Photovoltaic devices fabricated from perovskite absorbers have reached power conversion efficiencies above 25 per cent in single-junction devices and 28 per cent in tandem devices(1,2). This strong performance (albeit below the practical limits of about 30 per cent and 35 per cent, respectively(3)) is surprising in thin films processed from solution at low-temperature, a method that generally produces abundant crystalline defects(4). Although point defects often induce only shallow electronic states in the perovskite bandgap that do not affect performance(5), perovskite devices still have many states deep within the bandgap that trap charge carriers and cause them to recombine non-radiatively. These deep trap states thus induce local variations in photoluminescence and limit the device performance(6). The origin and distribution of these trap states are unknown, but they have been associated with light-induced halide segregation in mixed-halide perovskite compositions(7) and with local strain(8), both of which make devices less stable(9). Here we use photoemission electron microscopy to image the trap distribution in state-of-the-art halide perovskite films. Instead of a relatively uniform distribution within regions of poor photoluminescence efficiency, we observe discrete, nanoscale trap clusters. By correlating microscopy measurements with scanning electron analytical techniques, we find that these trap clusters appear at the interfaces between crystallographically and compositionally distinct entities. Finally, by generating time-resolved photoemission sequences of the photo-excited carrier trapping process(10,11), we reveal a hole-trapping character with the kinetics limited by diffusion of holes to the local trap clusters. Our approach shows that managing structure and composition on the nanoscale will be essential for optimal performance of halide perovskite devices.


  
A pathway coordinated by DELE1 relays mitochondrial stress to the cytosol 期刊论文
NATURE, 2020
作者:  Suskiewicz, Marcin J.;  Zobel, Florian;  Ogden, Tom E. H.;  Fontana, Pietro;  Ariza, Antonio;  Yang, Ji-Chun;  Zhu, Kang;  Bracken, Lily;  Hawthorne, William J.;  Ahel, Dragana;  Neuhaus, David;  Ahel, Ivan
收藏  |  浏览/下载:43/0  |  提交时间:2020/07/03

Haploid genetic screening of cells under different types of mitochondrial perturbation shows that a pathway involving OMA1, DELE1 and the eIF2 alpha kinase HRI communicates mitochondrial stress to the cytosol to trigger the integrated stress response.


Mitochondrial fidelity is tightly linked to overall cellular homeostasis and is compromised in ageing and various pathologies(1-3). Mitochondrial malfunction needs to be relayed to the cytosol, where an integrated stress response is triggered by the phosphorylation of eukaryotic translation initiation factor 2 alpha (eIF2 alpha) in mammalian cells(4,5). eIF2 alpha phosphorylation is mediated by the four eIF2 alpha kinases GCN2, HRI, PERK and PKR, which are activated by diverse types of cellular stress(6). However, the machinery that communicates mitochondrial perturbation to the cytosol to trigger the integrated stress response remains unknown(1,2,7). Here we combine genome engineering and haploid genetics to unbiasedly identify genes that affect the induction of C/EBP homologous protein (CHOP), a key factor in the integrated stress response. We show that the mitochondrial protease OMA1 and the poorly characterized protein DELE1, together with HRI, constitute the missing pathway that is triggered by mitochondrial stress. Mechanistically, stress-induced activation of OMA1 causes DELE1 to be cleaved into a short form that accumulates in the cytosol, where it binds to and activates HRI via its C-terminal portion. Obstruction of this pathway can be beneficial or adverse depending on the type of mitochondrial perturbation. In addition to the core pathway components, our comparative genetic screening strategy identifies a suite of additional regulators. Together, these findings could be used to inform future strategies to modulate the cellular response to mitochondrial dysfunction in the context of human disease.


  
A claustrum in reptiles and its role in slow-wave sleep 期刊论文
NATURE, 2020, 578 (7795) : 413-+
作者:  Loubeyre, Paul;  Occelli, Florent;  Dumas, Paul
收藏  |  浏览/下载:16/0  |  提交时间:2020/07/03

The mammalian claustrum, owing to its widespread connectivity with other forebrain structures, has been hypothesized to mediate functions that range from decision-making to consciousness(1). Here we report that a homologue of the claustrum, identified by single-cell transcriptomics and viral tracing of connectivity, also exists in a reptile-the Australian bearded dragon Pogona vitticeps. In Pogona, the claustrum underlies the generation of sharp waves during slow-wave sleep. The sharp waves, together with superimposed high-frequency ripples(2), propagate to the entire neighbouring pallial dorsal ventricular ridge (DVR). Unilateral or bilateral lesions of the claustrum suppress the production of sharp-wave ripples during slow-wave sleep in a unilateral or bilateral manner, respectively, but do not affect the regular and rapidly alternating sleep rhythm that is characteristic of sleep in this species(3). The claustrum is thus not involved in the generation of the sleep rhythm itself. Tract tracing revealed that the reptilian claustrum projects widely to a variety of forebrain areas, including the cortex, and that it receives converging inputs from, among others, areas of the mid- and hindbrain that are known to be involved in wake-sleep control in mammals(4-6). Periodically modulating the concentration of serotonin in the claustrum, for example, caused a matching modulation of sharp-wave production there and in the neighbouring DVR. Using transcriptomic approaches, we also identified a claustrum in the turtle Trachemys scripta, a distant reptilian relative of lizards. The claustrum is therefore an ancient structure that was probably already present in the brain of the common vertebrate ancestor of reptiles and mammals. It may have an important role in the control of brain states owing to the ascending input it receives from the mid- and hindbrain, its widespread projections to the forebrain and its role in sharp-wave generation during slow-wave sleep.


A structure homologous to the mammalian claustrum exists in reptiles and has a role in generating sharp waves in the brain during slow-wave sleep.


  
Dualities and non-Abelian mechanics 期刊论文
NATURE, 2020, 577 (7792) : 636-+
作者:  Song, Xinyang;  Sun, Ximei;  Oh, Sungwhan F.;  Wu, Meng;  Zhang, Yanbo;  Zheng, Wen;  Geva-Zatorsky, Naama;  Jupp, Ray;  Mathis, Diane;  Benoist, Christophe;  Kasper, Dennis L.
收藏  |  浏览/下载:13/0  |  提交时间:2020/07/03

Dualities-mathematical mappings between different systems-can act as hidden symmetries that enable materials design beyond that suggested by crystallographic space groups.


Dualities are mathematical mappings that reveal links between apparently unrelated systems in virtually every branch of physics(1-8). Systems mapped onto themselves by a duality transformation are called self-dual and exhibit remarkable properties, as exemplified by the scale invariance of an Ising magnet at the critical point. Here we show how dualities can enhance the symmetries of a dynamical matrix (or Hamiltonian), enabling the design of metamaterials with emergent properties that escape a standard group theory analysis. As an illustration, we consider twisted kagome lattices(9-15), reconfigurable mechanical structures that change shape by means of a collapse mechanism(9). We observe that pairs of distinct configurations along the mechanism exhibit the same vibrational spectrum and related elastic moduli. We show that these puzzling properties arise from a duality between pairs of configurations on either side of a mechanical critical point. The critical point corresponds to a self-dual structure with isotropic elasticity even in the absence of spatial symmetries and a twofold-degenerate spectrum over the entire Brillouin zone. The spectral degeneracy originates from a version of Kramers'  theorem(16,17) in which fermionic time-reversal invariance is replaced by a hidden symmetry emerging at the self-dual point. The normal modes of the self-dual systems exhibit non-Abelian geometric phases(18,19) that affect the semiclassical propagation of wavepackets(20), leading to non-commuting mechanical responses. Our results hold promise for holonomic computation(21) and mechanical spintronics by allowing on-the-fly manipulation of synthetic spins carried by phonons.