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Subpolar marginal seas fuel the North Pacific through the intermediate water at the termination of the ocean circulation 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2020, 117 (23) : 12665-12673
作者:  Nishioka, Jun;  Obata, Hajime;  Ogawa, Hiroshi;  Ono, Kazuya;  Yamashita, Youhei;  Lee, Keunjong;  Takeda, Shigenobu;  Yasuda, Ichiro
收藏  |  浏览/下载:11/0  |  提交时间:2020/06/01
dissolved iron  macronutrients  North Pacific Ocean  island chains mixing  GEOTRACES  
Mutations that prevent caspase cleavage of RIPK1 cause autoinflammatory disease 期刊论文
NATURE, 2020, 577 (7788) : 103-+
作者:  Lalaoui, Najoua;  Boyden, Steven E.;  Oda, Hirotsugu;  Wood, Geryl M.;  Stone, Deborah L.;  Chau, Diep;  Liu, Lin;  Stoffels, Monique;  Kratina, Tobias;  Lawlor, Kate E.;  Zaal, Kristien J. M.;  Hoffmann, Patrycja M.;  Etemadi, Nima;  Shield-Artin, Kristy;  Biben, Christine;  Tsai, Wanxia Li;  Blake, Mary D.;  Kuehn, Hye Sun;  Yang, Dan;  Anderton, Holly;  Silke, Natasha;  Wachsmuth, Laurens;  Zheng, Lixin;  Moura, Natalia Sampaio;  Beck, David B.;  Gutierrez-Cruz, Gustavo;  Ombrello, Amanda K.;  Pinto-Patarroyo, Gineth P.;  Kueh, Andrew J.;  Herold, Marco J.;  Hall, Cathrine;  Wang, Hongying;  Chae, Jae Jin;  Dmitrieva, Natalia I.;  McKenzie, Mark;  Light, Amanda;  Barham, Beverly K.;  Jones, Anne;  Romeo, Tina M.;  Zhou, Qing;  Aksentijevich, Ivona;  Mullikin, James C.;  Gross, Andrew J.;  Shum, Anthony K.;  Hawkins, Edwin D.;  Masters, Seth L.;  Lenardo, Michael J.;  Boehm, Manfred;  Rosenzweig, Sergio D.;  Pasparakis, Manolis;  Voss, Anne K.;  Gadina, Massimo;  Kastner, Daniel L.;  Silke, John
收藏  |  浏览/下载:24/0  |  提交时间:2020/07/03

RIPK1 is a key regulator of innate immune signalling pathways. To ensure an optimal inflammatory response, RIPK1 is regulated post-translationally by well-characterized ubiquitylation and phosphorylation events, as well as by caspase-8-mediated cleavage1-7. The physiological relevance of this cleavage event remains unclear, although it is thought to inhibit activation of RIPK3 and necroptosis8. Here we show that the heterozygous missense mutations D324N, D324H and D324Y prevent caspase cleavage of RIPK1 in humans and result in an early-onset periodic fever syndrome and severe intermittent lymphadenopathy-a condition we term '  cleavage-resistant RIPK1-induced autoinflammatory syndrome'  . To define the mechanism for this disease, we generated a cleavage-resistant Ripk1(D325A) mutant mouse strain. Whereas Ripk1(-/-) mice died postnatally from systemic inflammation, Ripk1(D325A/D325A) mice died during embryogenesis. Embryonic lethality was completely prevented by the combined loss of Casp8 and Ripk3, but not by loss of Ripk3 or Mlkl alone. Loss of RIPK1 kinase activity also prevented Ripk1(D325A/D325A) embryonic lethality, although the mice died before weaning from multi-organ inflammation in a RIPK3-dependent manner. Consistently, Ripk1(D325A/D325A) and Ripk1(D325A/+) cells were hypersensitive to RIPK3-dependent TNF-induced apoptosis and necroptosis. Heterozygous Ripk1(D325A/+) mice were viable and grossly normal, but were hyper-responsive to inflammatory stimuli in vivo. Our results demonstrate the importance of caspase-mediated RIPK1 cleavage during embryonic development and show that caspase cleavage of RIPK1 not only inhibits necroptosis but also maintains inflammatory homeostasis throughout life.


  
Structure of nevanimibe-bound tetrameric human ACAT1 期刊论文
NATURE, 2020, 581 (7808) : 339-U214
作者:  Ma, Xiyu;  Claus, Lucas A. N.;  Leslie, Michelle E.;  Tao, Kai;  Wu, Zhiping;  Liu, Jun;  Yu, Xiao;  Li, Bo;  Zhou, Jinggeng;  Savatin, Daniel V.;  Peng, Junmin;  Tyler, Brett M.;  Heese, Antje;  Russinova, Eugenia;  He, Ping;  Shan, Libo
收藏  |  浏览/下载:28/0  |  提交时间:2020/07/03

The structure of human ACAT1 in complex with the inhibitor nevanimibe is resolved by cryo-electron microscopy.


Cholesterol is an essential component of mammalian cell membranes, constituting up to 50% of plasma membrane lipids. By contrast, it accounts for only 5% of lipids in the endoplasmic reticulum (ER)(1). The ER enzyme sterol O-acyltransferase 1 (also named acyl-coenzyme A:cholesterol acyltransferase, ACAT1) transfers a long-chain fatty acid to cholesterol to form cholesteryl esters that coalesce into cytosolic lipid droplets. Under conditions of cholesterol overload, ACAT1 maintains the low cholesterol concentration of the ER and thereby has an essential role in cholesterol homeostasis(2,3). ACAT1 has also been implicated in Alzheimer'  s disease(4), atherosclerosis(5) and cancers(6). Here we report a cryo-electron microscopy structure of human ACAT1 in complex with nevanimibe(7), an inhibitor that is in clinical trials for the treatment of congenital adrenal hyperplasia. The ACAT1 holoenzyme is a tetramer that consists of two homodimers. Each monomer contains nine transmembrane helices (TMs), six of which (TM4-TM9) form a cavity that accommodates nevanimibe and an endogenous acyl-coenzyme A. This cavity also contains a histidine that has previously been identified as essential for catalytic activity(8). Our structural data and biochemical analyses provide a physical model to explain the process of cholesterol esterification, as well as details of the interaction between nevanimibe and ACAT1, which may help to accelerate the development of ACAT1 inhibitors to treat related diseases.


  
FACT caught in the act of manipulating the nucleosome 期刊论文
NATURE, 2020, 577 (7790) : 426-+
作者:  Shen, Helen
收藏  |  浏览/下载:4/0  |  提交时间:2020/07/03

The organization of genomic DNA into nucleosomes profoundly affects all DNA-related processes in eukaryotes. The histone chaperone known as '  facilitates chromatin transcription'  (FACT(1)) (consisting of subunits SPT16 and SSRP1) promotes both disassembly and reassembly of nucleosomes during gene transcription, DNA replication and DNA repair(2). However, the mechanism by which FACT causes these opposing outcomes is unknown. Here we report two cryo-electron-microscopic structures of human FACT in complex with partially assembled subnucleosomes, with supporting biochemical and hydrogen-deuterium exchange data. We find that FACT is engaged in extensive interactions with nucleosomal DNA and all histone variants. The large DNA-binding surface on FACT appears to be protected by the carboxy-terminal domains of both of its subunits, and this inhibition is released by interaction with H2A-H2B, allowing FACT-H2A-H2B to dock onto a complex containing DNA and histones H3 and H4 (ref. (3)). SPT16 binds nucleosomal DNA and tethers H2A-H2B through its carboxy-terminal domain by acting as a placeholder for DNA. SSRP1 also contributes to DNA binding, and can assume two conformations, depending on whether a second H2A-H2B dimer is present. Our data suggest a compelling mechanism for how FACT maintains chromatin integrity during polymerase passage, by facilitating removal of the H2A-H2B dimer, stabilizing intermediate subnucleosomal states and promoting nucleosome reassembly. Our findings reconcile discrepancies regarding the many roles of FACT and underscore the dynamic interactions between histone chaperones and nucleosomes.


  
Molecular architecture of the human 17S U2 snRNP 期刊论文
NATURE, 2020, 583 (7815) : 310-+
作者:  Muench, David E.;  Olsson, Andre;  Ferchen, Kyle;  Pham, Giang;  Serafin, Rachel A.;  Chutipongtanate, Somchai;  Dwivedi, Pankaj;  Song, Baobao;  Hay, Stuart;  Chetal, Kashish;  Trump-Durbin, Lisa R.;  Mookerjee-Basu, Jayati;  Zhang, Kejian;  Yu, Jennifer C.
收藏  |  浏览/下载:18/0  |  提交时间:2020/07/03

The U2 small nuclear ribonucleoprotein (snRNP) has an essential role in the selection of the precursor mRNA branch-site adenosine, the nucleophile for the first step of splicing'  . Stable addition of U2 during early spliceosome formation requiresthe DEAD-box ATPase PRP5(2-7). Yeast U2 small nuclear RNA (snRNA) nucleotides that form base pairs with the branch site are initially sequestered in a branchpoint-interacting stem-loop (BSL)(8), but whether the human U2 snRNA folds in a similar manner is unknown. The U2 SF3B1 protein, a common mutational target in haematopoietic cancers(9), contains a HEAT domain (SF3B1(HEAT)) with an open conformation in isolated SF3b(10), but a closed conformation in spliceosomes(11), which is required for stable interaction between U2 and the branch site. Here we report a 3D cryo-electron microscopy structure ofthe human 17S U2 snRNP at a core resolution of 4.1 angstrom and combine it with protein crosslinking data to determine the molecular architecture of this snRNP. Our structure reveals that SF3B1(HEAT) interacts with PRP5 and TAT-SF1, and maintains its open conformation in U2 snRNP, and that U2 snRNA forms a BSL that is sandwiched between PRP5, TAT-SF1 and SF3B1(HEAT). Thus, substantial remodelling of the BSL and displacement of BSL-interacting proteins must occur to allow formation of the U2-branch-site helix. Our studies provide a structural explanation of why TAT-SF1 must be displaced before the stable addition of U2 to the spliceosome, and identify RNP rearrangements facilitated by PRP5 that are required for stable interaction between U2 and the branch site.


  
TLR9 and beclin 1 crosstalk regulates muscle AMPK activation in exercise 期刊论文
NATURE, 2020
作者:  Keener, Megan;  Hunt, Camden;  Carroll, Timothy G.;  Kampel, Vladimir;  Dobrovetsky, Roman;  Hayton, Trevor W.;  Menard, Gabriel
收藏  |  浏览/下载:18/0  |  提交时间:2020/07/03

In mice, the interaction of the innate immune sensor TLR9 with beclin 1 is shown to have a role in glucose metabolism and AMPK activation in skeletal muscle during exercise.


The activation of adenosine monophosphate-activated protein kinase (AMPK) in skeletal muscle coordinates systemic metabolic responses to exercise(1). Autophagy-a lysosomal degradation pathway that maintains cellular homeostasis(2)-is upregulated during exercise, and a core autophagy protein, beclin 1, is required for AMPK activation in skeletal muscle(3). Here we describe a role for the innate immune-sensing molecule Toll-like receptor 9 (TLR9)(4), and its interaction with beclin 1, in exercise-induced activation of AMPK in skeletal muscle. Mice that lack TLR9 are deficient in both exercise-induced activation of AMPK and plasma membrane localization of the GLUT4 glucose transporter in skeletal muscle, but are not deficient in autophagy. TLR9 binds beclin 1, and this interaction is increased by energy stress (glucose starvation and endurance exercise) and decreased by a BCL2 mutation(3,5) that blocks the disruption of BCL2-beclin 1 binding. TLR9 regulates the assembly of the endolysosomal phosphatidylinositol 3-kinase complex (PI3KC3-C2)-which contains beclin 1 and UVRAG-in skeletal muscle during exercise, and knockout of beclin 1 or UVRAG inhibits the cellular AMPK activation induced by glucose starvation. Moreover, TLR9 functions in a muscle-autonomous fashion in ex vivo contraction-induced AMPK activation, glucose uptake and beclin 1-UVRAG complex assembly. These findings reveal a heretofore undescribed role for a Toll-like receptor in skeletal-muscle AMPK activation and glucose metabolism during exercise, as well as unexpected crosstalk between this innate immune sensor and autophagy proteins.


  
Dimensionality-reduction techniques for complex mass spectrometric datasets: application to laboratory atmospheric organic oxidation experiments 期刊论文
ATMOSPHERIC CHEMISTRY AND PHYSICS, 2020, 20 (2) : 1021-1041
作者:  Koss, Abigail R.;  Canagaratna, Manjula R.;  Zaytsev, Alexander;  Krechmer, Jordan E.;  Breitenlechner, Martin;  Nihill, Kevin J.;  Lim, Christopher Y.;  Rowe, James C.;  Roscioli, Joseph R.;  Keutsch, Frank N.;  Kroll, Jesse H.
收藏  |  浏览/下载:12/0  |  提交时间:2020/07/02
An Implicit Algebraic Turbulence Closure Scheme for Atmospheric Boundary Layer Simulation 期刊论文
JOURNAL OF THE ATMOSPHERIC SCIENCES, 2019, 76 (11) : 3367-3386
作者:  Shi, Xiaoming;  Enriquez, Rica Mae;  Street, Robert L.;  Bryan, George H.;  Chow, Fotini Katopodes
收藏  |  浏览/下载:5/0  |  提交时间:2019/11/27
Turbulence  Boundary layer  Cloud resolving models  Large eddy simulations  Parameterization  Subgrid-scale processes  
An oceanic subduction origin for Archaean granitoids revealed by silicon isotopes 期刊论文
NATURE GEOSCIENCE, 2019, 12 (9) : 774-+
作者:  Deng, Zhengbin;  Chaussidon, Marc;  Guitreau, Martin;  Puchtel, Igor S.;  Dauphas, Nicolas;  Moynier, Frederic
收藏  |  浏览/下载:7/0  |  提交时间:2019/11/27
Persistence of neuronal representations through time and damage in the hippocampus 期刊论文
SCIENCE, 2019, 365 (6455) : 821-+
作者:  Gonzalez, Walter G.;  Zhang, Hanwen;  Harutyunyan, Anna;  Lois, Carlos
收藏  |  浏览/下载:6/0  |  提交时间:2019/11/27