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Evaluation of a Wastewater-Based Epidemiological Approach to Estimate the Prevalence of SARS-CoV-2 Infections and the Detection of Viral Variants in Disparate Oregon Communities at City and Neighborhood Scales 期刊论文
Environmental Health Perspectives, 2022
作者:  Blythe A. Layton;  Devrim Kaya;  Christine Kelly;  Kenneth J. Williamson;  Dana Alegre;  Silke M. Bachhuber;  Peter G. Banwarth;  Jeffrey W. Bethel;  Katherine Carter;  Benjamin D. Dalziel;  Mark Dasenko;  Matthew Geniza;  Andrea George;  Anne-Marie Girard;  Roy Haggerty;  Kathryn A. Higley;  Denise M. Hynes;  Jane Lubchenco;  Katherine R. McLaughlin;  F. Javier Nieto;  Aslan Noakes;  Matthew Peterson;  Adriana D. Piemonti;  Justin L. Sanders;  Brett M. Tyler;  Tyler S. Radniecki
收藏  |  浏览/下载:12/0  |  提交时间:2022/07/08
X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease 期刊论文
Science, 2021
作者:  Sebastian Günther;  Patrick Y. A. Reinke;  Yaiza Fernández-García;  Julia Lieske;  Thomas J. Lane;  Helen M. Ginn;  Faisal H. M. Koua;  Christiane Ehrt;  Wiebke Ewert;  Dominik Oberthuer;  Oleksandr Yefanov;  Susanne Meier;  Kristina Lorenzen;  Boris Krichel;  Janine-Denise Kopicki;  Luca Gelisio;  Wolfgang Brehm;  Ilona Dunkel;  Brandon Seychell;  Henry Gieseler;  Brenna Norton-Baker;  Beatriz Escudero-Pérez;  Martin Domaracky;  Sofiane Saouane;  Alexandra Tolstikova;  Thomas A. White;  Anna Hänle;  Michael Groessler;  Holger Fleckenstein;  Fabian Trost;  Marina Galchenkova;  Yaroslav Gevorkov;  Chufeng Li;  Salah Awel;  Ariana Peck;  Miriam Barthelmess;  Frank Schlünzen;  P. Lourdu Xavier;  Nadine Werner;  Hina Andaleeb;  Najeeb Ullah;  Sven Falke;  Vasundara Srinivasan;  Bruno Alves França;  Martin Schwinzer;  Hévila Brognaro;  Cromarte Rogers;  Diogo Melo;  Joanna J. Zaitseva-Doyle;  Juraj Knoska;  Gisel E. Peña-Murillo;  Aida Rahmani Mashhour;  Vincent Hennicke;  Pontus Fischer;  Johanna Hakanpää;  Jan Meyer;  Philip Gribbon;  Bernhard Ellinger;  Maria Kuzikov;  Markus Wolf;  Andrea R. Beccari;  Gleb Bourenkov;  David von Stetten;  Guillaume Pompidor;  Isabel Bento;  Saravanan Panneerselvam;  Ivars Karpics;  Thomas R. Schneider;  Maria Marta Garcia-Alai;  Stephan Niebling;  Christian Günther;  Christina Schmidt;  Robin Schubert;  Huijong Han;  Juliane Boger;  Diana C. F. Monteiro;  Linlin Zhang;  Xinyuanyuan Sun;  Jonathan Pletzer-Zelgert;  Jan Wollenhaupt;  Christian G. Feiler;  Manfred S. Weiss;  Eike-Christian Schulz;  Pedram Mehrabi;  Katarina Karničar;  Aleksandra Usenik;  Jure Loboda;  Henning Tidow;  Ashwin Chari;  Rolf Hilgenfeld;  Charlotte Uetrecht;  Russell Cox;  Andrea Zaliani;  Tobias Beck;  Matthias Rarey;  Stephan Günther;  Dusan Turk;  Winfried Hinrichs;  Henry N. Chapman;  Arwen R. Pearson;  Christian Betzel;  Alke Meents
收藏  |  浏览/下载:14/0  |  提交时间:2021/05/14
Viral epitope profiling of COVID-19 patients reveals cross-reactivity and correlates of severity 期刊论文
Science, 2020
作者:  Ellen Shrock;  Eric Fujimura;  Tomasz Kula;  Richard T. Timms;  I-Hsiu Lee;  Yumei Leng;  Matthew L. Robinson;  Brandon M. Sie;  Mamie Z. Li;  Yuezhou Chen;  Jennifer Logue;  Adam Zuiani;  Denise McCulloch;  Felipe J. N. Lelis;  Stephanie Henson;  Daniel R. Monaco;  Meghan Travers;  Shaghayegh Habibi;  William A. Clarke;  Patrizio Caturegli;  Oliver Laeyendecker;  Alicja Piechocka-Trocha;  Jonathan Z. Li;  Ashok Khatri;  Helen Y. Chu;  MGH COVID-19 Collection &;  amp;  Processing Team16‡;  Alexandra-Chloé Villani;  Kyle Kays;  Marcia B. Goldberg;  Nir Hacohen;  Michael R. Filbin;  Xu G. Yu;  Bruce D. Walker;  Duane R. Wesemann;  H. Benjamin Larman;  James A. Lederer;  Stephen J. Elledge
收藏  |  浏览/下载:11/0  |  提交时间:2020/11/30
Distemper, extinction, and vaccination of the Amur tiger 期刊论文
Proceedings of the National Academy of Sciences, 2020
作者:  Martin Gilbert;  Nadezhda Sulikhan;  Olga Uphyrkina;  Mikhail Goncharuk;  Linda Kerley;  Enrique Hernandez Castro;  Richard Reeve;  Tracie Seimon;  Denise McAloose;  Ivan V. Seryodkin;  Sergey V. Naidenko;  Christopher A. Davis;  Gavin S. Wilkie;  Sreenu B. Vattipally;  Walt E. Adamson;  Chris Hinds;  Emma C. Thomson;  Brian J. Willett;  Margaret J. Hosie;  Nicola Logan;  Michael McDonald;  Robert J. Ossiboff;  Elena I. Shevtsova;  Stepan Belyakin;  Anna A. Yurlova;  Steven A. Osofsky;  Dale G. Miquelle;  Louise Matthews;  Sarah Cleaveland
收藏  |  浏览/下载:10/0  |  提交时间:2020/11/30
The physical oceanography of the transport of floating marine debris 期刊论文
ENVIRONMENTAL RESEARCH LETTERS, 2020, 15 (2)
作者:  van Sebille, Erik;  Aliani, Stefano;  Law, Kara Lavender;  Maximenko, Nikolai;  Alsina, Jose M.;  Bagaev, Andrei;  Bergmann, Melanie;  Chapron, Bertrand;  Chubarenko, Irina;  Cozar, Andres;  Delandmeter, Philippe;  Egger, Matthias;  Fox-Kemper, Baylor;  Garaba, Shungudzemwoyo P.;  Goddijn-Murphy, Lonneke;  Hardesty, Britta Denise;  Hoffman, Matthew J.;  Isobe, Atsuhiko;  Jongedijk, Cleo E.;  Kaandorp, Mikael L. A.;  Khatmullina, Liliya;  Koelmans, Albert A.;  Kukulka, Tobias;  Laufkotter, Charlotte;  Lebreton, Laurent;  Lobelle, Delphine;  Maes, Christophe;  Martinez-Vicente, Victor;  Maqueda, Miguel Angel Morales;  Poulain-Zarcos, Marie;  Rodriguez, Ernesto;  Ryan, Peter G.;  Shanks, Alan L.;  Shim, Won Joon;  Suaria, Giuseppe;  Thiel, Martin;  van den Bremer, Ton S.;  Wichmann, David
收藏  |  浏览/下载:18/0  |  提交时间:2020/07/02
marine debris  physical oceanography  ocean circulation  remote sensing  fluid dynamics  
Feeding-dependent VIP neuron-ILC3 circuit regulates the intestinal barrier 期刊论文
NATURE, 2020, 579 (7800) : 575-+
作者:  Bhaduri, Aparna;  Andrews, Madeline G.;  Mancia Leon, Walter;  Jung, Diane;  Shin, David;  Allen, Denise;  Jung, Dana;  Schmunk, Galina;  Haeussler, Maximilian;  Salma, Jahan;  Pollen, Alex A.;  Nowakowski, Tomasz J.;  Kriegstein, Arnold R.
收藏  |  浏览/下载:37/0  |  提交时间:2020/07/03

The intestinal mucosa serves both as a conduit for the uptake of food-derived nutrients and microbiome-derived metabolites, and as a barrier that prevents tissue invasion by microorganisms and tempers inflammatory responses to the myriad contents of the lumen. How the intestine coordinates physiological and immune responses to food consumption to optimize nutrient uptake while maintaining barrier functions remains unclear. Here we show in mice how a gut neuronal signal triggered by food intake is integrated with intestinal antimicrobial and metabolic responses that are controlled by type-3 innate lymphoid cells (ILC3)(1-3). Food consumption rapidly activates a population of enteric neurons that express vasoactive intestinal peptide (VIP)(4). Projections of VIP-producing neurons (VIPergic neurons) in the lamina propria are in close proximity to clusters of ILC3 that selectively express VIP receptor type 2 (VIPR2  also known as VPAC2). Production of interleukin (IL)-22 by ILC3, which is upregulated by the presence of commensal microorganisms such as segmented filamentous bacteria(5-7), is inhibited upon engagement of VIPR2. As a consequence, levels of antimicrobial peptide derived from epithelial cells are reduced but the expression of lipid-binding proteins and transporters is increased(8). During food consumption, the activation of VIPergic neurons thus enhances the growth of segmented filamentous bacteria associated with the epithelium, and increases lipid absorption. Our results reveal a feeding- and circadian-regulated dynamic neuroimmune circuit in the intestine that promotes a trade-off between innate immune protection mediated by IL-22 and the efficiency of nutrient absorption. Modulation of this pathway may therefore be effective for enhancing resistance to enteropathogens(2,3,9) and for the treatment of metabolic diseases.


Feeding controls a neuroimmune circuit comprising VIP-producing neurons and type-3 innate lymphoid cells that helps to regulate the efficiency of nutrient uptake and IL-22-mediated immune protection in the intestine.


  
The molecular basis for sugar import in malaria parasites 期刊论文
NATURE, 2020, 578 (7794) : 321-+
作者:  Zhao, Peishen;  Liang, Yi-Lynn;  Belousoff, Matthew J.;  Deganutti, Giuseppe;  Fletcher, Madeleine M.;  Willard, Francis S.;  Bell, Michael G.;  Christe, Michael E.;  Sloop, Kyle W.;  Inoue, Asuka;  Truong, Tin T.;  Clydesdale, Lachlan;  Furness, Sebastian G. B.;  Christopoulos, Arthur;  Wang, Ming-Wei;  Miller, Laurence J.;  Reynolds, Christopher A.;  Danev, Radostin;  Sexton, Patrick M.;  Wootten, Denise
收藏  |  浏览/下载:19/0  |  提交时间:2020/07/03

Elucidating the mechanism of sugar import requires a molecular understanding of how transporters couple sugar binding and gating events. Whereas mammalian glucose transporters (GLUTs) are specialists(1), the hexose transporter from the malaria parasite Plasmodium falciparum PfHT1(2,3) has acquired the ability to transport both glucose and fructose sugars as efficiently as the dedicated glucose (GLUT3) and fructose (GLUT5) transporters. Here, to establish the molecular basis of sugar promiscuity in malaria parasites, we determined the crystal structure of PfHT1 in complex with d-glucose at a resolution of 3.6 angstrom. We found that the sugar-binding site in PfHT1 is very similar to those of the distantly related GLUT3 and GLUT5 structures(4,5). Nevertheless, engineered PfHT1 mutations made to match GLUT sugar-binding sites did not shift sugar preferences. The extracellular substrate-gating helix TM7b in PfHT1 was positioned in a fully occluded conformation, providing a unique glimpse into how sugar binding and gating are coupled. We determined that polar contacts between TM7b and TM1 (located about 15 angstrom from d-glucose) are just as critical for transport as the residues that directly coordinate d-glucose, which demonstrates a strong allosteric coupling between sugar binding and gating. We conclude that PfHT1 has achieved substrate promiscuity not by modifying its sugar-binding site, but instead by evolving substrate-gating dynamics.


Crystal structure of the Plasmodium falciparum hexose transporter PfHT1 reveals the molecular basis of its ability to transport multiple types of sugar as efficiently as the dedicated mammalian glucose and fructose transporters.


  
Processive extrusion of polypeptide loops by a Hsp100 disaggregase 期刊论文
NATURE, 2020, 578 (7794) : 317-+
作者:  Zhao, Peishen;  Liang, Yi-Lynn;  Belousoff, Matthew J.;  Deganutti, Giuseppe;  Fletcher, Madeleine M.;  Willard, Francis S.;  Bell, Michael G.;  Christe, Michael E.;  Sloop, Kyle W.;  Inoue, Asuka;  Truong, Tin T.;  Clydesdale, Lachlan;  Furness, Sebastian G. B.;  Christopoulos, Arthur;  Wang, Ming-Wei;  Miller, Laurence J.;  Reynolds, Christopher A.;  Danev, Radostin;  Sexton, Patrick M.;  Wootten, Denise
收藏  |  浏览/下载:17/0  |  提交时间:2020/07/03

The ability to reverse protein aggregation is vital to cells(1,2). Hsp100 disaggregases such as ClpB and Hsp104 are proposed to catalyse this reaction by translocating polypeptide loops through their central pore(3,4). This model of disaggregation is appealing, as it could explain how polypeptides entangled within aggregates can be extracted and subsequently refolded with the assistance of Hsp70(4,5). However, the model is also controversial, as the necessary motor activity has not been identified(6-8) and recent findings indicate non-processive mechanisms such as entropic pulling or Brownian ratcheting(9,10). How loop formation would be accomplished is also obscure. Indeed, cryo-electron microscopy studies consistently show single polypeptide strands in the Hsp100 pore(11,12). Here, by following individual ClpB-substrate complexes in real time, we unambiguously demonstrate processive translocation of looped polypeptides. We integrate optical tweezers with fluorescent-particle tracking to show that ClpB translocates both arms of the loop simultaneously and switches to single-arm translocation when encountering obstacles. ClpB is notably powerful and rapid  it exerts forces of more than 50 pN at speeds of more than 500 residues per second in bursts of up to 28 residues. Remarkably, substrates refold while exiting the pore, analogous to co-translational folding. Our findings have implications for protein-processing phenomena including ubiquitin-mediated remodelling by Cdc48 (or its mammalian orthologue p97)(13) and degradation by the 26S proteasome(14).


A combination of optical tweezers and fluorescent-particle tracking is used to dissect the dynamics of the Hsp100 disaggregase ClpB, and show that the processive extrusion of polypeptide loops is the mechanistic basis of its activity.


  
Activation of the GLP-1 receptor by a non-peptidic agonist 期刊论文
NATURE, 2020, 577 (7790) : 432-+
作者:  Zhao, Peishen;  Liang, Yi-Lynn;  Belousoff, Matthew J.;  Deganutti, Giuseppe;  Fletcher, Madeleine M.;  Willard, Francis S.;  Bell, Michael G.;  Christe, Michael E.;  Sloop, Kyle W.;  Inoue, Asuka;  Truong, Tin T.;  Clydesdale, Lachlan;  Furness, Sebastian G. B.;  Christopoulos, Arthur;  Wang, Ming-Wei;  Miller, Laurence J.;  Reynolds, Christopher A.;  Danev, Radostin;  Sexton, Patrick M.;  Wootten, Denise
收藏  |  浏览/下载:9/0  |  提交时间:2020/07/03

Class B G-protein-coupled receptors are major targets for the treatment of chronic diseases, including diabetes and obesity(1). Structures of active receptors reveal peptide agonists engage deep within the receptor core, leading to an outward movement of extracellular loop 3 and the tops of transmembrane helices 6 and 7, an inward movement of transmembrane helix 1, reorganization of extracellular loop 2 and outward movement of the intracellular side of transmembrane helix 6, resulting in G-protein interaction and activation(2-6). Here we solved the structure of a non-peptide agonist, TT-OAD2, bound to the glucagon-like peptide-1 (GLP-1) receptor. Our structure identified an unpredicted non-peptide agonist-binding pocket in which reorganization of extracellular loop 3 and transmembrane helices 6 and 7 manifests independently of direct ligand interaction within the deep transmembrane domain pocket. TT-OAD2 exhibits biased agonism, and kinetics of G-protein activation and signalling that are distinct from peptide agonists. Within the structure, TT-OAD2 protrudes beyond the receptor core to interact with the lipid or detergent, providing an explanation for the distinct activation kinetics that may contribute to the clinical efficacy of this compound series. This work alters our understanding of the events that drive the activation of class B receptors.


  
Archaeological assessment reveals Earth's early transformation through land use 期刊论文
SCIENCE, 2019, 365 (6456) : 897-+
作者:  Stephens, Lucas;  Fuller, Dorian;  Boivin, Nicole;  Rick, Torben;  Gauthier, Nicolas;  Kay, Andrea;  Marwick, Ben;  Armstrong, Chelsey Geralda Denise;  Barton, C. Michael;  Denham, Tim;  Douglass, Kristina;  Driver, Jonathan;  Janz, Lisa;  Roberts, Patrick;  Rogers, J. Daniel;  Thakar, Heather;  Altaweel, Mark;  Johnson, Amber L.;  Sampietro Vattuone, Maria Marta;  Aldenderfer, Mark;  Archila, Sonia;  Artioli, Gilberto;  Bale, Martin T.;  Beach, Timothy;  Borrell, Ferran;  Braje, Todd;  Buckland, Philip I.;  Jimenez Cano, Nayeli Guadalupe;  Capriles, Jose M.;  Diez Castillo, Agustin;  Cilingiroglu, Ciler;  Cleary, Michelle Negus;  Conolly, James;  Coutros, Peter R.;  Covey, R. Alan;  Cremaschi, Mauro;  Crowther, Alison;  Der, Lindsay;  di Lernia, Savino;  Doershuk, John F.;  Doolittle, William E.;  Edwards, Kevin J.;  Erlandson, Jon M.;  Evans, Damian;  Fairbairn, Andrew;  Faulkner, Patrick;  Feinman, Gary;  Fernandes, Ricardo;  Fitzpatrick, Scott M.;  Fyfe, Ralph;  Garcea, Elena;  Goldstein, Steve;  Goodman, Reed Charles;  Guedes, Jade Dalpoim;  Herrmann, Jason;  Hiscock, Peter;  Hommel, Peter;  Horsburgh, K. Ann;  Hritz, Carrie;  Ives, John W.;  Junno, Aripekka;  Kahn, Jennifer G.;  Kaufman, Brett;  Kearns, Catherine;  Kidder, Tristram R.;  Lanoe, Francois;  Lawrence, Dan;  Lee, Gyoung-Ah;  Levin, Maureece J.;  Lindskoug, Henrik B.;  Antonio Lopez-Saez, Jose;  Macrae, Scott;  Marchant, Rob;  Marston, John M.;  McClure, Sarah;  Mccoy, Mark D.;  Miller, Alicia Ventresca;  Morrison, Michael;  Matuzeviciute, Giedre Motuzaite;  Mueller, Johannes;  Nayak, Ayushi;  Noerwidi, Sofwan;  Peres, Tanya M.;  Peterson, Christian E.;  Proctor, Lucas;  Randall, Asa R.;  Renette, Steve;  Schug, Gwen Robbins;  Ryzewski, Krysta;  Saini, Rakesh;  Scheinsohn, Vivian;  Schmidt, Peter;  Sebillaud, Pauline;  Seitsonen, Oula;  Simpson, Ian A.;  Soltysiak, Arkadiusz;  Speakman, Robert J.;  Spengler, Robert N.;  Steffen, Martina L.;  Storozum, Michael J.;  Strickland, Keir M.;  Thompson, Jessica;  Thurston, T. L.;  Ulm, Sean;  Ustunkaya, M. Cemre;  Welker, Martin H.;  West, Catherine;  Williams, Patrick Ryan;  Wright, David K.;  Wright, Nathan;  Zahir, Muhammad;  Zerboni, Andrea;  Beaudoin, Ella;  Garcia, Santiago Munevar;  Powell, Jeremy;  Thornton, Alexa;  Kaplan, Jed O.;  Gaillard, Marie-Jose;  Goldewijk, Kees Klein;  Ellis, Erle
收藏  |  浏览/下载:58/0  |  提交时间:2019/11/27