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arXiv 2017年

作者： Chen, Muyuan Dai, Wei Sun, Stella Y. Jonasch, Darius He, Cynthia Y. Schmid, Michael F. Chiu, Wah Ludtke, Steven J. Graduate Program in Structural and Computational Biology and Molecular Biophysics Baylor College of Medicine HoustonTX77030 United States Verna Marrs and McLean Department of Biochemistry and Molecular Biology Baylor College of Medicine HoustonTX77030 United States Department of Biological Science Centre for BioImaging Sciences National University of Singapore 14 Science Drive 4 Singapore117543 Singapore

Cellular Electron Cryotomography (CryoET) offers the ability to look inside cells and observe macromolecules frozen in action. A primary challenge for this technique is identifying and extracting the molecular components within the crowded cellular environment. We introduce a method using neural networks to dramatically reduce the time and human effort required for subcellular annotation and feature extraction. Subsequent subtomogram classification and averaging yields in-situ structures of molecular components of interest. © 2017, CC BY.

关键词： Cellular neural networks

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Author Correction: π-HuB: the proteomic navigator of the human body

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Nature 2025年第8046期637卷 E22页

作者： Fuchu He Ruedi Aebersold Mark S Baker Xiuwu Bian Xiaochen Bo Daniel W Chan Cheng Chang Luonan Chen Xiangmei Chen Yu-Ju Chen Heping Cheng Ben C Collins Fernando Corrales Jürgen Cox Weinan E Jennifer E Van Eyk Jia Fan Pouya Faridi Daniel Figeys George Fu Gao Wen Gao Zu-Hua Gao Keisuke Goda Wilson Wen Bin Goh Dongfeng Gu Changjiang Guo Tiannan Guo Yuezhong He Albert J R Heck Henning Hermjakob Tony Hunter Narayanan Gopalakrishna Iyer Ying Jiang Connie R Jimenez Lokesh Joshi Neil L Kelleher Ming Li Yang Li Qingsong Lin Cui Hua Liu Fan Liu Guang-Hui Liu Yansheng Liu Zhihua Liu Teck Yew Low Ben Lu Matthias Mann Anming Meng Robert L Moritz Edouard Nice Guang Ning Gilbert S Omenn Christopher M Overall Giuseppe Palmisano Yaojin Peng Charles Pineau Terence Chuen Wai Poon Anthony W Purcell Jie Qiao Roger R Reddel Phillip J Robinson Paola Roncada Chris Sander Jiahao Sha Erwei Song Sanjeeva Srivastava Aihua Sun Siu Kwan Sze Chao Tang Liujun Tang Ruijun Tian Juan Antonio Vizcaíno Chanjuan Wang Chen Wang Xiaowen Wang Xinxing Wang Yan Wang Tobias Weiss Mathias Wilhelm Robert Winkler Bernd Wollscheid Limsoon Wong Linhai Xie Wei Xie Tao Xu Tianhao Xu Liying Yan Jing Yang Xiao Yang John Yates Tao Yun Qiwei Zhai Bing Zhang Hui Zhang Lihua Zhang Lingqiang Zhang Pingwen Zhang Yukui Zhang Yu Zi Zheng Qing Zhong Yunping Zhu State Key Laboratory of Medical Proteomics Beijing Proteome Research Center National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics Beijing China. hefc@***. International Academy of Phronesis Medicine (Guangdong) Guangdong China. hefc@***. Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich Switzerland. aebersold@imsb.biol.ethz.ch. Macquarie Medical School Macquarie University Sydney New South Wales Australia. Institute of Pathology and Southwest Cancer Center Southwest Hospital Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology Ministry of Education of China Chongqing China. Institute of Health Service and Transfusion Medicine Beijing China. Department of Pathology and The Sidney Kimmel Comprehensive Cancer Center Johns Hopkins University Baltimore MD USA. State Key Laboratory of Medical Proteomics Beijing Proteome Research Center National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics Beijing China. Key Laboratory of Systems Biology Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai China. Department of Nephrology First Medical Center of Chinese PLA General Hospital Nephrology Institute of the Chinese People's Liberation Army State Key Laboratory of Kidney Diseases National Clinical Research Center for Kidney Diseases Beijing Key Laboratory of Kidney Disease Research Beijing China. Institute of Chemistry Academia Sinica Taipei China. National Biomedical Imaging Center State Key Laboratory of Membrane Biology Institute of Molecular Medicine Peking-Tsinghua Center for Life Sciences College of Future Technology Peking University Beijing China. School of Biological Sciences Queen's University of Belfast Belfast UK. Functional Proteomics Laboratory Centro Nacional de Biotecnología-CSIC Madrid Spain. Computational Systems Biochemistry Research Group Ma

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LifeTime and improving European healthcare through cell-based interceptive medicine (vol 587, pg 377, 2020)

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NATURE 2021年第7852期592卷 E8-E8页

作者： Rajewsky, Nikolaus Almouzni, Genevieve Gorski, Stanislaw A. Aerts, Stein Amit, Ido Bertero, Michela G. Bock, Christoph Bredenoord, Annelien L. Cavalli, Giacomo Chiocca, Susanna Clevers, Hans De Strooper, Bart Eggert, Angelika Ellenberg, Jan Fernandez, Xose M. Figlerowicz, Marek Gasser, Susan M. Hubner, Norbert Kjems, Jorgen Knoblich, Jurgen A. Krabbe, Grietje Lichter, Peter Linnarsson, Sten Marine, Jean-Christophe Marioni, John C. Marti-Renom, Marc A. Netea, Mihai G. Nickel, Dorthe Nollmann, Marcelo Novak, Halina R. Parkinson, Helen Piccolo, Stefano Pinheiro, Ines Pombo, Ana Popp, Christian Reik, Wolf Roman-Roman, Sergio Rosenstiel, Philip Schultze, Joachim L. Stegle, Oliver Tanay, Amos Testa, Giuseppe Thanos, Dimitris Theis, Fabian J. Torres-Padilla, Maria-Elena Valencia, Alfonso Vallot, Celine van Oudenaarden, Alexander Vidal, Marie Voet, Thierry Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany Charité-Universitätsmedizin Berlin Germany Berlin Institute of Health (BIH) Berlin Germany German Center for Cardiovascular Research (DZHK) Partner Site Berlin Berlin Germany Institute for Biology Humboldt University of Berlin Berlin Germany Cardiovascular and Metabolic Sciences Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin Germany Department of Pediatric Oncology/Hematology Charité-Universitätsmedizin Berlin Berlin Germany Institut Curie CNRS PSL Research University Sorbonne Université Nuclear Dynamics Unit Equipe Labellisée Ligue contre le cancer Paris France VIB Center for Brain and Disease Research Leuven Belgium Department of Human Genetics KU Leuven Leuven Belgium Department of Neurosciences KU Leuven Leuven Belgium UK Dementia Research Institute at UCL University College London London UK Wellcome Sanger Institute Wellcome Genome Campus Cambridge UK Department of Immunology Weizmann Institute of Science Rehovot Israel Centre for Genomic Regulation (CRG) Barcelona Institute of Science and Technology Barcelona Spain CNAG-CRG Centre for Genomic Regulation Barcelona Institute of Science and Technology Barcelona Spain Universitat Pompeu Fabra Barcelona Spain ICREA Barcelona Spain CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna Austria Department of Laboratory Medicine Medical University of Vienna Vienna Austria Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases Vienna Austria Department of Medical Humanities Julius Center for Health Sciences and Primary Care University Medical Center Utrecht Utrecht The Netherlands Institute of Human Genetics UMR 9002 CNRS and University of Montpellier Montpellier France Department of Experimental Oncology IEO European Institute of Oncology IRCCS Milan Italy Department of Oncology and Hemato

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The next generation's Frankenstein films

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Science (New York, N.Y.) 2018年第6372期359卷 170-171页

作者： Jenny Nguyen Matilda S Newton Michael Strong Martin Pačesa Bo Cao Kristy A Winter Ken Dutton-Regester Laura J Kingsley Lewis Katz School of Medicine at Temple University Philadelphia PA 19140 USA. jt.nguyen2020@***. University of Minnesota St. Paul MN 55108 USA. msnewton@umn.edu. Computational Bioscience Program University of Colorado Denver Denver CO 80206 USA. michael.strong@ucdenver.edu. Department of Biochemistry University of Zurich 8057 Zurich Switzerland. m.pacesa@bioc.uzh.ch. Core Research Laboratory The Second Affiliated Hospital School of Medicine Xi'an Jiaotong University Xi'an Shaanxi 710004 China. bocao@***. Skeletal Biology and Forensic Anthropology Research Laboratory Queensland University of Technology Brisbane QLD 4000 Australia. kristy.winter@hdr.qut.edu.au. QIMR Berghofer Medical Research Institute Brisbane QLD 4006 Australia. ken.dutton-regester@qimrberghofer.edu.au. Department of Structural Biology Genomics Institute of the Novartis Research Foundation San Diego CA 92121 USA. lkingsley@***.

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Effect of climate on traits of dominant and rare tree species in the world’s forests

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Nature Communications 2025年第1期16卷 1-15页

作者： Hordijk, Iris Poorter, Lourens Liang, Jingjing Reich, Peter B. de-Miguel, Sergio Nabuurs, Gert-Jan Gamarra, Javier G. P. Chen, Han Y. H. Zhou, Mo Wiser, Susan K. Pretzsch, Hans Paquette, Alain Picard, Nicolas Hérault, Bruno Bastin, Jean-Francois Alberti, Giorgio Abegg, Meinrad Adou Yao, Yves C. Almeyda Zambrano, Angelica M. Alvarado, Braulio V. Alvarez-Davila, Esteban Alvarez-Loayza, Patricia Alves, Luciana F. Amaral, Iêda Ammer, Christian Antón-Fernández, Clara Araujo-Murakami, Alejandro Arroyo, Luzmila Avitabile, Valerio Aymard C, Gerardo A. Baker, Timothy Banki, Olaf Barroso, Jorcely Bastian, Meredith L. Birigazzi, Luca Birnbaum, Philippe Bitariho, Robert Boeckx, Pascal Bongers, Frans Bouriaud, Olivier Brancalion, Pedro H. S. Brandl, Susanne Brearley, Francis Q. Brienen, Roel Broadbent, Eben N. Bruelheide, Helge Cazzolla Gatti, Roberto Cesar, Ricardo G. Cesljar, Goran Chazdon, Robin L. Chisholm, Chelsea Cienciala, Emil Clark, Connie J. Clark, David B. Colletta, Gabriel Coomes, David Cornejo Valverde, Fernando Corral-Rivas, Jose J. Crim, Philip Cumming, Jonathan Dayanandan, Selvadurai de Gasper, André L. Decuyper, Mathieu Derroire, Géraldine DeVries, Ben Djordjevic, Ilija Dourdain, Aurélie Dolezal, Jiri Engone Obiang, Nestor Laurier Enquist, Brian Eyre, Teresa Fandohan, Adandé Belarmain Fayle, Tom M. Ferreira, Leandro V. Feldpausch, Ted R. Finér, Leena Fischer, Markus Fletcher, Christine Frizzera, Lorenzo Gianelle, Damiano Glick, Henry B. Harris, David Hector, Andrew Hemp, Andreas Herbohn, John Hillers, Annika Honorio Coronado, Eurídice N. Hui, Cang Cho, Hyunkook Ibanez, Thomas Jung, Ilbin Imai, Nobuo Jagodzinski, Andrzej M. Jaroszewicz, Bogdan Johannsen, Vivian Joly, Carlos A. Jucker, Tommaso Karminov, Viktor Kartawinata, Kuswata Kearsley, Elizabeth Kenfack, David Kennard, Deborah Kepfer-Rojas, Sebastian Keppel, Gunnar Khan, Mohammed Latif Killeen, Timothy Kim, Hyun Seok Kitayama, Kanehiro Köhl, Michael Korjus, Henn Kraxner, Florian Laarmann, Diana Lang, Mait Lewis, Simon Lu, Huicui Lukina, Natalia Maitner, Br Institute of Integrative Biology ETH Zurich (Swiss Federal Institute of Technology) Zurich Switzerland Wageningen University and Research Wageningen Netherlands Department of Forestry and Natural Resources Purdue University West Lafayette IN United States Department of Forest Resources University of Minnesota St Paul MN United States Hawkesbury Institute for the Environment Western Sydney University Penrith NSW Australia Department of Agricultural and Forest Sciences and Engineering University of Lleida Lleida Spain Forest Science and Technology Centre of Catalonia (CTFC) Solsona Spain Forestry Division Food and Agriculture Organization of the United Nations Rome Italy Faculty of Natural Resources Management Lakehead University Thunder Bay ON Canada Manaaki Whenua–Landcare Research Lincoln New Zealand Chair for Forest Growth and Yield Science TUM School for Life Sciences Technical University of Munich Munich Germany Centre for Forest Research Université du Québec à Montréal Montréal QC Canada GIP ECOFOR Paris France CIRAD Forêts et Sociétés Montpellier France Forêts et Sociétés Univ Montpellier CIRAD Montpellier France Gembloux Agro Bio-Tech University of Liege Liege Belgium Faculty of Science and Technology Free University of Bolzano Bolzano Italy Department of Agricultural Food Environmental and Animal Sciences University of Udine Udine Italy Swiss Federal Institute for Forest Snow and Landscape Research WSL Birmensdorf Switzerland UFR Biosciences University Félix Houphouët-Boigny Abidjan Cote d'Ivoire Spatial Ecology and Conservation Laboratory Center for Latin American Studies University of Florida Gainesville FL United States Forestry School Tecnológico de Costa Rica TEC Cartago Costa Rica Fundacion ConVida Universidad Nacional Abierta y a Distancia UNAD Medellin Colombia Field Museum of Natural History Chicago IL United States Center for Tropical Research Institute of the Environment and Sustainability UCLA Los Angeles CA

Species’ traits and environmental conditions determine the abundance of tree species across the globe. The extent to which traits of dominant and rare tree species differ remains untested across a broad environmental range, limiting our understanding of how species traits and the environment shape forest functional composition. We use a global dataset of tree composition of >22,000 forest plots and 11 traits of 1663 tree species to ask how locally dominant and rare species differ in their trait values, and how these differences are driven by climatic gradients in temperature and water availability in forest biomes across the globe. We find three consistent trait differences between locally dominant and rare species across all biomes;dominant species are taller, have softer wood and higher loading on the multivariate stem strategy axis (related to narrow tracheids and thick bark). The difference between traits of dominant and rare species is more strongly driven by temperature compared to water availability, as temperature might affect a larger number of traits. Therefore, climate change driven global temperature rise may have a strong effect on trait differences between dominant and rare tree species and may lead to changes in species abundances and therefore strong community reassembly. © The Author(s) 2025.

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Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

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Nature biotechnology 2020年第4期38卷 504页

作者： Christian Lieven Moritz E Beber Brett G Olivier Frank T Bergmann Meric Ataman Parizad Babaei Jennifer A Bartell Lars M Blank Siddharth Chauhan Kevin Correia Christian Diener Andreas Dräger Birgitta E Ebert Janaka N Edirisinghe José P Faria Adam M Feist Georgios Fengos Ronan M T Fleming Beatriz García-Jiménez Vassily Hatzimanikatis Wout van Helvoirt Christopher S Henry Henning Hermjakob Markus J Herrgård Ali Kaafarani Hyun Uk Kim Zachary King Steffen Klamt Edda Klipp Jasper J Koehorst Matthias König Meiyappan Lakshmanan Dong-Yup Lee Sang Yup Lee Sunjae Lee Nathan E Lewis Filipe Liu Hongwu Ma Daniel Machado Radhakrishnan Mahadevan Paulo Maia Adil Mardinoglu Gregory L Medlock Jonathan M Monk Jens Nielsen Lars Keld Nielsen Juan Nogales Intawat Nookaew Bernhard O Palsson Jason A Papin Kiran R Patil Mark Poolman Nathan D Price Osbaldo Resendis-Antonio Anne Richelle Isabel Rocha Benjamín J Sánchez Peter J Schaap Rahuman S Malik Sheriff Saeed Shoaie Nikolaus Sonnenschein Bas Teusink Paulo Vilaça Jon Olav Vik Judith A H Wodke Joana C Xavier Qianqian Yuan Maksim Zakhartsev Cheng Zhang Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Lyngby Denmark. Systems Biology Lab Amsterdam Institute of Molecular and Life Sciences (AIMMS) Vrije Universiteit Amsterdam Amsterdam the Netherlands. BioQUANT/COS Heidelberg University Heidelberg Germany. Ecole Polytechnique Fédérale de Lausanne Laboratory of Computational Systems Biotechnology Lausanne Switzerland. iAMB-Institute of Applied Microbiology ABBt-Aachen Biology and Biotechnology RWTH Aachen University Aachen Germany. Department of Bioengineering University of California La Jolla CA USA. Department of Chemical Engineering and Applied Chemistry University of Toronto Toronto Ontario Canada. Human Systems Biology Laboratory Instituto Nacional de Medicina Genomica & Coordinación de la Investigación Científica-Red de Apoyo a la Investigación UNAM Mexico City Mexico. Institute for Systems Biology Seattle WA USA. Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens Institute for Biomedical Informatics (IBMI) Tübingen Germany. Department of Computer Science University of Tübingen Tübingen Germany. German Center for Infection Research (DZIF) partner site Tübingen Tübingen Germany. Australian Institute for Bioengineering and Nanotechnology The University of Queensland Brisbane Queensland Australia. Argonne National Laboratory Lemont IL USA. Analytical Biosciences Division of Systems Biomedicine and Pharmacology Leiden Academic Centre for Drug Research Leiden University Leiden the Netherlands. Department of Systems Biology Centro Nacional de Biotecnología Consejo Superior de Investigaciones Científicas (CNB-CSIC) Madrid Spain. Centro de Biotecnología y Genómica de Plantas (CBGP UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Madrid Spain. Department of Animal and Aquacultural Sciences Faculty of Biosciences Norwegian University of Life Sciences Oslo Norway

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Building and Validating Atomic Models for Cryo-EM Density Maps

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Microscopy and Microanalysis 2016年第S3期22卷 2080-2081页

作者： Matthew L. Baker Muyuan Chen Tunay Durmaz Phil Baldwin Tao Ju Steven J. Ludtke Verna and Marrs McLean Department of Biochemistry and Molecular Biology Baylor College of Medicine HoustonTXUSA Program in Structural and Computational Biology and Molecular Biophysics Baylor College of Medicine HoustonTXUSA Department of Computer Science and Engineering Washington University in St. Louis St. LouisMOUSA

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GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging

arXiv

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arXiv 2017年

作者： Pryor, Alan Yang, Yongsoo Rana, Arjun Gallagher-Jones, Marcus Zhou, Jihan Lo, Yuan Hung Melinte, Georgian Chiu, Wah Rodriguez, Jose A. Miao, Jianwei Department of Physics and Astronomy California NanoSystems Institute University of California Los AngelesCA90095 United States Department of Chemistry & Biochemistry UCLA-DOE Institute of Genomics and Proteomics Los AngelesCA90095-1570 United States Department of Bioengineering University of California Los AngelesCA90095 United States Institut de Physique et Chimie des Matériaux de Strasbourg CNRS-Université de Strasbourg 23 rue du Loess Cedex 08 Strasbourg67037 France Program in Structural and Computational Biology and Molecular Biophysics Baylor College of Medicine HoustonTX77030 United States

Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. In many scientific applications, however, the number of projections that can be measured is limited due to geometric constraints, tolerable radiation dose and/or acquisition speed. Thus it becomes an important problem to obtain the best-possible reconstruction from a limited number of projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE). By iterating between real and reciprocal space, GENFIRE searches for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques by numerical simulations, and by experimentally by reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. Equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines. Copyright © 2017, The Authors. All rights reserved.

关键词： Tomography

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Dominant variants in major spliceosome U4 and U5 small nuclear RNA genes cause neurodevelopmental disorders through splicing disruption

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Nature Genetics 2025年 1-15页

作者： Nava, Caroline Cogne, Benjamin Santini, Amandine Leitão, Elsa Lecoquierre, François Chen, Yuyang Stenton, Sarah L. Besnard, Thomas Heide, Solveig Baer, Sarah Jakhar, Abhilasha Neuser, Sonja Keren, Boris Faudet, Anne Forlani, Sylvie Faoucher, Marie Uguen, Kevin Platzer, Konrad Afenjar, Alexandra Alessandri, Jean-Luc Andres, Stephanie Angelini, Chloé Aral, Bernard Arveiler, Benoit Attie-Bitach, Tania Aubert Mucca, Marion Banneau, Guillaume Barakat, Tahsin Stefan Barcia, Giulia Baulac, Stéphanie Beneteau, Claire Benkerdou, Fouzia Bernard, Virginie Bézieau, Stéphane Bonneau, Dominique Bonnet-Dupeyron, Marie-Noelle Boussion, Simon Boute, Odile Brischoux-Boucher, Elise Bryen, Samantha J. Buratti, Julien Busa, Tiffany Caliebe, Almuth Capri, Yline Cassinari, Kévin Caumes, Roseline Cenni, Camille Chambon, Pascal Charles, Perrine Christodoulou, John Colson, Cindy Conrad, Solène Cospain, Auriane Coursimault, Juliette Courtin, Thomas Couse, Madeline Coutton, Charles Creveaux, Isabelle D’Gama, Alissa M. Dauriat, Benjamin de Sainte Agathe, Jean-Madeleine Del Gobbo, Giulia Delahaye-Duriez, Andrée Delanne, Julian Denommé-Pichon, Anne-Sophie Dieux-Coeslier, Anne Do Souto Ferreira, Laura Doco-Fenzy, Martine Drukewitz, Stephan Duboc, Véronique Dubourg, Christèle Duffourd, Yannis Dyment, David El Chehadeh, Salima Elmaleh, Monique Faivre, Laurence Fennelly, Samuel Fischer, Hanna Fradin, Mélanie Galludec Vaillant, Camille Ganne, Benjamin Ghoumid, Jamal Goel, Himanshu Gokce-Samar, Zeynep Goldenberg, Alice Gonfreville Robert, Romain Gorokhova, Svetlana Goujon, Louise Granier, Victoria Gras, Mathilde Greally, John M. Greiten, Bianca Gueguen, Paul Guerrot, Anne-Marie Guha, Saurav Guimier, Anne Haack, Tobias B. Hadj Abdallah, Hamza Halleb, Yosra Harbuz, Radu Harris, Madeleine Hentschel, Julia Héron, Bénédicte Hitz, Marc-Phillip Innes, A. Micheil Jadas, Vincent Januel, Louis Jean-Marçais, Nolwenn Jobanputra, Vaidehi Jobic, Florence Jornea, Ludmila Jost, Céline Julia, Sophie Kaiser, Frank J. Kaschta, Daniel Kaya, Sabine Ketteler, Petra Khadi Sorbonne Université Institut du Cerveau—Paris Brain Institute—ICM Inserm CNRS APHP Hôpital Pitié-Salpêtrière Paris France Assistance Publique-Hôpitaux de Paris (APHP) Sorbonne Université Département de Génétique Médicale Hôpital Pitié-Salpêtrière Paris France Laboratoire SeqOIA Paris France Nantes Université CHU de Nantes Service de Génétique Médicale Nantes France Nantes Université CHU de Nantes CNRS INSERM l’institut du thorax Nantes France Univ. Rouen Normandie Normandie Univ. Inserm U1245 Rouen France Institute of Human Genetics University Hospital Essen University Duisburg–Essen Essen Germany Univ. Rouen Normandie Normandie Univ. Inserm U1245 and CHU Rouen Department of Genetics and Reference Center for Developmental Abnormalities Rouen France Big Data Institute University of Oxford Oxford United Kingdom Centre for Human Genetics University of Oxford Oxford United Kingdom Broad Center for Mendelian Genomics Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA United States Division of Genetics and Genomics Boston Children’s Hospital Harvard Medical School Boston MA United States Service de Neuropédiatrie Hôpitaux Universitaires de Strasbourg Strasbourg France Institute of Genetics and Cellular and Molecular Biology (IGBMC) INSERM-U964 CNRS-UMR7104 University of Strasbourg Illkirch France CNRS Inserm Université de Strasbourg IGBMC UMR 7104-UMR-S 1258 Illkirch France Department of Integrated Structural Biology IGBMC Illkirch France Institute of Human Genetics University of Leipzig Medical Center Leipzig Germany Laboratoire de Génétique Moléculaire et Génomique FHU GenOMedS CHU Rennes Rennes France University of Rennes CNRS INSERM IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290 ERL U1305 Rennes France GCS AURAGEN Lyon France Univ. Brest Inserm EFS UMR 1078 GGB Brest France Service de Génétique Médicale et Biologie de la Reproduction CHRU de Brest Brest France Assistan

The major spliceosome contains five small nuclear RNAs (snRNAs;U1, U2, U4, U5 and U6) essential for splicing. Variants in RNU4-2, encoding U4, cause a neurodevelopmental disorder called ReNU syndrome. We investigated de novo variants in 50 snRNA-encoding genes in a French cohort of 23,649 individuals with rare disorders and gathered additional cases through international collaborations. Altogether, we identified 145 previously unreported probands with (likely) pathogenic variants in RNU4-2 and 21 individuals with de novo and/or recurrent variants in RNU5B-1 and RNU5A-1, encoding U5. Pathogenic variants typically arose de novo on the maternal allele and cluster in regions critical for splicing. RNU4-2 variants mainly localize to two structures, the stem III and T-loop/quasi-pseudoknot, which position the U6 ACAGAGA box for 5′ splice site recognition and associate with different phenotypic severity. RNU4-2 variants result in specific defects in alternative 5′ splice site usage and methylation patterns (episignatures) that correlate with variant location and clinical severity. This study establishes RNU5B-1 as a neurodevelopmental disorder gene, suggests RNU5A-1 as a strong candidate and highlights the role of de novo variants in snRNAs. © The Author(s) 2025.

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Analytical strategies for studying stem cell metabolism

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Frontiers in biology 2015年第2期10卷 141-153页

作者： James M. Arnold William T. Choi Arun Sreekumar Mirjana Maletic-Savatic Department of Molecular and Cell Biology Baylor College of Medicine Houston TX 77030 USA Program in Developmental Biology and Medical Scientist Training Program Baylor College of Medicine Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital Houston TX 77030 USA Departments of Pediatrics-Neurology and Neuroscience and Program in Structural and Computational Biology and Molecular Biophysics Baylor College of Medicine Houston TX 77030 USA

Owing to their capacity for self-renewal and pluripotency, stem cells possess untold potential for revolutionizing the field of regenerative medicine through the development of novel therapeutic strategies for treating cancer, diabetes, cardiovascular and neurodegenerative diseases. Central to developing these strategies is improving our understanding of biological mechanisms responsible for governing stem cell fate and self-renewal. Increasing attention is being given to the significance of metabolism, through the production of energy and generation of small molecules, as a critical regulator of stem cell functioning. Rapid advances in the field of metabolomics now allow for in-depth profiling of stem cells both in vitro and in vivo, providing a systems perspective on key metabolic and molecular pathways which influence stem cell biology. Understanding the analytical platforms and techniques that are currently used to study stem cell metabolomics, as well as how new insights can be derived from this knowledge, will accelerate new research in the field and improve future efforts to expand our understanding of the interplay between metabolism and stem cell biology.

关键词： stem cell metabolism NMR mass spectrometry MRS flux analysis

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