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Publisher Correction: A genome-wide association analysis reveals new pathogenic pathways in gout

Nature genetics 2024年第11期56卷 2577页

作者： Tanya J Major Riku Takei Hirotaka Matsuo Megan P Leask Nicholas A Sumpter Ruth K Topless Yuya Shirai Wei Wang Murray J Cadzow Amanda J Phipps-Green Zhiqiang Li Aichang Ji Marilyn E Merriman Emily Morice Eric E Kelley Wen-Hua Wei Sally P A McCormick Matthew J Bixley Richard J Reynolds Kenneth G Saag Tayaza Fadason Evgenia Golovina Justin M O'Sullivan Lisa K Stamp Nicola Dalbeth Abhishek Abhishek Michael Doherty Edward Roddy Lennart T H Jacobsson Meliha C Kapetanovic Olle Melander Mariano Andrés Fernando Pérez-Ruiz Rosa J Torres Timothy Radstake Timothy L Jansen Matthijs Janssen Leo A B Joosten Ruiqi Liu Orsolya I Gaal Tania O Crişan Simona Rednic Fina Kurreeman Tom W J Huizinga René Toes Frédéric Lioté Pascal Richette Thomas Bardin Hang Korng Ea Tristan Pascart Geraldine M McCarthy Laura Helbert Blanka Stibůrková Anne-K Tausche Till Uhlig Véronique Vitart Thibaud S Boutin Caroline Hayward Philip L Riches Stuart H Ralston Archie Campbell Thomas M MacDonald Akiyoshi Nakayama Tappei Takada Masahiro Nakatochi Seiko Shimizu Yusuke Kawamura Yu Toyoda Hirofumi Nakaoka Ken Yamamoto Keitaro Matsuo Nariyoshi Shinomiya Kimiyoshi Ichida Chaeyoung Lee Linda A Bradbury Matthew A Brown Philip C Robinson Russell R C Buchanan Catherine L Hill Susan Lester Malcolm D Smith Maureen Rischmueller Hyon K Choi Eli A Stahl Jeff N Miner Daniel H Solomon Jing Cui Kathleen M Giacomini Deanna J Brackman Eric M Jorgenson Hongbo Liu Katalin Susztak Suyash Shringarpure Alexander So Yukinori Okada Changgui Li Yongyong Shi Tony R Merriman Department of Biochemistry University of Otago Dunedin New Zealand. Division of Clinical Immunology and Rheumatology University of Alabama at Birmingham Birmingham AL USA. Department of Integrative Physiology and Bio-Nano Medicine National Defense Medical College Saitama Japan. Department of Biomedical Information Management National Defense Medical College Research Institute National Defense Medical College Saitama Japan. Department of Statistical Genetics Osaka University Graduate School of Medicine Osaka Japan. Genomics R&D 23andMe Inc Sunnyvale CA USA. The Biomedical Sciences Institute and The Affiliated Hospital of Qingdao University Qingdao University Qingdao Shandong China. Shandong Provincial Key Laboratory of Metabolic Diseases Shandong Provincial Clinical Research Center for Immune Diseases and Gout the Affiliated Hospital of Qingdao University Qingdao Shandong China. The Institute of Metabolic Diseases Qingdao University Qingdao Shandong China. Department of Physiology and Pharmacology West Virginia University Morgantown WV USA. Department of Women's and Children's Health University of Otago Dunedin New Zealand. Liggins Institute University of Auckland Auckland New Zealand. MRC Lifecourse Epidemiology Unit University of Southampton Southampton United Kingdom. Singapore Institute for Clinical Sciences Agency for Science Technology and Research Singapore Singapore. Australian Parkinsons Mission Garvan Institute of Medical Research Sydney New South Wales Australia. Department of Medicine University of Otago Christchurch Christchurch New Zealand. Department of Medicine University of Auckland Auckland New Zealand. Academic Rheumatology School of Medicine University of Nottingham Nottingham United Kingdom. School of Medicine Keele University Keele Staffordshire United Kingdom. Haywood Academic Rheumatology Centre Midlands Partnership University NHS Foundation Trust Stoke-on-Trent UK. Department of Rheumatology and Inflammation Research

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Pressing topics in the Belgian water sector anno 2015

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Sustainability of Water Quality and Ecology 2016年 7卷 32-36页

作者： De Mulder, C. Van Hoey, S. Van Hulle, S. Agathos, S.N. Cauwenberg, P. Mergen, P. Seuntjens, P. Smets, I. De Gueldre, G. Mouton, A. Schowanek, D. Meesschaert, B. Verstraete, W. Nopens, I. BIOMATH Department of Mathematical Modelling Statistics and Bioinformatics Faculty of Bioscience Engineering Ghent University Coupure Links 653 Gent 9000 Belgium LIWET Department of Industrial Biological Sciences Ghent University Graaf Karel de Goedelaan 5 Kortrijk 8500 Belgium Laboratory of Bioengineering Earth and Life Institute Université Catholique de Louvain Louvain-la-Neuve 1348 Belgium Unit Environmental Modeling Flemish Institute for Technological Research (VITO) Boeretang 200 Mol 2400 Belgium Royal Museum for Central Africa Leuvensesteenweg 13 Tervuren 3080 Belgium Botanic Garden Meise Bouchout Domain Nieuwelaan 38 Meise 1860 Belgium Department of Soil Management Faculty of Bioscience Engineering Ghent University Coupure Links 653 Gent 9000 Belgium Department of Bioscience Engineering University of Antwerp Groenenborgerlaan 171 Antwerpen 2000 Belgium CREaS Department of Chemical Engineering KU Leuven Celestijnenlaan 200F Leuven 3001 Belgium Aquafin NV Dijkstraat 8 Aartselaar 2630 Belgium Technology Campus Gent Odisee Hogeschool Gebroeders De Smetstraat 1 Gent 9000 Belgium Environmental Stewardship and Sustainability - Brussels Innovation Center Procter and Gamble Temselaan 100 Strombeek-Bever 1853 Belgium Cluster for Bioengineering Technology Department of Microbial and Molecular Systems KU Leuven Technology Campus Ostend Zeedijk 101 Oostende B-8400 Belgium LabMET Department of Biochemical and Microbial Technology Faculty of Bioscience Engineering Ghent University Coupure Links 653 Gent 9000 Belgium

Today's water sector is governed by some hot topics, and this is no different in Belgium. As for the International Water Association (IWA), the goal of its Belgian division (B-IWA) is to gather different stakeholders, i.e. academics, policy makers and people from industry active in the (Belgian) water sector and trigger the debate. In May 2015, a first Nocturnal was organised to accomplish just this. Seven hot water topics, proposed by participants at the time of their online registration, were addressed in rotating round table discussions. These topics included resource recovery, micropollutants, water scarcity, hydroinformatics, integrated water management and modeling, technology vs. legislation and Computational Fluid Dynamics in water applications. The lively discussions led to the idea of this short contribution describing the outcomes of these round table discussions, along with some additional research on the topics. Main conclusions include the need for education (both of scholars and young professionals), inter-domain communication and the growing importance of IT in the water sector. © 2016 Elsevier B.V.

关键词： Education Industry Informatics Legislation Water sector

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PERFECTOS-APE: Predicting regulatory functional effect of SNPs by approximate P-value estimation 6

PERFECTOS-APE: Predicting regulatory functional effect of SN...

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6th International Conference on bioinformatics Models, Methods and Algorithms, bioinformatics 2015

作者： Vorontsov, Ilya E. Kulakovskiy, Ivan V. Khimulya, Grigory Nikolaeva, Daria D. Makeev, Vsevolod J. Department of Computational Systems Biology Vavilov Institute of General Genetics Gubkina Str. 3 Moscow Russia Laboratory of Bioinformatics and Systems Biology Engelhardt Institute of Molecular Biology Vavilova Str. 32 Moscow Russia Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow Russia Department of Medical and Biological Physics Moscow Institute of Physics and Technology Moscow Region Russia

ISBN: (纸本)9789897580703

Single nucleotide polymorphisms (SNPs) and variants (SNVs) are often found in regulatory regions of human genome. Nucleotide substitutions in promoter and enhancer regions may affect transcription factor (TF) binding and alter gene expression regulation. Nowadays binding patterns are known for hundreds of human TFs. Thus one can assess possible functional effects of allele variations or mutations in TF binding sites using sequence analysis. We present PERFECTOS-APE, the software to PrEdict Regulatory Functional Effect of SNPs by Approximate P-value Estimation. Using a predefined collection of position weight matrices (PWMs) representing TF binding patterns, PERFECTOS-APE identifies transcription factors whose binding sites can be significantly affected by given nucleotide substitutions. PERFECTOS-APE supports both classic PWMs under the position independency assumption, and dinucleotide PWMs accounting for the dinucleotide composition and correlations between nucleotides in adjacent positions within binding sites. PERFECTOS-APE uses dynamic programming to calculate PWM score distribution and convert the scores to P-values with an optional binary search mode using a precomputed P-value list to speed-up the computations. Software is written in Java and is freely available as standalone program and online tool: http://***/perfectosape/. We have tested our algorithm on several disease associated SNVs as well as on a set of cancer somatic mutations occurring in intronic regions of the human genome.

关键词： Binding sites

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SP164 WHY DOES ISCHEMIC PRECONDITIONING NOT WORK IN AGED KIDNEY

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Nephrology Dialysis Transplantation 2017年第SUPPL_3期32卷 iii159-iii159页

作者： Jankauskas, Stanislovas Andrianova, Nadezhda Zorova, Ljubava Pevzner, Irina Popkov, Vasily Kolosova, Nataliya Plotnikov, Egor Zorov, Dmitry Laboratory of the structure and function of mitochondria A.N. Belozersky Institute Of Physico-Chemical Biology Moscow State University Moscow Russian Federation Department of Biochemistry Pirogov Russian National Research Medical University Moscow Russian Federation International Laser Center A.N. Belozersky Institute Of Physico-Chemical Biology Moscow State University Moscow Russian Federation Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow Russian Federation Sector of Molecular Mechanisms of Aging The Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences Novosibirsk Russian Federation

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Significance and Strategy in the Foundation of Department for Bio-Medical Engineering in Japan

Transactions of Japanese Society for Medical and Biological ...

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Transactions of Japanese Society for Medical and Biological Engineering 2016年第27 PM期54 Annual卷 164-164页

作者： Hashizume, Makoto Ikuta, Koji Imachi, Hiroshi Shimizu, Kouichi Sakuma, Ichirou Sunagawa, Kenji Ishihara, Ken Hanafusa, Akihiko Department of Advanced Medical Initiatives Faculty of Medical Sciences Kyushu University Japan Medical Micromachine Laboratory The Research Center for Advanced Science and Technology The University of Tokyo Japan Tohoku University Japan Division of Bioengineering and Bioinformatics Hokkaido University Japan Department of Human and Engineered Enviromental Studies Graduate School of Frontier Sciences The University of Tokyo Japan Center for Cardiovascular disruptive Innovation Kyushu University Japan Department of Medical Informatics Ehime University Graduate School of Medicine Japan Department of Mechanical Engineering Shibaura Institute of Technology Graduate School Japan

The purpose of this symposium is to discuss the significance and the strategy to found the department of bio-medical engineering in Japan. The department of bio-medical engineering has been already established in most of the leading universities in Europe and the United States of America since 1950, while there are a few institutes of the bio-medical engineering in Japan. It is the mandatory issue to be solved in order to grow the young generation up to the international level in the field of biomedical engineering and to strengthen the international competition in medical industry. We would like to show some direction toward the foundation of the department of bio-medical engineering by discussing the current problems and learning the history and the strategy from the founders. © 2016, Japan Soc. of Med. Electronics and Biol. Engineering. All rights reserved.

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A probabilistic method to quantify the colocalization of markers on intracellular vesicular structures visualized by light microscopy

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AIP Conference Proceedings 2015年第1期1641卷 580-587页

作者： Yannis Kalaidzidis Inna Kalaidzidis Marino Zerial Max Planck Institute of Molecular Cell Biology and Genetics 01307 Dresden Germany and Faculty of Bioengineering and Bioinformatics Moscow State University 119991 Moscow Russia Max Planck Institute of Molecular Cell Biology and Genetics 01307 Dresden Germany

The intracellular localization of proteins to their specific compartments is a rich source of information for the study of biological processes. The colocalization of a protein with an established compartment marker is routinely measured from multi-color fluorescent microscopy images. Unfortunately, the apparent colocalization is a mixture of real and random colocalization. Random colocalization results from the limited resolution of the light microscope and the close location or occlusion of objects in the crowded cytoplasmic environment. Commonly used methods for the correction of random colocalization work well if the random colocalization is significantly smaller than the real colocalization. In the case where they have comparable values, the final result could be a senseless negative value. To solve this problem, we first developed a probabilistic model for the estimation of random colocalization and demonstrated that it produces results that coincide with the standard scramble method. Second, we developed a probabilistic model for the correction of random colocalization for the double and multiple colocalization of intracellular markers on vesicular structures. Our probabilistic method of estimation of real colocalization has two main advantages: 1) it never gives a negative colocalization value and 2) provides the estimation of colocalization uncertainty.

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Thymidine Glycol: The Effect on DNA Structure and DNA Binding by Site-Specific Proteins

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Natural Science 2015年第11期7卷 491-509页

作者： Elena A. Kubareva Fan Yang Alexandra Yu. Ryazanova Nina G. Dolinnaya Andrei V. Golovin Nikolai V. Molochkov Elena A. Romanova Elizaveta A. Karpova Timofei S. Zatsepin Tatiana S. Oretskaya Belozersky Institute of Physico-Chemical Biology Lomonosov Moscow State University Moscow Russia Chemistry Department Lomonosov Moscow State University Moscow Russia Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow Russia Institute of Theoretical and Experimental Biophysics Russian Academy of Science Moscow Region Pushchino Russia

Thymidine glycol (5,6-dihydroxy-5,6-dihydrothymidine, Tg) is a major type of oxidative damage in DNA. During chemical oligonucleotide synthesis, Tg residue was incorporated in the different positions of 17 b.p. DNA duplexes, which differ in one base pair in the internal part. According to UV-melting curves, Tg destabilizes the double helix in a sequence independent manner. In contrast, the localized alterations in duplex structure were shown by CD spectroscopy to depend on the type of base pairs flanking the Tg lesion. Molecular dynamics simulations demonstrate that Tg is partially out of the double helix. For the first time, Tg impact on several site-specific DNA-binding proteins is studied, namely p50 and p65 subunits of nuclear factor kappa-B (NF-κB) and DNA methyltransferase SsoII (***). Our results show that p50/p50 and p65/p65 homodimers of NF-κB can tolerate a single Tg residue in the binding site quite well. Nevertheless the homodimers have different affinities to the oxidized κB site depending on the Tg position. *** can act as a transcription repressor when bound to the regulatory site. *** demonstrates decreased affinity and lowered methylation efficiency when its methylation site contains Tg in the central position. Single Tg in one half of the regulatory site decreases *** affinity to the oxidized DNA, whereas Tg presence in both half-sites prevents *** binding to such ligand.

关键词： Thymidine Glycol Oxidative Damage Molecular Dynamics Simulations Nuclear Factor Kappa-B DNA Methyltransferase SsoII

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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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SP169MITOCHONDRIA-TARGETED ANTIOXIDANT SKQR1 PEVENTS ENDOTHELIAL DYSFUNCTION DURING ISCHEMIC ACUTE KIDNEY INJURY

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Nephrology Dialysis Transplantation 2016年第SUPPL_1期31卷 i143-i143页

作者： Jankauskas, Stanislovas S. Matsievsky, Dmitry D Andrianova, Nadezhda V. Savchenko, Elena S. Alieva, Irina B. Plotnikov, Egor Y. Zorov, Dmitry B. A.N. Belozersky Institute Of Physico-Chemical Biology Moscow State University Laboratory of the structure and function of mitochondria Moscow RUSSIAN FEDERATION Institute of General Pathology and Pathophysiology Bioengineering Moscow RUSSIAN FEDERATION Pirogov Russian National Research Medical University Biochemistry Moscow RUSSIAN FEDERATION Lomonosov Moscow State University Faculty of Bioengineering and Bioinformatics Moscow RUSSIAN FEDERATION A.N. Belozersky Institute Of Physico-Chemical Biology Moscow State University Department of electron microscopy Moscow RUSSIAN FEDERATION

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Fluorescence color diversity of great barrier reef corals

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Journal of Innovative Optical Health Sciences 2015年第4期8卷 58-68页

作者： Grigory Lapshin Anya Salih Peter Kolosov Maria Golovkina Yuri Zavorotnyi Tatyana Ivashina Leonid Vinokurov Victor Bagratashvili Alexander Savitsky Physical Biochemistry Lab INBI RASLeninsky Prospekt 33Build.2 Moscow 119071Russia Faculty of Bioengineering and Bioinformatics Moscow State University Leninskiye Gory 1-73 MSU GSP-1 Moscow 119991Russia Confocal Bio-Imaging Facility(CBIF) Division Deputy Vice-Chancellor(Research&Development)University of Western SydneyLocked Bag 1797 Penrith South DCNSW 1797Australia Institute of Higher Nervous Activity and Neurophysiology The Russian Academy of Sciences 5A Butlerova St.Moscow 117485Russia Skobeltsyn Institute of Nuclear Physics Moscow State University 1(2)Leninskie Gory GSP-1Moscow 119991Russia Molecular Microbiology Lab Skryabin Institute of Biochemistry and Physiology of Micro-organisms RAS Prospect Nauki 5 Pushchino142290 Moscow RegionRussia Group of Bioengineering of Reporter Proteins Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences Prospekt Nauki 65 Pushchino 142290 Moscow RegionRussia Institute of Laser and Information Technologies RAS 2 Pionerskaya TroitskMoscow 142190Russia

A group of variously colored proteins belonging to the green fAuorescent protein(GFP)family are responsible for coloring coral *** of the Great Barrier Reef were studied with the custom-built fiber laser fluorescence *** analysis showed that most of the excarmined corals contained multiple fuorescent peaks ranging from 470 to *** obser-vation was attributed to the presence of multiple genes of GFP-like proteins in a single coral,as well as by the photo-induced post-translational modifcations of certain GFP-like *** isolated a novel photo-convertible fuorescent protein(FP)from one of the tested ***:propose that two processes may explain the observed diversity of the fuorescent spectra in corals:(1)dark post-translational modifcation(maturation),and(2)color photo-conversion of certain maturated proteins in response to sunlight.

关键词： Coral fuorescence GFP like proteins fuorophores Kaede

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