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Erratum to: Bacterial and Protozoan Lipoxygenases Could be Involved in Cell-to-Cell Signaling and Immune Response Suppression

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Biochemistry (Moscow) 2020年第10期85卷 1288-1288页

作者： Kurakin, G. F. Samoukina, A. M. Potapova, N. A. Department of Biochemistry and Laboratory Medicine Tver State Medical University Ministry of Health of the Russian Federation Tver Russia Department of Microbiology Virology and Immunology Tver State Medical University Ministry of Health of the Russian Federation Tver Russia Kharkevich Institute for Information Transmission Problems Russian Academy of Sciences Moscow Russia Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow Russia

On p. 1051, Fig. 2, legend: instead of “nor” should read “not”. On p. 1053, Fig. 4, legend: instead of “initial” should read “original”. On p. 1059, Fig. 7, legend: instead of “initial” should read “origina...

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P.703 Administration of thiamine to rats regulates the brain pyridoxal kinase and pyridoxal-5’-phosphate phosphatase without affecting pyridoxine-5’-phosphate oxidase

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European Neuropsychopharmacology 2020年 40卷 S399-S400页

作者： Aleshin, V. Kaehne, T. Kryukov, D. Nogues, I. Graf, A. Bunik, V. A.N.Belozersky Institute of Physico-Chemical Biology- Lomonosov Moscow State University Enzyme kinetics Moscow Russia Lomonosov Moscow State University Faculty of bioengineering and bioinformatics Moscow Russia Otto-von-Guericke University Magdeburg Institute of Experimental Internal Medicine Magdeburg Germany Lomonosov Moscow State University Faculty of chemistry Moscow Russia Italian National Research Council Research Institute of Terrestrial Ecosystems Rome Italy Lomonosov Moscow State University Faculty of biology Moscow Russia Moscow Institute of Physics and Technology Faculty of Nano- Bio- Informational and Cognitive Technologies Moscow Russia Sechenov University Department of Biochemistry Moscow Russia

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Biotechnology and bioengineering 2020年第5期117卷

作者： Jozef B. J. H. van Duuren Paul J. de Wild Sören Starck Christian Bradtmöller Mirjam Selzer Kerstin Mehlmann Roland Schneider Michael Kohlstedt Ignacio Poblete‐Castro Jessica Stolzenberger Nadja Barton Michel Fritz Stephan Scholl Joachim Venus Christoph Wittmann Institute of Systems Biotechnology Saarland University Saarbrücken Germany Biomass & Energy Efficiency TNO Petten The Netherlands Institute for Chemical and Thermal Process Engineering Technische Universität Braunschweig Braunschweig Germany Department of Bioengineering Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB) Potsdam Germany Biosystems Engineering Laboratory Center for Bioinformatics and Integrative Biology Faculty of Natural Sciences Universidad Andres Bello Santiago de Chile Chile

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Accuracy validation of a newly developed cuffless blood pressure estimation method using only an iPhone

Transactions of Japanese Society for Medical and Biological ...

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Transactions of Japanese Society for Medical and Biological Engineering 2018年第PROC期56卷 13-13页

作者： Harada, Ippei Yamakoshi, Takehiro Toda, Sogo Matsumura, Kenta Information and Systems Engineering Graduate School of Engineering Fukuoka Institute of Technology Japan Department of Information Systems Engineering Faculty of Information Engineering Fukuoka Institute of Technology Japan Division of Bioengineering and Bioinformatics Graduate School of Information Science and Technology Hokkaido University Japan Computer Science Laboratory Comprehensive Research Organization Fukuoka Institute of Technology Japan

The mainstream method for cuffless blood pressure is that based on pulse transit time. However, there are many inconveniences in this method such as requiring simultaneous measurement of electrocardiogram and photoplethysmogram and frequent calibration using a cuff sphygmomanometer. So, we developed a far simpler method to estimate blood pressure only using a heart rate and modified normalized pulse volume that can be measured using a smartphone alone. In this study, we examined its accuracy against conventional brachial cuff sphygmomanometer. Mental arithmetic task was used to alter blood pressure in 13 healthy subjects. Analysis revealed that the correlation coefficients between these two were.73,.73, and.72 for mean blood pressure, systolic blood pressure, and diastolic blood pressure, respectively. Results suggest that this simple method can yield moderately reliable measures of blood pressure. (132/150). © 2018, Japan Soc. of Med. Electronics and Biol. Engineering. All rights reserved.

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Quantification of Mitochondrial Morphology in situ

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Cell and Tissue Biology 2017年第1期11卷 51-58页

作者： Popkov, V.A. Plotnikov, E. Yu. Zorova, L.D. Pevzner, I.B. Silachev, D.N. Babenko, V.A. Jankauskas, S.S. Zorov, S.D. Zorov, D.B. Belozersky Institute of Physico-Chemical Biology Lomonosov Moscow State University Moscow 119991 Russian Federation Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow 119991 Russian Federation International Laser Center Lomonosov Moscow State University Moscow 119991 Russian Federation

The structural organization of mitochondria reflects their functional status and largely is an index of cell viability. The indirect parameter to assess the functional state of mitochondria in cells is the degree of their fragmentation, i.e., the ratio of long or branched mitochondrial structures to round mitochondria. Such evaluations requires an approach that allows to create an integral pattern of the three-dimensional organization of mitochondrial reticulum using confocal images of mitochondria stained with a fluorescent probe. In the present study, we tested three approaches to analyzing the structural architecture of mitochondria under normal conditions and fission induced by oxidative stress. We revealed that, while the most informative is a three-dimensional reconstruction based on series of confocal images taken along the Z-dimension, with some restrictions it is plausible to use more simple algorithms of analysis, including one that uses unitary twodimensional images. Further improvement of these methods of image analysis will allow more comprehensive study of mitochondrial architecture under normal conditions and different pathological states. It may also provide quantification of a number of mitochondrial parameters determining the morphofunctional state of mitochondria—primarily, their absolute and relative volumes—and give additional information on threedimensional organization of the mitochondrion. © 2017, Pleiades Publishing, Ltd. All Right Reserved.

关键词： 3D modeling confocal microscopy fragmentation mitochondria

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Enabling pan-repository reanalysis for big data science of public metabolomics data

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Nature communications 2025年第1期16卷 4838页

作者： Yasin El Abiead Michael Strobel Thomas Payne Eoin Fahy Claire O'Donovan Shankar Subramamiam Juan Antonio Vizcaíno Ozgur Yurekten Victoria Deleray Simone Zuffa Shipei Xing Helena Mannochio-Russo Ipsita Mohanty Haoqi Nina Zhao Andres M Caraballo-Rodriguez Paulo Wender P Gomes Nicole E Avalon Trent R Northen Benjamin P Bowen Katherine B Louie Pieter C Dorrestein Mingxun Wang Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego La Jolla CA USA. Department of Computer Science and Engineering University of California Riverside Riverside CA USA. European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD UK. Department of Bioengineering and San Diego Supercomputer Center University of California San Diego 9500 Gilman Drive La Jolla CA 92093-0505 USA. Faculty of Chemistry Federal University of Pará Belém PA Brazil. Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA. Department of Pharmaceutical Sciences University of California Irvine California 92697 Irvine USA. Environmental Genomics and Systems Biology Division Lawrence Berkeley National Lab Berkeley CA 94720 USA. The DOE Joint Genome Institute Lawrence Berkeley National Laboratory Berkeley CA 94720 USA. Collaborative Mass Spectrometry Innovation Center Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego La Jolla CA USA. Department of Pharmacology University of California San Diego La Jolla CA 92093 USA. Center for Microbiome Innovation University of California San Diego La Jolla CA 92093 USA. Department of Computer Science and Engineering University of California Riverside Riverside CA USA. mingxun.wang@cs.ucr.edu.

Public untargeted metabolomics data is a growing resource for metabolite and phenotype discovery; however, accessing and utilizing these data across repositories pose significant challenges. Therefore, here we develop pan-repository universal identifiers and harmonized cross-repository metadata. This ecosystem facilitates discovery by integrating diverse data sources from public repositories including MetaboLights, Metabolomics Workbench, and GNPS/MassIVE. Our approach simplified data handling and unlocks previously inaccessible reanalysis workflows, fostering unmatched research opportunities.

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Correction to: Primary antibody deficiencies in Turkey: molecular and clinical aspects

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Immunologic research 2022年第1期70卷 134页

作者： Sinem Firtina Yuk Yin Ng Ozden H Ng Ayca Kiykim Esra Yucel Ozek Manolya Kara Elif Aydiner Serdar Nepesov Yildiz Camcioglu Esra H Sayar Ezgi Yalcin Gungoren Ismail Reisli Selda H Torun Sule Haskologlu Tuba Cogurlu Aysenur Kaya Sukru Cekic Safa Baris Ugur Ozbek Ahmet Ozen Muge Sayitoglu Istanbul University Graduate School of Health Sciences Istanbul Turkey. Department of Bioinformatics and Genetics Engineering and Natural Sciences Faculty Istinye University Istanbul Turkey. Department of Genetics and Bioengineering Istanbul Bilgi University Istanbul Turkey. Department of Medical Biology Acibadem School of Medicine Acibadem Mehmet Ali Aydinlar University Istanbul Turkey. Department of Infectious Diseases and Clinical Immunology Cerrahpasa School of Medicine Istanbul University Istanbul Turkey. Department of Clinical Immunology Istanbul School of Medicine Istanbul University Istanbul Turkey. Istinye University Faculty of Medicine VM MedicalPark Pendik Hospital Pediatric Infectious Diseases Clinic Istanbul Turkey. Department of Pediatric Allergy and Immunology Marmara University Istanbul Turkey. Department of Pediatric Allergy Immunology Medipol University Istanbul Turkey. Department of Pediatric Immunology and Allergy Meram Medical Faculty Necmettin Erbakan University Konya Turkey. Department of Pediatric Immunology and Allergy Ankara University School of Medicine Ankara Turkey. Department of Pediatric Immunology and Allergy Kocaeli University Kocaeli Turkey. Department of Pediatric Immunology Uludag University School of Medicine Bursa Turkey. Department of Medical Genetics Acibadem School of Medicine Acibadem Mehmet Ali Aydinlar University Istanbul Turkey. Istanbul University Graduate School of Health Sciences Istanbul Turkey. mugeay@istanbul.edu.tr. Department of Genetics Aziz Sancar Institute of Experimental Medical Research Istanbul University Istanbul Turkey. mugeay@istanbul.edu.tr.

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Nuclear lamina maintains global spatial organization of chromatin in Drosophila cultured cells

Nuclear lamina maintains global spatial organization of chro...

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IEEE International Conference on bioinformatics and Biomedicine

作者： Sergey V. Ulianov Semen A. Doronin Ekaterina E. Khrameeva Pavel I. Kos Sergey S. Starikov Aleksandra A. Galitsyna Artem Luzhin Mikhail S. Gelfand Alexander V. Chertovich Sergey V. Razin Yuri Y. Shevelyov Russian Academy of Sciences Institute of Gene Biology Moscow Russia Russian Academy of Sciences Institute of Molecular Genetics Moscow Russia Russian Academy of Sciences Institute for Information Transmission Problems (the Kharkevich Institute) Moscow Russia Faculty of Physics M.V. Lomonosov Moscow State University Moscow Russia Faculty of Bioengineering and Bioinformatics M.V. Lomonosov Moscow State University Moscow Russia

ISBN: (纸本)9781538654897;9781538654880

Interphase chromatin in animals is constrained by interactions with the nuclear lamina (NL) - a protein mesh lining nuclear envelope and composed from lamins and lamin-associated proteins. About 30% of chromatin is located near the NL in a living cell forming densely packed lamina-associated domains (LADs). LADs largely overlap with topologically-associating domains (TADs) build up from repressed chromatin, and contain predominately inactive genes, thus playing a role in transcription regulation. Here, we show that the NL disruption in Drosophila leads to en mass chromatin compactisation and redistribution towards the nuclear interior. This results in an increase of contact frequency between active and repressed fractions of the genome accompanied by the transcription upregulation in LADs. A subset of TADs characterized by high level of LADs become less compact, that could be driven by the loss of interactions with the nuclear envelope as revealed by polymer modelling. These results indicate that the NL in Drosophila cells plays a role in the specific spatial positioning of the chromatin inside the nucleus, its compartmentalization and at least partially controls the packaging density and low-level transcription in LADs.

关键词： Conferences bioinformatics

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The accuracy of the rapid equilibrium assumption in steady-state enzyme kinetics in the case of a multipath arbitrary enzyme mechanism with a number of equilibrium segments

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Biophysics (Russian Federation) 2016年第3期61卷 373-379页

作者： Vrzheshch, P.V. Faculty of Bioengineering and Bioinformatics Moscow State University International Biotechnological Center Moscow 119991 Russian Federation

A quantitative evaluation of the accuracy of the rapid-equilibrium assumption in steady-state enzyme kinetics was obtained for a multipath arbitrary enzyme mechanism with a number of equilibrium segments. Explicit expressions for estimating the contribution of any equilibrium segment to the accuracy of the rapid-equilibrium assumption were obtained. This allowed us to determine the accuracy of the rapid-equilibrium assumption (Δ) in general: 1 + Δ = (1 + Δ₁)(1 + Δ₂).. (1 + Δ_k), where Δ₁, Δ₂,.., Δ_k is the contribution of each individual equilibrium segment. The accuracy depends only on the structure and properties of equilibrium segments, which have been accounted for in the rapid-equilibrium assumption, but it is independent of the number of paths in the mechanism of the enzymatic reaction and on the structure and properties of the remaining part (steady-state) of the kinetic scheme. © 2016, Pleiades Publishing, Inc.

关键词： accuracy of assumption equilibrium segments graph theory multipath enzyme mechanisms rapid-equilibrium assumption steady-state enzyme kinetics

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Author Correction: A virally encoded tRNA neutralizes the PARIS antiviral defence system

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Nature 2024年第8043期636卷 E8页

作者： Nathaniel Burman Svetlana Belukhina Florence Depardieu Royce A Wilkinson Mikhail Skutel Andrew Santiago-Frangos Ava B Graham Alexei Livenskyi Anna Chechenina Natalia Morozova Trevor Zahl William S Henriques Murat Buyukyoruk Christophe Rouillon Baptiste Saudemont Lena Shyrokova Tatsuaki Kurata Vasili Hauryliuk Konstantin Severinov Justine Groseille Agnès Thierry Romain Koszul Florian Tesson Aude Bernheim David Bikard Blake Wiedenheft Artem Isaev Department of Microbiology and Cell Biology Montana State University Bozeman MT USA. The Center for Molecular and Cellular Biology Moscow Russia. Synthetic Biology Institut Pasteur Université Paris Cité CNRS UMR 6047 Paris France. Center for Precision Genome Editing and Genetic Technologies for Biomedicine Institute of Gene Biology Russian Academy of Sciences Moscow Russia. Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow Russia. Peter the Great St Petersburg State Polytechnic University St. Petersburg Russia. Department of Experimental Medical Science Lund University Lund Sweden. Virus Centre Lund University Lund Sweden. Science for Life Laboratory Lund Sweden. Waksman Institute Rutgers The State University of New Jersey Piscataway NJ USA. Unité Régulation Spatiale des Génomes Institut Pasteur CNRS UMR 3525 Université Paris Cité Paris France. Center for Interdisciplinary Research in Biology (CIRB) Collège de France CNRS INSERM Université PSL Paris France. Collège Doctoral Sorbonne Université Paris France. Molecular Diversity of Microbes Institut Pasteur CNRS UMR3525 Université Paris Cité Paris France. Synthetic Biology Institut Pasteur Université Paris Cité CNRS UMR 6047 Paris France. david.bikard@pasteur.fr. Department of Microbiology and Cell Biology Montana State University Bozeman MT USA. bwiedenheft@***. The Center for Molecular and Cellular Biology Moscow Russia. tcft18@***.

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