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Metagenomic binning reveals versatile nutrient cycling and distinct adaptive features in alphaproteobacterial symbionts of marine sponges

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FEMS MICROBIOLOGY ECOLOGY 2018年第6期94卷

作者： Karimi, Elham Slaby, Beate M. Soares, Andre R. Blom, Jochen Hentschel, Ute Costa, Rodrigo Centre of Marine Sciences (CCMAR) Faculty of Science and Technology (FCT) Algarve University 8005-139 Faro Portugal RD3 Marine Microbiology GEOMAR Helmholtz Centre for Ocean Research Kiel 24105 Kiel Germany Institute of Geography and Earth Sciences Aberystwyth University SY23 3DB Aberystwyth Wales UK Bioinformatics and Systems Biology Justus-Liebig-University Giessen 35392 Giessen Germany RD3 Marine Microbiology GEOMAR Helmholtz Centre for Ocean Research Kiel 24105 Kiel Germany Christian-Albrechts-Universität zu Kiel 24118 Kiel Germany Centre of Marine Sciences (CCMAR) Faculty of Science and Technology (FCT) Algarve University 8005-139 Faro Portugal Institute for Bioengineering and Biosciences (IBB) Instituto Superior Técnico Universidade de Lisboa 1049-001 Lisbon Portugal Corresponding author: Department of Bioengineering Instituto Superior Técnico Av. Rovisco Pais 1 South Tower 8th Floor Room 8.6-22 1049-001 Lisbon Portugal. Tel: +351 21 841 7339 E-mail: rodrigoscosta@tecnico.ulisboa.pt

Marine sponges are early-branched metazoans known to harbor dense and diverse microbial communities. Yet the role of the so far uncultivable alphaproteobacterial lineages that populate these sessile invertebrates remains unclear. We applied a sequence composition-dependent binning approach to assemble one Rhodospirillaceaegenome from the Spongia officinalis microbial metagenome and contrast its functional features with those of closely related sponge-associated and free-living genomes. Both symbiotic and free-living Rhodospirillaceae shared a suite of common features, possessing versatile carbon, nitrogen, sulfur and phosphorus metabolisms. Symbiotic genomes could be distinguished from their free-living counterparts by the lack of chemotaxis and motility traits, enrichment of genes required for the uptake and utilization of organic sulfur compounds-particularly taurine-, higher diversity and abundance of ABC transporters, and a distinct repertoire of genes involved in natural product biosynthesis, plasmid stability, cell detoxification and oxidative stress remediation. These sessile symbionts may more effectively contribute to host fitness via nutrient exchange, and also host detoxification and chemical defense. Considering the worldwide occurrence and high diversity of sponge-associated Rhodospirillaceae verified here using a tailored in silico approach, we suggest that these organisms are not only relevant to holobiont homeostasis but also to nutrient cycling in benthic ecosystems.

关键词： Porifera metagenomics functional genomics Rhodospirillaceae host-microbe interactions sulfur metabolism

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Correction to: Recommendations for the nomenclature of enteroviruses and rhinoviruses

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Archives of virology 2020年第6期165卷 1515页

作者： P Simmonds A E Gorbalenya H Harvala T Hovi N J Knowles A M Lindberg M S Oberste A C Palmenberg G Reuter T Skern C Tapparel K C Wolthers P C Y Woo R Zell Nuffield Department of Experimental Medicine University of Oxford Oxford UK. Peter.Simmonds@ndm.ox.ac.uk. Department of Medical Microbiology Leiden University Medical Center Leiden The Netherlands. Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow Russia. Department of Biomedical Data Sciences Leiden University Medical Center Leiden The Netherlands. National Microbiology Service NHS Blood and Transplant London UK. Finnish Institute for Health and Welfare Helsinki Finland. The Pirbright Institute Pirbright Woking UK. Department of Chemistry and Biomedical Sciences Linnaeus University Kalmar Sweden. Division of Viral Diseases Centers for Disease Control and Prevention Atlanta GA USA. Department of Biochemistry Institute for Molecular Virology Madison WI USA. Department of Medical Microbiology and Immunology Medical School University of Pécs Pecs Hungary. Max Perutz Labs Medical University of Vienna Vienna Austria. Department of Microbiology and Molecular Medicine Faculty of Medicine University of Geneva Geneva Switzerland. Department of Medical Microbiology Academic Medical Center University of Amsterdam Amsterdam The Netherlands. Department of Microbiology The University of Hong Kong Hong Kong SAR China. Division of Experimental Virology Institute of Medical Microbiology Jena University Hospital Jena Germany.

Unfortunately, one of the affiliations of author "A. E. Gorbalenya" was missed in original version. The affiliation is updated here.

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Towards a Unified Framework for Determining Conformational Ensembles of Disordered Proteins

arXiv

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arXiv 2025年

作者： Ghafouri, Hamidreza Kadeřávek, Pavel Melo, Ana M. Aspromonte, Maria Cristina Bernadó, Pau Cortes, Juan Dosztányi, Zsuzsanna Erdos, Gabor Feig, Michael Janson, Giacomo Lindorff-Larsen, Kresten Mulder, Frans A.A. Nagy, Peter Pestell, Richard Piovesan, Damiano Schiavina, Marco Schuler, Benjamin Sibille, Nathalie Tesei, Giulio Tompa, Peter Vendruscolo, Michele Vondrasek, Jiri Vranken, Wim Zidek, Lukas Tosatto, Silvio C.E. Monzon, Alexander Miguel Department of Biomedical Sciences University of Padova Italy Via Ugo Bassi 58/B Padova35131 Italy Masaryk University Kamenice 5 Brno62500 Czech Republic National Centre for Biomolecular Research Faculty of Science Masaryk University Kamenice 5 Brno62500 Czech Republic iBB—Institute for Bioengineering and Biosciences Instituto Superior Técnico Universidade de Lisboa Av. Rovisco Pais Lisboa1049-001 Portugal Laboratory i4HB—Institute for Health and Bioeconomy Instituto Superior Técnico Universidade de Lisboa Av. Rovisco Pais Lisboa1049-001 Portugal Université de Montpellier INSERM CNRS Montpellier34090 France LAAS CNRS Université de Toulouse CNRS ToulouseF-31400 France Department of Biochemistry ELTE Eötvös Loránd University Budapest Hungary Department of Biochemistry and Molecular Biology Michigan State University East LansingMI48824 United States Structural Biology and NMR Laboratory Linderstrøm-Lang Centre for Protein Science Department of Biology University of Copenhagen Ole Maaløes Vej 5 CopenhagenDK-2200 Denmark Johannes Kepler University Institute of Biochemistry Linz4040 Austria Department of Molecular Immunology and Toxicology the National Tumor Biology Laboratory National Institute of Oncology Budapest1122 Hungary Department of Anatomy and Histology HUN-REN UVMB Laboratory of Redox Biology Research Group University of Veterinary Medicine Budapest1078 Hungary Chemistry Coordinating Institute University of Debrecen Debrecen4012 Hungary Baruch S. Blumberg Institute DoylestownPA18902 United States Xavier University School of Medicine at Aruba Oranjestad Aruba The Wistar Institute PhiladelphiaPA19107 United States Cell Cycle Laboratory National Institute of Oncology Budapest1122 Hungary Semmelweis University Budapest1117 Hungary Magnetic Resonance Center Department of Chemistry "Ugo Schiff" University of Florence Via Luigi Sacconi 6 Sesto Fiorentino Florence50019 Italy Department of Biochemistry University of

Disordered proteins play essential roles in myriad cellular processes, yet their structural characterization remains a major challenge due to their dynamic and heterogeneous nature. We here present a community-driven initiative to address this problem by advocating a unified framework for determining conformational ensembles of disordered proteins. Our aim is to integrate state-of-the-art experimental techniques with advanced computational methods, including knowledge-based sampling, enhanced molecular dynamics, and machine learning models. The modular framework comprises three interconnected components: experimental data acquisition, computational ensemble generation, and validation. The systematic development of this framework will ensure the accurate and reproducible determination of conformational ensembles of disordered proteins. We highlight the open challenges necessary to achieve this goal, including force field accuracy, efficient sampling, and environmental dependency, advocating for collaborative benchmarking and standardized protocols. © 2025, CC BY-NC-ND.

关键词： Knowledge acquisition

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FP037 INFLUENCE OF INFLAMMATION ON MMSC:ANTI-INFLAMMATORY PRIMING OR SWITCHING TO INFLAMMATORY PHENOTYPE

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Nephrology Dialysis Transplantation 2018年第SUPPL_1期33卷 i59-i60页

作者： Plotnikov, Egor Danilina, Tatyana Pulkova, Natalya Pevzner, Irina Zorova, Ljubava Silachev, Denis Sukhikh, Gennady Zorov, Dmitry A.N.Belozersky Institute of Physico-Chemical Biology Lomonosov Moscow State University Moscow Russian Federation Laboratory of Molecular Mechanisms of Adaptation National Medical Research Center for Obstetrics Gynecology and Perinatology Moscow Russian Federation Institute of Molecular Medicine Sechenov First Moscow State Medical University Moscow Russian Federation Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow Russian Federation

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The accuracy of rapid equilibrium assumption in steady-state enzyme kinetics is the function of equilibrium segment structure and properties

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Biofizika 2015年第2期60卷 262-269页

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

Quantitative evaluation of the accuracy of the rapid equilibrium assumption in the steady-state enzyme kinetics was obtained for an arbitrary mechanism of an enzyme-catalyzed reaction. This evaluation depends only on the structure and properties of the equilibrium segment, but doesn't depend on the structure and properties of the rest (stationary part) of the kinetic scheme. The smaller the values of the edges leaving equilibrium segment in relation to values of the edges within the equilibrium segment, the higher the accuracy of determination of intermediate concentrations and reaction velocity in a case of the rapid equilibrium assumption.

关键词： accuracy of assumption Cha method enzyme kinetics graph theory rapid equilibrium assumption steady-state kinetics

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Changes in number of neurons, astrocytes and microglia in brain after ischemic stroke assessed by immunohistochemistry and immunoblotting

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Cell and Tissue Biology 2016年第6期10卷 445-452页

作者： Savchenko, E.S. Pevzner, I.B. Zorova, L.D. Silachev, D.N. Babenko, V.A. Manskikh, V.N. Gulyaev, M.V. Pirogov, Yu. A. Plotnikov, E. Yu. Zorov, D.B. Belozersky Institute of Physico-Chemical Biology Moscow State University Moscow 119991 Russian Federation Faculty of Bioengineering and Bioinformatics Moscow State University Moscow 119991 Russian Federation International Laser Center Moscow State University Moscow 119991 Russian Federation Biospectrotomography Center of Collective Use Moscow State University Moscow 119992 Russian Federation

It is known that the mechanisms of brain damage after a stroke are regulated by interaction within several cell types, primarily neurons, astrocytes, the endothelium, and microglia. Ischemic exposure disrupts the balance in the brain cellular content;thus, in the lesion, cells die by necrosis, while delayed induction of apoptosis occurs in the tissue surrounding the ischemic zone. Named cells die in the lesion and their ratio determines the clinical outcome of the disease. Thus, the detection of deaths within various cell types of the neurovascular unit is an important part of fundamental studies of the mechanisms of brain damage and preclinical studies of potential neuroprotective drugs. For this reason, we conducted a comparative study of the two most often used methods: immunohistochemical staining of brain sections, which allows to determine the number and localization of specific cells in the tissue among other types of cells, and immunoblotting, which detects specific proteins in the tissue homogenate. We found that, depending on the cell type, changes in their number and composition after a stroke can be localized in a limited part of the tissue or cover the entire hemisphere, which imposes restrictions on the use of any method of determining the number of cells in brain tissue. In general, the most preferable is the use of immunohistochemistry;however, with certain limitations, immunoblotting can be used to determine the proportion of astroglia and microglia. © 2016, Pleiades Publishing, Ltd.

关键词： astrocytes microglia neurons neurovascular unit stroke

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Automatic recognition and characterization of different non-parenchymal cells in liver tissue

Automatic recognition and characterization of different non-...

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IEEE International Symposium on Biomedical Imaging

作者： Hernán Morales-Navarrete Hidenori Nonaka Fabian Segovia-Miranda Marino Zerial Yannis Kalaidzidis Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany Rohto Pharmaceutical Tokyo Japan Faculty of Bioengineering and Bioinformatics Moscow State University Moscow Russia

ISBN: (纸本)9781479923519

Understanding how cells form tissues is an essential component in systems biology that involves the generation of tissue models. Generating such a tissue model requires a proper reconstruction of the different cells forming the tissue visualized as fluorescent objects in microscopy images. This is limited by the number of fluorescent markers that can be simultaneously imaged in a tissue sample (up to 4-5 by confocal microscopy). This limitation can be overcome by using automatic algorithms for the recognition of the different cell types without the use of specific markers. In this study, we propose a toolbox of algorithms for an accurate identification, reconstruction and characterization of different cells types in 3D tissue images. We applied our toolbox to the recognition of sinusoidal endothelial cells (SECs), Kupffer and Stellate cells in adult mouse liver tissue. The cell recognition algorithm was based on the morphology, texture and relative localization of the nuclei. The analysis of the most relevant parameters used for cell classification gave new insights into liver cell structure and function. In particular, nuclear shape, distance to cell borders, chromatin texture and proximity to sinusoids were the most important parameters for the non-parenchymal liver cells classification.

关键词： Image reconstruction Liver Three-dimensional displays Microscopy Shape Bayes methods Feature extraction

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Correction to: Draft genome sequences of Hirudo medicinalis and salivary transcriptome of three closely related medicinal leeches

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BMC genomics 2020年第1期21卷 503页

作者： Vladislav V Babenko Oleg V Podgorny Valentin A Manuvera Artem S Kasianov Alexander I Manolov Ekaterina N Grafskaia Dmitriy A Shirokov Alexey S Kurdyumov Dmitriy V Vinogradov Anastasia S Nikitina Sergey I Kovalchuk Nickolay A Anikanov Ivan O Butenko Olga V Pobeguts Daria S Matyushkina Daria V Rakitina Elena S Kostryukova Victor G Zgoda Isolda P Baskova Vladimir M Trukhan Mikhail S Gelfand Vadim M Govorun Helgi B Schiöth Vassili N Lazarev Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency 1a Malaya Pirogovskaya Str Moscow 119435 Russia. daniorerio34@***. Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency 1a Malaya Pirogovskaya Str Moscow 119435 Russia. Koltzov Institute of Developmental Biology Russian Academy of Sciences 26 Vavilov str Moscow 119334 Russia. Moscow Institute of Physics and Technology 9 Institutskiy per. Dolgoprudny Moscow Region 141700 Russia. Vavilov Institute of General Genetics Russian Academy of Sciences 3 Gubkina str Moscow 119991 Russia. A.A. Kharkevich Institute for Information Transmission Problems Russian Academy of Sciences 19 Bol'shoi Karetnyi per Moscow 127051 Russia. Skolkovo Institute of Science and Technology 3 Nobelya Ulitsa str Moscow 121205 Russia. Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences 16/10 Miklukho-Maklaya str Moscow 117997 Russia. V.N. Orekhovich Research Institute of Biomedical Chemistry Russian Academy of Medical Sciences 10 Pogodinskaja str Moscow 119832 Russia. Faculty of Biology Lomonosov Moscow State University 1-12 Leninskie Gory Moscow 119991 Russia. I.M. Sechenov First Moscow State Medical University of the Ministry of Healthcare of the Russian Federation (Sechenovskiy University) Trubetskaya str. 8-2 Moscow 119991 Russia. Faculty of Computer Science National Research University Higher School of Economics 20 Myasnitskaya str Moscow 101000 Russia. Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University 1-73 Leninskie Gory Moscow 119991 Russia. Functional Pharmacology Department of Neuroscience Uppsala University Husargatan 3 75124 Uppsala Sweden.

An amendment to this paper has been published and can be accessed via the original article.

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Towards a consensus atlas of human and mouse adipose tissue at single-cell resolution

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Nature metabolism 2025年 2025 May 13页

作者： Anne Loft Margo P Emont Ada Weinstock Adeline Divoux Adhideb Ghosh Allon Wagner Ann V Hertzel Babukrishna Maniyadath Bart Deplancke Boxiang Liu Camilla Scheele Carey Lumeng Changhai Ding Chenkai Ma Christian Wolfrum Clarissa Strieder-Barboza Congru Li Danh D Truong David A Bernlohr Elisabet Stener-Victorin Erin E Kershaw Esti Yeger-Lotem Farnaz Shamsi Hannah X Hui Henrique Camara Jiawei Zhong Joanna Kalucka Joseph A Ludwig Julie A Semon Jutta Jalkanen Katie L Whytock Kyle D Dumont Lauren M Sparks Lindsey A Muir Lingzhao Fang Lucas Massier Luis R Saraiva Marc D Beyer Marc G Jeschke Marcelo A Mori Mariana Boroni Martin J Walsh Mary-Elizabeth Patti Matthew D Lynes Matthias Blüher Mikael Rydén Natnael Hamda Nicole L Solimini Niklas Mejhert Peng Gao Rana K Gupta Rinki Murphy Saeed Pirouzpanah Silvia Corvera Su'an Tang Swapan K Das Søren F Schmidt Tao Zhang Theodore M Nelson Timothy E O'Sullivan Vissarion Efthymiou Wenjing Wang Yihan Tong Yu-Hua Tseng Susanne Mandrup Evan D Rosen Center for Functional Genomics and Tissue Plasticity (ATLAS) Department of Biochemistry and Molecular Biology University of Southern Denmark (SDU) Odense Denmark. anlo@bmb.sdu.dk. Section of Endocrinology Diabetes and Metabolism University of Chicago Chicago IL USA. margo@uchicago.edu. Department of Medicine Section of Genetic Medicine University of Chicago Chicago IL USA. Translational Research Institute AdventHealth Orlando FL USA. Department of Health Sciences and Technology Institute of Food Nutrition and Health ETH Zurich Schwerzenbach Switzerland. Department of Electrical Engineering and Computer Sciences University of California Berkeley Berkeley CA USA. Department of Molecular and Cell Biology University of California Berkeley Berkeley CA USA. Center for Computational Biology University of California Berkeley Berkeley CA USA. Department of Biochemistry Molecular Biology and Biophysics Institute on the Biology of Aging and Metabolism The University of Minnesota-Twin Cities Minneapolis MN USA. Center for Functional Genomics and Tissue Plasticity (ATLAS) Department of Biochemistry and Molecular Biology University of Southern Denmark (SDU) Odense Denmark. Laboratory of Systems Biology and Genetics Institute of Bioengineering School of Life Sciences École Polytechnique Fédérale de Lausanne (EPFL) Lausanne Switzerland. Department of Pharmacy and Pharmaceutical Sciences Faculty of Science National University of Singapore Singapore Singapore. Department of Biomedical Informatics Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore. Genome Institute of Singapore (GIS) Agency for Science Technology and Research (A*STAR) Singapore Singapore. Precision Medicine Translational Research Programme Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore. Cardiovascular-Metabolic Disease Translational Research Programme Yong Loo Lin School of Medicine National University of Singapore Singapor

Adipose tissue (AT) is a complex connective tissue with a high relative proportion of adipocytes, which are specialized cells with the ability to store lipids in large droplets. AT is found in multiple discrete depots throughout the body, where it serves as the primary repository for excess calories. In addition, AT has an important role in functions as diverse as insulation, immunity and regulation of metabolic homeostasis. The Human Cell Atlas Adipose Bionetwork was established to support the generation of single-cell atlases of human AT as well as the development of unified approaches and consensus for cell annotation. Here, we provide a first roadmap from this bionetwork, including our suggested cell annotations for humans and mice, with the aim of describing the state of the field and providing guidelines for the production, analysis, interpretation and presentation of AT single-cell data.

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Author Correction: Vaccine elicitation of HIV broadly neutralizing antibodies from engineered B cells

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Nature communications 2020年第1期11卷 6360页

作者： Deli Huang Jenny Tuyet Tran Alex Olson Thomas Vollbrecht Mary Tenuta Mariia V Guryleva Roberta P Fuller Torben Schiffner Justin R Abadejos Lauren Couvrette Tanya R Blane Karen Saye Wenjuan Li Elise Landais Alicia Gonzalez-Martin William Schief Ben Murrell Dennis R Burton David Nemazee James E Voss Department of Immunology and Microbiology The Scripps Research Institute La Jolla CA USA. Department of Medicine The University of California San Diego La Jolla CA USA. Department of Microbiology Tumor and Cell Biology Karolinska Institutet Stockholm Sweden. Faculty of Bioengineering and Bioinformatics Moscow Lomonosov State University Moscow Russia. Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD) The Scripps Research Institute La Jolla CA USA. IAVI Neutralizing Antibody Center (IAVI) The Scripps Research Institute La Jolla CA USA. Faculty of Science University of Ottawa Ottawa Canada. Department of Biochemistry Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM) Madrid Spain. Ragon Institute of Massachusetts General Hospital Massachusetts Institute of Technology and Harvard Cambridge MA USA. Department of Microbiology Tumor and Cell Biology Karolinska Institutet Stockholm Sweden. benjamin.murrell@ki.se. Department of Immunology and Microbiology The Scripps Research Institute La Jolla CA USA. burton@scripps.edu. Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD) The Scripps Research Institute La Jolla CA USA. burton@scripps.edu. IAVI Neutralizing Antibody Center (IAVI) The Scripps Research Institute La Jolla CA USA. burton@scripps.edu. Ragon Institute of Massachusetts General Hospital Massachusetts Institute of Technology and Harvard Cambridge MA USA. burton@scripps.edu. Department of Immunology and Microbiology The Scripps Research Institute La Jolla CA USA. nemazee@scripps.edu. Department of Immunology and Microbiology The Scripps Research Institute La Jolla CA USA. jvoss@scripps.edu.

A Correction to this paper has been published: https://***/10.1038/s41467-020-20304-y.

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