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      Cryptococcus extracellular vesicles properties and their use as vaccine platforms

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          Abstract

          Whereas extracellular vesicle (EV) research has become commonplace in different biomedical fields, this field of research is still in its infancy in mycology. Here we provide a robust set of data regarding the structural and compositional aspects of EVs isolated from the fungal pathogenic species Cryptococcus neoformans, C. deneoformans and C. deuterogattii. Using cutting‐edge methodological approaches including cryogenic electron microscopy and cryogenic electron tomography, proteomics, and flow cytometry, we revisited cryptococcal EV features and suggest a new EV structural model, in which the vesicular lipid bilayer is covered by mannoprotein‐based fibrillar decoration, bearing the capsule polysaccharide as its outer layer. About 10% of the EV population is devoid of fibrillar decoration, adding another aspect to EV diversity. By analysing EV protein cargo from the three species, we characterized the typical Cryptococcus EV proteome. It contains several membrane‐bound protein families, including some Tsh proteins bearing a SUR7/PalI motif. The presence of known protective antigens on the surface of Cryptococcus EVs, resembling the morphology of encapsulated virus structures, suggested their potential as a vaccine. Indeed, mice immunized with EVs obtained from an acapsular C. neoformans mutant strain rendered a strong antibody response in mice and significantly prolonged their survival upon C. neoformans infection.

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          UCSF Chimera--a visualization system for exploratory research and analysis.

          The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/. Copyright 2004 Wiley Periodicals, Inc.
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            Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

            ABSTRACT The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.
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              MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.

              Efficient analysis of very large amounts of raw data for peptide identification and protein quantification is a principal challenge in mass spectrometry (MS)-based proteomics. Here we describe MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data. Using correlation analysis and graph theory, MaxQuant detects peaks, isotope clusters and stable amino acid isotope-labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space. By integrating multiple mass measurements and correcting for linear and nonlinear mass offsets, we achieve mass accuracy in the p.p.b. range, a sixfold increase over standard techniques. We increase the proportion of identified fragmentation spectra to 73% for SILAC peptide pairs via unambiguous assignment of isotope and missed-cleavage state and individual mass precision. MaxQuant automatically quantifies several hundred thousand peptides per SILAC-proteome experiment and allows statistically robust identification and quantification of >4,000 proteins in mammalian cell lysates.
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                Author and article information

                Contributors
                janbon@pasteur.fr
                Journal
                J Extracell Vesicles
                J Extracell Vesicles
                10.1002/(ISSN)2001-3078
                JEV2
                Journal of Extracellular Vesicles
                John Wiley and Sons Inc. (Hoboken )
                2001-3078
                02 August 2021
                August 2021
                : 10
                : 10 ( doiID: 10.1002/jev2.v10.10 )
                : e12129
                Affiliations
                [ 1 ] Unité Biologie des ARN des Pathogènes Fongiques Département de Mycologie, Institut Pasteur, F‐75015 Paris France
                [ 2 ] Unité Mycologie Moléculaire, CNRS UMR2000 Département de Mycologie, Institut Pasteur, F‐75015 Paris France
                [ 3 ] Ultrastructural Bio‐Imaging, UTechS UBI, CNRS UMR 3528 Département de Biologie cellulaire et infection, Institut Pasteur, F‐75015 Paris France
                [ 4 ] Plateforme Protéomique, Unité de Spectrométrie de Masse pour la Biologie (MSBio), CNRS UMR 2000 Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F‐75015 Paris France
                [ 5 ] Cytometry and Biomarkers Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F‐75015 Paris France
                [ 6 ] Instituto Carlos Chagas Fundação Oswaldo Cruz (FIOCRUZ) Curitiba Brazil
                [ 7 ] Centro de Desenvolvimento Tecnologico em Saude (CDTS‐Fiocruz) São Paulo Brazil
                [ 8 ] NanoImaging Core Facility Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F‐75015 Paris France
                [ 9 ] Institute of Microbiology and Infection and School of Biosciences University of Birmingham Birmingham B15 2TT UK
                [ 10 ] Instituto de Microbiologia Paulo de Góes (IMPG) Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
                Author notes
                [*] [* ] Correspondence

                Guilhem Janbon, Département de Mycologie, Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, F‐75015, Paris, France.

                Email: janbon@ 123456pasteur.fr

                Author information
                https://orcid.org/0000-0001-5538-6471
                https://orcid.org/0000-0002-9440-1774
                https://orcid.org/0000-0002-2922-3625
                https://orcid.org/0000-0002-3615-7021
                https://orcid.org/0000-0002-3886-4256
                https://orcid.org/0000-0001-5708-3597
                https://orcid.org/0000-0003-3958-7710
                https://orcid.org/0000-0001-6479-9470
                https://orcid.org/0000-0002-1972-2658
                https://orcid.org/0000-0001-5364-1838
                https://orcid.org/0000-0001-9281-6856
                https://orcid.org/0000-0002-6081-3439
                https://orcid.org/0000-0001-5813-7497
                https://orcid.org/0000-0002-4788-1154
                Article
                JEV212129
                10.1002/jev2.12129
                8329992
                34377375
                62d9e291-440e-424f-a11d-02e27f8213c4
                © 2021 The Authors. Journal of Extracellular Vesicles published by Wiley Periodicals, LLC on behalf of the International Society for Extracellular Vesicles

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 02 July 2021
                : 17 August 2020
                : 09 July 2021
                Page count
                Figures: 10, Tables: 0, Pages: 19, Words: 14656
                Funding
                Funded by: Conselho Nacional de Desenvolvimento Científico e Tecnológico , doi 10.13039/501100003593;
                Award ID: 405520/2018‐2
                Award ID: 301304/2017‐3
                Funded by: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
                Funded by: Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas
                Funded by: CAPES COFECUB
                Award ID: 39712ZK
                Award ID: 39712ZK
                Award ID: 39712ZK
                Award ID: 39712ZK
                Award ID: 88887.357947/2019‐00
                Funded by: CEFIPRA/ANR‐DFG
                Award ID: AfuINF
                Funded by: Pasteur‐Cantarini postdoctoral fellowship
                Funded by: CEFIPRA , doi 10.13039/501100001852;
                Award ID: 5403‐1
                Funded by: Agence Nationale de la Recherche , doi 10.13039/501100001665;
                Award ID: ANR‐11‐EQPX‐0008
                Funded by: Brazilian Ministry of Health
                Award ID: 440015/2018‐9
                Funded by: Pasteur‐Cantarini postdoctoral fellowship
                Categories
                Research Article
                Research Articles
                Custom metadata
                2.0
                August 2021
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.0.4 mode:remove_FC converted:02.08.2021

                cryo‐em,cryptococcus,extracellular vesicles,fungal infections,mannoproteins,vaccine

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