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      Cryo-EM of Aβ fibrils from mouse models find tg-APP ArcSwe fibrils resemble those found in patients with sporadic Alzheimer’s disease

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          Abstract

          The use of transgenic mice displaying amyloid-β (Aβ) brain pathology has been essential for the preclinical assessment of new treatment strategies for Alzheimer’s disease. However, the properties of Aβ in such mice have not been systematically compared to Aβ in the brains of patients with Alzheimer’s disease. Here, we determined the structures of nine ex vivo Aβ fibrils from six different mouse models by cryogenic-electron microscopy. We found novel Aβ fibril structures in the APP/PS1, ARTE10 and tg-SwDI models, whereas the human type II filament fold was found in the ARTE10, tg-APP Swe and APP23 models. The tg-APP ArcSwe mice showed an Aβ fibril whose structure resembles the human type I filament found in patients with sporadic Alzheimer’s disease. A detailed assessment of the Aβ fibril structure is key to the selection of adequate mouse models for the preclinical development of novel plaque-targeting therapeutics and positron emission tomography imaging tracers in Alzheimer’s disease.

          Abstract

          This study by Zielinski et al. used cryo-EM to compare Aβ fibril structures from mouse models to those from patients with Alzheimer’s disease. It revealed that tg-APP ArcSwe mice exhibit fibrils resembling those predominantly found in sporadic Alzheimer’s disease cases.

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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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            UCSF ChimeraX : Structure visualization for researchers, educators, and developers

            UCSF ChimeraX is the next-generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX brings (a) significant performance and graphics enhancements; (b) new implementations of Chimera's most highly used tools, many with further improvements; (c) several entirely new analysis features; (d) support for new areas such as virtual reality, light-sheet microscopy, and medical imaging data; (e) major ease-of-use advances, including toolbars with icons to perform actions with a single click, basic "undo" capabilities, and more logical and consistent commands; and (f) an app store for researchers to contribute new tools. ChimeraX includes full user documentation and is free for noncommercial use, with downloads available for Windows, Linux, and macOS from https://www.rbvi.ucsf.edu/chimerax.
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              New tools for automated high-resolution cryo-EM structure determination in RELION-3

              Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, de novo model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides higher resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resolution for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2–0.7 Å compared to previous RELION versions.
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                Author and article information

                Contributors
                l.gremer@fz-juelich.de
                D.Willbold@fz-juelich.de
                gu.schroeder@fz-juelich.de
                Journal
                Nat Neurosci
                Nat Neurosci
                Nature Neuroscience
                Nature Publishing Group US (New York )
                1097-6256
                1546-1726
                16 November 2023
                16 November 2023
                2023
                : 26
                : 12
                : 2073-2080
                Affiliations
                [1 ]Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, ( https://ror.org/02nv7yv05) Jülich, Germany
                [2 ]JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, ( https://ror.org/02nv7yv05) Jülich, Germany
                [3 ]Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, ( https://ror.org/024z2rq82) Düsseldorf, Germany
                [4 ]Institute of Neuroscience and Medicine, Medical Imaging Physics (INM-4), Forschungszentrum Jülich, ( https://ror.org/02nv7yv05) Jülich, Germany
                [5 ]Department of Vascular and Endovascular Surgery, University Hospital Düsseldorf, Heinrich Heine University, ( https://ror.org/024z2rq82) Düsseldorf, Germany
                [6 ]GRID grid.5510.1, ISNI 0000 0004 1936 8921, Department of Pharmacology, Institute of Clinical Medicine, , University of Oslo and Oslo University Hospital, ; Oslo, Norway
                [7 ]Department of Public Health and Caring Sciences, Molecular Geriatrics, Rudbeck Laboratory, Uppsala University, ( https://ror.org/048a87296) Uppsala, Sweden
                [8 ]GRID grid.231844.8, ISNI 0000 0004 0474 0428, Krembil Brain Institute, , University Health Network, ; Toronto, Ontario Canada
                [9 ]Tanz Centre for Research in Neurodegenerative Diseases, Departments of Medicine and Laboratory Medicine & Pathobiology, University of Toronto, ( https://ror.org/03dbr7087) Toronto, Ontario Canada
                [10 ]Physics Department, Heinrich Heine University Düsseldorf, ( https://ror.org/024z2rq82) Düsseldorf, Germany
                [11 ]Present Address: Life and Medical Sciences (LIMES) Institute, University of Bonn, ( https://ror.org/041nas322) Bonn, Germany
                Author information
                http://orcid.org/0000-0001-7443-917X
                http://orcid.org/0000-0001-8379-4827
                http://orcid.org/0000-0001-7065-5027
                http://orcid.org/0000-0002-7877-0262
                http://orcid.org/0000-0002-6725-0755
                http://orcid.org/0000-0002-8362-1042
                http://orcid.org/0000-0002-8196-4041
                http://orcid.org/0000-0002-9430-3859
                http://orcid.org/0000-0002-0065-7366
                http://orcid.org/0000-0003-1803-5431
                Article
                1484
                10.1038/s41593-023-01484-4
                10689242
                37973869
                da345e89-2b7d-491e-80c4-d6728496d9b4
                © The Author(s) 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 18 June 2023
                : 6 October 2023
                Funding
                Funded by: FundRef 501100009318, Helmholtz Association;
                Funded by: FundRef 501100002347, Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research);
                Award ID: 16LW028
                Award Recipient :
                Funded by: FundRef 501100004359, Vetenskapsrådet (Swedish Research Council);
                Award ID: 2021-03524
                Award ID: 2021-01083
                Award ID: 2021-03524
                Award ID: 2021-02793
                Award Recipient :
                Funded by: "Portfolio Drug Research" of the "Impuls und Vernetzungsfonds der Helmholtzgemeinschaft".
                Categories
                Article
                Custom metadata
                © Springer Nature America, Inc. 2023

                Neurosciences
                molecular neuroscience,cryoelectron microscopy
                Neurosciences
                molecular neuroscience, cryoelectron microscopy

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