Journal ArticleDOI
Automated electron microscope tomography using robust prediction of specimen movements.
TLDR
A new method was developed to acquire images automatically at a series of specimen tilts, as required for tomographic reconstruction, using changes in specimen position at previous tilt angles to predict the position at the current tilt angle.About:
This article is published in Journal of Structural Biology.The article was published on 2005-10-01. It has received 3995 citations till now. The article focuses on the topics: Tomographic reconstruction & Tilt (optics).read more
Citations
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Journal ArticleDOI
New tools for automated high-resolution cryo-EM structure determination in RELION-3.
Jasenko Zivanov,Takanori Nakane,Björn O. Forsberg,Dari Kimanius,Wim J. H. Hagen,Erik Lindahl,Erik Lindahl,Sjors H.W. Scheres +7 more
TL;DR: CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations in the third major release of RELION.
Journal ArticleDOI
Convergent antibody responses to SARS-CoV-2 in convalescent individuals.
Davide F. Robbiani,Davide F. Robbiani,Christian Gaebler,Frauke Muecksch,Julio C. C. Lorenzi,Zijun Wang,Alice Cho,Marianna Agudelo,Christopher O. Barnes,Anna Gazumyan,Shlomo Finkin,Thomas Hagglof,Thiago Y. Oliveira,Charlotte Viant,Arlene Hurley,Hans Heinrich Hoffmann,Katrina G. Millard,Rhonda G. Kost,Melissa Cipolla,Kristie Gordon,Filippo Bianchini,Spencer T. Chen,Victor A. Ramos,Roshni Patel,Juan Dizon,Irina Shimeliovich,Pilar Mendoza,Harald Hartweger,Lilian Nogueira,Maggi Pack,Jill Horowitz,Fabian Schmidt,Yiska Weisblum,Eleftherios Michailidis,Alison W. Ashbrook,Eric Waltari,John E. Pak,Kathryn E. Huey-Tubman,Nicholas Koranda,Pauline R. Hoffman,Anthony P. West,Charles M. Rice,Theodora Hatziioannou,Pamela J. Bjorkman,Paul D. Bieniasz,Paul D. Bieniasz,Marina Caskey,Michel C. Nussenzweig,Michel C. Nussenzweig +48 more
TL;DR: Most convalescent plasma samples obtained from individuals who recover from COVID-19 do not contain high levels of neutralizing activity, and rare but recurring RBD-specific antibodies with potent antiviral activity were found in all individuals tested, suggesting that a vaccine designed to elicit such antibodies could be broadly effective.
Journal ArticleDOI
Atheroprotective communication between endothelial cells and smooth muscle cells through miRNAs.
Eduard Hergenreider,Susanne Heydt,Karine Tréguer,Thomas Boettger,Anton J.G. Horrevoets,Andreas M. Zeiher,Margot P. Scheffer,Achilleas S. Frangakis,Xiaoke Yin,Manuel Mayr,Thomas Braun,Carmen Urbich,Reinier A. Boon,Stefanie Dimmeler +13 more
TL;DR: The results show that atheroprotective stimuli induce communication between endothelial cells and SMCs through an miRNA- and extracellular-vesicle-mediated mechanism and that this may comprise a promising strategy to combat atherosclerosis.
Journal ArticleDOI
Structure of the RNA-dependent RNA polymerase from COVID-19 virus.
Yan Gao,Yan Gao,Liming Yan,Yucen Huang,Fengjiang Liu,Yao Zhao,Lin Cao,Tao Wang,Qianqian Sun,Zhenhua Ming,Lianqi Zhang,Ji Ge,Litao Zheng,Ying Zhang,Haofeng Wang,Haofeng Wang,Yan Zhu,Chen Zhu,Tianyu Hu,Tian Hua,Bing Zhang,Xiuna Yang,Jun Li,Haitao Yang,Zhi-Jie Liu,Wenqing Xu,Luke W. Guddat,Quan Wang,Zhiyong Lou,Zihe Rao +29 more
TL;DR: The structure of the COVID-19 virus polymerase essential for viral replication provides a basis for the design of new antiviral drugs that target viral RdRp, also named nsp12, and it appears to be a primary target for the antiviral drug remdesivir.
Journal ArticleDOI
SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies.
Christopher O. Barnes,Claudia A. Jette,Morgan E. Abernathy,Kim Marie A. Dam,Shannon R. Esswein,Harry B. Gristick,Andrey G. Malyutin,Naima G. Sharaf,Kathryn E. Huey-Tubman,Yu E. Lee,Davide F. Robbiani,Davide F. Robbiani,Michel C. Nussenzweig,Michel C. Nussenzweig,Anthony P. West,Pamela J. Bjorkman +15 more
TL;DR: Eight new structures of distinct COVID-19 human neutralizing antibodies 5 in complex with the SARS-CoV-2 spike trimer or RBD are solved and rules for assigning current and future human RBD-targeting antibodies into classes, evaluating avidity effects and suggesting combinations for clinical use are provided.
References
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Journal ArticleDOI
Computer Visualization of Three-Dimensional Image Data Using IMOD
TL;DR: IMOD is useful for studying and modeling data from tomographic, serial section, and optical section reconstructions and allows image data to be visualized by several different methods.
Journal ArticleDOI
Dual-axis tomography: an approach with alignment methods that preserve resolution.
TL;DR: Analysis by Fourier sector correlation indicated that the variable tilt increment improved the reconstruction in some respects but degraded it in others, and a varying tilt increment thus does not give an unqualified improvement, at least when using back-projection algorithms for the reconstruction.
Journal ArticleDOI
TOM software toolbox: acquisition and analysis for electron tomography
Stephan Nickell,Friedrich Förster,Alexandros Linaroudis,William Del Net,Florian Beck,Reiner Hegerl,Wolfgang Baumeister,Jürgen M. Plitzko +7 more
TL;DR: TOM software toolbox integrates established algorithms and new concepts tailored to the special needs of low dose ET, which provides a user-friendly unified platform for all processing steps: acquisition, alignment, reconstruction, and analysis.
Journal ArticleDOI
New views of cells in 3D: an introduction to electron tomography
TL;DR: To be of maximal value, structural studies should provide isotropic, 3D information about well-preserved samples at the highest possible resolution about many kinds of cells and organelles.
Journal ArticleDOI
Perspectives of molecular and cellular electron tomography.
Abraham J. Koster,Rudo Grimm,Dieter Typke,Reiner Hegerl,Arne Stoschek,Jochen Walz,Wolfgang Baumeister +6 more
TL;DR: After a general introduction to three-dimensional electron microscopy and particularly to electron tomography (ET), the perspectives of applying ET to native (frozen-hydrated) cellular structures are discussed and the question of whether it is a realistic long-term goal to visualize or identify macromolecules in cells frozen in toto or in frozen sections of cells is addressed.