Literature DB >> 28827185

Best practices for managing large CryoEM facilities.

Bart Alewijnse1, Alun W Ashton2, Melissa G Chambers3, Songye Chen4, Anchi Cheng5, Mark Ebrahim6, Edward T Eng5, Wim J H Hagen7, Abraham J Koster1, Claudia S López8, Natalya Lukoyanova9, Joaquin Ortega10, Ludovic Renault1, Steve Reyntjens11, William J Rice5, Giovanna Scapin12, Raymond Schrijver11, Alistair Siebert2, Scott M Stagg13, Valerie Grum-Tokars14, Elizabeth R Wright15, Shenping Wu16, Zhiheng Yu17, Z Hong Zhou18, Bridget Carragher5, Clinton S Potter19.   

Abstract

This paper provides an overview of the discussion and presentations from the Workshop on the Management of Large CryoEM Facilities held at the New York Structural Biology Center, New York, NY on February 6-7, 2017. A major objective of the workshop was to discuss best practices for managing cryoEM facilities. The discussions were largely focused on supporting single-particle methods for cryoEM and topics included: user access, assessing projects, workflow, sample handling, microscopy, data management and processing, and user training. Crown
Copyright © 2017. Published by Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Automation; Cryotem; Data management; Facility management; Single-particle; User training

Mesh:

Year:  2017        PMID: 28827185      PMCID: PMC5605453          DOI: 10.1016/j.jsb.2017.07.011

Source DB:  PubMed          Journal:  J Struct Biol        ISSN: 1047-8477            Impact factor:   2.867


  27 in total

1.  'Collapsing rings' on Schottky electron emitters.

Authors:  M S Bronsgeest; P Kruit
Journal:  Ultramicroscopy       Date:  2010-05-16       Impact factor: 2.689

2.  Automated electron microscope tomography using robust prediction of specimen movements.

Authors:  David N Mastronarde
Journal:  J Struct Biol       Date:  2005-10       Impact factor: 2.867

Review 3.  High-resolution cryo-EM: the nuts and bolts.

Authors:  Dominika Elmlund; Sarah N Le; Hans Elmlund
Journal:  Curr Opin Struct Biol       Date:  2017-03-22       Impact factor: 6.809

4.  A novel storage system for cryoEM samples.

Authors:  Giovanna Scapin; Winifred W Prosise; Michael K Wismer; Corey Strickland
Journal:  J Struct Biol       Date:  2017-04-19       Impact factor: 2.867

5.  Near-Atomic Resolution Structure Determination of a Cypovirus Capsid and Polymerase Complex Using Cryo-EM at 200kV.

Authors:  Xiaowu Li; Niyun Zhou; Wenyuan Chen; Bin Zhu; Xurong Wang; Bin Xu; Jiawei Wang; Hongrong Liu; Lingpeng Cheng
Journal:  J Mol Biol       Date:  2016-12-01       Impact factor: 5.469

6.  Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy.

Authors:  J M de la Rosa-Trevín; A Quintana; L Del Cano; A Zaldívar; I Foche; J Gutiérrez; J Gómez-Blanco; J Burguet-Castell; J Cuenca-Alba; V Abrishami; J Vargas; J Otón; G Sharov; J L Vilas; J Navas; P Conesa; M Kazemi; R Marabini; C O S Sorzano; J M Carazo
Journal:  J Struct Biol       Date:  2016-04-20       Impact factor: 2.867

7.  Structure of the L Protein of Vesicular Stomatitis Virus from Electron Cryomicroscopy.

Authors:  Bo Liang; Zongli Li; Simon Jenni; Amal A Rahmeh; Benjamin M Morin; Timothy Grant; Nikolaus Grigorieff; Stephen C Harrison; Sean P J Whelan
Journal:  Cell       Date:  2015-07-02       Impact factor: 41.582

8.  Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli.

Authors:  M Radermacher; T Wagenknecht; A Verschoor; J Frank
Journal:  J Microsc       Date:  1987-05       Impact factor: 1.758

9.  CTFFIND4: Fast and accurate defocus estimation from electron micrographs.

Authors:  Alexis Rohou; Nikolaus Grigorieff
Journal:  J Struct Biol       Date:  2015-08-13       Impact factor: 2.867

10.  Cryo-EM structure of the large subunit of the spinach chloroplast ribosome.

Authors:  Tofayel Ahmed; Zhan Yin; Shashi Bhushan
Journal:  Sci Rep       Date:  2016-10-20       Impact factor: 4.379

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  12 in total

1.  Reducing cryoEM file storage using lossy image formats.

Authors:  Edward T Eng; Mykhailo Kopylov; Carl J Negro; Sarkis Dallaykan; William J Rice; Kelsey D Jordan; Kotaro Kelley; Bridget Carragher; Clinton S Potter
Journal:  J Struct Biol       Date:  2019-05-21       Impact factor: 2.867

2.  Industrial cryo-EM facility setup and management.

Authors:  Kasim Sader; Rishi Matadeen; Pablo Castro Hartmann; Tor Halsan; Chris Schlichten
Journal:  Acta Crystallogr D Struct Biol       Date:  2020-04-06       Impact factor: 7.652

3.  From Tube to Structure: SPA Cryo-EM Workflow Using Apoferritin as an Example.

Authors:  Christoph A Diebolder; Rebecca S Dillard; Ludovic Renault
Journal:  Methods Mol Biol       Date:  2021

4.  Next Generation Techniques for Determination of Protein-Protein Interactions: Beyond the Crystal Structure.

Authors:  Rachel Carter; Alessandra Luchini; Lance Liotta; Amanda Haymond
Journal:  Curr Pathobiol Rep       Date:  2019-07-01

Review 5.  Broadening access to cryoEM through centralized facilities.

Authors:  Christina M Zimanyi; Mykhailo Kopylov; Clinton S Potter; Bridget Carragher; Edward T Eng
Journal:  Trends Biochem Sci       Date:  2022-02       Impact factor: 13.807

6.  Development of CryoVR, a virtual reality training system for hands-on cryoEM operations.

Authors:  Jiahui Dong; Daoyi Li; Kadir Ozcan; Dayu Wan; Wen Jiang; Yingjie Chen
Journal:  Acta Crystallogr D Struct Biol       Date:  2022-06-27       Impact factor: 5.699

Review 7.  Big data in cryoEM: automated collection, processing and accessibility of EM data.

Authors:  Philip R Baldwin; Yong Zi Tan; Edward T Eng; William J Rice; Alex J Noble; Carl J Negro; Michael A Cianfrocco; Clinton S Potter; Bridget Carragher
Journal:  Curr Opin Microbiol       Date:  2017-10-31       Impact factor: 7.934

8.  Sub-2 Angstrom resolution structure determination using single-particle cryo-EM at 200 keV.

Authors:  Mengyu Wu; Gabriel C Lander; Mark A Herzik
Journal:  J Struct Biol X       Date:  2020-02-28

9.  Editorial: Technical Advances in Cryo-Electron Microscopy.

Authors:  Angel Rivera-Calzada; Marta Carroni
Journal:  Front Mol Biosci       Date:  2019-08-22

10.  Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion.

Authors:  D Maluenda; T Majtner; P Horvath; J L Vilas; A Jiménez-Moreno; J Mota; E Ramírez-Aportela; R Sánchez-García; P Conesa; L Del Caño; Y Rancel; Y Fonseca; M Martínez; G Sharov; C A García; D Strelak; R Melero; R Marabini; J M Carazo; C O S Sorzano
Journal:  Acta Crystallogr D Struct Biol       Date:  2019-10-01       Impact factor: 7.652

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