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Rihm SD, Tan YR, Ang W, Hofmeister M, Deng X, Laksana MT, Quek HY, Bai J, Pascazio L, Siong SC, Akroyd J, Mosbach S, Kraft M. The digital lab manager: Automating research support. SLAS Technol 2024; 29:100135. [PMID: 38703999 DOI: 10.1016/j.slast.2024.100135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/03/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
Laboratory management automation is essential for achieving interoperability in the domain of experimental research and accelerating scientific discovery. The integration of resources and the sharing of knowledge across organisations enable scientific discoveries to be accelerated by increasing the productivity of laboratories, optimising funding efficiency, and addressing emerging global challenges. This paper presents a novel framework for digitalising and automating the administration of research laboratories through The World Avatar, an all-encompassing dynamic knowledge graph. This Digital Laboratory Framework serves as a flexible tool, enabling users to efficiently leverage data from diverse systems and formats without being confined to a specific software or protocol. Establishing dedicated ontologies and agents and combining them with technologies such as QR codes, RFID tags, and mobile apps, enabled us to develop modular applications that tackle some key challenges related to lab management. Here, we showcase an automated tracking and intervention system for explosive chemicals as well as an easy-to-use mobile application for asset management and information retrieval. Implementing these, we have achieved semantic linking of BIM and BMS data with laboratory inventory and chemical knowledge. Our approach can capture the crucial data points and reduce inventory processing time. All data provenance is recorded following the FAIR principles, ensuring its accessibility and interoperability.
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Affiliation(s)
- Simon D Rihm
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore; Department of Chemical Engineering and Biotechnology, University of Cambridge, Philipppa Fawcett Drive, Cambridge, CB3 0AS, United Kingdom; Department of Chemical & Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore
| | - Yong Ren Tan
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore
| | - Wilson Ang
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore
| | - Markus Hofmeister
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore; Department of Chemical Engineering and Biotechnology, University of Cambridge, Philipppa Fawcett Drive, Cambridge, CB3 0AS, United Kingdom; Department of Chemical & Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore
| | - Xinhong Deng
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore
| | - Michael Teguh Laksana
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore
| | - Hou Yee Quek
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore
| | - Jiaru Bai
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philipppa Fawcett Drive, Cambridge, CB3 0AS, United Kingdom
| | - Laura Pascazio
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore
| | - Sim Chun Siong
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore
| | - Jethro Akroyd
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore; Department of Chemical Engineering and Biotechnology, University of Cambridge, Philipppa Fawcett Drive, Cambridge, CB3 0AS, United Kingdom; CMCL Innovations, Sheraton House, Cambridge, CB3 0AX, United Kingdom
| | - Sebastian Mosbach
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore; Department of Chemical Engineering and Biotechnology, University of Cambridge, Philipppa Fawcett Drive, Cambridge, CB3 0AS, United Kingdom; CMCL Innovations, Sheraton House, Cambridge, CB3 0AX, United Kingdom
| | - Markus Kraft
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore; Department of Chemical Engineering and Biotechnology, University of Cambridge, Philipppa Fawcett Drive, Cambridge, CB3 0AS, United Kingdom; CMCL Innovations, Sheraton House, Cambridge, CB3 0AX, United Kingdom; School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459, Singapore; The Alan Turing Institute, 2QR, John Dodson House, 96 Euston Rd, London, NW1 2DB, United Kingdom.
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2
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Smith II PL. Exploring electronic lab notebooks (ELNs) at a R1 institution in the Southeast USA. DIGITAL LIBRARY PERSPECTIVES 2022. [DOI: 10.1108/dlp-02-2022-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Purpose
This study aims to build a better understanding of researcher needs regarding support for data that you create, store, and/or manage using an electronic lab notebook (ELN), also referred to as electronic research notebook (ERN). The study also articulates the need for risk assessment for ELN products used by researchers for both open data and sensitive data that require standards.
Design/methodology/approach
The author used a participatory action research mixed-methods approach. A working group was formed from an ELN initial meeting. The working group team investigated several institutional ERN solutions by setting up trials, speaking with representatives from other research universities with ERN solutions and conducting internal and external research. This culminated in a broader-scale survey exploration.
Findings
Findings reveal there is no single institutional ELN license solution to satisfy all scientific disciplines. There is a need to develop foundational tools needed by all, provide additional tools and uses cases with best practices that can be tailored to various labs and research processes and develop a how-to guide on how to assemble the parts to create a useful ELN solution.
Research limitations/implications
The research implications include providing support for researchers selecting an ERN solution through a combination of online guides, short tutorials and training. There is a need to develop foundational tools, uses cases with best practices that can be tailored to various labs and research processes and how-to guide on how to assemble the parts to create a useful hybrid-ELN solution.
Practical implications
Practical implications include aligning available ERN solutions with other institution provided technologies across the research life cycle to provide researchers a suite of tools to conduct and manage their research. Further investigating educational license discounts for courses using eLabJournal, RSpace, Protocols.io, Open Science Framework, LabArchives or other ERNs currently funded by student course fees via grant funded projects are key implications.
Social implications
Social implications include the research computing environments of researchers that use ELN solutions approved through institutional risk assessment for open data are in compliance with university regulatory frameworks for use of the software in research.
Originality/value
The originality of this study includes risk assessments of ELNs solutions to better guide researchers in the selection process. To the best of the author’s knowledge, this survey was the first exploration of ELN on campus resulting in a final report to senior stakeholders. This study also highlights a developing grant proposal to further develop support across labs and campus.
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Higgins SG, Nogiwa-Valdez AA, Stevens MM. Considerations for implementing electronic laboratory notebooks in an academic research environment. Nat Protoc 2022; 17:179-189. [PMID: 35031789 DOI: 10.1038/s41596-021-00645-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 10/07/2021] [Indexed: 11/09/2022]
Abstract
As research becomes predominantly digitalized, scientists have the option of using electronic laboratory notebooks to record and access entries. These systems can more readily meet volume, complexity, accessibility and preservation requirements than paper notebooks. Although the technology can yield many benefits, these can be realized only by choosing a system that properly fulfills the requirements of a given context. This review explores the factors that should be considered when introducing electronic laboratory notebooks to an academically focused research group. We cite pertinent studies and discuss our own experience implementing a system within a multidisciplinary research environment. We also consider how the required financial and time investment is shared between individuals and institutions. Finally, we discuss how electronic laboratory notebooks fit into the broader context of research data management. This article is not a product review; it provides a framework for both the initial consideration of an electronic laboratory notebook and the evaluation of specific software packages.
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Affiliation(s)
- Stuart G Higgins
- Department of Materials, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
- Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Akemi A Nogiwa-Valdez
- Department of Materials, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
- Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Molly M Stevens
- Department of Materials, Imperial College London, London, UK.
- Department of Bioengineering, Imperial College London, London, UK.
- Institute of Biomedical Engineering, Imperial College London, London, UK.
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4
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Tirumalai MR, Kaelber JT, Park DR, Tran Q, Fox GE. Cryo-electron microscopy visualization of a large insertion in the 5S ribosomal RNA of the extremely halophilic archaeon Halococcus morrhuae. FEBS Open Bio 2020; 10:1938-1946. [PMID: 32865340 PMCID: PMC7530397 DOI: 10.1002/2211-5463.12962] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022] Open
Abstract
The extreme halophile Halococcus morrhuae (ATCC® 17082) contains a 108-nucleotide insertion in its 5S rRNA. Large rRNA expansions in Archaea are rare. This one almost doubles the length of the 5S rRNA. In order to understand how such an insertion is accommodated in the ribosome, we obtained a cryo-electron microscopy reconstruction of the native large subunit at subnanometer resolution. The insertion site forms a four-way junction that fully preserves the canonical 5S rRNA structure. Moving away from the junction site, the inserted region is conformationally flexible and does not pack tightly against the large subunit. The high-salt requirement of the H. morrhuae ribosomes for their stability conflicted with the low-salt threshold for cryo-electron microscopy procedures. Despite this obstacle, this is the first cryo-electron microscopy map of Halococcus ribosomes.
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Affiliation(s)
| | - Jason T. Kaelber
- National Center for Macromolecular ImagingBaylor College of MedicineHoustonTXUSA
- Present address:
Rutgers New Jersey Cryo‐electron Microscopy & Tomography Core FacilityInstitute for Quantitative Biomedicine, RutgersThe State University of New JerseyPiscatawayNJUSA
| | - Donghyun R. Park
- National Center for Macromolecular ImagingBaylor College of MedicineHoustonTXUSA
- Present address:
Department of Microbial PathogenesisYale UniversityNew HavenCTUSA
| | - Quyen Tran
- Department of Biology and BiochemistryUniversity of HoustonTXUSA
| | - George E. Fox
- Department of Biology and BiochemistryUniversity of HoustonTXUSA
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Ortega DR, Oikonomou CM, Ding HJ, Rees-Lee P, Jensen GJ. ETDB-Caltech: A blockchain-based distributed public database for electron tomography. PLoS One 2019; 14:e0215531. [PMID: 30986271 PMCID: PMC6464211 DOI: 10.1371/journal.pone.0215531] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/03/2019] [Indexed: 01/12/2023] Open
Abstract
Three-dimensional electron microscopy techniques like electron tomography provide valuable insights into cellular structures, and present significant challenges for data storage and dissemination. Here we explored a novel method to publicly release more than 11,000 such datasets, more than 30 TB in total, collected by our group. Our method, based on a peer-to-peer file sharing network built around a blockchain ledger, offers a distributed solution to data storage. In addition, we offer a user-friendly browser-based interface, https://etdb.caltech.edu, for anyone interested to explore and download our data. We discuss the relative advantages and disadvantages of this system and provide tools for other groups to mine our data and/or use the same approach to share their own imaging datasets.
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Affiliation(s)
- Davi R. Ortega
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Catherine M. Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - H. Jane Ding
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Prudence Rees-Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | | | - Grant J. Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Howard Hughes Medical Institute, Pasadena, California, United States of America
- * E-mail:
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6
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Structural basis for KCTD-mediated rapid desensitization of GABA B signalling. Nature 2019; 567:127-131. [PMID: 30814734 PMCID: PMC6405316 DOI: 10.1038/s41586-019-0990-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/24/2019] [Indexed: 11/23/2022]
Abstract
The GABAB receptor is one of the principal inhibitory neurotransmitter receptors in the brain, and it signals through heterotrimeric G proteins to activate a variety of effectors including G protein-coupled inwardly-rectifying potassium channels (GIRKs)1,2. GABAB receptor signaling is tightly regulated by auxiliary subunits called KCTDs, which control the kinetics of GIRK activation and desensitization3–5. However, the mechanistic basis for KCTD modulation of GABAB signaling remains incompletely understood. Here, using a combination of X-ray crystallography, electron microscopy, functional and biochemical experiments we reveal the molecular details of KCTD binding to both GABAB receptors and Gβγ subunits. KCTDs associate with the receptor by forming an asymmetric pentameric ring around a region of the receptor C-terminal tail, while a second KCTD domain, H1, engages in a symmetric interaction with five copies of Gβγ in which the G protein subunits also directly interact with one another. We further show that KCTD binding to Gβγ is highly cooperative, defining a model in which KCTDs cooperatively strip G proteins from GIRK channels to induce rapid desensitization following receptor activation. These results provide a framework for understanding the molecular basis for the precise temporal control of GABAB signaling by KCTD proteins.
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7
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Le VQ, Iacob RE, Tian Y, McConaughy W, Jackson J, Su Y, Zhao B, Engen JR, Pirruccello-Straub M, Springer TA. Tolloid cleavage activates latent GDF8 by priming the pro-complex for dissociation. EMBO J 2018; 37:384-397. [PMID: 29343545 DOI: 10.15252/embj.201797931] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 12/17/2022] Open
Abstract
Growth differentiation factor 8 (GDF8)/myostatin is a latent TGF-β family member that potently inhibits skeletal muscle growth. Here, we compared the conformation and dynamics of precursor, latent, and Tolloid-cleaved GDF8 pro-complexes to understand structural mechanisms underlying latency and activation of GDF8. Negative stain electron microscopy (EM) of precursor and latent pro-complexes reveals a V-shaped conformation that is unaltered by furin cleavage and sharply contrasts with the ring-like, cross-armed conformation of latent TGF-β1. Surprisingly, Tolloid-cleaved GDF8 does not immediately dissociate, but in EM exhibits structural heterogeneity consistent with partial dissociation. Hydrogen-deuterium exchange was not affected by furin cleavage. In contrast, Tolloid cleavage, in the absence of prodomain-growth factor dissociation, increased exchange in regions that correspond in pro-TGF-β1 to the α1-helix, latency lasso, and β1-strand in the prodomain and to the β6'- and β7'-strands in the growth factor. Thus, these regions are important in maintaining GDF8 latency. Our results show that Tolloid cleavage activates latent GDF8 by destabilizing specific prodomain-growth factor interfaces and primes the growth factor for release from the prodomain.
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Affiliation(s)
- Viet Q Le
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Roxana E Iacob
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, USA
| | - Yuan Tian
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | | | - Yang Su
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Bo Zhao
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, USA
| | | | - Timothy A Springer
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA .,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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8
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Tremouilhac P, Nguyen A, Huang YC, Kotov S, Lütjohann DS, Hübsch F, Jung N, Bräse S. Chemotion ELN: an Open Source electronic lab notebook for chemists in academia. J Cheminform 2017; 9:54. [PMID: 29086216 PMCID: PMC5612905 DOI: 10.1186/s13321-017-0240-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/18/2017] [Indexed: 11/18/2022] Open
Abstract
The development of an electronic lab notebook (ELN) for researchers working in the field of chemical sciences is presented. The web based application is available as an Open Source software that offers modern solutions for chemical researchers. The Chemotion ELN is equipped with the basic functionalities necessary for the acquisition and processing of chemical data, in particular the work with molecular structures and calculations based on molecular properties. The ELN supports planning, description, storage, and management for the routine work of organic chemists. It also provides tools for communicating and sharing the recorded research data among colleagues. Meeting the requirements of a state of the art research infrastructure, the ELN allows the search for molecules and reactions not only within the user’s data but also in conventional external sources as provided by SciFinder and PubChem. The presented development makes allowance for the growing dependency of scientific activity on the availability of digital information by providing Open Source instruments to record and reuse research data. The current version of the ELN has been using for over half of a year in our chemistry research group, serves as a common infrastructure for chemistry research and enables chemistry researchers to build their own databases of digital information as a prerequisite for the detailed, systematic investigation and evaluation of chemical reactions and mechanisms.
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Affiliation(s)
- Pierre Tremouilhac
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - An Nguyen
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Yu-Chieh Huang
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Serhii Kotov
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Dominic Sebastian Lütjohann
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.,Cubuslab GmbH, Lange Straße 2, 76199, Karlsruhe, Germany
| | - Florian Hübsch
- Ninja-Concept GmbH, Haid-und-Neu-Straße 18, 76131, Karlsruhe, Germany
| | - Nicole Jung
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany. .,Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany.
| | - Stefan Bräse
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany. .,Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany.
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9
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Abstract
Whether β1 integrin ectodomains visit conformational states similarly to β2 and β3 integrins has not been characterized. Furthermore, despite a wealth of activating and inhibitory antibodies to β1 integrins, the conformational states that these antibodies stabilize, and the relation of these conformations to function, remain incompletely characterized. Using negative-stain electron microscopy, we show that the integrin α5β1 ectodomain adopts extended-closed and extended-open conformations as well as a bent conformation. Antibodies SNAKA51, 8E3, N29, and 9EG7 bind to different domains in the α5 or β1 legs, activate, and stabilize extended ectodomain conformations. Antibodies 12G10 and HUTS-4 bind to the β1 βI domain and hybrid domains, respectively, activate, and stabilize the open headpiece conformation. Antibody TS2/16 binds a similar epitope as 12G10, activates, and appears to stabilize an open βI domain conformation without requiring extension or hybrid domain swing-out. mAb13 and SG/19 bind to the βI domain and βI-hybrid domain interface, respectively, inhibit, and stabilize the closed conformation of the headpiece. The effects of the antibodies on cell adhesion to fibronectin substrates suggest that the extended-open conformation of α5β1 is adhesive and that the extended-closed and bent-closed conformations are nonadhesive. The functional effects and binding sites of antibodies and fibronectin were consistent with their ability in binding to α5β1 on cell surfaces to cross-enhance or inhibit one another by competitive or noncompetitive (allosteric) mechanisms.
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10
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Tan YZ, Cheng A, Potter CS, Carragher B. Automated data collection in single particle electron microscopy. Microscopy (Oxf) 2015; 65:43-56. [PMID: 26671944 DOI: 10.1093/jmicro/dfv369] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/06/2015] [Indexed: 11/12/2022] Open
Abstract
Automated data collection is an integral part of modern workflows in single particle electron microscopy (EM) research. This review surveys the software packages available for automated single particle EM data collection. The degree of automation at each stage of data collection is evaluated, and the capabilities of the software packages are described. Finally, future trends in automation are discussed.
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Affiliation(s)
- Yong Zi Tan
- The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Anchi Cheng
- The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Clinton S Potter
- The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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11
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Ding HJ, Oikonomou CM, Jensen GJ. The Caltech Tomography Database and Automatic Processing Pipeline. J Struct Biol 2015; 192:279-86. [PMID: 26087141 DOI: 10.1016/j.jsb.2015.06.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 06/11/2015] [Accepted: 06/13/2015] [Indexed: 10/23/2022]
Abstract
Here we describe the Caltech Tomography Database and automatic image processing pipeline, designed to process, store, display, and distribute electron tomographic data including tilt-series, sample information, data collection parameters, 3D reconstructions, correlated light microscope images, snapshots, segmentations, movies, and other associated files. Tilt-series are typically uploaded automatically during collection to a user's "Inbox" and processed automatically, but can also be entered and processed in batches via scripts or file-by-file through an internet interface. As with the video website YouTube, each tilt-series is represented on the browsing page with a link to the full record, a thumbnail image and a video icon that delivers a movie of the tomogram in a pop-out window. Annotation tools allow users to add notes and snapshots. The database is fully searchable, and sets of tilt-series can be selected and re-processed, edited, or downloaded to a personal workstation. The results of further processing and snapshots of key results can be recorded in the database, automatically linked to the appropriate tilt-series. While the database is password-protected for local browsing and searching, datasets can be made public and individual files can be shared with collaborators over the Internet. Together these tools facilitate high-throughput tomography work by both individuals and groups.
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Affiliation(s)
- H Jane Ding
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, United States
| | - Catherine M Oikonomou
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, United States
| | - Grant J Jensen
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, United States; Howard Hughes Medical Institute, United States.
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12
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Adeno-associated virus serotype 1 (AAV1)- and AAV5-antibody complex structures reveal evolutionary commonalities in parvovirus antigenic reactivity. J Virol 2014; 89:1794-808. [PMID: 25410874 DOI: 10.1128/jvi.02710-14] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The clinical utility of the adeno-associated virus (AAV) gene delivery system has been validated by the regulatory approval of an AAV serotype 1 (AAV1) vector for the treatment of lipoprotein lipase deficiency. However, neutralization from preexisting antibodies is detrimental to AAV transduction efficiency. Hence, mapping of AAV antigenic sites and engineering of neutralization-escaping vectors are important for improving clinical efficacy. We report the structures of four AAV-monoclonal antibody fragment complexes, AAV1-ADK1a, AAV1-ADK1b, AAV5-ADK5a, and AAV5-ADK5b, determined by cryo-electron microscopy and image reconstruction to a resolution of ∼11 to 12 Å. Pseudoatomic modeling mapped the ADK1a epitope to the protrusions surrounding the icosahedral 3-fold axis and the ADK1b and ADK5a epitopes, which overlap, to the wall between depressions at the 2- and 5-fold axes (2/5-fold wall), and the ADK5b epitope spans both the 5-fold axis-facing wall of the 3-fold protrusion and portions of the 2/5-fold wall of the capsid. Combined with the six antigenic sites previously elucidated for different AAV serotypes through structural approaches, including AAV1 and AAV5, this study identified two common AAV epitopes: one on the 3-fold protrusions and one on the 2/5-fold wall. These epitopes coincide with regions with the highest sequence and structure diversity between AAV serotypes and correspond to regions determining receptor recognition and transduction phenotypes. Significantly, these locations overlap the two dominant epitopes reported for autonomous parvoviruses. Thus, rather than the amino acid sequence alone, the antigenic sites of parvoviruses appear to be dictated by structural features evolved to enable specific infectious functions. IMPORTANCE The adeno-associated viruses (AAVs) are promising vectors for in vivo therapeutic gene delivery, with more than 20 years of intense research now realized in a number of successful human clinical trials that report therapeutic efficacy. However, a large percentage of the population has preexisting AAV capsid antibodies and therefore must be excluded from clinical trials or vector readministration. This report represents our continuing efforts to understand the antigenic structure of the AAVs, specifically, to obtain a picture of "polyclonal" reactivity as is the situation in humans. It describes the structures of four AAV-antibody complexes determined by cryo-electron microscopy and image reconstruction, increasing the number of mapped epitopes to four and three, respectively, for AAV1 and AAV5, two vectors currently in clinical trials. The results presented provide information essential for generating antigenic escape vectors to overcome a critical challenge remaining in the optimization of this highly promising vector delivery system.
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Rochat RH, Hecksel CW, Chiu W. Cryo-EM techniques to resolve the structure of HSV-1 capsid-associated components. Methods Mol Biol 2014; 1144:265-81. [PMID: 24671690 DOI: 10.1007/978-1-4939-0428-0_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Electron cryo-microscopy has become a routine technique to determine the structure of biochemically purified herpes simplex virus capsid particles. This chapter describes the procedures of specimen preparation by cryopreservation; low dose and low temperature imaging in an electron cryo-microscope; and data processing for reconstruction. This methodology has yielded subnanometer resolution structures of the icosahedral capsid shell where α-helices and β-sheets of individual subunits can be recognized. A relaxation of the symmetry in the reconstruction steps allows us to resolve the DNA packaging protein located at one of the 12 vertices in the capsid.
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Affiliation(s)
- Ryan H Rochat
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
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