1
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Tüting C, Schmidt L, Skalidis I, Sinz A, Kastritis PL. Enabling cryo-EM density interpretation from yeast native cell extracts by proteomics data and AlphaFold structures. Proteomics 2023; 23:e2200096. [PMID: 37016452 DOI: 10.1002/pmic.202200096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/06/2023]
Abstract
In the cellular context, proteins participate in communities to perform their function. The detection and identification of these communities as well as in-community interactions has long been the subject of investigation, mainly through proteomics analysis with mass spectrometry. With the advent of cryogenic electron microscopy and the "resolution revolution," their visualization has recently been made possible, even in complex, native samples. The advances in both fields have resulted in the generation of large amounts of data, whose analysis requires advanced computation, often employing machine learning approaches to reach the desired outcome. In this work, we first performed a robust proteomics analysis of mass spectrometry (MS) data derived from a yeast native cell extract and used this information to identify protein communities and inter-protein interactions. Cryo-EM analysis of the cell extract provided a reconstruction of a biomolecule at medium resolution (∼8 Å (FSC = 0.143)). Utilizing MS-derived proteomics data and systematic fitting of AlphaFold-predicted atomic models, this density was assigned to the 2.6 MDa complex of yeast fatty acid synthase. Our proposed workflow identifies protein complexes in native cell extracts from Saccharomyces cerevisiae by combining proteomics, cryo-EM, and AI-guided protein structure prediction.
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Affiliation(s)
- Christian Tüting
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Biozentrum, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Lisa Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Ioannis Skalidis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Biozentrum, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
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2
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Mermans F, Mattelin V, Van den Eeckhoudt R, García-Timermans C, Van Landuyt J, Guo Y, Taurino I, Tavernier F, Kraft M, Khan H, Boon N. Opportunities in optical and electrical single-cell technologies to study microbial ecosystems. Front Microbiol 2023; 14:1233705. [PMID: 37692384 PMCID: PMC10486927 DOI: 10.3389/fmicb.2023.1233705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/03/2023] [Indexed: 09/12/2023] Open
Abstract
New techniques are revolutionizing single-cell research, allowing us to study microbes at unprecedented scales and in unparalleled depth. This review highlights the state-of-the-art technologies in single-cell analysis in microbial ecology applications, with particular attention to both optical tools, i.e., specialized use of flow cytometry and Raman spectroscopy and emerging electrical techniques. The objectives of this review include showcasing the diversity of single-cell optical approaches for studying microbiological phenomena, highlighting successful applications in understanding microbial systems, discussing emerging techniques, and encouraging the combination of established and novel approaches to address research questions. The review aims to answer key questions such as how single-cell approaches have advanced our understanding of individual and interacting cells, how they have been used to study uncultured microbes, which new analysis tools will become widespread, and how they contribute to our knowledge of ecological interactions.
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Affiliation(s)
- Fabian Mermans
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
- Department of Oral Health Sciences, KU Leuven, Leuven, Belgium
| | - Valérie Mattelin
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Ruben Van den Eeckhoudt
- Micro- and Nanosystems (MNS), Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
| | - Cristina García-Timermans
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Josefien Van Landuyt
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Yuting Guo
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Irene Taurino
- Micro- and Nanosystems (MNS), Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
- Semiconductor Physics, Department of Physics and Astronomy, KU Leuven, Leuven, Belgium
| | - Filip Tavernier
- MICAS, Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
| | - Michael Kraft
- Micro- and Nanosystems (MNS), Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
- Leuven Institute of Micro- and Nanoscale Integration (LIMNI), KU Leuven, Leuven, Belgium
| | - Hira Khan
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
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3
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Rima L, Zimmermann M, Fränkl A, Clairfeuille T, Lauer M, Engel A, Engel HA, Braun T. cryoWriter: a blotting free cryo-EM preparation system with a climate jet and cover-slip injector. Faraday Discuss 2022; 240:55-66. [PMID: 35924676 PMCID: PMC9641993 DOI: 10.1039/d2fd00066k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Electron microscopy (EM) introduced a fast and lasting change to structural and cellular biology. However, the sample preparation is still the bottleneck in the cryogenic electron microscopy (cryo-EM) workflow. Classical specimen preparation methods employ a harsh paper-blotting step, and the protein particles are exposed to a damaging air-water interface. Therefore, improved preparation strategies are urgently needed. Here, we present an amended microfluidic sample preparation method, which entirely avoids paper blotting and allows the passivation of the air-water interface during the preparation process. First, a climate jet excludes oxygen from the sample environment and controls the preparation temperature by varying the relative humidity of the grid environment. Second, the integrated "coverslip injector" allows the modulation of the air-water interface of the thin sample layer with effector molecules. We will briefly discuss the climate jet's effect on the stability and dynamics of the sample thin films. Furthermore, we will address the coverslip injector and demonstrate significant improvement in the sample quality.
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Affiliation(s)
- Luca Rima
- Biozentrum, University of BaselSpitalstrasse 414056 BaselSwitzerland+41 79 7337269
| | - Michael Zimmermann
- Biozentrum, University of BaselSpitalstrasse 414056 BaselSwitzerland+41 79 7337269
| | - Andri Fränkl
- Swiss Nanoscience Institute, University of Basel4056 BaselSwitzerland
| | - Thomas Clairfeuille
- Roche Pharma Research and Early Development, Therapeutic Modalities, Lead Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd.Grenzacherstrasse 1244070 BaselSwitzerland
| | - Matthias Lauer
- Roche Pharma Research and Early Development, Therapeutic Modalities, Lead Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd.Grenzacherstrasse 1244070 BaselSwitzerland
| | - Andreas Engel
- cryoWrite Ltd.Klingelbergstrasse 504056 BaselSwitzerland
| | | | - Thomas Braun
- Biozentrum, University of BaselSpitalstrasse 414056 BaselSwitzerland+41 79 7337269
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4
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Interfacing microfluidics with information-rich detection systems for cells, bioparticles, and molecules. Anal Bioanal Chem 2022; 414:4575-4589. [PMID: 35389095 PMCID: PMC8987515 DOI: 10.1007/s00216-022-04043-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/01/2022] [Accepted: 03/24/2022] [Indexed: 11/16/2022]
Abstract
The development of elegant and numerous microfluidic manipulations has enabled significant advances in the processing of small volume samples and the detection of minute amounts of biomaterials. Effective isolation of single cells in a defined volume as well as manipulations of complex bioparticle or biomolecule mixtures allows for the utilization of information-rich detection methods including mass spectrometry, electron microscopy imaging, and amplification/sequencing. The art and science of translating biosamples from microfluidic platforms to highly advanced, information-rich detection system is the focus of this review, where we term the translation between the microfluidics elements to the external world “off-chipping.” When presented with the challenge of presenting sub-nanoliter volumes of manipulated sample to a detection scheme, several delivery techniques have been developed for effective analysis. These techniques include spraying (electrospray, nano-electrospray, pneumatic), meniscus-defined volumes (droplets, plugs), constrained volumes (narrow channels, containers), and phase changes (deposition, freezing). Each technique has been proven effective in delivering highly defined samples from microfluidic systems to the detection elements. This review organizes and presents selective publications that illustrate the advancements of these delivery techniques with respect to the type of sample analyzed, while introducing each strategy and providing historical perspective. The publications highlighted in this review were chosen due to their significance and relevance in the development of their respective off-chip technique.
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5
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An AI-assisted cryo-EM pipeline for structural studies of cellular extracts. Structure 2022; 30:532-534. [PMID: 35395193 DOI: 10.1016/j.str.2022.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Proteins, the building blocks of life, often form large assemblies to perform their function but are traditionally studied separately in structural biology. In this issue of Structure, Skalidis et al. (2022) present a workflow to identify members of intact protein communities and solve their structures de novo to near-atomic resolution.
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6
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Ziegler SJ, Mallinson SJ, St. John PC, Bomble YJ. Advances in integrative structural biology: Towards understanding protein complexes in their cellular context. Comput Struct Biotechnol J 2020; 19:214-225. [PMID: 33425253 PMCID: PMC7772369 DOI: 10.1016/j.csbj.2020.11.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 01/26/2023] Open
Abstract
Microorganisms rely on protein interactions to transmit signals, react to stimuli, and grow. One of the best ways to understand these protein interactions is through structural characterization. However, in the past, structural knowledge was limited to stable, high-affinity complexes that could be crystallized. Recent developments in structural biology have revolutionized how protein interactions are characterized. The combination of multiple techniques, known as integrative structural biology, has provided insight into how large protein complexes interact in their native environment. In this mini-review, we describe the past, present, and potential future of integrative structural biology as a tool for characterizing protein interactions in their cellular context.
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Key Words
- CLEM, correlated light and electron microscopy
- Crosslinking mass spectrometry
- Cryo-electron microscopy
- Cryo-electron tomography
- EPR, electron paramagnetic resonance
- FRET, Forster resonance energy transfer
- ISB, Integrative structural biology
- Integrative structural biology
- ML, machine learning
- MR, molecular replacement
- MSAs, multiple sequence alignments
- MX, macromolecular crystallography
- NMR, nuclear magnetic resonance
- PDB, Protein Data Bank
- Protein docking
- Protein structure prediction
- Quinary interactions
- SAD, single-wavelength anomalous dispersion
- SANS, small angle neutron scattering
- SAXS, small angle X-ray scattering
- X-ray crystallography
- XL-MS, cross-linking mass spectrometry
- cryo-EM SPA, cryo-EM single particle analysis
- cryo-EM, cryo-electron microscopy
- cryo-ET, cryo-electron tomography
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Affiliation(s)
- Samantha J. Ziegler
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Sam J.B. Mallinson
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Peter C. St. John
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
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7
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Rubinstein JL, Guo H, Ripstein ZA, Haydaroglu A, Au A, Yip CM, Di Trani JM, Benlekbir S, Kwok T. Shake-it-off: a simple ultrasonic cryo-EM specimen-preparation device. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:1063-1070. [PMID: 31793900 PMCID: PMC6889916 DOI: 10.1107/s2059798319014372] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/21/2019] [Indexed: 01/27/2023]
Abstract
A method is presented for high-speed low-volume cryo-EM specimen preparation with a device constructed from readily available components. Although microscopes and image-analysis software for electron cryomicroscopy (cryo-EM) have improved dramatically in recent years, specimen-preparation methods have lagged behind. Most strategies still rely on blotting microscope grids with paper to produce a thin film of solution suitable for vitrification. This approach loses more than 99.9% of the applied sample and requires several seconds, leading to problematic air–water interface interactions for macromolecules in the resulting thin film of solution and complicating time-resolved studies. Recently developed self-wicking EM grids allow the use of small volumes of sample, with nanowires on the grid bars removing excess solution to produce a thin film within tens of milliseconds from sample application to freezing. Here, a simple cryo-EM specimen-preparation device that uses components from an ultrasonic humidifier to transfer protein solution onto a self-wicking EM grid is presented. The device is controlled by a Raspberry Pi single-board computer and all components are either widely available or can be manufactured by online services, allowing the device to be constructed in laboratories that specialize in cryo-EM rather than instrument design. The simple open-source design permits the straightforward customization of the instrument for specialized experiments.
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Affiliation(s)
- John L Rubinstein
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Hui Guo
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Zev A Ripstein
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Ali Haydaroglu
- Engineering Science Division, The University of Toronto, Toronto, Ontario, Canada
| | - Aaron Au
- Institute of Biomaterials and Biomedical Engineering, The University of Toronto, Toronto, Ontario, Canada
| | - Christopher M Yip
- Department of Biochemistry, The University of Toronto, Toronto, Ontario, Canada
| | - Justin M Di Trani
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Samir Benlekbir
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Timothy Kwok
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
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8
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Syntychaki A, Rima L, Schmidli C, Stohler T, Bieri A, Sütterlin R, Stahlberg H, Castaño-Díez D, Braun T. "Differential Visual Proteomics": Enabling the Proteome-Wide Comparison of Protein Structures of Single-Cells. J Proteome Res 2019; 18:3521-3531. [PMID: 31355640 DOI: 10.1021/acs.jproteome.9b00447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteins are involved in all tasks of life, and their characterization is essential to understand the underlying mechanisms of biological processes. We present a method called "differential visual proteomics" geared to study proteome-wide structural changes of proteins and protein-complexes between a disturbed and an undisturbed cell or between two cell populations. To implement this method, the cells are lysed and the lysate is prepared in a lossless manner for single-particle electron microscopy (EM). The samples are subsequently imaged in the EM. Individual particles are computationally extracted from the images and pooled together, while keeping track of which particle originated from which specimen. The extracted particles are then aligned and classified. A final quantitative analysis of the particle classes found identifies the particle structures that differ between positive and negative control samples. The algorithm and a graphical user interface developed to perform the analysis and to visualize the results were tested with simulated and experimental data. The results are presented, and the potential and limitations of the current implementation are discussed. We envisage the method as a tool for the untargeted profiling of the structural changes in the proteome of single-cells as a response to a disturbing force.
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Affiliation(s)
- Anastasia Syntychaki
- Center for Cellular Imaging and NanoAnalytics, Biozentrum , University of Basel , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Luca Rima
- Center for Cellular Imaging and NanoAnalytics, Biozentrum , University of Basel , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Claudio Schmidli
- Center for Cellular Imaging and NanoAnalytics, Biozentrum , University of Basel , Mattenstrasse 26 , 4058 Basel , Switzerland.,Swiss Nanoscience Institute , University of Basel , 4056 Basel , Switzerland
| | - Thomas Stohler
- Center for Cellular Imaging and NanoAnalytics, Biozentrum , University of Basel , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Andrej Bieri
- Center for Cellular Imaging and NanoAnalytics, Biozentrum , University of Basel , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Rosmarie Sütterlin
- Center for Cellular Imaging and NanoAnalytics, Biozentrum , University of Basel , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics, Biozentrum , University of Basel , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Daniel Castaño-Díez
- Center for Cellular Imaging and NanoAnalytics, Biozentrum , University of Basel , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Thomas Braun
- Center for Cellular Imaging and NanoAnalytics, Biozentrum , University of Basel , Mattenstrasse 26 , 4058 Basel , Switzerland
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9
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Abstract
The recent improvements in cryogenic electron microscopy (cryo-EM) caused a revolution in structural biology. However, 1) protein isolation and 2) sample preparation methods lag behind, and cryo-EM is performed at far from full efficiency. Here, we present a microfluidic method for the rapid isolation of a target protein from minimal amounts of cell lysate and for its direct preparation for high-resolution cryo-EM. Our technology opens more avenues for structural biology: High-throughput structure determination of proteins in a multitude of conditions, ultrafast isolation and structure determination of sensitive proteins, and the analysis of proteins that cannot be produced in sufficient amounts using conventional approaches. High-resolution structural information is essential to understand protein function. Protein-structure determination needs a considerable amount of protein, which can be challenging to produce, often involving harsh and lengthy procedures. In contrast, the several thousand to a few million protein particles required for structure determination by cryogenic electron microscopy (cryo-EM) can be provided by miniaturized systems. Here, we present a microfluidic method for the rapid isolation of a target protein and its direct preparation for cryo-EM. Less than 1 μL of cell lysate is required as starting material to solve the atomic structure of the untagged, endogenous human 20S proteasome. Our work paves the way for high-throughput structure determination of proteins from minimal amounts of cell lysate and opens more opportunities for the isolation of sensitive, endogenous protein complexes.
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10
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Abstract
Cryogenic electron microscopy (cryo-EM) enables structure determination of macromolecular objects and their assemblies. Although the techniques have been developing for nearly four decades, they have gained widespread attention in recent years due to technical advances on numerous fronts, enabling traditional microscopists to break into the world of molecular structural biology. Many samples can now be routinely analyzed at near-atomic resolution using standard imaging and image analysis techniques. However, numerous challenges to conventional workflows remain, and continued technical advances open entirely novel opportunities for discovery and exploration. Here, I will review some of the main methods surrounding cryo-EM with an emphasis specifically on single-particle analysis, and I will highlight challenges, open questions, and opportunities for methodology development.
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Affiliation(s)
- Dmitry Lyumkis
- From the Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, La Jolla, California 92037
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11
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Yi X, Verbeke EJ, Chang Y, Dickinson DJ, Taylor DW. Electron microscopy snapshots of single particles from single cells. J Biol Chem 2018; 294:1602-1608. [PMID: 30541924 PMCID: PMC6364765 DOI: 10.1074/jbc.ra118.006686] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/07/2018] [Indexed: 12/15/2022] Open
Abstract
Cryo-electron microscopy (cryo-EM) has become an indispensable tool for structural studies of biological macromolecules. Two additional predominant methods are available for studying the architectures of multiprotein complexes: 1) single-particle analysis of purified samples and 2) tomography of whole cells or cell sections. The former can produce high-resolution structures but is limited to highly purified samples, whereas the latter can capture proteins in their native state but has a low signal-to-noise ratio and yields lower-resolution structures. Here, we present a simple, adaptable method combining microfluidic single-cell extraction with single-particle analysis by EM to characterize protein complexes from individual Caenorhabditis elegans embryos. Using this approach, we uncover 3D structures of ribosomes directly from single embryo extracts. Moreover, we investigated structural dynamics during development by counting the number of ribosomes per polysome in early and late embryos. This approach has significant potential applications for counting protein complexes and studying protein architectures from single cells in developmental, evolutionary, and disease contexts.
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Affiliation(s)
- Xiunan Yi
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Eric J Verbeke
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Yiran Chang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Daniel J Dickinson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712.
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712; LIVESTRONG Cancer Institute, Dell Medical School, Austin, Texas 78712.
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12
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Schmidli C, Rima L, Arnold SA, Stohler T, Syntychaki A, Bieri A, Albiez S, Goldie KN, Chami M, Stahlberg H, Braun T. Miniaturized Sample Preparation for Transmission Electron Microscopy. J Vis Exp 2018. [PMID: 30102271 PMCID: PMC6126565 DOI: 10.3791/57310] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Due to recent technological progress, cryo-electron microscopy (cryo-EM) is rapidly becoming a standard method for the structural analysis of protein complexes to atomic resolution. However, protein isolation techniques and sample preparation methods for EM remain a bottleneck. A relatively small number (100,000 to a few million) of individual protein particles need to be imaged for the high-resolution analysis of proteins by the single particle EM approach, making miniaturized sample handling techniques and microfluidic principles feasible. A miniaturized, paper-blotting-free EM grid preparation method for sample pre-conditioning, EM grid priming and post processing that only consumes nanoliter-volumes of sample is presented. The method uses a dispensing system with sub-nanoliter precision to control liquid uptake and EM grid priming, a platform to control the grid temperature thereby determining the relative humidity above the EM grid, and a pick-and-plunge-mechanism for sample vitrification. For cryo-EM, an EM grid is placed on the temperature-controlled stage and the sample is aspirated into a capillary. The capillary tip is positioned in proximity to the grid surface, the grid is loaded with the sample and excess is re-aspirated into the microcapillary. Subsequently, the sample film is stabilized and slightly thinned by controlled water evaporation regulated by the offset of the platform temperature relative to the dew-point. At a given point the pick-and-plunge mechanism is triggered, rapidly transferring the primed EM grid into liquid ethane for sample vitrification. Alternatively, sample-conditioning methods are available to prepare nanoliter-sized sample volumes for negative stain (NS) EM. The methodologies greatly reduce sample consumption and avoid approaches potentially harmful to proteins, such as the filter paper blotting used in conventional methods. Furthermore, the minuscule amount of sample required allows novel experimental strategies, such as fast sample conditioning, combination with single-cell lysis for "visual proteomics," or "lossless" total sample preparation for quantitative analysis of complex samples.
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Affiliation(s)
- Claudio Schmidli
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel; Swiss Nanoscience Institute, University of Basel
| | - Luca Rima
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel
| | - Stefan A Arnold
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel; Swiss Nanoscience Institute, University of Basel
| | - Thomas Stohler
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel
| | - Anastasia Syntychaki
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel
| | - Andrej Bieri
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel
| | - Stefan Albiez
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel
| | - Kenneth N Goldie
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel
| | | | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel
| | - Thomas Braun
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel;
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13
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Zeng X, Leung MR, Zeev-Ben-Mordehai T, Xu M. A convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation. J Struct Biol 2018; 202:150-160. [PMID: 29289599 PMCID: PMC6661905 DOI: 10.1016/j.jsb.2017.12.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 12/24/2017] [Accepted: 12/27/2017] [Indexed: 01/08/2023]
Abstract
Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to automatically isolate different in situ cellular components. In this paper, we propose a convolutional autoencoder-based unsupervised approach to provide a coarse grouping of 3D small subvolumes extracted from tomograms. We demonstrate that the autoencoder can be used for efficient and coarse characterization of features of macromolecular complexes and surfaces, such as membranes. In addition, the autoencoder can be used to detect non-cellular features related to sample preparation and data collection, such as carbon edges from the grid and tomogram boundaries. The autoencoder is also able to detect patterns that may indicate spatial interactions between cellular components. Furthermore, we demonstrate that our autoencoder can be used for weakly supervised semantic segmentation of cellular components, requiring a very small amount of manual annotation.
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Affiliation(s)
- Xiangrui Zeng
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh 15213, USA
| | - Miguel Ricardo Leung
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Cryo-electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Tzviya Zeev-Ben-Mordehai
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Cryo-electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Min Xu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh 15213, USA.
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14
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Arnold SA, Müller SA, Schmidli C, Syntychaki A, Rima L, Chami M, Stahlberg H, Goldie KN, Braun T. Miniaturizing EM Sample Preparation: Opportunities, Challenges, and “Visual Proteomics”. Proteomics 2018; 18:e1700176. [DOI: 10.1002/pmic.201700176] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/15/2018] [Indexed: 01/31/2023]
Affiliation(s)
- Stefan A. Arnold
- Center for Cellular Imaging and NanoAnalytics (C-CINA); Biozentrum; University of Basel; Basel Switzerland
- Swiss Nanoscience Institute; University of Basel; Basel Switzerland
| | - Shirley A. Müller
- Center for Cellular Imaging and NanoAnalytics (C-CINA); Biozentrum; University of Basel; Basel Switzerland
| | - Claudio Schmidli
- Center for Cellular Imaging and NanoAnalytics (C-CINA); Biozentrum; University of Basel; Basel Switzerland
- Swiss Nanoscience Institute; University of Basel; Basel Switzerland
| | - Anastasia Syntychaki
- Center for Cellular Imaging and NanoAnalytics (C-CINA); Biozentrum; University of Basel; Basel Switzerland
| | - Luca Rima
- Center for Cellular Imaging and NanoAnalytics (C-CINA); Biozentrum; University of Basel; Basel Switzerland
| | - Mohamed Chami
- BioEM Lab; Biozentrum; University of Basel; Basel Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA); Biozentrum; University of Basel; Basel Switzerland
| | - Kenneth N. Goldie
- Center for Cellular Imaging and NanoAnalytics (C-CINA); Biozentrum; University of Basel; Basel Switzerland
| | - Thomas Braun
- Center for Cellular Imaging and NanoAnalytics (C-CINA); Biozentrum; University of Basel; Basel Switzerland
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15
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Pedde RD, Li H, Borchers CH, Akbari M. Microfluidic-Mass Spectrometry Interfaces for Translational Proteomics. Trends Biotechnol 2017; 35:954-970. [PMID: 28755975 DOI: 10.1016/j.tibtech.2017.06.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/05/2017] [Accepted: 06/09/2017] [Indexed: 12/29/2022]
Abstract
Interfacing mass spectrometry (MS) with microfluidic chips (μchip-MS) holds considerable potential to transform a clinician's toolbox, providing translatable methods for the early detection, diagnosis, monitoring, and treatment of noncommunicable diseases by streamlining and integrating laborious sample preparation workflows on high-throughput, user-friendly platforms. Overcoming the limitations of competitive immunoassays - currently the gold standard in clinical proteomics - μchip-MS can provide unprecedented access to complex proteomic assays having high sensitivity and specificity, but without the labor, costs, and complexities associated with conventional MS sample processing. This review surveys recent μchip-MS systems for clinical applications and examines their emerging role in streamlining the development and translation of MS-based proteomic assays by alleviating many of the challenges that currently inhibit widespread clinical adoption.
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Affiliation(s)
- R Daniel Pedde
- Laboratory for Innovations in Microengineering (LiME), Department of Mechanical Engineering, University of Victoria, 3800 Finnerty Rd., Victoria, BC, V8P 5C2, Canada; University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, 3101-4464 Markham St., Victoria, BC, V8Z 7X8, Canada
| | - Huiyan Li
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, 3101-4464 Markham St., Victoria, BC, V8Z 7X8, Canada
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, 3101-4464 Markham St., Victoria, BC, V8Z 7X8, Canada; Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Rd., Victoria, BC, V8P 5C2, Canada; Gerald Bronfman Department of Oncology, McGill University, 5100 de Maisonneuve Blvd. West, Suite 720, Montreal, QC, H4A 3T2, Canada; Proteomics Centre, Jewish General Hospital, McGill University, 3755 Cote-Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada.
| | - Mohsen Akbari
- Laboratory for Innovations in Microengineering (LiME), Department of Mechanical Engineering, University of Victoria, 3800 Finnerty Rd., Victoria, BC, V8P 5C2, Canada; Centre for Biomedical Research (CBR), University of Victoria, 3800 Finnerty Rd., Victoria, BC, V8P 5C2, Canada; Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd., Victoria, BC, V8P 5C2, Canada.
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16
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Shehadul Islam M, Aryasomayajula A, Selvaganapathy PR. A Review on Macroscale and Microscale Cell Lysis Methods. MICROMACHINES 2017. [PMCID: PMC6190294 DOI: 10.3390/mi8030083] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The lysis of cells in order to extract the nucleic acids or proteins inside it is a crucial unit operation in biomolecular analysis. This paper presents a critical evaluation of the various methods that are available both in the macro and micro scale for cell lysis. Various types of cells, the structure of their membranes are discussed initially. Then, various methods that are currently used to lyse cells in the macroscale are discussed and compared. Subsequently, popular methods for micro scale cell lysis and different microfluidic devices used are detailed with their advantages and disadvantages. Finally, a comparison of different techniques used in microfluidics platform has been presented which will be helpful to select method for a particular application.
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17
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Blotting-free and lossless cryo-electron microscopy grid preparation from nanoliter-sized protein samples and single-cell extracts. J Struct Biol 2016; 197:220-226. [PMID: 27864160 DOI: 10.1016/j.jsb.2016.11.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/24/2016] [Accepted: 11/14/2016] [Indexed: 12/28/2022]
Abstract
We present a sample preparation method for cryo-electron microscopy (cryo-EM) that requires only 3-20nL of sample to prepare a cryo-EM grid, depending on the protocol used. The sample is applied and spread on the grid by a microcapillary. The procedure does not involve any blotting steps, and real-time monitoring allows the water film thickness to be assessed and decreased to an optimum value prior to vitrification. We demonstrate that the method is suitable for high-resolution cryo-EM and will enable alternative electron microscopy approaches, such as single-cell visual proteomics.
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18
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Arnold SA, Albiez S, Opara N, Chami M, Schmidli C, Bieri A, Padeste C, Stahlberg H, Braun T. Total Sample Conditioning and Preparation of Nanoliter Volumes for Electron Microscopy. ACS NANO 2016; 10:4981-4988. [PMID: 27074622 DOI: 10.1021/acsnano.6b01328] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Electron microscopy (EM) entered a new era with the emergence of direct electron detectors and new nanocrystal electron diffraction methods. However, sample preparation techniques have not progressed and still suffer from extensive blotting steps leading to a massive loss of sample. Here, we present a simple but versatile method for the almost lossless sample conditioning and preparation of nanoliter volumes of biological samples for EM, keeping the sample under close to physiological condition. A microcapillary is used to aspirate 3-5 nL of sample. The microcapillary tip is immersed into a reservoir of negative stain or trehalose, where the sample becomes conditioned by diffusive exchange of salt and heavy metal ions or sugar molecules, respectively, before it is deposited as a small spot onto an EM grid. We demonstrate the use of the method to prepare protein particles for imaging by transmission EM and nanocrystals for analysis by electron diffraction. Furthermore, the minute sample volume required for this method enables alternative strategies for biological experiments, such as the analysis of the content of a single cell by visual proteomics, fully exploiting the single molecule detection limit of EM.
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Affiliation(s)
| | | | - Nadia Opara
- Paul Scherrer Institute (PSI) , 5232 Villigen, Switzerland
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19
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Chen B, Frank J. Two promising future developments of cryo-EM: capturing short-lived states and mapping a continuum of states of a macromolecule. Microscopy (Oxf) 2015; 65:69-79. [PMID: 26520784 DOI: 10.1093/jmicro/dfv344] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/05/2015] [Indexed: 01/04/2023] Open
Abstract
The capabilities and application range of cryogenic electron microscopy (cryo-EM) method have expanded vastly in the last two years, thanks to the advances provided by direct detection devices and computational classification tools. We take this review as an opportunity to sketch out promising developments of cryo-EM in two important directions: (i) imaging of short-lived states (10-1000 ms) of biological molecules by using time-resolved cryo-EM, particularly the mixing-spraying method and (ii) recovering an entire continuum of coexisting states from the same sample by employing a computational technique called manifold embedding. It is tempting to think of combining these two methods, to elucidate the way the states of a molecular machine such as the ribosome branch and unfold. This idea awaits further developments of both methods, particularly by increasing the data yield of the time-resolved cryo-EM method and by developing the manifold embedding technique into a user-friendly workbench.
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Affiliation(s)
- Bo Chen
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 W. 168th Street, New York, NY 10032, USA
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 W. 168th Street, New York, NY 10032, USA Department of Biological Sciences, Columbia University, New York, NY 10027, USA Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
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20
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Witte C, Kremer C, Chanasakulniyom M, Reboud J, Wilson R, Cooper JM, Neale SL. Spatially selecting a single cell for lysis using light-induced electric fields. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:3026-31. [PMID: 24719234 DOI: 10.1002/smll.201400247] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 02/27/2014] [Indexed: 05/16/2023]
Abstract
An optoelectronic tweezing (OET) device, within an integrated microfluidic channel, is used to precisely select single cells for lysis among dense populations. Cells to be lysed are exposed to higher electrical fields than their neighbours by illuminating a photoconductive film underneath them. Using beam spot sizes as low as 2.5 μm, 100% lysis efficiency is reached in <1 min allowing the targeted lysis of cells.
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Affiliation(s)
- Christian Witte
- University of Glasgow, Division of Biomedical Engineering, G12 8LT, Scotland
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21
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Giss D, Kemmerling S, Dandey V, Stahlberg H, Braun T. Exploring the Interactome: Microfluidic Isolation of Proteins and Interacting Partners for Quantitative Analysis by Electron Microscopy. Anal Chem 2014; 86:4680-7. [DOI: 10.1021/ac4027803] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Dominic Giss
- Center
for Cellular Imaging
and Nano Analytics, Biozentrum, University of Basel, Basel 4056, Switzerland
| | - Simon Kemmerling
- Center
for Cellular Imaging
and Nano Analytics, Biozentrum, University of Basel, Basel 4056, Switzerland
| | - Venkata Dandey
- Center
for Cellular Imaging
and Nano Analytics, Biozentrum, University of Basel, Basel 4056, Switzerland
| | - Henning Stahlberg
- Center
for Cellular Imaging
and Nano Analytics, Biozentrum, University of Basel, Basel 4056, Switzerland
| | - Thomas Braun
- Center
for Cellular Imaging
and Nano Analytics, Biozentrum, University of Basel, Basel 4056, Switzerland
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22
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Ramakrishnan C, Bieri A, Sauter N, Roizard S, Ringler P, Müller SA, Goldie KN, Enimanev K, Stahlberg H, Rinn B, Braun T. openBEB: open biological experiment browser for correlative measurements. BMC Bioinformatics 2014; 15:84. [PMID: 24666611 PMCID: PMC3987129 DOI: 10.1186/1471-2105-15-84] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 03/11/2014] [Indexed: 11/12/2022] Open
Abstract
Background New experimental methods must be developed to study interaction networks in systems biology. To reduce biological noise, individual subjects, such as single cells, should be analyzed using high throughput approaches. The measurement of several correlative physical properties would further improve data consistency. Accordingly, a considerable quantity of data must be acquired, correlated, catalogued and stored in a database for subsequent analysis. Results We have developed openBEB (open Biological Experiment Browser), a software framework for data acquisition, coordination, annotation and synchronization with database solutions such as openBIS. OpenBEB consists of two main parts: A core program and a plug-in manager. Whereas the data-type independent core of openBEB maintains a local container of raw-data and metadata and provides annotation and data management tools, all data-specific tasks are performed by plug-ins. The open architecture of openBEB enables the fast integration of plug-ins, e.g., for data acquisition or visualization. A macro-interpreter allows the automation and coordination of the different modules. An update and deployment mechanism keeps the core program, the plug-ins and the metadata definition files in sync with a central repository. Conclusions The versatility, the simple deployment and update mechanism, and the scalability in terms of module integration offered by openBEB make this software interesting for a large scientific community. OpenBEB targets three types of researcher, ideally working closely together: (i) Engineers and scientists developing new methods and instruments, e.g., for systems-biology, (ii) scientists performing biological experiments, (iii) theoreticians and mathematicians analyzing data. The design of openBEB enables the rapid development of plug-ins, which will inherently benefit from the “house keeping” abilities of the core program. We report the use of openBEB to combine live cell microscopy, microfluidic control and visual proteomics. In this example, measurements from diverse complementary techniques are combined and correlated.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Thomas Braun
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, Universität Basel, Basel, Switzerland.
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