1
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Senft RA, Diaz-Rohrer B, Colarusso P, Swift L, Jamali N, Jambor H, Pengo T, Brideau C, Llopis PM, Uhlmann V, Kirk J, Gonzales KA, Bankhead P, Evans EL, Eliceiri KW, Cimini BA. A biologist's guide to planning and performing quantitative bioimaging experiments. PLoS Biol 2023; 21:e3002167. [PMID: 37368874 PMCID: PMC10298797 DOI: 10.1371/journal.pbio.3002167] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023] Open
Abstract
Technological advancements in biology and microscopy have empowered a transition from bioimaging as an observational method to a quantitative one. However, as biologists are adopting quantitative bioimaging and these experiments become more complex, researchers need additional expertise to carry out this work in a rigorous and reproducible manner. This Essay provides a navigational guide for experimental biologists to aid understanding of quantitative bioimaging from sample preparation through to image acquisition, image analysis, and data interpretation. We discuss the interconnectedness of these steps, and for each, we provide general recommendations, key questions to consider, and links to high-quality open-access resources for further learning. This synthesis of information will empower biologists to plan and execute rigorous quantitative bioimaging experiments efficiently.
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Affiliation(s)
- Rebecca A. Senft
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Barbara Diaz-Rohrer
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Pina Colarusso
- Live Cell Imaging Laboratory, University of Calgary, Calgary, Alberta, Canada
| | - Lucy Swift
- Live Cell Imaging Laboratory, University of Calgary, Calgary, Alberta, Canada
| | - Nasim Jamali
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Helena Jambor
- National Center for Tumor Diseases, University Cancer Center, NCT-UCC, Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden, Dresden, Germany
| | - Thomas Pengo
- Informatics Institute, University of Minnesota Twin Cities, Minneapolis, Minnesota, United States of America
| | - Craig Brideau
- Live Cell Imaging Laboratory, University of Calgary, Calgary, Alberta, Canada
| | - Paula Montero Llopis
- MicRoN Core, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Virginie Uhlmann
- European Bioinformatic Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Jason Kirk
- Optical Imaging & Vital Microscopy Core, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kevin Andrew Gonzales
- Mammalian Cell Biology and Development, Rockefeller University, New York, New York, United States of America
| | - Peter Bankhead
- Edinburgh Pathology, Centre for Genomic and Experimental Medicine, and CRUK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Edward L. Evans
- Morgridge Institute and University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kevin W. Eliceiri
- Morgridge Institute and University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Beth A. Cimini
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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2
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Fuchs YF, Brunner J, Weigelt M, Schieferdecker A, Morgenstern R, Sturm A, Winter B, Jambor H, Stölzel F, Ruhnke L, von Bonin M, Rücker-Braun E, Heidenreich F, Fuchs A, Bonifacio E, Bornhäuser M, Poitz DM, Altmann H. Next Generation Biobanking: Employing a Robotic System for Automated Mononuclear Cell Isolation. Biopreserv Biobank 2023; 21:106-110. [PMID: 36251308 PMCID: PMC9963478 DOI: 10.1089/bio.2021.0181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yannick F. Fuchs
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Jonathan Brunner
- Medical Department I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Marc Weigelt
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Anja Schieferdecker
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Robert Morgenstern
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Andrea Sturm
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Helena Jambor
- Mildred Scheel Early Career Center, Medical Faculty, Technische Universität Dresden, Dresden, Germany
| | - Friedrich Stölzel
- Medical Department I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Leo Ruhnke
- Medical Department I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Malte von Bonin
- Medical Department I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Elke Rücker-Braun
- Medical Department I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Clinical Trials Unit, DKMS gGmbH, Dresden, Germany
| | - Falk Heidenreich
- Medical Department I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Clinical Trials Unit, DKMS gGmbH, Dresden, Germany
| | - Anke Fuchs
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany.,Mildred Scheel Early Career Center, Medical Faculty, Technische Universität Dresden, Dresden, Germany
| | - Ezio Bonifacio
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Martin Bornhäuser
- Medical Department I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David M. Poitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
| | - Heidi Altmann
- Medical Department I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Address correspondence to: Heidi Altmann, PhD, Medical Department I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstr. 74, Dresden 01307, Germany
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3
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Krüger T, Wehner R, Herbig M, Kräter M, Kramer M, Middeke JM, Stölzel F, List C, Egger-Heidrich K, Teipel R, Oelschlägel U, Wermke M, Jambor H, Wobus M, Schetelig J, Jöhrens K, Tonn T, Subburayalu J, Schmitz M, Bornhauser M, von Bonin M. Perturbations of mesenchymal stromal cells after allogeneic hematopoietic cell transplantation predispose for bone marrow graft-versus-host-disease. Front Immunol 2022; 13:1005554. [PMID: 36311725 PMCID: PMC9599394 DOI: 10.3389/fimmu.2022.1005554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/27/2022] [Indexed: 12/04/2022] Open
Abstract
Functional impairment of the bone marrow (BM) niche has been suggested as a major reason for prolonged cytopenia and secondary graft failure after allogeneic hematopoietic cell transplantation (alloHCT). Because mesenchymal stromal cells (MSCs) serve as multipotent progenitors for several niche components in the BM, they might play a key role in this process. We used collagenase digested trephine biopsies to directly quantify MSCs in 73 patients before (n = 18) and/or after alloHCT (n = 65). For the first time, we demonstrate that acute graft-versus-host disease (aGvHD, n = 39) is associated with a significant decrease in MSC numbers. MSC reduction can be observed even before the clinical onset of aGvHD (n = 10). Assessing MSCs instantly after biopsy collection revealed phenotypic and functional differences depending on the occurrence of aGvHD. These differences vanished during ex vivo expansion. The MSC endotypes observed revealed an enhanced population of donor-derived classical dendritic cells type 1 and alloreactive T cells as the causing agent for compartmental inflammation and MSC damage before clinical onset of aGvHD was ascertained. In conclusion, MSCs endotypes may constitute a predisposing conductor of alloreactivity after alloHCT preceding the clinical diagnosis of aGvHD.
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Affiliation(s)
- Thomas Krüger
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- *Correspondence: Thomas Krüger,
| | - Rebekka Wehner
- German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Maik Herbig
- Max Planck Institute for Science of Light and Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
- Biotechnology Center, Center for Molecular and Cellular Bioengineering Technical University (TU) Dresden Tatzberg, Dresden, Germany
- Center for Regenerative Therapies (CRTD), Dresden, Germany
| | - Martin Kräter
- Max Planck Institute for Science of Light and Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
- Biotechnology Center, Center for Molecular and Cellular Bioengineering Technical University (TU) Dresden Tatzberg, Dresden, Germany
| | - Michael Kramer
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Jan Moritz Middeke
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Friedrich Stölzel
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Catrin List
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | | | - Raphael Teipel
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Uta Oelschlägel
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Martin Wermke
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
- University Cancer Centrum (UCC), Early Clinical Trial Unit (ECTU), University Hospital Carl Gustav Carus, Dresden, Germany
| | - Helena Jambor
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Manja Wobus
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Johannes Schetelig
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Korinna Jöhrens
- Institute of Pathology, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Torsten Tonn
- Institute of Transfusion Medicine, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Red Cross Blood Donation Service North-East, Dresden, Germany
| | - Julien Subburayalu
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center for Regenerative Therapies (CRTD), Dresden, Germany
- Mildred Scheel Early Career Center, Medical Faculty, Technische Universität Dresden, Dresden, Germany
| | - Marc Schmitz
- German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
- Center for Regenerative Therapies (CRTD), Dresden, Germany
| | - Martin Bornhauser
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
- Center for Regenerative Therapies (CRTD), Dresden, Germany
| | - Malte von Bonin
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
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4
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Chwastek G, Surma MA, Rizk S, Grosser D, Lavrynenko O, Rucińska M, Jambor H, Sáenz J. Principles of Membrane Adaptation Revealed through Environmentally Induced Bacterial Lipidome Remodeling. Cell Rep 2021; 32:108165. [PMID: 32966790 DOI: 10.1016/j.celrep.2020.108165] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/20/2020] [Accepted: 08/27/2020] [Indexed: 12/17/2022] Open
Abstract
Cells, from microbes to mammals, adapt their membrane lipid composition in response to environmental changes to maintain optimal properties. Global patterns of lipidome remodeling are poorly understood, particularly in organisms with simple lipid compositions that can provide insight into fundamental principles of membrane adaptation. Using shotgun lipidomics, we examine the simple yet, as we show here, adaptive lipidome of the plant-associated Gram-negative bacterium Methylobacterium extorquens. We observe that minimally 11 lipids account for 90% of total variability, thus constraining the upper limit of variable lipids required for an adaptive living membrane. Through lipid features analysis, we reveal that acyl chain remodeling is not evenly distributed across lipid classes, resulting in headgroup-specific effects of acyl chain variability on membrane properties. Results herein implicate headgroup-specific acyl chain remodeling as a mechanism for fine-tuning the membrane's physical state and provide a resource for using M. extorquens to explore the design principles of living membranes.
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Affiliation(s)
- Grzegorz Chwastek
- Technische Universität Dresden, B CUBE, Tatzberg 41, Dresden, Germany
| | | | - Sandra Rizk
- Technische Universität Dresden, B CUBE, Tatzberg 41, Dresden, Germany
| | - Daniel Grosser
- DZD-Paul Langerhans Institute Dresden, Fetscherstraße 74, Dresden, Germany
| | - Oksana Lavrynenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, Dresden, Germany
| | | | - Helena Jambor
- Technische Universität Dresden, Medizinische Fakultät, Fetscherstraße 74, Dresden, Germany
| | - James Sáenz
- Technische Universität Dresden, B CUBE, Tatzberg 41, Dresden, Germany.
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5
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Jambor H, Antonietti A, Alicea B, Audisio TL, Auer S, Bhardwaj V, Burgess SJ, Ferling I, Gazda MA, Hoeppner LH, Ilangovan V, Lo H, Olson M, Mohamed SY, Sarabipour S, Varma A, Walavalkar K, Wissink EM, Weissgerber TL. Creating clear and informative image-based figures for scientific publications. PLoS Biol 2021; 19:e3001161. [PMID: 33788834 PMCID: PMC8041175 DOI: 10.1371/journal.pbio.3001161] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/12/2021] [Accepted: 02/26/2021] [Indexed: 11/18/2022] Open
Abstract
Scientists routinely use images to display data. Readers often examine figures first; therefore, it is important that figures are accessible to a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for image acquisition; however, data on the legibility and interpretability of images are scarce. We systematically examined these factors in non-blot images published in the top 15 journals in 3 fields; plant sciences, cell biology, and physiology (n = 580 papers). Common problems included missing scale bars, misplaced or poorly marked insets, images or labels that were not accessible to colorblind readers, and insufficient explanations of colors, labels, annotations, or the species and tissue or object depicted in the image. Papers that met all good practice criteria examined for all image-based figures were uncommon (physiology 16%, cell biology 12%, plant sciences 2%). We present detailed descriptions and visual examples to help scientists avoid common pitfalls when publishing images. Our recommendations address image magnification, scale information, insets, annotation, and color and may encourage discussion about quality standards for bioimage publishing.
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Affiliation(s)
- Helena Jambor
- Mildred Scheel Early Career Center, Medical Faculty, Technische Universität Dresden, Dresden, Germany
| | - Alberto Antonietti
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Italy
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Bradly Alicea
- Orthogonal Research and Education Laboratory, Champaign, IL, United States of America
| | - Tracy L. Audisio
- Evolutionary Genomics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Susann Auer
- Department of Plant Physiology, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Vivek Bhardwaj
- Max Plank Institute of Immunology and Epigenetics, Freiburg, Germany
- Hubrecht Institute, Utrecht, the Netherlands
| | - Steven J. Burgess
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Iuliia Ferling
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute (HKI), Jena, Germany
| | - Małgorzata Anna Gazda
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Luke H. Hoeppner
- The Hormel Institute, University of Minnesota, Austin, MN, United States of America
- The Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
| | | | - Hung Lo
- Neuroscience Research Center, Charité—Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt—Universität zu Berlin, Berlin Institute of Health, Berlin, Germany
- Einstein Center for Neurosciences Berlin, Berlin, Germany
| | - Mischa Olson
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States of America
| | - Salem Yousef Mohamed
- Gastroenterology and Hepatology Unit, Internal Medicine Department, Faculty of Medicine, University of Zagazig, Zagazig, Egypt
| | - Sarvenaz Sarabipour
- Institute for Computational Medicine and the Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
| | - Aalok Varma
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bangalore, Karnataka, India
| | - Kaivalya Walavalkar
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bangalore, Karnataka, India
| | - Erin M. Wissink
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Tracey L. Weissgerber
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, QUEST Center, Berlin, Germany
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6
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Sarov M, Barz C, Jambor H, Hein MY, Schmied C, Suchold D, Stender B, Janosch S, K J VV, Krishnan RT, Krishnamoorthy A, Ferreira IRS, Ejsmont RK, Finkl K, Hasse S, Kämpfer P, Plewka N, Vinis E, Schloissnig S, Knust E, Hartenstein V, Mann M, Ramaswami M, VijayRaghavan K, Tomancak P, Schnorrer F. A genome-wide resource for the analysis of protein localisation in Drosophila. eLife 2016; 5:e12068. [PMID: 26896675 PMCID: PMC4805545 DOI: 10.7554/elife.12068] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 02/19/2016] [Indexed: 02/07/2023] Open
Abstract
The Drosophila genome contains >13000 protein-coding genes, the majority of which remain poorly investigated. Important reasons include the lack of antibodies or reporter constructs to visualise these proteins. Here, we present a genome-wide fosmid library of 10000 GFP-tagged clones, comprising tagged genes and most of their regulatory information. For 880 tagged proteins, we created transgenic lines, and for a total of 207 lines, we assessed protein expression and localisation in ovaries, embryos, pupae or adults by stainings and live imaging approaches. Importantly, we visualised many proteins at endogenous expression levels and found a large fraction of them localising to subcellular compartments. By applying genetic complementation tests, we estimate that about two-thirds of the tagged proteins are functional. Moreover, these tagged proteins enable interaction proteomics from developing pupae and adult flies. Taken together, this resource will boost systematic analysis of protein expression and localisation in various cellular and developmental contexts. DOI:http://dx.doi.org/10.7554/eLife.12068.001 The fruit fly Drosophila melanogaster is a popular model organism in biological research. Studies using Drosophila have led to important insights into human biology, because related proteins often fulfil similar roles in flies and humans. Thus, studying the role of a protein in Drosophila can teach us about what it might do in a human. To fulfil their biological roles, proteins often occupy particular locations inside cells, such as the cell’s nucleus or surface membrane. Many proteins are also only found in specific types of cell, such as neurons or muscle cells. A protein’s location thus provides clues about what it does, however cells contain many thousands of proteins and identifying the location of each one is a herculean task. Sarov et al. took on this challenge and developed a new resource to study the localisation of all Drosophila proteins during this animal’s development. First, genetic engineering was used to tag thousands of Drosophila proteins with a green fluorescent protein, so that they could be tracked under a microscope. Sarov et al. tagged about 10000 Drosophila proteins in bacteria, and then introduced almost 900 of them into flies to create genetically modified flies. Each fly line contains an extra copy of the tagged gene that codes for one tagged protein. About two-thirds of these tagged proteins appeared to work normally after they were introduced into flies. Sarov et al. then looked at over 200 of these fly lines in more detail and observed that many of the proteins were found in particular cell types and localized to specific parts of the cells. Video imaging of the tagged proteins in living fruit fly embryos and pupae revealed the proteins’ movements, while other techniques showed which proteins bind to the tagged proteins, and may therefore work together in protein complexes. This resource is openly available to the community, and so researchers can use it to study their favourite protein and gain new insights into how proteins work and are regulated during Drosophila development. Following on from this work, the next challenge will be to create more flies carrying tagged proteins, and to swap the green fluorescent tag with other experimentally useful tags. DOI:http://dx.doi.org/10.7554/eLife.12068.002
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Affiliation(s)
- Mihail Sarov
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
| | - Christiane Barz
- Muscle Dynamics Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Helena Jambor
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
| | - Marco Y Hein
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - Dana Suchold
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
| | - Bettina Stender
- Muscle Dynamics Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stephan Janosch
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
| | - Vinay Vikas K J
- Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - R T Krishnan
- Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Aishwarya Krishnamoorthy
- Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Irene R S Ferreira
- Muscle Dynamics Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - Katja Finkl
- Muscle Dynamics Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Susanne Hasse
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
| | - Philipp Kämpfer
- Heidelberg Institute of Theoretical Studies, Heidelberg, Germany
| | - Nicole Plewka
- Muscle Dynamics Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Elisabeth Vinis
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
| | | | - Elisabeth Knust
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
| | - Volker Hartenstein
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Mani Ramaswami
- Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - K VijayRaghavan
- Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Pavel Tomancak
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
| | - Frank Schnorrer
- Muscle Dynamics Group, Max Planck Institute of Biochemistry, Martinsried, Germany
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7
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Jambor H, Mejstrik P, Tomancak P. Rapid Ovary Mass-Isolation (ROMi) to Obtain Large Quantities of Drosophila Egg Chambers for Fluorescent In Situ Hybridization. Methods Mol Biol 2016; 1478:253-262. [PMID: 27730587 DOI: 10.1007/978-1-4939-6371-3_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Isolation of large quantities of tissue from organisms is essential for many techniques such as genome-wide screens and biochemistry. However, obtaining large quantities of tissues or cells is often the rate-limiting step when working in vivo. Here, we present a rapid method that allows the isolation of intact, single egg chambers at various developmental stages from ovaries of adult female Drosophila flies. The isolated egg chambers are amenable for a variety of procedures such as fluorescent in situ hybridization, RNA isolation, extract preparation, or immunostaining. Isolation of egg chambers from adult flies can be completed in 5 min and results, depending on the input amount of flies, in several milliliters of material. The isolated egg chambers are then further processed depending on the exact requirements of the subsequent application. We describe high-throughput in situ hybridization in 96-well plates as example application for the mass-isolated egg chambers.
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Affiliation(s)
- Helena Jambor
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.
| | - Pavel Mejstrik
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.
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Dunst S, Kazimiers T, von Zadow F, Jambor H, Sagner A, Brankatschk B, Mahmoud A, Spannl S, Tomancak P, Eaton S, Brankatschk M. Endogenously tagged rab proteins: a resource to study membrane trafficking in Drosophila. Dev Cell 2015; 33:351-65. [PMID: 25942626 PMCID: PMC4431667 DOI: 10.1016/j.devcel.2015.03.022] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/21/2015] [Accepted: 03/29/2015] [Indexed: 11/25/2022]
Abstract
Membrane trafficking is key to the cell biological mechanisms underlying development. Rab GTPases control specific membrane compartments, from core secretory and endocytic machinery to less-well-understood compartments. We tagged all 27 Drosophila Rabs with YFP(MYC) at their endogenous chromosomal loci, determined their expression and subcellular localization in six tissues comprising 23 cell types, and provide this data in an annotated, searchable image database. We demonstrate the utility of these lines for controlled knockdown and show that similar subcellular localization can predict redundant functions. We exploit this comprehensive resource to ask whether a common Rab compartment architecture underlies epithelial polarity. Strikingly, no single arrangement of Rabs characterizes the five epithelia we examine. Rather, epithelia flexibly polarize Rab distribution, producing membrane trafficking architectures that are tissue- and stage-specific. Thus, the core machinery responsible for epithelial polarization is unlikely to rely on polarized positioning of specific Rab compartments.
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Affiliation(s)
- Sebastian Dunst
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Tom Kazimiers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany; HHMI Janelia Research Campus, Ashburn, VA 20147, USA
| | - Felix von Zadow
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Helena Jambor
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Andreas Sagner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany; MRC National Institute for Medical Research, London NW7 1AA, UK
| | - Beate Brankatschk
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany; Paul Langerhans Institute, Dresden 01307, Germany
| | - Ali Mahmoud
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Stephanie Spannl
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany.
| | - Suzanne Eaton
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany.
| | - Marko Brankatschk
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany.
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Kanke M, Jambor H, Reich J, Marches B, Gstir R, Ryu YH, Ephrussi A, Macdonald PM. oskar RNA plays multiple noncoding roles to support oogenesis and maintain integrity of the germline/soma distinction. RNA 2015; 21:1096-109. [PMID: 25862242 PMCID: PMC4436663 DOI: 10.1261/rna.048298.114] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/12/2015] [Indexed: 05/05/2023]
Abstract
The Drosophila oskar (osk) mRNA is unusual in that it has both coding and noncoding functions. As an mRNA, osk encodes a protein required for embryonic patterning and germ cell formation. Independent of that function, the absence of osk mRNA disrupts formation of the karyosome and blocks progression through oogenesis. Here we show that loss of osk mRNA also affects the distribution of regulatory proteins, relaxing their association with large RNPs within the germline, and allowing them to accumulate in the somatic follicle cells. This and other noncoding functions of the osk mRNA are mediated by multiple sequence elements with distinct roles. One role, provided by numerous binding sites in two distinct regions of the osk 3' UTR, is to sequester the translational regulator Bruno (Bru), which itself controls translation of osk mRNA. This defines a novel regulatory circuit, with Bru restricting the activity of osk, and osk in turn restricting the activity of Bru. Other functional elements, which do not bind Bru and are positioned close to the 3' end of the RNA, act in the oocyte and are essential. Despite the different roles played by the different types of elements contributing to RNA function, mutation of any leads to accumulation of the germline regulatory factors in the follicle cells.
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Affiliation(s)
- Matt Kanke
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Helena Jambor
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - John Reich
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Brittany Marches
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Ronald Gstir
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Young Hee Ryu
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Paul M Macdonald
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
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Jambor H, Surendranath V, Kalinka AT, Mejstrik P, Saalfeld S, Tomancak P. Systematic imaging reveals features and changing localization of mRNAs in Drosophila development. eLife 2015; 4. [PMID: 25838129 PMCID: PMC4384636 DOI: 10.7554/elife.05003] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 03/09/2015] [Indexed: 01/02/2023] Open
Abstract
mRNA localization is critical for eukaryotic cells and affects numerous transcripts, yet how cells regulate distribution of many mRNAs to their subcellular destinations is still unknown. We combined transcriptomics and systematic imaging to determine the tissue-specific expression and subcellular distribution of 5862 mRNAs during Drosophila oogenesis. mRNA localization is widespread in the ovary and detectable in all of its cell types—the somatic epithelial, the nurse cells, and the oocyte. Genes defined by a common RNA localization share distinct gene features and differ in expression level, 3′UTR length and sequence conservation from unlocalized mRNAs. Comparison of mRNA localizations in different contexts revealed that localization of individual mRNAs changes over time in the oocyte and between ovarian and embryonic cell types. This genome scale image-based resource (Dresden Ovary Table, DOT, http://tomancak-srv1.mpi-cbg.de/DOT/main.html) enables the transition from mechanistic dissection of singular mRNA localization events towards global understanding of how mRNAs transcribed in the nucleus distribute in cells. DOI:http://dx.doi.org/10.7554/eLife.05003.001 To make a protein, the DNA sequence that encodes it must first be ‘transcribed’ to build a molecule of messenger RNA (called mRNA for short). Although many mRNA molecules are found throughout a cell, some are ‘localized’ to certain areas; and recent evidence suggests that this mRNA localization may be more common than previously thought. Not much is known about how cells identify which mRNAs need to be localized, or how these molecules are then transported to their destination. The localization process has been studied in most detail in the developing egg cell—also known as an oocyte—of the fruit fly species Drosophila melanogaster. These studies have identified few mRNA molecules that, if they are not carefully localized within the cell, cause the different parts of the fly embryo to fail to develop correctly when the oocyte is fertilized. Jambor et al. created an open-access online resource called the ‘Dresden Ovary Table’ that shows how 5862 mRNA molecules are distributed in several cell types involved in oocyte production in the ovary of female D. melanogaster flies. This resource consists of a combination of three-dimensional fluorescent images and measurements of mRNA amounts recorded at different stages in the development of the oocyte. Using the resource, Jambor et al. demonstrate that all of the cell types that make up the ovary localize many different mRNA molecules to several distinct destinations within the cells. The localized mRNAs share certain features, with mRNAs localized in the same part of the cell showing the most similarities. For example, localized mRNAs have longer so-called 3′ untranslated regions (3′UTR) that carry regulatory information and these sequences are also more evolutionarily conserved. Further, when the mRNA molecules in the oocyte were examined at different times during its development and compared with the embryo, the majority of these mRNAs were found to change where they are localized as the organism develops. The resource can be used to gain insight into specific genetic features that control the distribution of mRNAs. This information will be instrumental for cracking the ‘RNA localization code’ and understanding how it affects the activity of proteins in cells. DOI:http://dx.doi.org/10.7554/eLife.05003.002
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Affiliation(s)
- Helena Jambor
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Alex T Kalinka
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Pavel Mejstrik
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Stephan Saalfeld
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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Jambor H, Mueller S, Bullock SL, Ephrussi A. A stem-loop structure directs oskar mRNA to microtubule minus ends. RNA 2014; 20:429-39. [PMID: 24572808 PMCID: PMC3964905 DOI: 10.1261/rna.041566.113] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 01/06/2014] [Indexed: 05/22/2023]
Abstract
mRNA transport coupled with translational control underlies the intracellular localization of many proteins in eukaryotic cells. This is exemplified in Drosophila, where oskar mRNA transport and translation at the posterior pole of the oocyte direct posterior patterning of the embryo. oskar localization is a multistep process. Within the oocyte, a spliced oskar localization element (SOLE) targets oskar mRNA for plus end-directed transport by kinesin-1 to the posterior pole. However, the signals mediating the initial minus end-directed, dynein-dependent transport of the mRNA from nurse cells into the oocyte have remained unknown. Here, we show that a 67-nt stem-loop in the oskar 3' UTR promotes oskar mRNA delivery to the developing oocyte and that it shares functional features with the fs(1)K10 oocyte localization signal. Thus, two independent cis-acting signals, the oocyte entry signal (OES) and the SOLE, mediate sequential dynein- and kinesin-dependent phases of oskar mRNA transport during oogenesis. The OES also promotes apical localization of injected RNAs in blastoderm stage embryos, another dynein-mediated process. Similarly, when ectopically expressed in polarized cells of the follicular epithelium or salivary glands, reporter RNAs bearing the oskar OES are apically enriched, demonstrating that this element promotes mRNA localization independently of cell type. Our work sheds new light on how oskar mRNA is trafficked during oogenesis and the RNA features that mediate minus end-directed transport.
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Affiliation(s)
- Helena Jambor
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Sandra Mueller
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Simon L. Bullock
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Anne Ephrussi
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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Jambor H, Brunel C, Ephrussi A. Dimerization of oskar 3' UTRs promotes hitchhiking for RNA localization in the Drosophila oocyte. RNA 2011; 17:2049-2057. [PMID: 22028360 PMCID: PMC3222118 DOI: 10.1261/rna.2686411] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 08/23/2011] [Indexed: 05/29/2023]
Abstract
mRNA localization coupled with translational control is a highly conserved and widespread mechanism for restricting protein expression to specific sites within eukaryotic cells. In Drosophila, patterning of the embryo requires oskar mRNA transport to the posterior pole of the oocyte and translational repression prior to localization. oskar RNA splicing and the 3' untranslated region (UTR) are required for posterior enrichment of the mRNA. However, reporter RNAs harboring the oskar 3' UTR can localize by hitchhiking with endogenous oskar transcripts. Here we show that the oskar 3' UTR contains a stem-loop structure that promotes RNA dimerization in vitro and hitchhiking in vivo. Mutations in the loop that abolish in vitro dimerization interfere with reporter RNA localization, and restoring loop complementarity restores hitchhiking. Our analysis provides insight into the molecular basis of RNA hitchhiking, whereby localization-incompetent RNA molecules can become locally enriched in the cytoplasm, by virtue of their association with transport-competent RNAs.
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Affiliation(s)
- Helena Jambor
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Christine Brunel
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg Cedex, France
| | - Anne Ephrussi
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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Jambor H. Life on top: working at the European Molecular Biology Laboratory, Heidelberg, Germany. N Biotechnol 2008; 25:124. [PMID: 18771757 DOI: 10.1016/j.nbt.2008.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Accepted: 08/08/2008] [Indexed: 11/24/2022]
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