|
1
|
Jeyaraman N, Jeyaraman M, Ramasubramanian S, Balaji S, Nallakumarasamy A. Visualizing medicine: The case for implementing graphical abstracts in clinical reporting. World J Methodol 2025; 15:95966. [DOI: 10.5662/wjm.v15.i2.95966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 09/21/2024] [Accepted: 10/21/2024] [Indexed: 11/27/2024] Open
Abstract
Graphical abstracts (GAs) are emerging as a pivotal tool in medical literature, enhancing the dissemination and comprehension of complex clinical data through visual summaries. This editorial highlights the significant advantages of GAs, including improved clarity, increased reader engagement, and enhanced visibility of research findings. By transforming intricate scientific data into accessible visual formats, these abstracts facilitate quick and effective knowledge transfer, crucial in clinical decision-making and patient care. However, challenges such as potential data misrepresentation due to oversimplification, the skill gap in graphic design among researchers, and the lack of standardized creation guidelines pose barriers to their widespread adoption. Additionally, while software such as Adobe Illustrator, BioRender, and Canva are commonly employed to create these visuals, not all researchers may be proficient in their use. To address these issues, we recommend that academic journals establish clear guidelines and provide necessary design training to researchers. This proactive approach will ensure the creation of high-quality GAs, promote their standardization, and expand their use in clinical reporting, ultimately benefiting the medical community and improving healthcare outcomes.
Collapse
Affiliation(s)
- Naveen Jeyaraman
- Department of Orthopaedics, ACS Medical College and Hospital, Dr MGR Educational and Research Institute, Chennai 600077, Tamil Nadu, India
| | - Madhan Jeyaraman
- Department of Orthopaedics, ACS Medical College and Hospital, Dr MGR Educational and Research Institute, Chennai 600077, Tamil Nadu, India
| | - Swaminathan Ramasubramanian
- Department of Orthopaedics, Government Medical College, Omandurar Government Estate, Chennai 600002, Tamil Nadu, India
| | - Sangeetha Balaji
- Department of Orthopaedics, Government Medical College, Omandurar Government Estate, Chennai 600002, Tamil Nadu, India
| | - Arulkumar Nallakumarasamy
- Department of Orthopaedics, Jawaharlal Institute of Postgraduate Medical Education and Research–Karaikal, Puducherry 609602, India
| |
Collapse
|
|
2
|
Marconi A, Vernaz G, Karunaratna A, Ngochera MJ, Durbin R, Santos ME. Genetic and Developmental Divergence in the Neural Crest Program between Cichlid Fish Species. Mol Biol Evol 2024; 41:msae217. [PMID: 39412298 PMCID: PMC11558072 DOI: 10.1093/molbev/msae217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 10/07/2024] [Accepted: 10/09/2024] [Indexed: 10/30/2024] Open
Abstract
Neural crest (NC) is a vertebrate-specific embryonic progenitor cell population at the basis of important vertebrate features such as the craniofacial skeleton and pigmentation patterns. Despite the wide-ranging variation of NC-derived traits across vertebrates, the contribution of NC to species diversification remains underexplored. Here, leveraging the adaptive diversity of African Great Lakes' cichlid species, we combined comparative transcriptomics and population genomics to investigate the evolution of the NC genetic program in the context of their morphological divergence. Our analysis revealed substantial differences in transcriptional landscapes across somitogenesis, an embryonic period coinciding with NC development and migration. This included dozens of genes with described functions in the vertebrate NC gene regulatory network, several of which showed signatures of positive selection. Among candidates showing between-species expression divergence, we focused on teleost-specific paralogs of the NC-specifier sox10 (sox10a and sox10b) as prime candidates to influence NC development. These genes, expressed in NC cells, displayed remarkable spatio-temporal variation in cichlids, suggesting their contribution to interspecific morphological differences, such as craniofacial structures and pigmentation. Finally, through CRISPR/Cas9 mutagenesis, we demonstrated the functional divergence between cichlid sox10 paralogs, with the acquisition of a novel skeletogenic function by sox10a. When compared with teleost models zebrafish and medaka, our findings reveal that sox10 duplication, although retained in most teleost lineages, had variable functional fates across their phylogeny. Altogether, our study suggests that NC-related processes-particularly those controlled by sox10s-are involved in generating morphological diversification between species and lays the groundwork for further investigations into the mechanisms underpinning vertebrate NC diversification.
Collapse
Affiliation(s)
| | - Grégoire Vernaz
- Zoological Institute, University of Basel, Basel, Switzerland
| | | | - Maxon J Ngochera
- Malawi Fisheries Department, Senga Bay Fisheries Research Center, P.O. Box 316, Salima, Malawi
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - M Emília Santos
- Department of Zoology, University of Cambridge, Cambridge, UK
| |
Collapse
|
|
3
|
Marconi A, Vernaz G, Karunaratna A, Ngochera MJ, Durbin R, Santos ME. Genetic and developmental divergence in the neural crest programme between cichlid fish species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.578004. [PMID: 38352436 PMCID: PMC10862805 DOI: 10.1101/2024.01.30.578004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Neural crest (NC) is a vertebrate-specific embryonic progenitor cell population at the basis of important vertebrate features such as the craniofacial skeleton and pigmentation patterns. Despite the wide-ranging variation of NC-derived traits across vertebrates, the contribution of NC to species diversification remains underexplored. Here, leveraging the adaptive diversity of African Great Lakes' cichlid species, we combined comparative transcriptomics and population genomics to investigate the evolution of the NC genetic programme in the context of their morphological divergence. Our analysis revealed substantial differences in transcriptional landscapes across somitogenesis, an embryonic period coinciding with NC development and migration. This included dozens of genes with described functions in the vertebrate NC gene regulatory network, several of which showed signatures of positive selection. Among candidates showing between-species expression divergence, we focused on teleost-specific paralogs of the NC-specifier sox10 (sox10a and sox10b) as prime candidates to influence NC development. These genes, expressed in NC cells, displayed remarkable spatio-temporal variation in cichlids, suggesting their contribution to inter-specific morphological differences. Finally, through CRISPR/Cas9 mutagenesis, we demonstrated the functional divergence between cichlid sox10 paralogs, with the acquisition of a novel skeletogenic function by sox10a. When compared to the teleost models zebrafish and medaka, our findings reveal that sox10 duplication, although retained in most teleost lineages, had variable functional fates across their phylogeny. Altogether, our study suggests that NC-related processes - particularly those controlled by sox10s - might be involved in generating morphological diversification between species and lays the groundwork for further investigations into mechanisms underpinning vertebrate NC diversification.
Collapse
Affiliation(s)
| | | | | | - Maxon J. Ngochera
- Senga Bay Fisheries Research Center, Malawi Fisheries Department, P.O. Box 316, Salima, Malawi
| | - Richard Durbin
- Department of Genetics, University of Cambridge, United Kingdom
| | | |
Collapse
|
|
4
|
Taatjes DJ, Koji T, Schrader M, Roth J. Editorial: Histochemistry and Cell Biology implements new submission guidelines for image presentation and image analysis. Histochem Cell Biol 2023; 160:495-497. [PMID: 37878055 DOI: 10.1007/s00418-023-02247-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Affiliation(s)
- Douglas J Taatjes
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA.
| | - Takehiko Koji
- Office for Research Initiative and Development, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Michael Schrader
- Faculty of Health and Life Sciences, Biosciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Jürgen Roth
- University of Zurich, 8091, Zurich, Switzerland
| |
Collapse
|
|
5
|
Acharya S, Preda MB, Papatheodorou I, Palioura D, Giardoglou P, Tsata V, Erceg S, Barbalata T, Ben-Aicha S, Martino F, Nicastro L, Lazou A, Beis D, Martelli F, Sopic M, Emanueli C, Kardassis D, Devaux Y, EU-CardioRNA COST Action CA17129.. The science behind soft skills: Do's and Don'ts for early career researchers and beyond. A review paper from the EU-CardioRNA COST Action CA17129. OPEN RESEARCH EUROPE 2023; 3:55. [PMID: 38689633 PMCID: PMC11058455 DOI: 10.12688/openreseurope.15746.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 10/10/2023] [Indexed: 05/02/2024]
Abstract
Soft skills are the elementary management, personal, and interpersonal abilities that are vital for an individual to be efficient at workplace or in their personal life. Each work place requires different set of soft skills. Thus, in addition to scientific/technical skills that are easier to access within a short time frame, several key soft skills are essential for the success of a researcher in today's international work environment. In this paper, the trainees and trainers of the EU-CardioRNA COST Action CA17129 training school on soft skills present basic and advanced soft skills for early career researchers. Here, we particularly emphasize on the importance of transferable and presentation skills, ethics, literature reading and reviewing, research protocol and grant writing, networking, and career opportunities for researchers. All these skills are vital but are often overlooked by some scholars. We also provide tips to ace in aforementioned skills that are crucial in a day-to-day life of early and late career researchers in academia and industry.
Collapse
Affiliation(s)
- Shubhra Acharya
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, 1445, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, 4365, Luxembourg
| | - Mihai Bogdan Preda
- "Nicolae Simionescu” Institute of Cellular Biology and Pathology, Bucharest, 050568, Romania
| | - Ioanna Papatheodorou
- School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Dimitra Palioura
- School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Panagiota Giardoglou
- Developmental Biology, Clinical, Experimental Surgery and Translational Research Center, Biomedical Research Foundation of the Academy of Athens, Athens, 11527, Greece
| | - Vasiliki Tsata
- Developmental Biology, Clinical, Experimental Surgery and Translational Research Center, Biomedical Research Foundation of the Academy of Athens, Athens, 11527, Greece
| | - Sanja Erceg
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, 11000, Serbia
| | - Teodora Barbalata
- "Nicolae Simionescu” Institute of Cellular Biology and Pathology, Bucharest, 050568, Romania
| | - Soumaya Ben-Aicha
- National Heart and Lung Institute, Imperial College London, London, W120NN, UK
| | - Fabiana Martino
- National Heart and Lung Institute, Imperial College London, London, W120NN, UK
| | - Laura Nicastro
- National Heart and Lung Institute, Imperial College London, London, W120NN, UK
| | - Antigone Lazou
- School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Dimitris Beis
- Developmental Biology, Clinical, Experimental Surgery and Translational Research Center, Biomedical Research Foundation of the Academy of Athens, Athens, 11527, Greece
| | - Fabio Martelli
- Laboratory of Molecular Cardiology, IRCCS Policlinico San Donato, Milan, 20097, Italy
| | - Miron Sopic
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, 11000, Serbia
| | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, London, W120NN, UK
| | - Dimitris Kardassis
- Laboratory of Biochemistry, Medical School, University of Crete, Heraklion, 71003, Greece
- Institute of Molecular Biology and Biotechnology, Foundation For Research & Technology Hellas (FORTH), Heraklion, 71003, Greece
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, 1445, Luxembourg
| | - EU-CardioRNA COST Action CA17129.
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, 1445, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, 4365, Luxembourg
- "Nicolae Simionescu” Institute of Cellular Biology and Pathology, Bucharest, 050568, Romania
- School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
- Developmental Biology, Clinical, Experimental Surgery and Translational Research Center, Biomedical Research Foundation of the Academy of Athens, Athens, 11527, Greece
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, 11000, Serbia
- National Heart and Lung Institute, Imperial College London, London, W120NN, UK
- Laboratory of Molecular Cardiology, IRCCS Policlinico San Donato, Milan, 20097, Italy
- Laboratory of Biochemistry, Medical School, University of Crete, Heraklion, 71003, Greece
- Institute of Molecular Biology and Biotechnology, Foundation For Research & Technology Hellas (FORTH), Heraklion, 71003, Greece
| |
Collapse
|
|
6
|
Acharya S, Preda MB, Papatheodorou I, Palioura D, Giardoglou P, Tsata V, Erceg S, Barbalata T, Ben-Aicha S, Martino F, Nicastro L, Lazou A, Beis D, Martelli F, Sopic M, Emanueli C, Kardassis D, Devaux Y, EU-CardioRNA COST Action CA17129.. The science behind soft skills: Do's and Don'ts for early career researchers and beyond. A review paper from the EU-CardioRNA COST Action CA17129. OPEN RESEARCH EUROPE 2023; 3:55. [PMID: 38689633 PMCID: PMC11058455 DOI: 10.12688/openreseurope.15746.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/10/2023] [Indexed: 01/18/2025]
Abstract
Soft skills are the elementary management, personal, and interpersonal abilities that are vital for an individual to be efficient at workplace or in their personal life. Each work place requires different set of soft skills. Thus, in addition to scientific/technical skills that are easier to access within a short time frame, several key soft skills are essential for the success of a researcher in today's international work environment. In this paper, the trainees and trainers of the EU-CardioRNA COST Action CA17129 training school on soft skills present basic and advanced soft skills for early career researchers. Here, we particularly emphasize on the importance of transferable and presentation skills, ethics, literature reading and reviewing, research protocol and grant writing, networking, and career opportunities for researchers. All these skills are vital but are often overlooked by some scholars. We also provide tips to ace in aforementioned skills that are crucial in a day-to-day life of early and late career researchers in academia and industry.
Collapse
Affiliation(s)
- Shubhra Acharya
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, 1445, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, 4365, Luxembourg
| | - Mihai Bogdan Preda
- "Nicolae Simionescu” Institute of Cellular Biology and Pathology, Bucharest, 050568, Romania
| | - Ioanna Papatheodorou
- School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Dimitra Palioura
- School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Panagiota Giardoglou
- Developmental Biology, Clinical, Experimental Surgery and Translational Research Center, Biomedical Research Foundation of the Academy of Athens, Athens, 11527, Greece
| | - Vasiliki Tsata
- Developmental Biology, Clinical, Experimental Surgery and Translational Research Center, Biomedical Research Foundation of the Academy of Athens, Athens, 11527, Greece
| | - Sanja Erceg
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, 11000, Serbia
| | - Teodora Barbalata
- "Nicolae Simionescu” Institute of Cellular Biology and Pathology, Bucharest, 050568, Romania
| | - Soumaya Ben-Aicha
- National Heart and Lung Institute, Imperial College London, London, W120NN, UK
| | - Fabiana Martino
- National Heart and Lung Institute, Imperial College London, London, W120NN, UK
| | - Laura Nicastro
- National Heart and Lung Institute, Imperial College London, London, W120NN, UK
| | - Antigone Lazou
- School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Dimitris Beis
- Developmental Biology, Clinical, Experimental Surgery and Translational Research Center, Biomedical Research Foundation of the Academy of Athens, Athens, 11527, Greece
| | - Fabio Martelli
- Laboratory of Molecular Cardiology, IRCCS Policlinico San Donato, Milan, 20097, Italy
| | - Miron Sopic
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, 11000, Serbia
| | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, London, W120NN, UK
| | - Dimitris Kardassis
- Laboratory of Biochemistry, Medical School, University of Crete, Heraklion, 71003, Greece
- Institute of Molecular Biology and Biotechnology, Foundation For Research & Technology Hellas (FORTH), Heraklion, 71003, Greece
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, 1445, Luxembourg
| | - EU-CardioRNA COST Action CA17129.
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, 1445, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, 4365, Luxembourg
- "Nicolae Simionescu” Institute of Cellular Biology and Pathology, Bucharest, 050568, Romania
- School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
- Developmental Biology, Clinical, Experimental Surgery and Translational Research Center, Biomedical Research Foundation of the Academy of Athens, Athens, 11527, Greece
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, 11000, Serbia
- National Heart and Lung Institute, Imperial College London, London, W120NN, UK
- Laboratory of Molecular Cardiology, IRCCS Policlinico San Donato, Milan, 20097, Italy
- Laboratory of Biochemistry, Medical School, University of Crete, Heraklion, 71003, Greece
- Institute of Molecular Biology and Biotechnology, Foundation For Research & Technology Hellas (FORTH), Heraklion, 71003, Greece
| |
Collapse
|
|
7
|
Schmied C, Nelson MS, Avilov S, Bakker GJ, Bertocchi C, Bischof J, Boehm U, Brocher J, Carvalho M, Chiritescu C, Christopher J, Cimini BA, Conde-Sousa E, Ebner M, Ecker R, Eliceiri K, Fernandez-Rodriguez J, Gaudreault N, Gelman L, Grunwald D, Gu T, Halidi N, Hammer M, Hartley M, Held M, Jug F, Kapoor V, Koksoy AA, Lacoste J, Dévédec SL, Guyader SL, Liu P, Martins GG, Mathur A, Miura K, Montero Llopis P, Nitschke R, North A, Parslow AC, Payne-Dwyer A, Plantard L, Ali R, Schroth-Diez B, Schütz L, Scott RT, Seitz A, Selchow O, Sharma VP, Spitaler M, Srinivasan S, Strambio-De-Castillia C, Taatjes D, Tischer C, Jambor HK. Community-developed checklists for publishing images and image analyses. ARXIV 2023:arXiv:2302.07005v2. [PMID: 36824427 PMCID: PMC9949169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However for scientists wishing to publish the obtained images and image analyses results, there are to date no unified guidelines. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here we present community-developed checklists for preparing light microscopy images and image analysis for publications. These checklists offer authors, readers, and publishers key recommendations for image formatting and annotation, color selection, data availability, and for reporting image analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby heighten the quality and explanatory power of microscopy data is in publications.
Collapse
Affiliation(s)
- Christopher Schmied
- Fondazione Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milano, Italy
- Present address: Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Michael S Nelson
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sergiy Avilov
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Gert-Jan Bakker
- Medical BioSciences department, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Cristina Bertocchi
- Laboratory for Molecular mechanics of cell adhesions, Pontificia Universidad Católica de Chile Santiago
- Osaka University, Graduate School of Engineering Science, Japan
| | - Johanna Bischof
- Euro-BioImaging ERIC, Bio-Hub, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Ulrike Boehm
- Carl Zeiss AG, Carl-Zeiss-Straße 22, 73447 Oberkochen, Germany
| | - Jan Brocher
- BioVoxxel, Scientific Image Processing and Analysis, Eugen-Roth-Strasse 8, 67071 Ludwigshafen, Germany
| | - Mariana Carvalho
- Nanophotonics and BioImaging Facility at INL, International Iberian Nanotechnology Laboratory, 4715-330, Portugal
| | | | | | - Beth A Cimini
- Imaging Platform, Broad Institute, Cambridge, MA 02142
| | - Eduardo Conde-Sousa
- i3S, Instituto de Investigação e Inovação Em Saúde and INEB, Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
| | - Michael Ebner
- Fondazione Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milano, Italy
| | - Rupert Ecker
- Translational Research Institute, Queensland University of Technology, 37 Kent Street, Woolloongabba, QLD 4102, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4059, Australia
- TissueGnostics GmbH, 1020 Vienna, Austria
| | - Kevin Eliceiri
- Department of Medical Physics and Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | | | - Laurent Gelman
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | | | - Nadia Halidi
- Advanced Light Microscopy Unit, Centre for Genomic Regulation, Barcelona, Spain
| | - Mathias Hammer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Matthew Hartley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Marie Held
- Centre for Cell Imaging, The University of Liverpool, UK
| | - Florian Jug
- Fondazione Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milano, Italy
| | - Varun Kapoor
- Department of AI research, Kapoor Labs, Paris, 75005, France
| | | | | | - Sylvia Le Dévédec
- Division of Drug Discovery and Safety, Cell Observatory, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | | | - Penghuan Liu
- Key Laboratory for Modern Measurement Technology and Instruments of Zhejiang Province, College of Optical and Electronic Technology, China Jiliang University, Hangzhou, China
| | - Gabriel G Martins
- Advanced Imaging Facility, Instituto Gulbenkian de Ciência, Oeiras 2780-156 - Portugal
| | - Aastha Mathur
- Euro-BioImaging ERIC, Bio-Hub, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Kota Miura
- Bioimage Analysis & Research, 69127 Heidelberg/Germany
| | | | - Roland Nitschke
- Life Imaging Center, Signalling Research Centres CIBSS and BIOSS, University of Freiburg, Germany
| | - Alison North
- Bio-Imaging Resource Center, The Rockefeller University, New York, NY USA
| | - Adam C Parslow
- Baker Institute Microscopy Platform, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia
| | - Alex Payne-Dwyer
- School of Physics, Engineering and Technology, University of York, Heslington, YO10 5DD, UK
| | - Laure Plantard
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Rizwan Ali
- King Abdullah International Medical Research Center (KAIMRC), Medical Research Core Facility and Platforms (MRCFP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11481, Saudi Arabia
| | - Britta Schroth-Diez
- Light Microscopy Facility, Max Planck Institute of Molecular Cell Biology and Genetics Dresden, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Lucas Schütz
- ariadne.ai (Germany) GmbH, 69115 Heidelberg, Germany
| | - Ryan T Scott
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Arne Seitz
- BioImaging & Optics Platform (BIOP), Ecole Polytechnique Fédérale de Lausanne (EPFL), Faculty of Life sciences (SV), CH-1015 Lausanne
| | - Olaf Selchow
- Microscopy & BioImaging Consulting, Image Processing & Large Data Handling, Tobias-Hoppe-Strassse 3, 07548 Gera, Germany
| | - Ved P Sharma
- Bio-Imaging Resource Center, The Rockefeller University, New York, NY USA
| | - Martin Spitaler
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Sathya Srinivasan
- Imaging and Morphology Support Core, Oregon National Primate Research Center - (ONPRC - OHSU West Campus), Beaverton, Oregon 97006, USA
| | | | - Douglas Taatjes
- Department of Pathology and Laboratory Medicine, Microscopy Imaging Center (RRID# SCR_018821), Center for Biomedical Shared Resources, University of Vermont, Burlington, VT 05405 USA
| | - Christian Tischer
- Centre for Bioimage Analysis, EMBL Heidelberg, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Helena Klara Jambor
- NCT-UCC, Medizinische Fakultät TU Dresden, Fetscherstrasse 105, 01307 Dresden/Germany
| |
Collapse
|
|
8
|
Clark E, Battistara M, Benton MA. A timer gene network is spatially regulated by the terminal system in the Drosophila embryo. eLife 2022; 11:e78902. [PMID: 36524728 PMCID: PMC10065802 DOI: 10.7554/elife.78902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
In insect embryos, anteroposterior patterning is coordinated by the sequential expression of the 'timer' genes caudal, Dichaete, and odd-paired, whose expression dynamics correlate with the mode of segmentation. In Drosophila, the timer genes are expressed broadly across much of the blastoderm, which segments simultaneously, but their expression is delayed in a small 'tail' region, just anterior to the hindgut, which segments during germband extension. Specification of the tail and the hindgut depends on the terminal gap gene tailless, but beyond this the regulation of the timer genes is poorly understood. We used a combination of multiplexed imaging, mutant analysis, and gene network modelling to resolve the regulation of the timer genes, identifying 11 new regulatory interactions and clarifying the mechanism of posterior terminal patterning. We propose that a dynamic Tailless expression gradient modulates the intrinsic dynamics of a timer gene cross-regulatory module, delineating the tail region and delaying its developmental maturation.
Collapse
Affiliation(s)
- Erik Clark
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Margherita Battistara
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Department of Physiology, Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
| | - Matthew A Benton
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Developmental Biology Unit, EMBLHeidelbergGermany
| |
Collapse
|
|
9
|
Valli J, Sanderson J. Super-Resolution Fluorescence Microscopy Methods for Assessing Mouse Biology. Curr Protoc 2021; 1:e224. [PMID: 34436832 DOI: 10.1002/cpz1.224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Super-resolution (diffraction unlimited) microscopy was developed 15 years ago; the developers were awarded the Nobel Prize in Chemistry in recognition of their work in 2014. Super-resolution microscopy is increasingly being applied to diverse scientific fields, from single molecules to cell organelles, viruses, bacteria, plants, and animals, especially the mammalian model organism Mus musculus. In this review, we explain how super-resolution microscopy, along with fluorescence microscopy from which it grew, has aided the renaissance of the light microscope. We cover experiment planning and specimen preparation and explain structured illumination microscopy, super-resolution radial fluctuations, stimulated emission depletion microscopy, single-molecule localization microscopy, and super-resolution imaging by pixel reassignment. The final section of this review discusses the strengths and weaknesses of each super-resolution technique and how to choose the best approach for your research. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.
Collapse
Affiliation(s)
- Jessica Valli
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Jeremy Sanderson
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| |
Collapse
|
|
10
|
Tidswell ORA, Benton MA, Akam M. The neuroblast timer gene nubbin exhibits functional redundancy with gap genes to regulate segment identity in Tribolium. Development 2021; 148:271199. [PMID: 34351412 PMCID: PMC8406537 DOI: 10.1242/dev.199719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/23/2021] [Indexed: 12/05/2022]
Abstract
The neuroblast timer genes hunchback, Krüppel, nubbin and castor are expressed in temporal sequence in neural stem cells, and in corresponding spatial sequence along the Drosophila blastoderm. As canonical gap genes, hunchback and Krüppel play a crucial role in insect segmentation, but the roles of nubbin and castor in this process remain ambiguous. We have investigated the expression and functions of nubbin and castor during segmentation in the beetle Tribolium. We show that Tc-hunchback, Tc-Krüppel, Tc-nubbin and Tc-castor are expressed sequentially in the segment addition zone, and that Tc-nubbin regulates segment identity redundantly with two previously described gap/gap-like genes, Tc-giant and Tc-knirps. Simultaneous knockdown of Tc-nubbin, Tc-giant and Tc-knirps results in the formation of ectopic legs on abdominal segments. This homeotic transformation is caused by loss of abdominal Hox gene expression, likely due to expanded Tc-Krüppel expression. Our findings support the theory that the neuroblast timer series was co-opted for use in insect segment patterning, and contribute to our growing understanding of the evolution and function of the gap gene network outside of Drosophila. Summary:nubbin and the gap genes knirps and giant redundantly repress Krüppel expression during segmentation. Simultaneous knockdown of all three genes causes ectopic Krüppel expression and loss of abdominal segment identity.
Collapse
Affiliation(s)
| | - Matthew A Benton
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Michael Akam
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| |
Collapse
|
|
11
|
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: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|