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Imreh G, Hu J, Le Guyader S. Improving light microscopy training routines with evidence-based education. J Microsc 2024; 294:295-307. [PMID: 37534621 DOI: 10.1111/jmi.13216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/04/2023]
Abstract
The low reproducibility of scientific data published in articles has recently become a cause of concern in many scientific fields. Data involving light microscopy is no exception. The low awareness of researchers of the technologies they use in their research has been identified as one of the main causes of the problem. Potential solutions have hinted at the need to improve technological and methodological education within research. Despite the pivotal role of microscopy core facilities in the education of researchers being well documented, facility staff (FS) often learn their trade on the job, without receiving themselves any structured education about the technology they teach others to use. Additionally, despite endorsing an important role at the highest level of education, most FS never receive any training in pedagogy, the field of research on teaching and learning methods. In this article, we argue that the low level of awareness that researchers have of microscopy stems from a knowledge gap formed between them and microscopy FS during training routines. On the one hand, FS consider that their teaching task is to explain what is needed to produce reliable data. On the other, despite understanding what is being taught, researchers fail to learn the most challenging aspects of microscopy, those involving their judgement and reasoning. We suggest that the misunderstanding between FS and researchers is due to FS not being educated in pedagogy and thus often confusing understanding and learning. To bridge this knowledge gap and improve the quality of the microscopy education available to researchers, we propose a paradigm shift where training staff at technological core facilities be acknowledged as full-fledged teachers and offered structured education not only in the technology they teach but also in pedagogy. We then suggest that training routines at facilities be upgraded to follow the principles of the Constructive Alignment pedagogical method. We give an example of how this can be applied to existing microscopy training routines. We also describe a model to define where the responsibility of FS in training researchers begins and ends. This involves a major structural change where university staff involved in teaching research technologies themselves receive appropriate education. For this to be achieved, we advocate that funding agencies, universities, microscopy and core facility organisations mobilise resources of time and funding. Such changes may involve funding the creation and development of 'Train-the-trainer' type of courses and giving incentives for FS to upgrade their technological and pedagogical knowledge, for example by including them in career paths. We believe that this paradigm shift is necessary to improve the level of microscopy education and ultimately the reproducibility of published data.
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Affiliation(s)
- Gabriela Imreh
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Jianjiang Hu
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Sylvie Le Guyader
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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2
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Liu Y, Koch JC, Arregui L, Oune A, Bodenstein S, Gutierrez-Wing MT, Tiersch TR. Exploring pathways toward open-hardware ecosystems to safeguard genetic resources for biomedical research communities using aquatic model species. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:278-290. [PMID: 38185943 PMCID: PMC11099901 DOI: 10.1002/jez.b.23234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 11/03/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024]
Abstract
Development of reliable germplasm repositories is critical for preservation of genetic resources of aquatic species, which are widely utilized to support biomedical innovation by providing a foundational source for naturally occurring variation and development of new variants through genetic manipulations. A significant barrier in repository development is the lack of cryopreservation capability and reproducibility across the research community, posing great risks of losing advances developed from billions of dollars of research investment. The emergence of open scientific hardware has fueled a new movement across biomedical research communities. With the increasing accessibility of consumer-level fabrication technologies, such as three-dimensional printers, open hardware devices can be custom designed, and design files distributed to community members for enhancing rigor, reproducibility, and standardization. The overall goal of this review is to explore pathways to create open-hardware ecosystems among the communities using aquatic model resources for biomedical research. To gain feedback and insights from community members, an interactive workshop focusing on open-hardware applications in germplasm repository development was held at the 2022 Aquatic Models for Human Disease Conference, Woods Hole, Massachusetts. This work integrates conceptual strategies with practical insights derived from workshop interactions using examples of germplasm repository development. These insights can be generalized for establishment of open-hardware ecosystems for a broad biomedical research community. The specific objectives were to: (1) introduce an open-hardware ecosystem concept to support biomedical research; (2) explore pathways toward open-hardware ecosystems through four major areas, and (3) identify opportunities and future directions.
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Affiliation(s)
- Yue Liu
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Jack C Koch
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Lucía Arregui
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Allyssa Oune
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Sarah Bodenstein
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Maria T Gutierrez-Wing
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Terrence R Tiersch
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
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Abrams B, Pengo T, Wee TL, Deagle RC, Vuillemin N, Callahan LM, Smith MA, Kubow KE, Girard AM, Rappoport JZ, Bayles CJ, Cameron LA, Cole R, Brown CM. Tissue-Like 3D Standard and Protocols for Microscope Quality Management. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:616-634. [PMID: 37749742 PMCID: PMC10617369 DOI: 10.1093/micmic/ozad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/30/2022] [Accepted: 01/24/2023] [Indexed: 09/27/2023]
Abstract
This article outlines a global study conducted by the Association of Biomedical Resource Facilities (ABRF) Light Microscopy Research Group (LMRG). The results present a novel 3D tissue-like biologically relevant standard sample that is affordable and straightforward to prepare. Detailed sample preparation, instrument-specific image acquisition protocols and image analysis methods are presented and made available to the community. The standard consists of sub-resolution and large well characterized relative intensity fluorescence microspheres embedded in a 120 µm thick 3D gel with a refractive index of 1.365. The standard allows the evaluation of several properties as a function of depth. These include the following: 1) microscope resolution with automated analysis of the point-spread function (PSF), 2) automated signal-to-noise ratio analysis, 3) calibration and correction of fluorescence intensity loss, and 4) quantitative relative intensity. Results demonstrate expected refractive index mismatch dependent losses in intensity and resolution with depth, but the relative intensities of different objects at similar depths are maintained. This is a robust standard showing reproducible results across laboratories, microscope manufacturers and objective lens types (e.g., magnification, immersion medium). Thus, these tools will be valuable for the global community to benchmark fluorescence microscopes and will contribute to improved scientific rigor and reproducibility.
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Affiliation(s)
- Benjamin Abrams
- Life Sciences Microscopy Center, 150 Sinsheimer Labs, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA, RRID:SCR_021135
| | - Thomas Pengo
- Informatics Institute, University of Minnesota Twin Cities, Cancer and Cardiovascular Research Building, 2231 6th St SE, Minneapolis, MN 55449, USA
| | - Tse-Luen Wee
- Advanced BioImaging Facility (ABIF), McGill University, 3649 Prom, Sir William Osler, Bellini Building, Room 137, Montreal, QC H3G 0B1, Canada, RRID:SCR_017697
- Department of Physiology, McGill University, Montreal, QC
- Current affiliation: St. Giles Foundation Advanced Microscopy Center, Cold Spring Harbor Laboratory, One Bungtown Rd., Cold Spring Harbor, NY, 11724, USA, RRID:SCR_023023
| | - Rebecca C. Deagle
- Advanced BioImaging Facility (ABIF), McGill University, 3649 Prom, Sir William Osler, Bellini Building, Room 137, Montreal, QC H3G 0B1, Canada, RRID:SCR_017697
- Department of Physiology, McGill University, Montreal, QC
| | - Nelly Vuillemin
- Advanced BioImaging Facility (ABIF), McGill University, 3649 Prom, Sir William Osler, Bellini Building, Room 137, Montreal, QC H3G 0B1, Canada, RRID:SCR_017697
- Department of Physiology, McGill University, Montreal, QC
| | - Linda M. Callahan
- Department of Neuroscience, Del Monte Institute for Neuroscience, Univ. Rochester Medical Center, Rochester, NY 14642, USA
| | - Megan A. Smith
- Advanced BioImaging Facility (ABIF), McGill University, 3649 Prom, Sir William Osler, Bellini Building, Room 137, Montreal, QC H3G 0B1, Canada, RRID:SCR_017697
| | - Kristopher E. Kubow
- Biology Department, James Madison University, Bioscience Building, 951 Carrier Drive, Harrisonburg, VA 22807, USA, RRID:SCR_021904
| | - Anne-Marie Girard
- Center for Genome Research and Biocomputing, Oregon State University, 1500 SW Jefferson Way Corvallis, OR 97331, USA
| | - Joshua Z. Rappoport
- Center for Advanced Microscopy and Nikon Imaging Center, Feinberg School of Medicine, Northwestern Medicine, Northwestern University, Chicago, IL, USA
- Current affiliation: Boston College, 140 Commonwealth Avenue, Chestnut Hill, Massachusetts, USA
| | - Carol J. Bayles
- Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Lisa A. Cameron
- Light Microscopy Core Facility, Duke University, 4215 French Family Science Center, 124 Science Drive, Durham, NC 27708, USA
| | - Richard Cole
- New York State Dept of Health/Wadsworth Center, Advanced Light Microscopy & Image Analysis Core Facility, 150 New Scotland Ave, Albany, NY 12208, USA, RRID:SCR_021104
| | - Claire M. Brown
- Advanced BioImaging Facility (ABIF), McGill University, 3649 Prom, Sir William Osler, Bellini Building, Room 137, Montreal, QC H3G 0B1, Canada, RRID:SCR_017697
- Department of Physiology, McGill University, Montreal, QC
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4
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Santos ACA, Camarena DEM, Roncoli Reigado G, Chambergo FS, Nunes VA, Trindade MA, Stuchi Maria-Engler S. Tissue Engineering Challenges for Cultivated Meat to Meet the Real Demand of a Global Market. Int J Mol Sci 2023; 24:ijms24076033. [PMID: 37047028 PMCID: PMC10094385 DOI: 10.3390/ijms24076033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 04/14/2023] Open
Abstract
Cultivated meat (CM) technology has the potential to disrupt the food industry-indeed, it is already an inevitable reality. This new technology is an alternative to solve the environmental, health and ethical issues associated with the demand for meat products. The global market longs for biotechnological improvements for the CM production chain. CM, also known as cultured, cell-based, lab-grown, in vitro or clean meat, is obtained through cellular agriculture, which is based on applying tissue engineering principles. In practice, it is first necessary to choose the best cell source and type, and then to furnish the necessary nutrients, growth factors and signalling molecules via cultivation media. This procedure occurs in a controlled environment that provides the surfaces necessary for anchor-dependent cells and offers microcarriers and scaffolds that favour the three-dimensional (3D) organisation of multiple cell types. In this review, we discuss relevant information to CM production, including the cultivation process, cell sources, medium requirements, the main obstacles to CM production (consumer acceptance, scalability, safety and reproducibility), the technological aspects of 3D models (biomaterials, microcarriers and scaffolds) and assembly methods (cell layering, spinning and 3D bioprinting). We also provide an outlook on the global CM market. Our review brings a broad overview of the CM field, providing an update for everyone interested in the topic, which is especially important because CM is a multidisciplinary technology.
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Affiliation(s)
- Andressa Cristina Antunes Santos
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Denisse Esther Mallaupoma Camarena
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Gustavo Roncoli Reigado
- Department of Biotechnology, School of Arts, Sciences and Humanities, University of São Paulo, São Paulo 03828-000, Brazil
| | - Felipe S Chambergo
- Department of Biotechnology, School of Arts, Sciences and Humanities, University of São Paulo, São Paulo 03828-000, Brazil
| | - Viviane Abreu Nunes
- Department of Biotechnology, School of Arts, Sciences and Humanities, University of São Paulo, São Paulo 03828-000, Brazil
| | - Marco Antonio Trindade
- Faculty of Animal Science and Food Engineering, University of São Paulo, Av. Duque de Caxias Norte, Pirassununga 13635-900, Brazil
| | - Silvya Stuchi Maria-Engler
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
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5
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LaLonde-Paul D, Mouttham L, Promislow DEL, Castelhano MG. Banking on a new understanding: translational opportunities from veterinary biobanks. GeroScience 2023:10.1007/s11357-023-00763-z. [PMID: 36890420 PMCID: PMC10400517 DOI: 10.1007/s11357-023-00763-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 01/03/2023] [Indexed: 03/10/2023] Open
Abstract
Current advances in geroscience are due in part to the discovery of biomarkers with high predictive ability in short-lived laboratory animals such as flies and mice. These model species, however, do not always adequately reflect human physiology and disease, highlighting the need for a more comprehensive and relevant model of human aging. Domestic dogs offer a solution to this obstacle, as they share many aspects not only of the physiological and pathological trajectories of their human counterpart, but also of their environment. Furthermore, they age at a considerably faster rate. Studying aging in the companion dog provides an opportunity to better understand the biological and environmental determinants of healthy lifespan in our pets, and to translate those findings to human aging. Biobanking, the systematic collection, processing, storage, and distribution of biological material and associated data has contributed to basic, clinical, and translational research by streamlining the management of high-quality biospecimens for biomarker discovery and validation. In this review, we discuss how veterinary biobanks can support research on aging, particularly when integrated into large-scale longitudinal studies. As an example of this concept, we introduce the Dog Aging Project Biobank.
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Affiliation(s)
- D LaLonde-Paul
- Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - L Mouttham
- Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | | | - D E L Promislow
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Department of Biology, University of Washington, Seattle, WA, USA
| | - M G Castelhano
- Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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6
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Ott AW, Sol-Church K, Deshpande GM, Knudtson KL, Meyn SM, Mische SM, Taatjes DJ, Sturges MR, Gregory CW. Rigor, Reproducibility, and Transparency in Shared Research Resources: Follow-Up Survey and Recommendations for Improvements. J Biomol Tech 2022; 33:3fc1f5fe.fa789303. [PMID: 36910580 PMCID: PMC10001929 DOI: 10.7171/3fc1f5fe.fa789303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Rigor, reproducibility, and transparency (RR&T) are essential components of all scientific pursuits. Shared research resources, also known as core facilities, are on the frontlines of ensuring robust RR&T practices. The Association of Biomolecular Resource Facilities Committee on Core Rigor and Reproducibility conducted a follow-up survey 4 years after the initial 2017 survey to determine if core facilities have seen a positive impact of new RR&T initiatives (including guidance from the National Institutes of Health, new scientific journal requirements on transparency and data provenance, and educational tools from professional organizations). While there were fewer participants in the most recent survey, the respondents' opinions on the role of core facilities and level of best practices adoption remained the same. Overall, the respondents agreed that procedures should be implemented by core facilities to ensure scientific RR&T. They also indicated that there is a strong correlation between institutions that emphasize RR&T and core customers using this expertise in grant applications and publications. The survey also assessed the impact of the COVID-19 pandemic on core operations and RR&T. The answers to these pandemic-related questions revealed that many of the strategies aimed at increasing efficiencies are also best practices related to RR&T, including the development of standard operating procedures, supply chain management, and cross training. Given the consistent and compelling awareness of the importance of RR&T expressed by core directors in 2017 and 2021 contrasted with the lack of apparent improvements over this time period, the authors recommend an adoption of RR&T statements by all core laboratories. Adhering to the RR&T guidelines will result in more efficient training, better compliance, and improved experimental approaches empowering cores to become "rigor champions."
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Affiliation(s)
- Andrew W Ott
- Northwestern University EvanstonIllinois60208 USA
| | | | | | | | - Susan M Meyn
- Vanderbilt University Medical Center NashvilleTennessee37232 USA
| | - Sheenah M Mische
- New York University Langone Medical Center New YorkNew York10016 USA
| | - Douglas J Taatjes
- Larner College of Medicine University of Vermont BurlingtonVermont05405 USA
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7
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Schmidt C, Hanne J, Moore J, Meesters C, Ferrando-May E, Weidtkamp-Peters S. Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey. F1000Res 2022; 11:638. [PMID: 36405555 PMCID: PMC9641114 DOI: 10.12688/f1000research.121714.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/16/2022] [Indexed: 01/13/2023] Open
Abstract
Background: Knowing the needs of the bioimaging community with respect to research data management (RDM) is essential for identifying measures that enable adoption of the FAIR (findable, accessible, interoperable, reusable) principles for microscopy and bioimage analysis data across disciplines. As an initiative within Germany's National Research Data Infrastructure, we conducted this community survey in summer 2021 to assess the state of the art of bioimaging RDM and the community needs. Methods: An online survey was conducted with a mixed question-type design. We created a questionnaire tailored to relevant topics of the bioimaging community, including specific questions on bioimaging methods and bioimage analysis, as well as more general questions on RDM principles and tools. 203 survey entries were included in the analysis covering the perspectives from various life and biomedical science disciplines and from participants at different career levels. Results: The results highlight the importance and value of bioimaging RDM and data sharing. However, the practical implementation of FAIR practices is impeded by technical hurdles, lack of knowledge, and insecurity about the legal aspects of data sharing. The survey participants request metadata guidelines and annotation tools and endorse the usage of image data management platforms. At present, OMERO (Open Microscopy Environment Remote Objects) is the best known and most widely used platform. Most respondents rely on image processing and analysis, which they regard as the most time-consuming step of the bioimage data workflow. While knowledge about and implementation of electronic lab notebooks and data management plans is limited, respondents acknowledge their potential value for data handling and publication. Conclusion: The bioimaging community acknowledges and endorses the value of RDM and data sharing. Still, there is a need for information, guidance, and standardization to foster the adoption of FAIR data handling. This survey may help inspiring targeted measures to close this gap.
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Affiliation(s)
- Christian Schmidt
- Enabling Technology, German Cancer Research Center, Heidelberg, Baden-Württemberg, Germany,Bioimaging Center, University of Konstanz, Konstanz, Germany,
| | - Janina Hanne
- German BioImaging - Society for Microscopy and Image Analysis e.V., Konstanz, Germany,
| | - Josh Moore
- German BioImaging - Society for Microscopy and Image Analysis e.V., Konstanz, Germany,Open Microscopy Environment Consortium, University of Dundee, Dundee, UK
| | - Christian Meesters
- High Performance Computing, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Elisa Ferrando-May
- Enabling Technology, German Cancer Research Center, Heidelberg, Baden-Württemberg, Germany,Bioimaging Center, University of Konstanz, Konstanz, Germany,German BioImaging - Society for Microscopy and Image Analysis e.V., Konstanz, Germany
| | - Stefanie Weidtkamp-Peters
- German BioImaging - Society for Microscopy and Image Analysis e.V., Konstanz, Germany,Center for Advanced Imaging, Heinrich Heine University Dusseldorf, Dusseldorf, Germany
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8
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Taatjes DJ, Ghule PN, Bouffard NA, Lee K, DeLance NM, Evans MF, Weaver DL, Deakin N, Carr FE, Sprague BL, Stein GS, Stein JL. The Shared Core Resource as a Partner in Innovative Scientific Research: Illustration from an Academic Microscopy Imaging Center. J Biomol Tech 2022; 33:3fc1f5fe.2507f36c. [PMID: 35836997 PMCID: PMC9258914 DOI: 10.7171/3fc1f5fe.2507f36c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Core facilities have a ubiquitous and increasingly valuable presence at research institutions. Although many shared cores were originally created to provide routine services and access to complex and expensive instrumentation for the research community, they are frequently called upon by investigators to design protocols and procedures to help answer complex research questions. For instance, shared microscopy resources are evolving from providing access to and training on complex imaging instruments to developing detailed innovative protocols and experimental strategies, including sample preparation techniques, staining, complex imaging parameters, and high-level image analyses. These approaches require close intellectual collaboration between core staff and research investigators to formulate and coordinate plans for protocol development suited to the research question. Herein, we provide an example of such coordinated collaboration between a shared microscopy facility and a team of scientists and clinician-investigators to approach a complex multiprobe immunostaining, imaging, and image analysis project investigating the tumor microenvironment from human breast cancer samples. Our hope is that this example may be used to convey to institute administrators the critical importance of the intellectual contributions of the scientific staff in core facilities to research endeavors.
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Affiliation(s)
- Douglas J. Taatjes
- Department of Pathology and Laboratory Medicine,
Microscopy Imaging Center, and University of Vermont Cancer Center, University of VermontBurlington, VT 05405USA
| | - Prachi N. Ghule
- University of Vermont Cancer Center and Department of Biochemistry,
University of VermontBurlington,
VT 05405USA
| | - Nicole A. Bouffard
- Department of Pathology and Laboratory Medicine and Microscopy Imaging Center,
University of VermontBurlington,
VT 05405USA
| | - Kyra Lee
- Department of Biochemistry,
University of VermontBurlington,
VT 05405USA
| | - Nicole M. DeLance
- Department of Pathology and Laboratory Medicine and Microscopy Imaging Center,
University of VermontBurlington,
VT 05405USA
| | - Mark F. Evans
- Department of Pathology and Laboratory Medicine and University of Vermont Cancer Center,
University of VermontBurlington,
VT 05405USA
| | - Donald L. Weaver
- Department of Pathology and Laboratory Medicine and University of Vermont Cancer Center,
University of VermontBurlington,
VT 05405USA
| | | | - Frances E. Carr
- University of Vermont Cancer Center and Department of Pharmacology,
University of VermontBurlington,
VT 05405USA
| | - Brian L. Sprague
- University of Vermont Cancer Center and Department of Surgery,
Larner College of Medicine, University of VermontBurlington,
VT 05405USA
| | - Gary S. Stein
- University of Vermont Cancer Center and Department of Biochemistry,
University of VermontBurlington,
VT 05405USA
| | - Janet L. Stein
- University of Vermont Cancer Center and Department of Biochemistry,
University of VermontBurlington,
VT 05405USA
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9
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Restivo L, Gerlach B, Tsoory M, Bikovski L, Badurek S, Pitzer C, Kos-Braun IC, Mausset-Bonnefont ALM, Ward J, Schunn M, Noldus LP, Bespalov A, Voikar V. Towards best practices in research: Role of academic core facilities. EMBO Rep 2021; 22:e53824. [PMID: 34734666 PMCID: PMC8647140 DOI: 10.15252/embr.202153824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/24/2021] [Accepted: 10/18/2021] [Indexed: 11/09/2022] Open
Affiliation(s)
- Leonardo Restivo
- Neuro-BAU, Department of Fundamental Neuroscience, Faculty of Biology & Medicine, University of Lausanne, Lausanne, Switzerland
| | | | - Michael Tsoory
- Behavioral and Physiological Phenotyping Unit, Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Lior Bikovski
- The Myers Neuro-Behavioral Core Facility, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,School of Behavioral Sciences, Netanya Academic College, Netanya, Israel
| | - Sylvia Badurek
- Preclinical Phenotyping Facility at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Vienna, Austria
| | - Claudia Pitzer
- Interdisciplinary Neurobehavioral Core, University of Heidelberg, Heidelberg, Germany
| | - Isabelle C Kos-Braun
- Interdisciplinary Neurobehavioral Core, University of Heidelberg, Heidelberg, Germany
| | | | | | - Michael Schunn
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Lucas Pjj Noldus
- Noldus Information Technology BV, Wageningen, The Netherlands.,Department of Biophysics, Radboud University, Nijmegen, The Netherlands
| | | | - Vootele Voikar
- Neuroscience Center and Laboratory Animal Center, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
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10
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Gregory CW. Building a Quality Management System in a Core Facility: A Genomics Core Case Study. J Biomol Tech 2021; 31:57-65. [PMID: 32655325 DOI: 10.7171/jbt.20-3102-004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Core facilities are key resources supporting the academic research enterprise, providing access to innovative and essential technologies and expertise. Given the constraints placed on core facilities as recharge centers and the ever-changing research environment, an important competitive differentiator that can support rigorous and reproducible approaches in core labs is the implementation of a quality management system (QMS). This paper describes a systematic approach to building a QMS in a genomics core facility at the University of North Carolina School of Medicine. This model is based on principles of the International Organization for Standardization 9001 system with initiatives focused on process mapping, training (communication, customer service, performance management, development of standard operating procedures, and quality audits), root cause analysis, visual control boards, mock quality audits, and continuous improvement through metrics tracking and "voice of the customer" exercises. The goal of this paper is to share practical step-by-step recommendations and outcomes of this core facility QMS that are generally applicable to academic core facilities, regardless of technical focus. Application of these good laboratory practice principles will foster "competitiveness through compliance" and promote outstanding interdisciplinary research between academic cores and their nonacademic pharmaceutical and federal research partners. Additionally, implementation of the QMS qualified this core to apply for federally funded contracts, thereby diversifying its types of projects and sources of revenue.
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Affiliation(s)
- Christopher W Gregory
- Department of Genetics and Office of Research Technologies, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
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11
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Samuel S, König-Ries B. Understanding experiments and research practices for reproducibility: an exploratory study. PeerJ 2021; 9:e11140. [PMID: 33976964 PMCID: PMC8067906 DOI: 10.7717/peerj.11140] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 03/01/2021] [Indexed: 11/20/2022] Open
Abstract
Scientific experiments and research practices vary across disciplines. The research practices followed by scientists in each domain play an essential role in the understandability and reproducibility of results. The "Reproducibility Crisis", where researchers find difficulty in reproducing published results, is currently faced by several disciplines. To understand the underlying problem in the context of the reproducibility crisis, it is important to first know the different research practices followed in their domain and the factors that hinder reproducibility. We performed an exploratory study by conducting a survey addressed to researchers representing a range of disciplines to understand scientific experiments and research practices for reproducibility. The survey findings identify a reproducibility crisis and a strong need for sharing data, code, methods, steps, and negative and positive results. Insufficient metadata, lack of publicly available data, and incomplete information in study methods are considered to be the main reasons for poor reproducibility. The survey results also address a wide number of research questions on the reproducibility of scientific results. Based on the results of our explorative study and supported by the existing published literature, we offer general recommendations that could help the scientific community to understand, reproduce, and reuse experimental data and results in the research data lifecycle.
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Affiliation(s)
- Sheeba Samuel
- Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena, Jena, Thuringia, Germany
- Michael Stifel Center Jena, Jena, Thuringia, Germany
| | - Birgitta König-Ries
- Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena, Jena, Thuringia, Germany
- Michael Stifel Center Jena, Jena, Thuringia, Germany
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12
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Kos-Braun IC, Gerlach B, Pitzer C. A survey of research quality in core facilities. eLife 2020; 9:e62212. [PMID: 33241998 PMCID: PMC7714392 DOI: 10.7554/elife.62212] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/25/2020] [Indexed: 11/17/2022] Open
Abstract
Core facilities are an effective way of making expensive experimental equipment available to a large number of researchers, and are thus well placed to contribute to efforts to promote good research practices. Here we report the results of a survey that asked core facilities in Europe about their approaches to the promotion of good research practices, and about their interactions with users from the first contact to the publication of the results. Based on 253 responses we identified four ways that good research practices could be encouraged: (i) motivating users to follow the advice and procedures for best research practice; (ii) providing clear guidance on data-management practices; (iii) improving communication along the whole research process; and (iv) clearly defining the responsibilities of each party.
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Affiliation(s)
| | | | - Claudia Pitzer
- Interdisciplinary Neurobehavioral Core, Heidelberg UniversityHeidelbergGermany
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13
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The ABCs of reproducibility: effecting attitudes, behaviors and change to realize reproducibility. Biotechniques 2020; 69:359-361. [DOI: 10.2144/btn-2020-0082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
New tools and increased awareness are yet to enact meaningful changes in reproducibility. Tristan Free investigates why and explores promising initiatives.
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14
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Mische SM, Fisher NC, Meyn SM, Sol-Church K, Hegstad-Davies RL, Weis-Garcia F, Adams M, Ashton JM, Delventhal KM, Dragon JA, Holmes L, Jagtap P, Kubow KE, Mason CE, Palmblad M, Searle BC, Turck CW, Knudtson KL. A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups. J Biomol Tech 2020; 31:11-26. [PMID: 31969795 PMCID: PMC6959150 DOI: 10.7171/jbt.20-3101-003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Shared research resource facilities, also known as core laboratories (Cores), are responsible for generating a significant and growing portion of the research data in academic biomedical research institutions. Cores represent a central repository for institutional knowledge management, with deep expertise in the strengths and limitations of technology and its applications. They inherently support transparency and scientific reproducibility by protecting against cognitive bias in research design and data analysis, and they have institutional responsibility for the conduct of research (research ethics, regulatory compliance, and financial accountability) performed in their Cores. The Association of Biomolecular Resource Facilities (ABRF) is a FASEB-member scientific society whose members are scientists and administrators that manage or support Cores. The ABRF Research Groups (RGs), representing expertise for an array of cutting-edge and established technology platforms, perform multicenter research studies to determine and communicate best practices and community-based standards. This review provides a summary of the contributions of the ABRF RGs to promote scientific rigor and reproducibility in Cores from the published literature, ABRF meetings, and ABRF RGs communications.
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Affiliation(s)
- Sheenah M. Mische
- New York University (NYU) Langone Medical Center, New
York, New York 10016, USA
| | - Nancy C. Fisher
- University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599, USA
| | - Susan M. Meyn
- Vanderbilt University Medical Center, Nashville,
Tennessee 37212, USA
| | - Katia Sol-Church
- University of Virginia School of Medicine,
Charlottesville, Virginia 22908, USA
| | | | | | - Marie Adams
- Van Andel Institute, Grand Rapids, Michigan 49503,
USA
| | - John M. Ashton
- University of Rochester Medical Center, West
Henrietta, New York 14642, USA
| | - Kym M. Delventhal
- Stowers Institute for Medical Research, Kansas City,
Missouri 64110, USA
| | | | - Laura Holmes
- Stowers Institute for Medical Research, Kansas City,
Missouri 64110, USA
| | - Pratik Jagtap
- University of Minnesota, Minneapolis, Minnesota
55455, USA
| | | | | | - Magnus Palmblad
- Leiden University Medical Center, Leiden 2333, The
Netherlands
| | - Brian C. Searle
- Institute for Systems Biology, Seattle, Washington
98109, USA
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