1
|
Blatch-Jones AJ, Lakin K, Thomas S. A scoping review on what constitutes a good research culture. F1000Res 2024; 13:324. [PMID: 38826614 PMCID: PMC11140362 DOI: 10.12688/f1000research.147599.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/18/2024] [Indexed: 06/04/2024] Open
Abstract
Background The crisis in research culture is well documented, covering issues such as a tendency for quantity over quality, unhealthy competitive environments, and assessment based on publications, journal prestige and funding. In response, research institutions need to assess their own practices to promote and advocate for change in the current research ecosystem. The purpose of the scoping review was to explore ' What does the evidence say about the 'problem' with 'poor' research culture, what are the benefits of 'good' research culture, and what does 'good' look like?' Aims To examine the peer-reviewed and grey literature to explore the interplay between research culture, open research, career paths, recognition and rewards, and equality, diversity, and inclusion, as part of a larger programme of activity for a research institution. Methods A scoping review was undertaken. Six databases were searched along with grey literature. Eligible literature had relevance to academic research institutions, addressed research culture, and were published between January 2017 to May 2022. Evidence was mapped and themed to specific categories. The search strategy, screening and analysis took place between April-May 2022. Results 1666 titles and abstracts, and 924 full text articles were assessed for eligibility. Of these, 253 articles met the eligibility criteria for inclusion. A purposive sampling of relevant websites was drawn from to complement the review, resulting in 102 records included in the review. Key areas for consideration were identified across the four themes of job security, wellbeing and equality of opportunity, teamwork and interdisciplinary, and research quality and accountability. Conclusions There are opportunities for research institutions to improve their own practice, however institutional solutions cannot act in isolation. Research institutions and research funders need to work together to build a more sustainable and inclusive research culture that is diverse in nature and supports individuals' well-being, career progression and performance.
Collapse
Affiliation(s)
- Amanda Jane Blatch-Jones
- School of Healthcare Enterprise and Innovation, University of Southampton, Southampton, England, SO16 7NS, UK
| | - Kay Lakin
- Hatch, School of Healthcare Enterprise and Innovation, University of Southampton, Southampton, England, SO16 7NS, UK
| | - Sarah Thomas
- Hatch, School of Healthcare Enterprise and Innovation, University of Southampton, Southampton, England, SO16 7NS, UK
| |
Collapse
|
2
|
Uszkoreit J, Palmblad M, Schwämmle V. Tackling reproducibility: lessons for the proteomics community. Expert Rev Proteomics 2024; 21:9-11. [PMID: 38362700 DOI: 10.1080/14789450.2024.2320166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/03/2024] [Indexed: 02/17/2024]
Affiliation(s)
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
3
|
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: 2] [Impact Index Per Article: 2.0] [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.
Collapse
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
| |
Collapse
|
4
|
Chiriboga L, Callis GM, Wang Y, Chlipala E. Guide for collecting and reporting metadata on protocol variables and parameters from slide-based histotechnology assays to enhance reproducibility. J Histotechnol 2022; 45:132-147. [DOI: 10.1080/01478885.2022.2134022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Luis Chiriboga
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- NYULH Center for Biospecimen Research and Development, New York, NY, USA
| | | | - Yongfu Wang
- Stowers Institute for Medical Research, Kansas, MO, USA
| | | |
Collapse
|
5
|
Colomé N, Abian J, Aloria K, Arizmendi JM, Barceló-Batllori S, Braga-Lagache S, Burlet-Schiltz O, Carrascal M, Casal JI, Chicano-Gálvez E, Chiva C, Clemente LF, Elortza F, Estanyol JM, Fernandez-Irigoyen J, Fernández-Puente P, Fidalgo MJ, Froment C, Fuentes M, Fuentes-Almagro C, Gay M, Hainard A, Heller M, Hernández ML, Ibarrola N, Iloro I, Kieselbach T, Lario A, Locard-Paulet M, Marina-Ramírez A, Martín L, Morato-López E, Muñoz J, Navajas R, Odena MA, Odriozola L, de Oliveira E, Paradela A, Pasquarello C, de Los Rios V, Ruiz-Romero C, Sabidó E, Sánchez Del Pino M, Sancho J, Santamaría E, Schaeffer-Reiss C, Schneider J, de la Torre C, Valero ML, Vilaseca M, Wu S, Wu L, Ximénez de Embún P, Canals F, Corrales FJ. Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis. J Proteomics 2022; 251:104409. [PMID: 34758407 DOI: 10.1016/j.jprot.2021.104409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/12/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022]
Abstract
Global analysis of protein phosphorylation by mass spectrometry proteomic techniques has emerged in the last decades as a powerful tool in biological and biomedical research. However, there are several factors that make the global study of the phosphoproteome more challenging than measuring non-modified proteins. The low stoichiometry of the phosphorylated species and the need to retrieve residue specific information require particular attention on sample preparation, data acquisition and processing to ensure reproducibility, qualitative and quantitative robustness and ample phosphoproteome coverage in phosphoproteomic workflows. Aiming to investigate the effect of different variables in the performance of proteome wide phosphoprotein analysis protocols, ProteoRed-ISCIII and EuPA launched the Proteomics Multicentric Experiment 11 (PME11). A reference sample consisting of a yeast protein extract spiked in with different amounts of a phosphomix standard (Sigma/Merck) was distributed to 31 laboratories around the globe. Thirty-six datasets from 23 laboratories were analyzed. Our results indicate the suitability of the PME11 reference sample to benchmark and optimize phosphoproteomics strategies, weighing the influence of different factors, as well as to rank intra and inter laboratory performance.
Collapse
Affiliation(s)
- Núria Colomé
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain
| | - Joaquín Abian
- ProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, 08036 Barcelona, Spain
| | - Kerman Aloria
- ProteoRed-ISCIII, Proteomics Core Facility-SGIKER, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Jesús M Arizmendi
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | | | - Sophie Braga-Lagache
- Department for BioMedical Research (DBMR), Proteomics and Mass Spectrometry Core Facility, University of Bern, CH-3010 Bern, Switzerland
| | - Odile Burlet-Schiltz
- Proteomics and Mass Spectrometry of Biomolecules, Proteomics Infrastructure of Toulouse, Proteomics French Infrastructure, ProFI. Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France
| | - Montse Carrascal
- ProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, 08036 Barcelona, Spain
| | - J Ignacio Casal
- ProteoRed-ISCIII, Centro de Investigaciones Biológicas-CSIC, Madrid 28040, Spain
| | - Eduard Chicano-Gálvez
- ProteoRed-ISCIII, Proteomics Unit, IMIBIC/UCO/HURS, IMIBIC Building Fl.3, 14004 Córdoba, Spain
| | - Cristina Chiva
- Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; ProteoRed ISCIII, Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Felix Elortza
- ProteoRed-ISCIII, CIC bioGUNE, Proteomics Platform, Basque Research & Technology Alliance (BRTA), CIBERehd,Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Josep M Estanyol
- ProteoRed-ISCIII, Scientific and Technological Centers (CCiTUB), University of Barcelona, 08036 Barcelona, Spain
| | - Joaquín Fernandez-Irigoyen
- Proteored-ISCIII. Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain
| | - Patricia Fernández-Puente
- Grupo de Investigación de Reumatología (GIR), Agrupación CICA-INIBIC, Universidad de A Coruña, A Coruña, Spain
| | - María José Fidalgo
- ProteoRed-ISCIII, Scientific and Technological Centers (CCiTUB), University of Barcelona, 08036 Barcelona, Spain
| | - Carine Froment
- Proteomics and Mass Spectrometry of Biomolecules, Proteomics Infrastructure of Toulouse, Proteomics French Infrastructure, ProFI. Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Proteomics Unit, CIBERONC, Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Universidad de Salamanca, Spain
| | - Carlos Fuentes-Almagro
- Proteomics Unit, SCAI, University of Córdoba, Ramón y Cajal Building, Rabanales Campus, 14071, Córdoba, Spain
| | - Marina Gay
- ProteoRed-ISCIII, Institute for Research in Biomedicine (IRB Barcelona), BIST (The Barcelona Institute of Science and Technology), Baldiri i Reixac 10, 08028 Barcelona, Spain
| | | | - Manfred Heller
- Department for BioMedical Research (DBMR), Proteomics and Mass Spectrometry Core Facility, University of Bern, CH-3010 Bern, Switzerland
| | | | - Nieves Ibarrola
- ProteoRed-ISCIII, Proteomics Unit. Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Universidad de Salamanca-CSIC, Salamanca, Spain
| | - Ibon Iloro
- ProteoRed-ISCIII, CIC bioGUNE, Proteomics Platform, Basque Research & Technology Alliance (BRTA), CIBERehd,Bizkaia Science and Technology Park, 48160 Derio, Spain
| | | | | | - Marie Locard-Paulet
- Proteomics and Mass Spectrometry of Biomolecules, Proteomics Infrastructure of Toulouse, Proteomics French Infrastructure, ProFI. Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France
| | | | - Luna Martín
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain
| | | | - Javier Muñoz
- ProteoRed-ISCIII, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Rosana Navajas
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain
| | - M Antonia Odena
- ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, 08028, Barcelona, Spain
| | - Leticia Odriozola
- ProteoRed-ISCIII, CIMA, University of Navarra, 31008, Pamplona, Spain
| | - Eliandre de Oliveira
- ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, 08028, Barcelona, Spain
| | - Alberto Paradela
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain
| | | | - Vivian de Los Rios
- ProteoRed-ISCIII, Centro de Investigaciones Biológicas-CSIC, Madrid 28040, Spain
| | - Cristina Ruiz-Romero
- Grupo de Investigación de Reumatología (GIR) - ProteoRed-ISCIII, Unidad de Proteómica, INIBIC-Complejo Hospitalario Universitario de A Coruña, SERGAS, A Coruña, Spain
| | - Eduard Sabidó
- Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; ProteoRed ISCIII, Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Manuel Sánchez Del Pino
- Biotechnology and Biomedicine Interdisciplinary Research Unit (ERI BIOTECMED), University of Valencia, 46100 Burjassot, Spain
| | - Jaime Sancho
- ProteoRed-ISCIII, IPBLN -CSIC, 18016 Granada, Spain
| | - Enrique Santamaría
- Proteored-ISCIII. Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
| | - Justine Schneider
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
| | - Carolina de la Torre
- ProteoRed-ISCIII, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - M Luz Valero
- ProteoRed-ISCIII, Proteomics Unit, Central Service for Experimental Research (SCSIE), University of Valencia, 46100, Burjassot, Spain
| | - Marta Vilaseca
- ProteoRed-ISCIII, Institute for Research in Biomedicine (IRB Barcelona), BIST (The Barcelona Institute of Science and Technology), Baldiri i Reixac 10, 08028 Barcelona, Spain
| | - Shuai Wu
- Agilent Technologies, Inc., Santa Clara, CA 95051, USA
| | - Linfeng Wu
- Agilent Technologies, Inc., Santa Clara, CA 95051, USA
| | | | - Francesc Canals
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain.
| | - Fernando J Corrales
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain; ProteoRed-ISCIII, CIMA, University of Navarra, 31008, Pamplona, Spain.
| | -
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain; ProteoRed-ISCIII-PRB3, Spanish Proteomics Networked Platform, Centro Nacional de Biotecnología (CSIC), 28049, Madrid, Spain
| | -
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain; European Proteomics Association, Standardization Initiative, , Centro Nacional de Biotecnología (CSIC), 28049, Madrid, Spain
| |
Collapse
|
6
|
Indrayan A, Vishwakarma G, Malhotra RK, Gupta P, Sachdev HPS, Karande S, Asthana S, Labani S. The development of QERM scoring system for comprehensive assessment of the Quality of Empirical Research in Medicine - Part 1. J Postgrad Med 2022; 68:221-230. [PMID: 36348606 PMCID: PMC9841535 DOI: 10.4103/jpgm.jpgm_460_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Purpose Whereas a large number of features are mentioned to connote the quality of medical research, no tool is available to comprehensively measure it objectively across different types of studies. Also, all the available tools are for reporting, and none includes quality of the inputs and the process of research. The present paper is aimed to initiate a discussion on the need to develop such a comprehensive scoring system (in the first place), to show that it is feasible, and to describe the process of developing a credible system. Method An expert group comprising researchers, reviewers, and editors of medical journals extensively reviewed the literature on the quality of medical research and held detailed discussions to parse quality at all stages of medical research into specific domains and items that can be assigned scores on the pattern of quality-of-life score. Results Besides identifying the domains of the quality of medical research, a comprehensive tool for scoring emerged that can be possibly used to objectively measure the quality of empirical research comprising surveys, trials, and observational studies. Thus, this can be used as a tool to assess Quality of Empirical Research in Medicine (QERM). The expert group confirmed its face and content validity. The tool can be used by the researchers for self-assessment and improvement before submission of a paper for publication, and the reviewers and editors can use this for assessing the submissions. Published papers can also be rated such as those included in a meta-analysis. Conclusion It is feasible to devise a comprehensive scoring system comprising domains and items for assessing the quality of medical research end-to-end from choosing a problem to publication. The proposed scoring system needs to be reviewed by the researchers and needs to be validated.
Collapse
Affiliation(s)
| | - A Indrayan
- Clinical Research, Max Healthcare, New Delhi, India,Address for correspondence: Dr. Indrayan A, E-mail:
| | - G Vishwakarma
- Biostatistics, Indian Spinal Injuries Centre, New Delhi, India
| | - RK Malhotra
- Surgical Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - P Gupta
- Pediatrics, University College of Medical Sciences, Delhi, India
| | - HPS Sachdev
- Pediatrics and Clinical Epidemiology, Sitaram Bhartia Institute of Sciences and Research, New Delhi, India
| | - S Karande
- Pediatrics, Seth G. S. Medical College and KEM Hospital, Mumbai, Maharashtra, India
| | - S Asthana
- Epidemiology and Biostatistics, National Institute of Cancer Prevention and Research (Indian Council of Medical Research), Noida, Uttar Pradesh, India
| | - S Labani
- Epidemiology and Biostatistics, National Institute of Cancer Prevention and Research (Indian Council of Medical Research), Noida, Uttar Pradesh, India
| |
Collapse
|
7
|
Bae MJ, Lee YM, Choi YS, Lee E, Le MT, Duc Nguyen TH, Lee D, Cho J, Han HS, Park NJY, Chong GO. Simple Electric Device to Isolate Nucleic Acids from Whole Blood Optimized for Point of Care Testing of Brain Damage. Curr Neurovasc Res 2022; 19:333-343. [PMID: 36056832 PMCID: PMC10009893 DOI: 10.2174/1567202619666220903105805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/02/2022] [Accepted: 08/07/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Detection or monitoring of brain damage is a clinically crucial issue. Nucleic acids in the whole blood can be used as biomarkers for brain injury. Polymerase chain reaction (PCR) which is one of the most commonly used molecular diagnostic assays requires isolated nucleic acids to initiate amplification. Currently used nucleic acid isolation procedures are complicated and require laboratory equipments. OBJECTIVE In this study, we tried to develop a simple and convenient method to isolate nucleic acids from the whole blood sample using a tiny battery-powered electric device. The quality of the isolated nucleic acids should be suitable for PCR assay without extra preparation. METHODS A plastic device with separation chamber was designed and printed with a 3D printer. Two platinum electrodes were placed on both sides and a battery was used to supply the electricity. To choose the optimal nucleic acid isolation condition, diverse lysis buffers and separation buffers were evaluated, and the duration and voltage of the electricity were tested. Western blot analysis and PCR assay were used to determine the quality of the separated nucleic acids. RESULTS 2ul of whole blood was applied to the cathode side of the separation chamber containing 78 ul of normal saline. When the electricity at 5 V was applied for 5 min, nucleic acids were separated from segment 1 to 3 of the separation chamber. The concentration of nucleic acids peaked around 7~8 mm from cathode side. PCR assay using the separation buffer as the template was performed successfully both in conventional and realtime PCR methods. The hemoglobin in the whole blood did not show the inhibitory effect in our separation system and it may be due to structural modification of hemoglobin during electric separation. CONCLUSION Our simple electric device can separate nucleic acids from the whole blood sample by applying electricity at 5 V for 5 min. The separation buffer solution taken from the device can be used for PCR assay successfully.
Collapse
Affiliation(s)
- Mi Jung Bae
- Department of Physiology, School of Medicine, Kyungpook National University, Daegu 41944, Korea.,Clinical Omics Institute, Kyungpook National University, Daegu 41405, Korea
| | - Young Mi Lee
- Department of Physiology, School of Medicine, Kyungpook National University, Daegu 41944, Korea.,Clinical Omics Institute, Kyungpook National University, Daegu 41405, Korea
| | - Ye Seul Choi
- Department of Biomedical Science, Graduate School, Kyungpook National University, Daegu 41944, Korea.,BK21 Four Program, School of Medicine, Kyungpook National University, Daegu 41944, Korea
| | - Eunmi Lee
- Department of Biomedical Science, Graduate School, Kyungpook National University, Daegu 41944, Korea.,BK21 Four Program, School of Medicine, Kyungpook National University, Daegu 41944, Korea
| | - Minh Tan Le
- Department of Biomedical Science, Graduate School, Kyungpook National University, Daegu 41944, Korea.,BK21 Four Program, School of Medicine, Kyungpook National University, Daegu 41944, Korea
| | - Thi Hong Duc Nguyen
- Department of Biomedical Science, Graduate School, Kyungpook National University, Daegu 41944, Korea.,BK21 Four Program, School of Medicine, Kyungpook National University, Daegu 41944, Korea
| | - Donghyeon Lee
- Department of Biomedical Science, Graduate School, Kyungpook National University, Daegu 41944, Korea.,BK21 Four Program, School of Medicine, Kyungpook National University, Daegu 41944, Korea
| | - Junghwan Cho
- Clinical Omics Institute, Kyungpook National University, Daegu 41405, Korea
| | - Hyung Soo Han
- Department of Physiology, School of Medicine, Kyungpook National University, Daegu 41944, Korea.,Department of Biomedical Science, Graduate School, Kyungpook National University, Daegu 41944, Korea.,Clinical Omics Institute, Kyungpook National University, Daegu 41405, Korea.,BK21 Four Program, School of Medicine, Kyungpook National University, Daegu 41944, Korea
| | - Nora Jee-Young Park
- Clinical Omics Institute, Kyungpook National University, Daegu 41405, Korea.,Department of Pathology, Kyungpook National University Chilgok Hospital, Daegu 41404, Korea
| | - Gun Oh Chong
- Clinical Omics Institute, Kyungpook National University, Daegu 41405, Korea.,Department of Obstetrics and Gynecology, Kyungpook National University Chilgok Hospital, Daegu 41404, Korea
| |
Collapse
|
8
|
Montero Llopis P, Senft RA, Ross-Elliott TJ, Stephansky R, Keeley DP, Koshar P, Marqués G, Gao YS, Carlson BR, Pengo T, Sanders MA, Cameron LA, Itano MS. Best practices and tools for reporting reproducible fluorescence microscopy methods. Nat Methods 2021; 18:1463-1476. [PMID: 34099930 DOI: 10.1038/s41592-021-01156-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/15/2021] [Indexed: 02/04/2023]
Abstract
Although fluorescence microscopy is ubiquitous in biomedical research, microscopy methods reporting is inconsistent and perhaps undervalued. We emphasize the importance of appropriate microscopy methods reporting and seek to educate researchers about how microscopy metadata impact data interpretation. We provide comprehensive guidelines and resources to enable accurate reporting for the most common fluorescence light microscopy modalities. We aim to improve microscopy reporting, thus improving the quality, rigor and reproducibility of image-based science.
Collapse
Affiliation(s)
| | - Rebecca A Senft
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | | | | | - Daniel P Keeley
- Neuroscience Microscopy Core, University of North Carolina, Chapel Hill, NC, USA
| | - Preman Koshar
- Neuroscience Microscopy Core, University of North Carolina, Chapel Hill, NC, USA
| | - Guillermo Marqués
- University Imaging Centers and Department of Neuroscience, University of Minnesota, Minneapolis, MN, USA
| | - Ya-Sheng Gao
- Duke Light Microscopy Core Facility, Duke University, Durham, NC, USA
| | | | - Thomas Pengo
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, MN, USA
| | - Mark A Sanders
- University Imaging Centers and Department of Neuroscience, University of Minnesota, Minneapolis, MN, USA
| | - Lisa A Cameron
- Duke Light Microscopy Core Facility, Duke University, Durham, NC, USA
| | - Michelle S Itano
- Neuroscience Microscopy Core, University of North Carolina, Chapel Hill, NC, USA
| |
Collapse
|
9
|
Charalambakis NE, Ambulos NP, Hockberger P, Meyn SM, Bowen SK, Constable S, Fisher NC, Fletcher L, Kigenyi J, Mundoma C, Ramirez-Aguilar KA, Vinard A, Winn ME, Mische SM. Establishing a national strategy for shared research resources in biomedical sciences. FASEB J 2021; 35:e21973. [PMID: 34624149 DOI: 10.1096/fj.202101393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 09/20/2021] [Indexed: 11/11/2022]
Abstract
Contemporary science has become increasingly multi-disciplinary and team-based, resulting in unprecedented growth in biomedical innovation and technology over the last several decades. Collaborative research efforts have enabled investigators to respond to the demands of an increasingly complex 21st century landscape, including pressing scientific challenges such as the COVID-19 pandemic. A major contributing factor to the success of team science is the mobilization of core facilities and shared research resources (SRRs), the scientific instrumentation and expertise that exist within research organizations that enable widespread access to advanced technologies for trainees, faculty, and staff. For over 40 years, SRRs have played a key role in accelerating biomedical research discoveries, yet a national strategy that addresses how to leverage these resources to enhance team science and achieve shared scientific goals is noticeably absent. We believe a national strategy for biomedical SRRs-led by the National Institutes of Health-is crucial to advance key national initiatives, enable long-term research efficiency, and provide a solid foundation for the next generation of scientists.
Collapse
Affiliation(s)
| | - Nicholas P Ambulos
- Department of Microbiology and Immunology, Center for Innovative Biomedical Resources, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Philip Hockberger
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Susan M Meyn
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Sara K Bowen
- Flow Cytometry Core, Barrow Neurological Institute, Phoenix, Arizona, USA
| | | | - Nancy C Fisher
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Luellen Fletcher
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Justine Kigenyi
- Hoglund Biomedical Imaging Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Claudius Mundoma
- Research & Innovation Office, University of Colorado Boulder, Boulder, Colorado, USA
| | | | - Andrew Vinard
- Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Mary E Winn
- Van Andel Institute, Grand Rapids, Michigan, USA
| | - Sheenah M Mische
- Langone Medical Center, New York University, New York, New York, USA
| |
Collapse
|