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Zhivkoplias E, da Silva JM, Blasiak R. How transdisciplinarity can help biotech-driven biodiversity research. Trends Biotechnol 2025:S0167-7799(25)00135-0. [PMID: 40393855 DOI: 10.1016/j.tibtech.2025.04.008] [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: 01/24/2025] [Revised: 04/07/2025] [Accepted: 04/07/2025] [Indexed: 05/22/2025]
Abstract
The Kunming-Montreal Global Biodiversity Framework marks a significant step toward conserving genetic diversity on a global scale. Sequencing advancements have broadened biodiversity studies by enabling the mapping of species distributions, increasing understanding of ecological interactions, and monitoring genetic diversity. However, these tools are hindered by inequalities and biases, particularly in biodiversity-rich developing countries. To navigate these challenges, we propose strategies using the existing biotechnological toolbox to make biodiversity data more accessible and useful for research and development. This includes increasing funding for database curation, improving metadata standards, addressing inequalities in technological capacity, and supporting holistic capacity-building programmes. Implementing these strategies can unlock new opportunities for biodiversity research aligned with sustainable development principles and can contribute to improved conservation outcomes.
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Affiliation(s)
- Erik Zhivkoplias
- Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden.
| | - Jessica M da Silva
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Private Bag X7 Claremont, 7735, Cape Town, South Africa; Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, Auckland Park 2006, South Africa
| | - Robert Blasiak
- Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden
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2
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Silva-de-Jesus AC, Ferrari RG, Panzenhagen P, dos Santos AMP, Portes AB, Conte-Junior CA. Distribution of Antimicrobial Resistance and Biofilm Production Genes in the Genomic Sequences of S. aureus: A Global In Silico Analysis. Antibiotics (Basel) 2025; 14:364. [PMID: 40298499 PMCID: PMC12024283 DOI: 10.3390/antibiotics14040364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2025] [Revised: 03/11/2025] [Accepted: 03/12/2025] [Indexed: 04/30/2025] Open
Abstract
Background:Staphylococcus aureus constitutes a significant public health threat due to its exceptional adaptability, antimicrobial resistance (AMR), and capacity to form biofilms, all of which facilitate its persistence in clinical and environmental settings. Methods: This study undertook an extensive in silico analysis of 44,069 S. aureus genomic sequences acquired from the NCBI database to assess the global distribution of biofilm-associated and resistance-associated genes. The genomes were categorized into human clinical and environmental groups, with clinical samples representing a predominant 96%. Results: The analysis revealed notable regional discrepancies in sequencing efforts, with Europe and North America contributing 76% of the genomes. Key findings include the high prevalence of the ica locus, which is associated with biofilm formation, and its robust correlation with other genes, such as sasG, which was exclusively linked to SCCmec type IIa. The AMR gene analysis revealed substantial genetic diversity within environmental samples, with genes like vga(E) and erm being identified as particularly prominent. The clonal complex analysis revealed ST8 (USA300) and ST5 as the predominant types in human clinical isolates, while ST398 and ST59 were most frequently observed in environmental isolates. SCCmec type IV was globally prevalent, with subtype Iva being strongly associated with ST8 in North America and subtype IVh with ST239 in Europe. Conclusions: These findings underscore the dynamic evolution of S. aureus via mobile genetic elements and highlight the necessity for standardized metadata in public genomic databases to improve surveillance efforts. Furthermore, they reinforce the critical need for a One Health approach in monitoring S. aureus evolution, particularly concerning the co-dissemination of biofilm and resistance genes across various ecological niches.
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Affiliation(s)
- Ana Carolina Silva-de-Jesus
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-853, Brazil; (A.C.S.-d.-J.); (R.G.F.); (P.P.); (A.M.P.d.S.); (A.B.P.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-853, Brazil
- Graduate Technology Biotechnology, Universidade Estadual do Rio de Janeiro Campus-ZO, Manuel Caldeira de Alvarenga, Rio de Janeiro 23070-200, Brazil
- Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-909, Brazil
| | - Rafaela G. Ferrari
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-853, Brazil; (A.C.S.-d.-J.); (R.G.F.); (P.P.); (A.M.P.d.S.); (A.B.P.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-853, Brazil
| | - Pedro Panzenhagen
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-853, Brazil; (A.C.S.-d.-J.); (R.G.F.); (P.P.); (A.M.P.d.S.); (A.B.P.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-853, Brazil
- Graduate Program in Veterinary Hygiene (PPGHV), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Vital Brazil Filho, Niterói 24220-000, Brazil
| | - Anamaria M. P. dos Santos
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-853, Brazil; (A.C.S.-d.-J.); (R.G.F.); (P.P.); (A.M.P.d.S.); (A.B.P.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-853, Brazil
- Graduate Program in Veterinary Hygiene (PPGHV), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Vital Brazil Filho, Niterói 24220-000, Brazil
| | - Ana Beatriz Portes
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-853, Brazil; (A.C.S.-d.-J.); (R.G.F.); (P.P.); (A.M.P.d.S.); (A.B.P.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-853, Brazil
- Laboratory of Microorganism Structure, Department of General Microbiology, Institute of Microbiology Paulo de Góes (IMPG), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-853, Brazil
| | - Carlos Adam Conte-Junior
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-853, Brazil; (A.C.S.-d.-J.); (R.G.F.); (P.P.); (A.M.P.d.S.); (A.B.P.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-853, Brazil
- Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-909, Brazil
- Graduate Program in Veterinary Hygiene (PPGHV), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Vital Brazil Filho, Niterói 24220-000, Brazil
- Molecular & Analytical Laboratory Center, Department of Food Technology, Faculty of Veterinary, Universidade Federal Fluminense, Niterói 24220-900, Brazil
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3
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Brooksbank C, Brazas MD, Mulder N, Schwartz R, Ras V, Morgan SL, Lloret Llinares M, Carvajal López P, Larcombe L, Ghouila A, Hancocks T, Satagopam V, De Las Rivas J, Mazandu G, Gaeta B. The ISCB competency framework v. 3: a revised and extended standard for bioinformatics education and training. BIOINFORMATICS ADVANCES 2024; 4:vbae166. [PMID: 39678208 PMCID: PMC11646570 DOI: 10.1093/bioadv/vbae166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 07/05/2024] [Accepted: 11/14/2024] [Indexed: 12/17/2024]
Abstract
Motivation Developing competency in the broad area of bioinformatics is challenging globally, owing to the breadth of the field and the diversity of its audiences for education and training. Course design can be facilitated by the use of a competency framework-a set of competency requirements that define the knowledge, skills and attitudes needed by individuals in (or aspiring to be in) a particular profession or role. These competency requirements can help to define curricula as they can inform both the content and level to which competency needs to be developed. The International Society for Computational Biology (ISCB) developed a list of bioinformatics competencies in 2014, and these have undergone several rounds of improvement. In consultation with a broad bioinformatics training community, these have now been further refined and extended to include knowledge skills and attitudes, and mappings to previous and other existing competency frameworks. Results Here, we present version 3 of the ISCB competency framework. We describe how it was developed and how to access it, as well as providing some examples of how it has been used. Availability and implementation The framework is openly accessible at https://competency.ebi.ac.uk/framework/iscb/3.0/competencies.
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Affiliation(s)
- Cath Brooksbank
- EMBL’s European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
| | | | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Russell Schwartz
- Department of Biological Sciences and Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Verena Ras
- Computational Biology Division, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Sarah L Morgan
- EMBL’s European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Marta Lloret Llinares
- EMBL’s European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Patricia Carvajal López
- EMBL’s European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Lee Larcombe
- Nexastem Ltd, St Neots, Cambridgeshire PE19 6AD, United Kingdom
| | - Amel Ghouila
- Computational Biology Division, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Tom Hancocks
- EMBL’s European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Venkata Satagopam
- Luxembourg Centre For Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4365, Luxembourg
| | - Javier De Las Rivas
- Cancer Research Center (CiC-IBMCC), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca (USAL), Salamanca 37007, Spain
| | - Gaston Mazandu
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Bruno Gaeta
- School of Computer Science and Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
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Faundes V, Repetto GM, Valdivia LE. Discovery of novel genetic syndromes in Latin America: Opportunities and challenges. Genet Mol Biol 2024; 47Suppl 1:e20230318. [PMID: 38466870 PMCID: PMC10964411 DOI: 10.1590/1678-4685-gmb-2023-0318] [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: 11/06/2023] [Accepted: 02/06/2024] [Indexed: 03/13/2024] Open
Abstract
Latin America (LatAm) has a rich and historically significant role in delineating both novel and well-documented genetic disorders. However, the ongoing advancements in the field of human genetics pose challenges to the relatively slow adaption of LatAm in the field. Here, we describe past and present contributions of LatAm to the discovery of novel genetic disorders, often referred as novel gene-disease associations (NGDA). We also describe the current methodologies for discovery of NGDA, taking into account the latest developments in genomics. We provide an overview of opportunities and challenges for NGDA research in LatAm considering the steps currently performed to identify and validate such associations. Given the multiple and diverse needs of populations and countries in LatAm, it is imperative to foster collaborations amongst patients, indigenous people, clinicians and scientists. Such collaborative effort is essential for sustaining and enhancing the LatAm´s contributions to the field of NGDA.
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Affiliation(s)
- Víctor Faundes
- Universidad de Chile, Instituto de Nutrición y Tecnología de los Alimentos, Laboratorio de Genética y Enfermedades Metabólicas, Santiago, Chile
| | - Gabriela M. Repetto
- Universidad del Desarrollo, Facultad de Medicina, Instituto de Ciencias e Innovación en Medicina, Centro de Genética y Genómica, Programa de Enfermedades Raras, Santiago, Chile
| | - Leonardo E. Valdivia
- Universidad Mayor, Facultad de Ciencias, Centro de Biología Integrativa, Santiago, Chile
- Universidad Mayor, Facultad de Ciencias, Escuela de Biotecnología, Santiago, Chile
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Sano T, Sampad MJN, Gonzalez-Ferrer J, Hernandez S, Vera-Choqqueccota S, Vargas PA, Urcuyo R, Duran NM, Teodorescu M, Haussler D, Schmidt H, Mostajo-Radji MA. Open-loop lab-on-a-chip technology enables remote computer science training in Latinx life sciences students. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.28.538776. [PMID: 37205466 PMCID: PMC10187215 DOI: 10.1101/2023.04.28.538776] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Despite many interventions, science education remains highly inequitable throughout the world. Among all life sciences fields, Bioinformatics and Computational Biology suffer from the strongest underrepresentation of racial and gender minorities. Internet-enabled project-based learning (PBL) has the potential to reach underserved communities and increase the diversity of the scientific workforce. Here, we demonstrate the use of lab-on-a-chip (LoC) technologies to train Latinx life science undergraduate students in concepts of computer programming by taking advantage of open-loop cloud-integrated LoCs. We developed a context-aware curriculum to train students at over 8,000 km from the experimental site. We showed that this approach was sufficient to develop programming skills and increase the interest of students in continuing careers in Bioinformatics. Altogether, we conclude that LoC-based Internet-enabled PBL can become a powerful tool to train Latinx students and increase the diversity in STEM.
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Affiliation(s)
- Tyler Sano
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064
| | | | - Jesus Gonzalez-Ferrer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060
| | - Sebastian Hernandez
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060
- Centro de Electroquímica y Energía Química (CELEQ), Universidad de Costa Rica, San José, 11501 2060, Costa Rica
| | - Samira Vera-Choqqueccota
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060
| | - Paola A Vargas
- Biotechnology, Universidad Católica Boliviana San Pablo, Santa Cruz de la Sierra, Bolivia
| | - Roberto Urcuyo
- Centro de Electroquímica y Energía Química (CELEQ), Universidad de Costa Rica, San José, 11501 2060, Costa Rica
| | | | - Mircea Teodorescu
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060
| | - David Haussler
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060
| | - Holger Schmidt
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064
| | - Mohammed A Mostajo-Radji
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060
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Qi Z, Yan Z, Wang Y, Ji N, Yang X, Zhang A, Li M, Xu F, Zhang J. Integrative applications of network pharmacology and molecular docking: An herbal formula ameliorates H9c2 cells injury through pyroptosis. J Ginseng Res 2023; 47:228-236. [PMID: 36926601 PMCID: PMC10014185 DOI: 10.1016/j.jgr.2022.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/23/2022] [Accepted: 03/17/2022] [Indexed: 01/13/2023] Open
Abstract
Background QiShen YiQi pills (QSYQ) is a Traditional Chinese Medicine (TCM) formula, which has a significant effect on the treatment of patients with myocardial infarction (MI) in clinical practice. However, the molecular mechanism of QSYQ regulation pyroptosis after MI is still not fully known. Hence, this study was designed to reveal the mechanism of the active ingredient in QSYQ. Methods Integrated approach of network pharmacology and molecular docking, were conducted to screen active components and corresponding common target genes of QSYQ in intervening pyroptosis after MI. Subsequently, STRING and Cytoscape were applied to construct a PPI network, and obtain candidate active compounds. Molecular docking was performed to verify the binding ability of candidate components to pyroptosis proteins and oxygen-glucose deprivation (OGD) induced cardiomyocytes injuries were applied to explore the protective effect and mechanism of the candidate drug. Results Two drug-likeness compounds were preliminarily selected, and the binding capacity between Ginsenoside Rh2 (Rh2) and key target High Mobility Group Box 1 (HMGB1)was validated in the form of hydrogen bonding. 2 μM Rh2 prevented OGD-induced H9c2 death and reduced IL-18 and IL-1β levels, possibly by decreasing the activation of the NLRP3 inflammasome, inhibiting the expression of p12-caspase1, and attenuating the level of pyroptosis executive protein GSDMD-N. Conclusions We propose that Rh2 of QSYQ can protect myocardial cells partially by ameliorating pyroptosis, which seems to have a new insight regarding the therapeutic potential for MI.
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Affiliation(s)
- Zhongwen Qi
- Postdoctoral Research Station of China Academy of Chinese Medical Sciences, Institute of Gerontology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Zhipeng Yan
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yueyao Wang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Nan Ji
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaoya Yang
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Ao Zhang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Meng Li
- Institute of Hypertension, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- Corresponding author. Institute of Hypertension, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China.
| | - Fengqin Xu
- Postdoctoral Research Station of China Academy of Chinese Medical Sciences, Institute of Gerontology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Corresponding author. Postdoctoral Research Station of China Academy of Chinese Medical Sciences, Institute of Gerontology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Junping Zhang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- Corresponding author. First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.
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7
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Ayala-Ruano S, Hernandez F, Ortega A, Infante D, Carrascal D, Sánchez-Luquez K, Puche-Quiñonez R. Highlights of the 1st Ecuadorian-Venezuelan Symposium of Young Researchers in Bioinformatics (1SEVJIB). F1000Res 2022; 11:1086. [PMID: 36176547 PMCID: PMC9500400 DOI: 10.12688/f1000research.125381.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/15/2022] [Indexed: 01/13/2023] Open
Abstract
The COVID-19 pandemic profoundly changed how scientific conferences are organized, fostering virtual meetings. These online events have allowed students and researchers to overcome geographical, administrative and economic barriers to attend and organize high-quality international symposiums. Moreover, these virtual conferences have contributed to the creation of inclusive activities that strengthen scientific communities. Here, we summarize the main activities and learnings from the 1st Ecuadorian-Venezuelan Symposium of Young Bioinformatics Researchers (1SEVJIB), organized by the Ecuadorian and Venezuelan ISCB-SC Regional Student Groups (RSGs). This symposium aimed to provide an opportunity for undergraduate and postgraduate students from Ecuador, Venezuela, and other Latin American countries to share their Bioinformatics research. The 1SEVJIB was the first bi-national conference organized by two RSGs from Latin America (LatAm). This symposium was a two-day virtual meeting with five activities: 1) oral student presentations, 2) poster session, 3) keynote lectures, 4) workshop, and 5) round table. This conference promoted the scientific exchange and cooperation networks between young Bioinformatics researchers and students from Ecuador, Venezuela, and LatAm, giving them opportunities to boost their scientific careers.
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Affiliation(s)
- Sebastian Ayala-Ruano
- Grupo de Medicina Molecular y Traslacional (MeM&T), Universidad San Francisco de Quito, Quito, Ecuador
| | - Fernando Hernandez
- Centro de Medicina Experimental, Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Venezuela
| | - Arantxa Ortega
- Grupo Modelado Inteligente de Sistemas, Universidad de Cádiz, Algeciras, Spain
| | - Deliana Infante
- Centro de Medicina Experimental, Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Venezuela
| | - Daniela Carrascal
- Unidad de Estudios Genéticos y Forenses, Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Venezuela
| | - Karen Sánchez-Luquez
- Unidad de Estudios Genéticos y Forenses, Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Venezuela
| | - Rafael Puche-Quiñonez
- Unidad de Estudios Genéticos y Forenses, Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Venezuela,
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8
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Yek C, Pacheco AR, Vanaerschot M, Bohl JA, Fahsbender E, Aranda-Díaz A, Lay S, Chea S, Oum MH, Lon C, Tato CM, Manning JE. Metagenomic Pathogen Sequencing in Resource-Scarce Settings: Lessons Learned and the Road Ahead. FRONTIERS IN EPIDEMIOLOGY 2022; 2:926695. [PMID: 36247976 PMCID: PMC9558322 DOI: 10.3389/fepid.2022.926695] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/29/2022] [Indexed: 06/16/2023]
Abstract
Metagenomic next-generation sequencing (mNGS) is the process of sequencing all genetic material in a biological sample. The technique is growing in popularity with myriad applications including outbreak investigation, biosurveillance, and pathogen detection in clinical samples. However, mNGS programs are costly to build and maintain, and additional obstacles faced by low- and middle-income countries (LMICs) may further widen global inequities in mNGS capacity. Over the past two decades, several important infectious disease outbreaks have highlighted the importance of establishing widespread sequencing capacity to support rapid disease detection and containment at the source. Using lessons learned from the COVID-19 pandemic, LMICs can leverage current momentum to design and build sustainable mNGS programs, which would form part of a global surveillance network crucial to the elimination of infectious diseases.
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Affiliation(s)
- Christina Yek
- Department of Critical Care Medicine, National Institutes of Health Clinical Center, Bethesda, MD, United States
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
| | - Andrea R. Pacheco
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | | | - Jennifer A. Bohl
- Vaccine Immunology Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | | | - Andrés Aranda-Díaz
- Chan Zuckerberg Initiative, Redwood City, CA, United States
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Sreyngim Lay
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Sophana Chea
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Meng Heng Oum
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Chanthap Lon
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | | | - Jessica E. Manning
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
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9
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A Bibliometric Analysis of Mexican Bioinformatics: A Portrait of Actors, Structure, and Dynamics. BIOLOGY 2022; 11:biology11010131. [PMID: 35053129 PMCID: PMC8772911 DOI: 10.3390/biology11010131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/24/2021] [Accepted: 12/25/2021] [Indexed: 11/17/2022]
Abstract
Bioinformatics is a very important informatics tool for health and biological sciences, focusing on biological data management. The objective of this work was to perform a bibliometric analysis regarding the development of Mexican bioinformatics. An exhaustive revision of the literature associated with Mexican bioinformatics in a period of 25-years was performed. Bibliometric tools, such as performance analysis and science mapping were included in the analysis. We identified the main actors as well as the structure and dynamics of Mexican bioinformatics. Some of the main findings were as follows: the thematic structure in the field is defined by the research lines of outstanding authors; the outstanding collaborations of Mexican institutions with foreign countries and institutions are influenced by the geographic proximity and binational agreements, as well as philanthropic and academic programs that promote collaborations, and there is an inclination for health issues promoted by public health financing and philanthropic organizations. It is identified that publications had an explosion since 2012, we consider that this growth may be influenced by the democratization of data, derived from the mass sequencing of biological molecules stored in public databases.
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Rocha M, Massarani L, Souza SJD, Vasconcelos ATRD. The past, present and future of genomics and bioinformatics: A survey of Brazilian scientists. Genet Mol Biol 2022; 45:e20210354. [PMID: 35671453 PMCID: PMC9169998 DOI: 10.1590/1678-4685-gmb-2021-0354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/05/2022] [Indexed: 11/22/2022] Open
Abstract
Brazil has one of the highest rates of scientific production, occupying the ninth position among countries with genome-sequencing projects. Considering the rapid development of this research area and the diversity of professionals involved, the present study aims to understand the expectations, past experiences and the current scenario of Brazilian research in bioinformatics and genomics. The present research was carried out by analyzing the perceptions of 576 researchers in genomics and bioinformatics in Brazil through content and sentiment analysis techniques. This group of participants is equivalent to 48% of the members of the research community. The results suggest that most researchers have a positive perception of the potential of this research area. However, there is concern about the lack of funding for investing in equipment and professional training. As part of a wish list for the future, researchers highlighted the need for higher funding, formal education, and collaboration among research networks. When asked about genomics and bioinformatics in other countries, the participants recognize that sequencing technologies and infrastructure are more accessible, allowing better data volume expansion.
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Affiliation(s)
| | | | - Sandro José de Souza
- Universidade Federal do Rio Grande do Norte, Brazil; Universidade Federal do Rio Grande do Norte, Brazil; Sichuan University, China
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Carvalho-Silva D, Garcia L, Morgan SL, Brooksbank C, Dunham I. Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars. PLoS Comput Biol 2018; 14:e1006419. [PMID: 30439935 PMCID: PMC6237289 DOI: 10.1371/journal.pcbi.1006419] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Denise Carvalho-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Leyla Garcia
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Sarah L. Morgan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Cath Brooksbank
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
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