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Song Y, Zhong S, Li Y, Jiang M, Wei Q. Constructing an Interactive and Integrated Analysis and Identification Platform for Pathogenic Microorganisms to Support Surveillance Capacity. Genes (Basel) 2023; 14:2156. [PMID: 38136978 PMCID: PMC10742832 DOI: 10.3390/genes14122156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/09/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
INTRODUCTION Whole genome sequencing (WGS) holds significant promise for epidemiological inquiries, as it enables the identification and tracking of pathogenic origins and dissemination through comprehensive genome analysis. This method is widely preferred for investigating outbreaks and monitoring pathogen activity. However, the effective utilization of microbiome sequencing data remains a challenge for clinical and public health experts. Through the National Pathogen Resource Center, we have constructed a dynamic and interactive online analysis platform to facilitate the in-depth analysis and use of pathogen genomic data, by public health and associated professionals, to support infectious disease surveillance framework building and capacity warnings. METHOD The platform was implemented using the Java programming language, and the front-end pages were developed using the VUE framework, following the MVC (Model-View-Controller) pattern to enable interactive service functionalities for front-end data collection and back-end data computation. Cloud computing services were employed to integrate biological information analysis tools for conducting fundamental analysis on sequencing data. RESULT The platform achieved the goal of non-programming analysis, providing an interactive visual interface that allows users to visually obtain results by setting parameters in web pages. Moreover, the platform allows users to export results in various formats to further support their research. DISCUSSION We have established a dynamic and interactive online platform for bioinformatics analysis. By encapsulating the complex background experiments and analysis processes in a cloud-based service platform, the complex background experiments and analysis processes are presented to the end-user in a simple and interactive manner. It facilitates real-time data mining and analysis by allowing users to independently select parameters and generate analysis results at the click of a button, based on their needs, without the need for a programming foundation.
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Affiliation(s)
- Yang Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China;
| | - Songchao Zhong
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (S.Z.); (Y.L.); (M.J.)
| | - Yixiao Li
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (S.Z.); (Y.L.); (M.J.)
| | - Mengnan Jiang
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (S.Z.); (Y.L.); (M.J.)
| | - Qiang Wei
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (S.Z.); (Y.L.); (M.J.)
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Sharma A, Chakraborty A, Jaganathan BG. Review of the potential of mesenchymal stem cells for the treatment of infectious diseases. World J Stem Cells 2021; 13:568-593. [PMID: 34249228 PMCID: PMC8246252 DOI: 10.4252/wjsc.v13.i6.568] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/07/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023] Open
Abstract
The therapeutic value of mesenchymal stem cells (MSCs) for the treatment of infectious diseases and the repair of disease-induced tissue damage has been explored extensively. MSCs inhibit inflammation, reduce pathogen load and tissue damage encountered during infectious diseases through the secretion of antimicrobial factors for pathogen clearance and they phagocytose certain bacteria themselves. MSCs dampen tissue damage during infection by downregulating the levels of pro-inflammatory cytokines, and inhibiting the excessive recruitment of neutrophils and proliferation of T cells at the site of injury. MSCs aid in the regeneration of damaged tissue by differentiating into the damaged cell types or by releasing paracrine factors that direct tissue regeneration, differentiation, and wound healing. In this review, we discuss in detail the various mechanisms by which MSCs help combat pathogens, tissue damage associated with infectious diseases, and challenges in utilizing MSCs for therapy.
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Affiliation(s)
- Amit Sharma
- Stem Cell and Cancer Biology Group, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Anuja Chakraborty
- Stem Cell and Cancer Biology Group, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Bithiah Grace Jaganathan
- Stem Cell and Cancer Biology Group, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
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Nayak K, Jain V, Kaur M, Khan N, Gottimukkala K, Aggarwal C, Sagar R, Gupta S, Rai RC, Dixit K, Islamuddin M, Khan WH, Verma A, Maheshwari D, Chawla YM, Reddy ES, Panda H, Sharma P, Bhatnagar P, Singh P, Raghavendhar B S, Patel AK, Ratageri VH, Chandele A, Ray P, Murali-Krishna K. Antibody response patterns in chikungunya febrile phase predict protection versus progression to chronic arthritis. JCI Insight 2020; 5:130509. [PMID: 32155134 DOI: 10.1172/jci.insight.130509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 03/04/2020] [Indexed: 11/17/2022] Open
Abstract
Chikungunya virus (CHIKV) infection causes acute febrile illness in humans, and some of these individuals develop a debilitating chronic arthritis that can persist for months to years for reasons that remain poorly understood. In this study from India, we characterized antibody response patterns in febrile chikungunya patients and further assessed the association of these initial febrile-phase antibody response patterns with protection versus progression to developing chronic arthritis. We found 5 distinct patterns of the antibody responses in the febrile phase: no CHIKV binding or neutralizing (NT) antibodies but PCR positive, IgM alone with no NT activity, IgM alone with NT activity, IgM and IgG without NT activity, and IgM and IgG with NT activity. A 20-month follow-up showed that appearance of NT activity regardless of antibody isotype or appearance of IgG regardless of NT activity during the initial febrile phase was associated with a robust protection against developing chronic arthritis in the future. These findings, while providing potentially novel insights on correlates of protective immunity against chikungunya-induced chronic arthritis, suggest that qualitative differences in the antibody response patterns that have evolved during the febrile phase can serve as biomarkers that allow prediction of protection or progression to chronic arthritis in the future.
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Affiliation(s)
- Kaustuv Nayak
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Vineet Jain
- Department of Medicine, Hamdard Institute of Medical Sciences and Research (HIMSAR), Jamia Hamdard, New Delhi, India
| | - Manpreet Kaur
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Naushad Khan
- Department of Biotechnology, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
| | - Kamalvishnu Gottimukkala
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Charu Aggarwal
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Rohit Sagar
- Department of Biotechnology, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
| | - Shipra Gupta
- Department of Biotechnology, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
| | - Ramesh Chandra Rai
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Kritika Dixit
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Mohammad Islamuddin
- Department of Biotechnology, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
| | - Wajihul Hasan Khan
- Department of Biotechnology, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
| | - Anil Verma
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Deepti Maheshwari
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Yadya M Chawla
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Elluri Seetharami Reddy
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Harekrushna Panda
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Pragati Sharma
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Priya Bhatnagar
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Prabhat Singh
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Siva Raghavendhar B
- Kusuma School of Biological Sciences, Indian Institute of Technology (IIT), New Delhi, India
| | - Ashok Kumar Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology (IIT), New Delhi, India
| | - Vinod H Ratageri
- Department of Pediatrics, Karnataka Institute of Medical Sciences (KIMS), Hubli, Karnataka, India
| | - Anmol Chandele
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Pratima Ray
- Department of Biotechnology, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
| | - Kaja Murali-Krishna
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India.,Emory Vaccine Center and.,Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
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