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Taunk K, Kalita B, Kale V, Chanukuppa V, Naiya T, Zingde SM, Rapole S. The development and clinical applications of proteomics: an Indian perspective. Expert Rev Proteomics 2020; 17:433-451. [PMID: 32576061 DOI: 10.1080/14789450.2020.1787157] [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: 10/24/2022]
Abstract
INTRODUCTION Proteomic research has been extensively used to identify potential biomarkers or targets for various diseases. Advances in mass spectrometry along with data analytics have led proteomics to become a powerful tool for exploring the critical molecular players associated with diseases, thereby, playing a significant role in the development of proteomic applications for the clinic. AREAS COVERED This review presents recent advances in the development and clinical applications of proteomics in India toward understanding various diseases including cancer, metabolic diseases, and reproductive diseases. Keywords combined with 'clinical proteomics in India' 'proteomic research in India' and 'mass spectrometry' were used to search PubMed. EXPERT OPINION The past decade has seen a significant increase in research in clinical proteomics in India. This approach has resulted in the development of proteomics-based marker technologies for disease management in the country. The majority of these investigations are still in the discovery phase and efforts have to be made to address the intended clinical use so that the identified potential biomarkers reach the clinic. To move toward this necessity, there is a pressing need to establish some key infrastructure requirements and meaningful collaborations between the clinicians and scientists which will enable more effective solutions to address health issues specific to India.
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Affiliation(s)
- Khushman Taunk
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India.,Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal , Haringhata, West Bengal, India
| | - Bhargab Kalita
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India
| | - Vaikhari Kale
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India
| | | | - Tufan Naiya
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal , Haringhata, West Bengal, India
| | - Surekha M Zingde
- CH3-53, Kendriya Vihar, Sector 11, Kharghar , Navi Mumbai, Maharashtra, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India
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Ray S, Srivastava S. Virtualization of science education: a lesson from the COVID-19 pandemic. ACTA ACUST UNITED AC 2020; 11:77-80. [PMID: 33132627 PMCID: PMC7261257 DOI: 10.1007/s42485-020-00038-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/18/2020] [Accepted: 05/23/2020] [Indexed: 11/29/2022]
Abstract
Nowadays, e-learning and virtual labs have gained substantial popularity in science education. Amid the COVID-19 shutdowns, regular in-person classroom teaching and lab courses are suspended in several countries worldwide. In this scenario, virtual classes and online resources could serve more effectively as a possible alternative way of learning science from home.
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Affiliation(s)
- Sandipan Ray
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076 India
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Reddy PJ, Atak A, Ghantasala S, Kumar S, Gupta S, Prasad TSK, Zingde SM, Srivastava S. Proteomics research in India: an update. J Proteomics 2015; 127:7-17. [PMID: 25868663 DOI: 10.1016/j.jprot.2015.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 04/06/2015] [Indexed: 02/04/2023]
Abstract
After a successful completion of the Human Genome Project, deciphering the mystery surrounding the human proteome posed a major challenge. Despite not being largely involved in the Human Genome Project, the Indian scientific community contributed towards proteomic research along with the global community. Currently, more than 76 research/academic institutes and nearly 145 research labs are involved in core proteomic research across India. The Indian researchers have been major contributors in drafting the "human proteome map" along with international efforts. In addition to this, virtual proteomics labs, proteomics courses and remote triggered proteomics labs have helped to overcome the limitations of proteomics education posed due to expensive lab infrastructure. The establishment of Proteomics Society, India (PSI) has created a platform for the Indian proteomic researchers to share ideas, research collaborations and conduct annual conferences and workshops. Indian proteomic research is really moving forward with the global proteomics community in a quest to solve the mysteries of proteomics. A draft map of the human proteome enhances the enthusiasm among intellectuals to promote proteomic research in India to the world.This article is part of a Special Issue entitled: Proteomics in India.
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Affiliation(s)
- Panga Jaipal Reddy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Apurva Atak
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Saicharan Ghantasala
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Saurabh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Shabarni Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore 560066, India
| | - Surekha M Zingde
- CH3-53 Kendriya Vihar, Kharghar, Navi Mumbai, 410210, India. http://www.psindia.org
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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Zingde SM. Has Proteomics come of age in India? J Proteomics 2015; 127:3-6. [PMID: 25748142 DOI: 10.1016/j.jprot.2015.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 02/25/2015] [Indexed: 12/24/2022]
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Diwakar S, Parasuram H, Medini C, Raman R, Nedungadi P, Wiertelak E, Srivastava S, Achuthan K, Nair B. Complementing Neurophysiology Education for Developing Countries via Cost-Effective Virtual Labs: Case Studies and Classroom Scenarios. JOURNAL OF UNDERGRADUATE NEUROSCIENCE EDUCATION : JUNE : A PUBLICATION OF FUN, FACULTY FOR UNDERGRADUATE NEUROSCIENCE 2014; 12:A130-9. [PMID: 24693260 PMCID: PMC3970995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 09/19/2013] [Accepted: 01/28/2014] [Indexed: 06/03/2023]
Abstract
Classroom-level neuroscience experiments vary from detailed protocols involving chemical, physiological and imaging techniques to computer-based modeling. The application of Information and Communication Technology (ICT) is revolutionizing the current laboratory scenario in terms of active learning especially for distance education cases. Virtual web-based labs are an asset to educational institutions confronting economic issues in maintaining equipment, facilities and other conditions needed for good laboratory practice. To enhance education, we developed virtual laboratories in neuroscience and explored their first-level use in (Indian) University education in the context of developing countries. Besides using interactive animations and remotely-triggered experimental devices, a detailed mathematical simulator was implemented on a web-based software platform. In this study, we focused on the perceptions of technology adoption for a virtual neurophysiology laboratory as a new pedagogy tool for complementing college laboratory experience. The study analyses the effect of virtual labs on users assessing the relationship between cognitive, social and teaching presence. Combining feedback from learners and teachers, the study suggests enhanced motivation for students and improved teaching experience for instructors.
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Affiliation(s)
- Shyam Diwakar
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham (Amrita University), Kollam, Kerala, India 690525
| | - Harilal Parasuram
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham (Amrita University), Kollam, Kerala, India 690525
| | - Chaitanya Medini
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham (Amrita University), Kollam, Kerala, India 690525
| | - Raghu Raman
- Center for Research in Advanced Technologies for Education (CREATE), Amrita Vishwa Vidyapeetham (Amrita University), Kollam, Kerala, 690525, India
| | - Prema Nedungadi
- Center for Research in Advanced Technologies for Education (CREATE), Amrita Vishwa Vidyapeetham (Amrita University), Kollam, Kerala, 690525, India
| | | | | | - Krishnashree Achuthan
- Amrita School of Engineering, Amrita Vishwa Vidyapeetham (Amrita University), Kollam, Kerala, 690525, India
| | - Bipin Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham (Amrita University), Kollam, Kerala, India 690525
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Gupta S, Venkatesh A, Ray S, Srivastava S. Challenges and prospects for biomarker research: a current perspective from the developing world. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:899-908. [PMID: 24412545 DOI: 10.1016/j.bbapap.2013.12.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 12/11/2013] [Accepted: 12/27/2013] [Indexed: 12/20/2022]
Abstract
Majority of deaths due to communicable and non-communicable diseases occur in the low and middle-income nations (LMNs), mainly due to the lack of early diagnoses and timely treatments. In such a scenario, biomarkers serve as an indispensible resource that can be used as indicators of biological processes, specific disease conditions or response to therapeutic interventions. Evaluation, diagnosis and management of diseases in developing world by following/extrapolating the findings obtained on the basis of the research work involving only the populations from the developed countries, could often be highly misleading due to existence of diverse patterns of diseases in developing countries compared to the developed world. Biomarker candidates identified from high-throughput integrated omics technologies have promising potential; however, their actual clinical applications are found to be limited, primarily due to the challenges of disease heterogeneity and pre-analytical variability associated with the biomarker discovery pipeline. Additionally, in the developing world, economic crunches, lack of awareness and education, paucity of biorepositories, enormous diversities in socio-epidemiological background, ethnicity, lifestyle, diet, exposure to various environmental risk factors and infectious agents, and ethical and social issues also cumulatively hinder biomarker discovery ventures. Establishment of standard operating procedures, comprehensive data repositories and exchange of scientific findings are crucial for reducing the variability and fragmentation of data. This review highlights the challenges associated with the discovery, validation and translational phases of biomarker research in LMNs with some of their amenable solutions and future prospects. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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Affiliation(s)
- Shabarni Gupta
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Apoorva Venkatesh
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sandipan Ray
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanjeeva Srivastava
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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