Qualification: 
Ph.D
bipin@am.amrita.edu

Bipin Nair received his Ph.D. in Microbiology in 1986 from the Department of Microbiology, M.S. University of Baroda, India and received his post-doctoral training at the University of Tennessee, Memphis, USA, in the Dept. of Pharmacology from 1987-1992. His major contributions during that phase were in the areas of growth factor receptor signaling, GTP binding proteins and second messenger pathways.

Dr. Nair then moved to the Biotechnology industry in 1993 and held the position of Senior Scientist- Lead Discovery at MDS Pharma Services in Seattle, Washington, USA. His experience with High Throughput Screening and application of novel technologies to a wide range of target areas, resulted in many significant achievements for MDS, during his tenure as Research Manager--Lead Discovery, at MDS Pharma Services.

In 2004, Dr. Nair moved back to India and took over as Professor and Chairman of the Centre for Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri Campus. Under his leadership, the School of Biotechnology has been a trail-blazer in the Biotechnology arena for both undergraduate and postgraduate academic programs as well as an active Ph.D. program at the School. Dr. Nair is also the Coordinator of the TIFAC Centre of Relevance and Excellence in Biomedical Technology at Amrita Vishwa Vidyapeetham, under the Mission Reach program of the Department of Science and Technology, Govt. of India. Apart from setting up the State of the Art Amrita Biomedical Engineering (AMBE) Research Centre as part of the TIFAC CORE, Dr. Nair also led the group that developed a prototype of an Automated Insulin Pump, which resulted in Amrita University’s first patent from the USPTO. Subsequently, a number of patents (both India and USA) in the area of biomedical devices and diagnostics have been filed and awarded. With active national and international collaborations, Dr. Nair’s laboratory also has well-funded(DST, DBT, CSIR, MHRD) research initiatives in Natural Products Lead Discovery with a focus on wound healing, cancer, antimicrobial drug discovery and the multi-drug resistance crisis. He is also the Discipline wise National Coordinator for the development of Biotechnology Virtual Labs being developed under the MHRD –NMEICT program.

Another significant feather in Dr. Nair’s cap has been the selection of the Amrita School of Biotechnology by the Bill and Melinda Gates Foundation for the Gates Foundation-DBT-BIRAC "Reinvent the Toilet" Grand Challenge India Sanitation Award as well as continued funding in collaboration with Columbia University, New York and the University of Durban, South Africa. The School also has ongoing productive collaborations with Oxford, Cambridge universities in UK, and UCSD, USA as well as industry collaborations/interactions with companies like Agilent and Wipro Technologies. 

Dr. Nair has numerous publications in national and international scientific journals. Dr. Nair is an Associate Editor for the International Journal ‘Current Pharmacogenomics and Personalized Medicine’ and also serves on several national and international advisory committees.

 

Major Research Interests

Development of low cost Biomedical Devices and Diagnostics in the management of

  1. Diabetes
  2. Design and development of an automated Insulin Pump which resulted in the award of an United States Patent (USPTO No. 8,034,019 B2, October 11, 2011).
  3. Development of low cost non-enzymatic glucose and cholesterol sensors.
  4. Design and development of a Lab-on-a-Chip device for simultaneous detection of glucose, HbA1c, Cholesterol and Creatinine

Identification of Natural Product Lead molecules as potential modulators and elucidation of molecular mechanisms involved in impaired wound healing in Diabetes.

  1. Elucidating the role of Matrix Metalloproteinases (MMP2 and MMP9) in wound healing.
  2. Identification of the molecular mechanisms involving Nitric Oxide and Epidermal Growth Factor in the wound healing process.

Understanding the molecular mechanisms underlying the regulation of Matrix Metalloproteinases and oncogenic signaling systems by Natural Products and dissecting the regulatory crosstalk between EGF Receptor signaling cascades and gelatinases.

Studying the role of quorum sensing and biofilm formation in microbial pathogenesis and identification of natural product inhibitors that block this process.

GATES Foundation-DBT-BIRAC Grand Challenge Award to develop Sanitation solutions: Identification of bacteriophages to target and eliminate pathogens and odor causing bacteria in fecal waste. Project also focuses on developing viral and non-viral lytic agents to combat helminth and protozoan contamination in waste water

Education

YEAR DEGREE/PROGRAM INSTITUTION
1981 - 1986 Ph.D. in Microbiology
Thesis Title: “Some regulatory aspects of carbohydrate metabolism in Neurospora crassa.”
Graduate Supervisor: Dr. H.S. Chhatpar.
Maharaja Sayajirao University of Baroda, Baroda, India
1979 - 1981 M.Sc. in Microbiology Maharaja Sayajirao University of Baroda, Baroda, India
1976 - 1979 B.Sc. in Microbiology Gujarat University, Ahmedabad, India

Honors

  • Aegis Graham Bell Award for ‘Innovation in Mobile Health’ for research conducted on "Low Cost Device and Cloud Enabled Smart Solution for Diabetes Care", New Delhi, February, 2018.
  • Poster presentation 1st Prize and cash award, Program Management Unit at Biotechnology Industry Research Assistance Council (PMU-BIRAC), New Delhi, March, 2017
  • Invited to participate 5 year transformative technologies Portfolio Review in Seattle from 18-22 July 2016 by the Bill and Melinda Gates Foundation, Seattle, USA, July, 2016
  • Expert advisory panel member on 'Sustainable Non-sewered Sanitation Standard' conclave, The American National Standards Institute (ANSI), with support from the Bill & Melinda Gates Foundation, Singapore, May 2015
  • Non-ex-officio member of the Finance Committee, National Center for Cell Science, Pune, India, August 2015
  • Member, DBT Task Force, Department of Biotechnology, Government of India, June 2014
  • Recipient of Bill and Melinda GATES Foundation – Department of Biotechnology, GOI/BIRAC Grand Challenge Award, March 2014
  • Member of Appraisal Committee, The Modified Special Incentive Package Scheme (M-SIPS), Govt. of India Ministry of Communication and Information Technology- Department of Electronics and Information Technology (DeitY) 2013
  • Member, Governing Body, National Center for Cell Science, Pune, India, May 2013
  • Associate Editor, Current Pharmacogenomics and Personalized Medicine, August 2013
  • Coordinator, TIFAC, Centre of Relevance and Excellence in Biomedical Technology, Dept. of Science and Technology, Government of India
  • Recipient of the Cora Louis Carson award for the best ranked grant at the Peer Review of the American Heart Association, Tennessee Affiliate, USA, March 1992
  • Recipient of Grant-in Aid awarded by American Heart Association, Tennessee Affiliate, USA, 1992-1993
  • Recipient of Post-doctoral Research Fellowship awarded by American Heart Association, Tennessee Affiliate, USA, 1990-1992
  • Recipient of Senior Research Fellowship, awarded by Dept of Atomic Energy, Govt. of India, 1983-1985
  • Recipient of Junior Research Fellowship, awarded by Dept of Atomic Energy, Govt. of India, 1982-1983

Roles

  • External Examiner for Ph.D. thesis evaluation, Manipal University, June, 2018
  • External Examiner for Ph.D. thesis evaluation, IIT Mumbai, June,2014
  • External Examiner for Ph.D. thesis evaluation, Bharathidasan  University,Tiruchirappalli, Tamilnadu.

Teaching

Professional Appointments

Year Affiliation
Nov 2017 - Present Dean, Faculty of Sciences, Amrita Vishwa Vidyapeetham
Jul 2007 - Present Dean, School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam, Kerala, India and Coordinator Dept. of Science and Technology-TIFAC CORE in Biomedical Technology
Nov 2004 -  Jun 2007 Professor and Chairman, Centre for Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam, Kerala, India, Coordinator Dept. of Science and Technology-TIFAC CORE in Biomedical Technology
2000 - 2004 Research Manager, Lead Discovery, MDS Pharma Services, Bothell, WA.
Management of High Throughput Screening projects for worldwide client base Exploration/ Investigation of novel technologies and platforms to integrate High Throughput Screening technologies and dramatically accelerate identification of quality lead compounds
1995 - 2000 Senior Scientist, Drug Discovery Services, MDS Panlabs, Bothell, WA.
Management of screening data using an in-house Laboratory Information Management system (LIMS)
Exploration/ Investigation of novel technologies and platforms to integrate High Throughput Screening technologies and dramatically accelerate identification of quality lead compounds. Successful coordination of wide diversity of High Throughput Screening projects for world-wide client base.
1993 - 1995 Scientist, Panlabs Inc.  Bothell, WA.
Development of novel assays employing new technologies and assay procedures.
High Throughput Screening of Natural Products and Chemical libraries against wide diversity of targets employing absorbance, radiometric, fluorometric and chemiluminescence formats in isolated membranes and whole cell analysis.
1991 - 1993 Instructor, Department of Pharmacology, School of Medicine, University of Tennessee, Memphis; USA
Supervisor: Dr. M. Heimberg
1987 - 1991 Postdoctoral Research Associate;  Department of Pharmacology, School of Medicine, University of Tennessee, Memphis, USA with Dr. T.B. Patel
1986 – 1987 Postdoctoral Fellow;  Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi, USA  with Dr. A.J. Wahba. Worked on regulation of protein synthesis initiation in rabbit reticulocytes
1982 - 1983 Teaching Assistant; Maharaja Sayajirao University of Baroda, India; Teaching courses in Microbiology and Biochemistry

Abstracts and Invited Talks

2018 Keynote talk: “Natural Products and the Molecular Basis of Therapeutics--Old Wine in a Defined New Bottle” First Cambridge OBOR International Conference, University of Cambridge, July 5-7, 2018.
2017 Keynote talk: “Harnessing the potential of microbes power for the micro(be)-grid” Technological Advancements in Power and Energy “TAP Energy 2017”, IEEE, Amritapuri, Kerala, Dec 21-23, 2017.
2017 Invited talk: “End to end low cost diabetes solution” Aegis Graham Bell Award Jury Round, Bombay, Nov 13-18, 2017.
2017 Invited talk: “Cost-Effective Device and Cloud Enabled Smart Solutions for Diabetes Care” ICACCI, Manipal University, Karnataka, Sept 13-16, 2017.
2016 Invited talk: “A low-cost device and cloud enabled smart solution for diabetes care” AIMS Research Synergy Day, AIMS Hospital, Kochi October 7, 2016
2016 Invited talk: “Integration of basic and translational research in modern Biotechnology” National Ilan University, May 23, 2016
2015 Invited talk: “Biomedicines and Diagnostics---Low-cost strategies and the path ahead” Annual Diri Symposium 2015 International Symposium On Translational Research, December 6-9, 2015, Teri Retreat, Gual Pahari, New Delhi
2015 Invited talk: ‘Harnessing natural resources for a better tomorrow’ Date: November 12 2015, University of Cambridge
2015 United Nations Academic Impact and Amrita Vishwa Vidyapeetham hosted Skills and Technology Accelerating Rapid Transformation [START] Conference on Technology for Sustainable Development."Harnessing Natural Resources for a Better Tomorrow" July 8, 2015 at the United Nations Head Quarters in New York.
2015 Natural Product Modulator of Matrix Metalloproteinases. Tokyo University of Agriculture and Technology, Tokyo, Japan, April 24, 2015.
2014 Invited Talk: Natural products lead discovery. PSI 6th Annual meeting, Proteomics from Discovery to Function ,International Proteomics Conference (December 7-9, 2014) Indo-US Workshop and 6th PS(I) Conference to be held at IIT Bombay from December 6-9, 2014. Venue: Board Room, Fourth Floor, Victor Menezes Convention Centre, Indian Institute of Technology Bombay, Powai
2014 Invited talk: “Small molecule inhibitors of MMPs and EGF signaling pathway in a highly metastatic human epithelial cancer cell line” Indo-Australian Workshop on Biotechnology, School of Life Sciences Manipal University, April 11-13, 2014
2014 Invited talk: APA International conference on Polymers: Vision and Innovations (February 19-20, 2014),IIT Delhi
2013 Invited talk: “International conference on Integrating Basic and Translational Research in Modern Biology”, Department of Microbiology and Biotechnology center, The Maharaja Sayajirao University of Baroda, Vadodara. December 27-28, 2013.
2012 Life Science Conclave 2012 “Promoting business innovation to drive growth in LifeSciences” December 11-12, 2012, Topic Drying Drug Pipelines: Innovative Bio/Pharma Business Model, Stein Auditorium, India Habitat Centre, New Delhi Organized by Confederation of Industry, DBT, DST, BIRAC, Department of Pharmaceuticals Ministry of Chemicals and Fertilizers.
2009 Invited talk “Nanotechnology and its applications in Modern Drug Development and Delivery” Nano-09 UGC sponsored seminar on “Nanotechnology for Biomedical Applications” dated March 17, 2009, Sree Narayana College Chengannur, Alappuzha, Kerala.
2008 Invited talk “The Wound Healing Process - Prospects for the Mathematical Modelling” University of Milan, Italy, November 17, 2008.
2008 Invited talk “Green Pharmacy and the Environment”, in the National Seminar on Biotechnology for a Clean Environment at SN College, Kollam, October 15, 2008.
2008 Invited talk “Cell Manipulation in Drug Discovery”, in the Golden Jubilee Celebrations of the Department of Botany, Kerala University, Trivandrum, March 27, 2008.
2008 Invited talk “Cross talk between Signaling Systems” in the National Science Day Celebrations, Rajiv Gandhi Centre for Biotechnology, Trivandrum, February 28, 2008.
2007 Invited to present the theme paper “Nanotechnology in Drug Development & Delivery” in the 7th Annual conference of the Society of Veterinary Pharmacology and Toxicology, November 30, 2007.
2007 Invited talk “Drug discovery from Natural Sources”, in the Department of Botany/ Biotechnology, Kerala University, Trivandrum, April 9, 2007.
  Vishnu Prasad CN, Asoke Banerjee, Bipin G Nair, Anilkumar G Bauhinia fornificata leaf extract exhibits GLUT4 transloation activity Name of the Conference: 75th Annual Meeting of Society of Biological Chemists (India), Theme: Metabolism to Metabolome Name of the Organizer: Society of Biological Chemistry, New Delhi Conference Venue: Jawaharlal Nehru University, New Delhi Page No: 200.
2006 Suma Mohan, Jeff Perry, Bipin G Nair, Anilkumar G (2006) Structural Analysis of Class I facilitative Glucose Transporters Name of the Conference: INCOB 2006 Satellite meeting: Computational Insights into Biological Systems Duration of the Conference: Dec 2006 Name of the Organizer: Indian Institute of Science Conference Venue: Bangalore Page No: 48
2007 Vishnu Prasad, Asoke Banerjee, Bipin G Nair, Anilkumar G (2007) An aliphatic compound from Bauhinia acuminate enhances GLUT4 translocation and glucose uptake activity. Name of the Organizer: American Association of Cell Biology Conference Venue: Washington Page No: B412
2003 Karen Yoshino and Bipin Nair (2003) Extracellular Nucleotides Mediate Calcium Signaling Through Endogenous P2Y2 Receptors in Chinese Hamster Ovary Cells Society for Biomolecular Screening; 9th Annual Conference—Drug Discovery : At the Cutting Edge; September 21-25, 2003, Portland, Oregon, USA.
2001 B.G. Nair and Khisal Alvi. (2001) High Throughput Screening of Natural Products—More Than A Numbers Game. High Throughput Screening Instrumentation and Miniaturization; ISI sponsored 1st International Conference on Advances in High Throughput Screening Technologies, Atlantic City, New Jersey. Feb. 2001.
1994 B.G. Nair, C. Mckenzie, K. Leung and J. Paslay (1994) Characterization of Calcium -Activated Potassium Channel activity by a High Throughput Assay employing 86Rubidium Efflux. IBC Meeting on Signal Transduction Therapy; Advances in Understanding and Drug Discovery; San Francisco California, August 4-5, 1994.
1992 A.R. Amin, C.D. Swenson, B. Xue, B.G. Nair, T.B. Patel, and G.H. Thorbecke (1992) Upregulation of IgD-receptors on murine T Helper cells by IgD requires tyrosine kinase activity. 8th International Congress of Immunology, Budapest, Hungary, August 23-28, 1992.
1991 M. E. Steinhelper, B.G. Nair, H. M. Rashed, T.B. Patel, and L.J. Field (1991). Guanylate cyclase coupled ANF receptors are down regulated in hypotensive transgenic mice expressing a transthyretin-ANF fusion gene. FASEB Meeting, April 21-25, 1991. Abstract No. 1749. FASEB J. 5(4) p A671.
1991 C.D. Swenson, A.R. Amin, B. Xue, B. Nair and G.J. Thorbecke (1991). Mechanism of IgD-R upregulation on T cells from young and aged mice. FASEB Meeting, April 21-25, 1991, Atlanta, Georgia. Abstract No 2104. FASEB J. 5(4), p A732.
1991 B. G. Nair and T.B. Patel (1991) EGF receptor tyrosine kinase is essential for stimulation of rat cardiac adenylate cyclase by EGF. FASEB Meeting, April 21-25, 1991, Atlanta, Georgia. Abstract No 4718. FASEB J. 5 (5) p. A1184.
1990 L. Steinke, Y. Yu, H.M. Rashed, B.G. Nair, J.M. Seyer, and T.B. Patel (1990) Upregulation of the ANF receptor/Guanylate cyclase in regenerating rat liver. Joint meeting of American Society for Biochemistry and Molecular Biology and American Association of Immunologists. June 3-7, 1990. New Orleans, LA. Abstract No. 1702. FASEB J. 4(7), April 1990, p.A1986.
1990 B. G. Nair, G. Milligan, and T. B. Patel (1990). Gs mediates epidermal growth factor elicited stimulation of rat cardiac adenylate cyclase. Joint Meeting of the American Society for Biochemistry and Molecular Biology and American Association of Immunologists. June 3-7, 1990, New Orleans, Louisiana. Abstract No 515. FASEB J. 4(7), April 1990, pA1782.
1988 B. G. Nair, H.M. Rashed, and T.B. Patel (1989) Guanine nucleotide binding protein mediated regulation of rat cardiac adenylate cyclase by epidermal growth factor. Joint Meeting of the American Society of Biochemistry and Molecular Biology and American Society for Cell Biology. Jan 29 - February 2 1989, San Francisco, California. Abstract No. 3936. J. Cell. Biol. 107(6), December 1988, p.. 696a.
1988 T. B. Patel and B.G. Nair (1989) Regulation of rat hepatic adenylate cyclase by pyridine nucleotides. Joint Meeting of the American Society of Biochemistry and Molecular Biology and American Society for Cell Biology. January 29 - February 2, 1989. San Fransisco, California. Abstract No. 2786. J. Cell Biol. 107(6), December 1988, p495a.

Funded Projects

2016 - 2018 Cost-Effective Device and Cloud Enabled Smart solutions for diabetes care
Principal Investigator
Funded by BIRAC, Govt. of India
2015 - 2018 An innovative green technology for treating muncipal and industrial wastewater entering rivers and streams
Co-Principal Investigator
Funded by DBT, Govt. of India
2015 - 2018 Identification and Characterisation of the role of Allium sativum-microbiome on the production of the therapeutic metabolite
Co-Principal Investigator
Funded by SERB, DST, Govt. of India
2014 - 2016 Use of viral agents, microbial fuel cell and effec tive recycling strategy to improve the economics of human waste disposal
Principal Investigator
Funded by BIRAC & DBT, Govt. of India and The Bill & Melinda Gates Foundation
2013 - 2018 To strenthen the Post Graduate Teaching and Research Facilities in the department on 50:50 mode being a Private Academic Institution
Funded By FIST, Dept. of Science & Technology and Amrita Vishwa Vidyapeetham
2013 - 2016 Anarcadic Acid- A novel template for cancer therapy
Principal Investigator
Funded by CSIR, Govt. of India
2012 - 2016 Lab-on-a-chip(LOC) for the monitoring of diabetes, cholesterol and kidney function
Principal Investigator
Funded by DBT, Govt. of India
2012 - 2015 Development of peptide inhibitors against functional components of snake venom
Principal Investigator
Funded by SERB, DST, Govt. of India
2009 - 2013 Value addition to seabukthorn through isolation & characterisation of pharmacologically active compounds
Principal Investigator
Funded by Department of Biotechnology
2004 - 2010 Adaptive and automatic insulin pump
Principal Investigator
Funded by TIFAC-CORE, DST, Govt. of India

Research Article

Publications

Publication Type: Journal Article

Year of Publication Publication Type Title

2018

Journal Article

C. Porayath, Suresh, M. K., Dr. Raja Biswas, Dr. Bipin G. Nair, Dr. Nandita Mishra, and Dr. Sanjay Pal, “Autolysin Mediated Adherence of Staphylococcus Aureus with Fibronectin, Gelatin and Heparin”, International Journal of Biological Macromolecules, 2018.

2018

Journal Article

N. Babu, Advani, J., Solanki, H. S., Patel, K., Jain, A. P., Khan, A. Ahmad, Radhakrishnan, A., Sahasrabuddhe, N. A., Mathur, P. Prakash, Dr. Bipin G. Nair, Prasad, T. S. Keshava, Chang, X., Sidransky, D., Gowda, H., and Chatterjee, A., “miRNA and proteomic dysregulation in non-small cell lung cancer in response to cigarette smoke.”, Microrna, 2018.[Abstract]


BACKGROUND: Dysregulation of miRNAs is associated with the development of non-small cell lung cancer (NSCLC). It is imperative to study the dysregulation of miRNAs by cigarette smoke which will affect their targets, either leading to the overexpression of oncoproteins or downregulation of tumor suppressor proteins.

OBJECTIVE AND METHODS: In this study, we carried out miRNA sequencing and SILAC-based proteomic analysis of H358 cells chronically exposed to cigarette smoke condensate. Using bioinformatics analysis, we mapped the dysregulated miRNAs to differentially expressed target proteins identified in our data. Gene ontology-based enrichment and pathway analysis was performed using the deregulated targets to study the role of cigarette smoke-mediated miRNA dysregulation in NSCLC cell line.

RESULTS: miRNA sequencing resulted in the identification of 208 miRNAs, of which 6 miRNAs were found to be significantly dysregulated (2 fold, Log Base 2; p-value ≤ 0.05) in H358-Smoke cells. Proteomic analysis of the smoke exposed cells compared to the untreated parental cells resulted in the quantification of 2,610 proteins, of which 690 proteins were found to be differentially expressed (fold change ≥ 2). Gene ontology based analysis of target proteins revealed enrichment of proteins driving metabolism and a decrease in expression of proteins associated with immune response in the cells exposed to cigarette smoke. Pathway study using Ingenuity Pathway Analysis (IPA) revealed activation of NRF2-mediated oxidative stress response and actin-cytoskeleton signaling, and repression of protein kinase A signaling in H358-Smoke cells. We also identified 5 novel miRNAs in H358-Smoke cells using unassigned reads of small RNA-Seq dataset.

CONCLUSION: In summary, this study indicates that chronic exposure to cigarette smoke leads to widespread dysregulation of miRNAs and their targets, resulting in signaling aberrations in NSCLC cell line. The miRNAs and their targets identified in the study need to be further investigated to explore their role as potential therapeutic targets and/or molecular markers in NSCLC especially in smokers.

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2018

Journal Article

J. Haripriyan, Omanakuttan, A., Menon, N. D., Vanuopadath, M., Nair, S. Sadasivan, Corriden, R., Dr. Bipin G. Nair, Nizet, V., and Geetha B Kumar, “Clove Bud Oil Modulates Pathogenicity Phenotypes of the Opportunistic Human Pathogen Pseudomonas aeruginosa.”, Sci Rep, vol. 8, no. 1, p. 3437, 2018.[Abstract]


Earlier studies from our laboratory have demonstrated that clove bud oil (CBO) attenuates expression of certain virulence factors of Pseudomonas aeruginosa PAO1. Here, we probe more deeply into the effect of CBO on four pseudomonal proteases - elastase A, elastase B, protease IV and alkaline protease - each known to play key roles in disease pathogenesis. CBO inhibited the activity of these proteases present in the bacterial culture supernatant. Zymography studies indicated that these proteases can activate host matrix metalloproteases (MMPs) to establish infection, through conversion of pro-MMP-2 to active MMP-2. PAO1 is a predominant pathogen in burn wound infections and we show the modulatory effect of CBO on MMPs in an in vitro model of burn injury. Furthermore, CBO induced dose-dependent neutrophil extracellular trap formation in human neutrophils. CBO also increased the survival of C. elegans infected with PAO1, establishing an anti-infective role in a whole animal model of pathogenesis. LC-MS/MS analysis indicated that CBO treatment elicited a significant reduction of signalling molecules (Acyl-Homoserine-Lactone) involved in quorum sensing regulation. Our observations demonstrate that CBO attenuates key virulence mechanisms of this important human pathogen, while concomitantly enhancing host innate immunomodulatory functions, with potential implications for topical therapy against antibiotic-resistant infections.

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2018

Journal Article

D. Nedungadi, Binoy, A., Nanjan Pandurangan, Pal, S., Dr. Bipin G. Nair, and Dr. Nandita Mishra, “6-Shogaol Induces Caspase-independent Paraptosis in Cancer Cells Via Proteasomal Inhibition”, Exp Cell Res, vol. 364, no. 2, pp. 243-251, 2018.[Abstract]


An α, β-unsaturated carbonyl compound of ginger, 6-Shogaol (6S), induced extensive cytoplasmic vacuolation and cell death in breast cancer cell (MDA-MB-231) and non-small lung cancer (A549) cells. In the presence of autophagic inhibitors the cells continued to exhibit cytoplasmic vacuolation and cell death clearly distinguishing it from the classic autophagic process. 6S induced death did not exhibit the characteristic apoptotic features like caspase cleavage, phosphatidyl serine exposure and DNA fragmentation. The immunofluorescence with the Endoplasmic Reticulum (ER) resident protein, calreticulin indicated that the vacuoles were of ER origin, typical of paraptosis. This was supported by the increase in level of microtubule associated protein light chain 3B (LC3 I and LC3 II) and polyubiquitin binding protein, p62. The level of ER stress markers like polyubiquitinated proteins, Bip and CHOP also consistently increased. We have found that 6S inhibits the 26S proteasome. The proteasomal inhibitory activity was elucidated by a) molecular docking of 6S onto the active site of β5 subunit and b) reduced fluorescence by the fluorogenic substrate of the chymotrypsin-like subunit. In conclusion these studies demonstrate for the first time that proteasomal inhibition by 6S induces cell death via paraptosis. So 6-shogaol may act as a template for anti-cancer lead discovery against the apoptosis resistant cancer cells.

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2018

Journal Article

P. H, Dr. Bipin G. Nair, G, N., E, D. ’A., and Dr. Shyam Diwakar, “Understanding Cerebellum Granular Layer Network Computations through Mathematical Reconstructions of Evoked Local Field Potentials”, Annals of Neuroscience, vol. 25, pp. 11-24, 2018.[Abstract]


Background: The cerebellar granular layer input stage of cerebellum receives information from tactile and sensory regions of the body. The somatosensory activity in the cerebellar granular layer corresponds to sensory and tactile input has been observed by recording Local Field Potential (LFP) from the Crus-IIa regions of cerebellum in brain slices and in anesthetized animals. Purpose: In this paper, a detailed biophysical model of Wistar rat cerebellum granular layer network model and LFP modelling schemas were used to simulate circuit’s evoked response. Methods: Point Source Approximation and Line Source Approximation were used to reconstruct the network LFP. The LFP mechanism in in vitro was validated in network model and generated the in vivo LFP using the same mechanism. Results: The network simulations distinctly displayed the Trigeminal and Cortical (TC) wave components generated by 2 independent bursts implicating the generation of TC waves by 2 independent granule neuron populations. Induced plasticity was simulated to estimate granule neuron activation related population responses. As a prediction, cerebellar dysfunction (ataxia) was also studied using the model. Dysfunction at individual neurons in the network was affected by the population response. Conclusion: Our present study utilizes available knowledge on known mechanisms in a single cell and associates network function to population responses.

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2018

Journal Article

Dr. Shyam Diwakar, Dr. Bipin G. Nair, Medini, K. Chaitanya, Asha Vijayan, and Rajendran, A. G., “Computational Modelling of Cerebellum Granule Neuron Temporal Responses for Auditory and Visual Stimuli”, International Journal of Advanced Intelligence Paradigms, vol. 10, p. 1, 2018.

2018

Journal Article

M. Younis Bhat, Advani, J., Rajagopalan, P., Patel, K., Nanjappa, V., Solanki, H. S., Patil, A. H., Bhat, F. A., Mathur, P. P., Dr. Bipin G. Nair, Prasad, T. S. Keshava, Califano, J. A., Sidransky, D., Gowda, H., and Chatterjee, A., “Cigarette smoke and chewing tobacco alter expression of different sets of miRNAs in oral keratinocytes.”, Sci Rep, vol. 8, no. 1, p. 7040, 2018.[Abstract]


Carcinogenic effect of tobacco in oral cancer is through chewing and/or smoking. Significant differences exist in development of oral cancer between tobacco users and non-users. However, molecular alterations induced by different forms of tobacco are yet to be fully elucidated. We developed cellular models of chronic exposure to chewing tobacco and cigarette smoke using immortalized oral keratinocytes. Chronic exposure to tobacco resulted in increased cell scattering and invasiveness in immortalized oral keratinocytes. miRNA sequencing using Illumina HiSeq 2500 resulted in the identification of 10 significantly dysregulated miRNAs (4 fold; p ≤ 0.05) in chewing tobacco treated cells and 6 in cigarette smoke exposed cells. We integrated this data with global proteomic data and identified 36 protein targets that showed inverse expression pattern in chewing tobacco treated cells and 16 protein targets that showed inverse expression in smoke exposed cells. In addition, we identified 6 novel miRNAs in chewing tobacco treated cells and 18 novel miRNAs in smoke exposed cells. Integrative analysis of dysregulated miRNAs and their targets indicates that signaling mechanisms leading to oncogenic transformation are distinct between both forms of tobacco. Our study demonstrates alterations in miRNA expression in oral cells in response to two frequently used forms of tobacco.

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2018

Journal Article

P. Rajagopalan, Patel, K., Jain, A. P., Nanjappa, V., Datta, K. K., Subbannayya, T., Mangalaparthi, K. K., Kumari, A., Manoharan, M., Coral, K., Murugan, S., Dr. Bipin G. Nair, Prasad, T. S. Keshava, Mathur, P. P., Gupta, R., Gupta, R., Khanna-Gupta, A., Califano, J., Sidransky, D., Gowda, H., and Chatterjee, A., “Molecular alterations associated with chronic exposure to cigarette smoke and chewing tobacco in normal oral keratinocytes.”, Cancer Biol Ther, pp. 1-13, 2018.[Abstract]


Tobacco usage is a known risk factor associated with development of oral cancer. It is mainly consumed in two different forms (smoking and chewing) that vary in their composition and methods of intake. Despite being the leading cause of oral cancer, molecular alterations induced by tobacco are poorly understood. We therefore sought to investigate the adverse effects of cigarette smoke/chewing tobacco exposure in oral keratinocytes (OKF6/TERT1). OKF6/TERT1 cells acquired oncogenic phenotype after treating with cigarette smoke/chewing tobacco for a period of 8 months. We employed whole exome sequencing (WES) and quantitative proteomics to investigate the molecular alterations in oral keratinocytes chronically exposed to smoke/ chewing tobacco. Exome sequencing revealed distinct mutational spectrum and copy number alterations in smoke/ chewing tobacco treated cells. We also observed differences in proteomic alterations. Proteins downstream of MAPK1 and EGFR were dysregulated in smoke and chewing tobacco exposed cells, respectively. This study can serve as a reference for fundamental damages on oral cells as a consequence of exposure to different forms of tobacco.

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2018

Journal Article

J. Nambiar, Vijayakumar, G., Drishya, G., Shaji, S. K., Pandurangan, N., Kumar, G. B., and Dr. Bipin G. Nair, “(I-3,II-3)-Biacacetin-mediated cell death involves mitochondria.”, Mol Cell Biochem, 2018.[Abstract]


Dysregulation of the dynamic balance between cell proliferation and cell death leads to several malignancies including cancer. Biflavones are known to possess anti-proliferative activity against numerous cancer cell lines. The current study was undertaken to understand the mechanism of action of the biflavonoid (I-3,II-3)-biacacetin on MDA-MB-231. Biacacetin induces dose-dependent cell death in MDA-MB-231 cells from concentrations as low as 0.5 μM, which was further confirmed by an increase in sub-G1 cells. Furthermore, the cell death induced by biacacetin was found to be mitochondria-dependent, since cells devoid of mitochondria were viable in the presence of biacacetin even at the highest concentration tested (25 μM). Fluorescence studies clearly indicated nuclear changes and apoptotic body formation that are characteristic of apoptosis. These results were further corroborated by studies that demonstrate biacacetin to regulate several key markers of apoptosis like Caspase 3, p53, Bax, and poly-ADP-ribose polymerase-1. Furthermore, biacacetin did not induce cell death in normal macrophage cell line, RAW at concentrations up to 15 μM. In addition to MDA-MB-231 cells, biacacetin also induces apoptotic cell death in the highly chemo-resistant cell line, OVISE, where the cells stained positive for annexin. Biacacetin also induces cell death in the highly malignant fibrosarcoma cell line HT1080. Furthermore, biacacetin also induces significant cell death (50%) in 3D tumor spheroids, at a concentration of 25 μM. Taken together, these results provide an understanding of biacacetin-mediated cell death and thereby provides a strong basis for the use of such compounds as novel templates for anti-cancer therapeutics.

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2018

Journal Article

D. Nair, Krishna, J. Gopala, Panikkar, M. Velayudhan, Dr. Bipin G. Nair, Pai, J. Gopalakris, and Nair, S. Sadasivan, “Identification, purification, biochemical and mass spectrometric characterization of novel phycobiliproteins from a marine red alga, Centroceras clavulatum.”, Int J Biol Macromol, vol. 114, pp. 679-691, 2018.[Abstract]


Phycobilisomes are light-harvesting protein complexes and are widely distributed in red algae and cyanobacteria. Each phycobilisome contains highly fluorescent protein components called phycobiliproteins. Based upon the distinct physiochemical properties, phycobiliproteins are classified as allophycocyanin, phycocyanin, phycoerythrin and phycoerythrocyanin. In the present study, we describe purification and structural characterization of a novel phycocyanin and phycoerythrin isolated from a marine red macroalga, Centroceras clavulatum. The absorbance and fluorescence studies indicated that the purified proteins belong to R-Phycocyanin (R-PC) and R-Phycoerythrin (R-PE). The single bands under native-polyacrylamide gel electrophoresis revealed the intact molecular weights of R-PC and R-PE as 110kDa and 250kDa. The polypeptide compositions of the two proteins were demonstrated by SDS-PAGE. The result showed that R-PC contains two bands at 17 and 21kDa and were identified as α and β subunits through mass spectrometry based proteomics experiments. SDS-PAGE of R-PE showed three distinct bands at 18, 19 and 35kDa and was subsequently identified as α, β and γ subunits. The near-complete amino acid sequences of α and β subunits of R-PC and R-PE were derived from mass spectrometric data combined with Mascot software and multiple de novo sequencing tools followed by homology search and manual validation.

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2018

Journal Article

Manjusha Nair, Jinesh, M. K., Jayaraman, B., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Temporal constrained objects for modelling neuronal dynamics”, PeerJ Computer Science, vol. 4, p. e159, 2018.[Abstract]


Background Several new programming languages and technologies have emerged in the past few decades in order to ease the task of modelling complex systems. Modelling the dynamics of complex systems requires various levels of abstractions and reductive measures in representing the underlying behaviour. This also often requires making a trade-off between how realistic a model should be in order to address the scientific questions of interest and the computational tractability of the model. Methods In this paper, we propose a novel programming paradigm, called \textit{temporal constrained objects,} which facilitates a principled approach to modelling complex dynamical systems. \textit{Temporal constrained objects} are an extension of \textit{constrained objects} with a focus on the analysis and prediction of the dynamic behaviour of a system. The structural aspects of a neuronal system are represented using objects, as in object-oriented languages, while the dynamic behaviour of neurons and synapses are modelled using declarative temporal constraints. Computation in this paradigm is a process of constraint satisfaction within a time-based simulation. Results We identified the feasibility and practicality in automatically mapping different kinds of neuron and synapse models to the constraints of \textit{temporal constrained objects}. Simple neuronal networks were modelled by composing circuit components, implicitly satisfying the internal constraints of each component and interface constraints of the composition. Simulations show that \textit{temporal constrained objects} provide significant conciseness in the formulation of these models. The underlying computational engine employed here automatically finds the solutions to the problems stated, reducing the code for modelling and simulation control. All examples reported in this paper have been programmed and successfully tested using the prototype language called TCOB. The code along with the programming environment are available at http://github.com/compneuro/TCOB_Neuron. Discussion \textit{Temporal constrained objects} provide powerful capabilities for modelling the structural and dynamic aspects of neural systems. Capabilities of the constraint programming paradigm, such as declarative specification, the ability to express partial information and non-directionality, and capabilities of the object-oriented paradigm especially aggregation and inheritance, make this paradigm the right candidate for complex systems and computational modelling studies. With the advent of multi-core parallel computer architectures and techniques or parallel constraint-solving, the paradigm of \textit{temporal constrained objects} lends itself to highly efficient execution which is necessary for modelling and simulation of large brain circuits.

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2017

Journal Article

Asha Vijayan, Chaitanya Nutakki, Dhanush Kumar, Dr. Krishnashree Achuthan, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Enabling a freely accessible open source remotely controlled robotic articulator with a neuro-inspired control algorithm”, International Journal of Interactive Mobile Technologies, vol. 13, no. 1, pp. 61-75, 2017.[Abstract]


Internet-enabled technologies for robotics education are gaining importance as online platforms facilitating and promoting skill training. Understanding the use and design of robotics is now introduced at university undergraduate levels, but in developing economies establishing usable hardware and software platforms face several challenges like cost, equipment etc. Remote labs help providing alternatives to some of the challenges. We developed an online laboratory for bioinspired robotics using a low-cost 6 degree-of-freedom robotic articulator with a neuro-inspired controller. Cerebellum-inspired neural network algorithm approximates forward and inverse kinematics for movement coordination. With over 210000 registered users, the remote lab has been perceived as an interactive online learning tool and a practice platform. Direct feedback from 60 students and 100 university teachers indicated that the remote laboratory motivated self-organized learning and was useful as teaching material to aid robotics skill education.

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PDF iconenabling-a-freely-accessible-open-source-remotely-controlled-robotic-articulator-with-a-neuro-inspired-control-algorithm.pdf

2017

Journal Article

M. Dammalli, Murthy, K. R., Pinto, S. M., Murthy, K. Babu, Nirujogi, R. Sekhar, Madugundu, A. K., Dey, G., Dr. Bipin G. Nair, Gowda, H., and Prasad, T. Subrahmany, “Toward Postgenomics Ophthalmology: A Proteomic Map of the Human Choroid-Retinal Pigment Epithelium Tissue.”, OMICS, vol. 21, no. 2, pp. 114-122, 2017.[Abstract]


Ophthalmology and visual health research have received relatively limited attention from the personalized medicine community, but this trend is rapidly changing. Postgenomics technologies such as proteomics are being utilized to establish a baseline biological variation map of the human eye and related tissues. In this context, the choroid is the vascular layer situated between the outer sclera and the inner retina. The choroidal circulation serves the photoreceptors and retinal pigment epithelium (RPE). The RPE is a layer of cuboidal epithelial cells adjacent to the neurosensory retina and maintains the outer limit of the blood-retina barrier. Abnormal changes in choroid-RPE layers have been associated with age-related macular degeneration. We report here the proteome of the healthy human choroid-RPE complex, using reverse phase liquid chromatography and mass spectrometry-based proteomics. A total of 5309 nonredundant proteins were identified. Functional analysis of the identified proteins further pointed to molecular targets related to protein metabolism, regulation of nucleic acid metabolism, transport, cell growth, and/or maintenance and immune response. The top canonical pathways in which the choroid proteins participated were integrin signaling, mitochondrial dysfunction, regulation of eIF4 and p70S6K signaling, and clathrin-mediated endocytosis signaling. This study illustrates the largest number of proteins identified in human choroid-RPE complex to date and might serve as a valuable resource for future investigations and biomarker discovery in support of postgenomics ophthalmology and precision medicine.

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2017

Journal Article

J. Raveendran, P.E., R., Dr. Ramachandran T., Dr. Bipin G. Nair, and Dr. Satheesh Babu T. G., “Fabrication of a disposable non-enzymatic electrochemical creatinine sensor”, Sensors and Actuators B: Chemical, vol. 243, pp. 589 - 595, 2017.[Abstract]


Abstract A disposable non-enzymatic sensor for creatinine was developed by electrodepositing copper on screen printed carbon electrodes. The sensor was characterized using electrochemical and microscopic techniques. Electrochemical detection of creatinine was carried out in phosphate buffer solution of pH 7.4. The estimation was based on the formation of soluble copper-creatinine complex. The formation of copper-creatinine complex was established using the pseudoperoxidase activity of copper-creatinine complex. The sensor showed a detection limit of 0.0746 μM with a linear range of 6–378 μΜ. The sensor exhibited a stable response to creatinine and found to be free from interference from molecules like urea, glucose, ascorbic acid and dopamine. Real sample analysis was carried out with blood serum.

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PDF iconfabrication-of-a-disposable-non-enzymatic-electrochemical-creatinine-sensor-29november2017.pdf

2017

Journal Article

D. Sunilkumar, Bose, C., Shaji, S. K., Nanjan Pandurangan, Geetha B Kumar, Asoke Banerji, and Dr. Bipin G. Nair, “Coconut Shell Derived Bioactive Compound Oxyresveratrol Mediates Regulation Of Matrix Metalloproteinase 9”, International Journal of Pharma and Bio Sciences, vol. 8, no. 1, pp. 202 – 210, 2017.

2017

Journal Article

J. Advani, Subbannayya, Y., Patel, K., Khan, A. Ahmad, Patil, A. H., Jain, A. P., Solanki, H. S., Radhakrishnan, A., Pinto, S. M., Sahasrabuddhe, N. A., Thomas, J. K., Mathur, P. P., Dr. Bipin G. Nair, Chang, X., Prasad, T. S. Keshava, Sidransky, D., Gowda, H., and Chatterjee, A., “Long-Term Cigarette Smoke Exposure and Changes in MiRNA Expression and Proteome in Non-Small-Cell Lung Cancer”, OMICS, vol. 21, no. 7, pp. 390-403, 2017.[Abstract]


Chronic exposure to cigarette smoke markedly increases the risk for lung cancer. Regulation of gene expression at the post-transcriptional level by miRNAs influences a variety of cancer-related interactomes. Yet, relatively little is known on the effects of long-term cigarette smoke exposure on miRNA expression and gene regulation. NCI-H292 (H292) is a cell line sensitive to cigarette smoke with mucoepidermoid characteristics in culture. We report, in this study, original observations on long-term (12 months) cigarette smoke effects in the H292 cell line, using microarray-based miRNA expression profiling, and stable isotopic labeling with amino acids in cell culture-based quantitative proteomic analysis. We identified 112 upregulated and 147 downregulated miRNAs (by twofold) in cigarette smoke-treated H292 cells. The liquid chromatography-tandem mass spectrometry analysis identified 3,959 proteins, of which, 303 proteins were overexpressed and 112 proteins downregulated (by twofold). We observed 39 miRNA target pairs (proven targets) that were differentially expressed in response to chronic cigarette smoke exposure. Gene ontology analysis of the target proteins revealed enrichment of proteins in biological processes driving metabolism, cell communication, and nucleic acid metabolism. Pathway analysis revealed the enrichment of phagosome maturation, antigen presentation pathway, nuclear factor erythroid 2-related factor 2-mediated oxidative stress response, and cholesterol biosynthesis pathways in cigarette smoke-exposed cells. In conclusion, this report makes an important contribution to knowledge on molecular changes in a lung cell line in response to long term cigarette smoke exposure. The findings might inform future strategies for drug target, biomarker and diagnostics innovation in lung cancer, and clinical oncology. These observations also call for further research on the extent to which continuing or stopping cigarette smoking in patients diagnosed with lung cancer translates into molecular and clinical outcomes.

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2017

Journal Article

J. Raveendran, Krishnan, R. G., Dr. Bipin G. Nair, and Dr. Satheesh Babu T. G., “Voltammetric determination of ascorbic acid by using a disposable screen printed electrode modified with Cu(OH)2 nanorods”, Microchimica Acta, pp. 1-7, 2017.[Abstract]


The authors describe a disposable non-enzymatic sensor for ascorbic acid (AA) that was obtained by modifying a screen printed electrode (SPE) with Cu(OH)2 nanorods (NRs). The NRs were synthesized by a wet chemical process which involves sequential addition of NH3 and NaOH to CuSO4 solution. NR formation was confirmed by thermogravimetric, spectroscopic, microscopic, and diffraction studies. The Cu(OH)2 NRs were mixed with carbon ink and printed onto an SPE. Electrochemical detection of AA was carried out at pH 7.4, at a typical voltage as low as 0 mV versus saturated calomel electrode with a scan rate of 100 mV/s, and is assumed to involve the chemical reduction of Cu(II) by AA followed by electrochemical oxidation of Cu(I). The sensor has a linear response in the 0.0125 to 10 mΜ AA concentration range. Response to AA is free from interference by urea, glucose, uric acid, dopamine, metal ions such as Fe2+, Zn2+ and Ni2+, NaCl, KCl and ethanol. It was applied to the determination of AA in a vitamin C tablet and in urine. [Figure not available: see fulltext.] © 2017 Springer-Verlag GmbH Austria

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2017

Journal Article

H. Sasidharakurup, Melethadathil, N., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “A Systems Model of Parkinson's Disease Using Biochemical Systems Theory”, OMICS, vol. 21, no. 8, pp. 454-464, 2017.[Abstract]


Parkinson's disease (PD), a neurodegenerative disorder, affects millions of people and has gained attention because of its clinical roles affecting behaviors related to motor and nonmotor symptoms. Although studies on PD from various aspects are becoming popular, few rely on predictive systems modeling approaches. Using Biochemical Systems Theory (BST), this article attempts to model and characterize dopaminergic cell death and understand pathophysiology of progression of PD. PD pathways were modeled using stochastic differential equations incorporating law of mass action, and initial concentrations for the modeled proteins were obtained from literature. Simulations suggest that dopamine levels were reduced significantly due to an increase in dopaminergic quinones and 3,4-dihydroxyphenylacetaldehyde (DOPAL) relating to imbalances compared to control during PD progression. Associating to clinically observed PD-related cell death, simulations show abnormal parkin and reactive oxygen species levels with an increase in neurofibrillary tangles. While relating molecular mechanistic roles, the BST modeling helps predicting dopaminergic cell death processes involved in the progression of PD and provides a predictive understanding of neuronal dysfunction for translational neuroscience.

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2017

Journal Article

Chandni P, Amrita Salim, Archana P. V., Pradeesh Babu, Dr. Bipin G. Nair, Madhavan, A., and Dr. Sanjay Pal, “Characterization of the bacteriophages binding to human matrix molecules.”, International Journal of Biological Macromolecules, 2017.[Abstract]


Recent literature has suggested a novel symbiotic relationship between bacteriophage and metazoan host that provides antimicrobial defense protecting mucosal surface by binding to host matrix mucin glycoproteins. Here, we isolated and studied different bacteriophages that specifically interact with human extracellular matrix molecules such as fibronectin, gelatin, heparin and demonstrated their potency for protection to host against microbial infections. We showed that subpopulations of bacteriophages that work against clinical isolates of Escherichia coli can bind to pure gelatin, fibronectin and heparin and reduced bacterial load in human colon cell line HT29. The bacteriophages were characterized with respect to their genome sizes, melting curve patterns and host tropism (cross-reactivity with different hosts). Since, the bacteriophages are non-toxic to the host and can effectively reduce bacterial load in HT29 cell line their therapeutic potency against bacterial infection could be explored.

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2017

Journal Article

A. Ahmad Khan, Advani, J., Patel, K., Nanjappa, V., Solanki, H. S., Mathur, P. Prakash, Dr. Bipin G. Nair, Prasad, T. S. Keshava, Chatterjee, A., and Gowda, H., “Chronic exposure of cigarette smoke and chewing tobacco alters expression of microRNAs in esophageal epithelial cells.”, Microrna, 2017.[Abstract]


BACKGROUND: Esophageal squamous cell carcinoma (ESCC) is one of the most common cancers with high mortality rate. Cigarette smoke and chewing tobacco are well known risk factors associated with ESCC. However, molecular mechanisms associated with development of ESCC among smokers and chewers are poorly understood. MicroRNAs play an important role in regulating physiological and disease processes including esophageal cancer.

OBJECTIVE AND METHODS: In this study, we developed an in vitro model by treating non-neoplastic Het-1A esophageal cell line with cigarette smoke and chewing tobacco. We carried out miRNA sequencing on Illumina HiSeq 2500 platform and compared miRNA expression pattern across cigarette smoke and chewing tobacco treated Het-1A cells with untreated cells.

RESULTS: We identified and quantified 433 miRNAs in both smoke exposed and chewing tobacco treated cells, of which 13 miRNAs showed significantly altered expression in cigarette smoke exposed cells while 25 miRNAs showed significantly altered expression in chewing tobacco treated cells. In addition, we predicted novel miRNAs from these data-sets. We evaluated miRNAs that showed selective or context dependent expression pattern in cigarette smoke exposed or chewing tobacco treated cells.

CONCLUSIONS: In this study, we have comprehensively mapped miRNA expression pattern in response to cigarette smoke and chewing tobacco in Het-1A cells. We identified miRNAs that show altered expression in these cell models.

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2017

Journal Article

P. Chellaiah, Dr. Bipin G. Nair, Achuthan, K., and Diwakar, S., “Using theme-based narrative construct of images as passwords: Implementation and assessment of remembered sequences”, International Journal of Online Engineering, vol. 13, pp. 77-93, 2017.[Abstract]


With many online engineering platforms such as virtual and remote laboratories designed for young or aged users, user authentication and passwords-based methods are being re-evaluated for tracking usage patterns and security. For ICT-enabled online engineering platforms, image-based humancentric approaches are gaining relevance for access frameworks. With the rubber- hose attacks, increased senior users, many existing systems are vulnerable to many attacks. This paper employs human uniqueness of narrative skills on an image-based password system for online platforms with focus on theme in the password generation process. To generate the secret password, a specially designed computer game was used. We used narrative constructs composed of cartoon image sequences to generate user-speci!c secret key. The durability of generated passwords and the authentication process while assessing the reconstruction process by a potential hacker was verified. For validating use of coerced attacks, under imposed psychological duress, users failed retrieving the password sequence suggesting the reliability as an anti-coercive attack cybersecurity tool. A set of experiments were used to analyze user behavior behind the image-based password system. EEG measurements demonstrated increased activity of " rhythms in F3 and FC5 channel bins and augmented levels of α rhythms in F3 and O1 channels, suggesting users added personalization to authentication more than in alpha-numeric password-based logins.

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2017

Journal Article

A. G. Rajendran, Nutakki, C., Sasidharakurup, H., Bodda, S., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Cerebellum in Neurological Disorders: A Review on the Role of Inter-Connected Neural Circuits”, Journal of Neurology and Stroke, vol. 6, pp. 1-4, 2017.[Abstract]


Recent studies have indicated the additional role of cerebellum beyond motor coordination non-motor and socio-cognitive tasks. Exploration of cerebellar roles in timing and plasticity have been attributed specific roles in neurological conditions such as ataxia, severe disorders such as Parkinson's and epilepsy. Cerebellar dysfunctions elaborate the need of research on cerebellar circuitry and physiology to better understand neurological functions and dysfunctions. Structural and functional studies of cerebellum also implicate the connection between cerebellum with interconnected circuits such as thalamo cortical and basal ganglia networks during motor and non-motor functions. In this review, we list some of recently perceived roles of cerebellum in information processing, neurological conditions in disorders.

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2017

Journal Article

R. R, D, K., N, N., Dr. Krishnashree Achuthan, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Implementation of ICT-based Virtual Labs for Sustainable Laboratory Education in Universities”, CSI journal of Computing, vol. 3, no. 2, pp. 67-75, 2017.

2016

Journal Article

Ja H., Omanakuttan, Aa, Pandurangan, Na, Vargis, VbS., Maneesh, Mc, Dr. Bipin G. Nair, and Kumar, GaB., “Clove bud oil reduces kynurenine and inhibits pqs A gene expression in P. aeruginosa”, Applied microbiology and biotechnology, vol. 100, no. 8, pp. 3681-3692, 2016.[Abstract]


Quorum sensing (QS), a communication system involved in virulence of pathogenic bacteria like Pseudomonas aeruginosa is a promising target to combat multiple drug resistance. In vitro studies using clove bud oil (CBO) in P. aeruginosa revealed a concentration dependent attenuation of a variety of virulence factors including motility, extracellular DNA, exopolysaccharides and pigment production. Furthermore, treatment with CBO demonstrated a distinct dose-dependent reduction in biofilm formation as well as promoting dispersion of already formed biofilm, observations that were also supported by porcine skin ex vivo studies. Expression studies of genes involved in signalling systems of P. aeruginosa indicated a specific decrease in transcription of pqsA, but not in the lasI or rhlI levels. Additionally, the expression of vfr and gacA genes, involved in regulation, was also not affected by CBO treatment. CBO also influenced the PQS signalling pathway by decreasing the levels of kynurenine, an effect which was reversed by the addition of exogenous kynurenine. Though the synthesis of the signalling molecules of the Las and Rhl pathways was not affected by CBO, their activity was significantly affected, as observed by decrease in levels of their various effectors. Molecular modelling studies demonstrated that eugenol, the major component of CBO, favourably binds to the QS receptor by hydrophobic interactions as well as by hydrogen bonding with Arg61 and Tyr41 which are key amino acid residues of the LasR receptor. These results thus elucidate the molecular mechanism underlying the action of CBO and provide the basis for the identification of an attractive QS inhibitor. © 2016 Springer-Verlag Berlin Heidelberg

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2016

Journal Article

H. Jayalekshmi, Victus, N. Mary G., Anoop, R., Sarath, T. M., Sali, S., .Harikrishnan, C., Kaushik, N., Kumar, G. B., and Dr. Bipin G. Nair, “Combinatorial Effect of D-Amino Acids and Tetracycline Against P.aeruginosa Biofilm”, International Journal of Pharmacy and Pharmaceutical Sciences, vol. 8, no. 11, pp. 216-220., 2016.[Abstract]


Antimicrobial resistance is increasing worldwide and is of particular concern in gram-negative bacilli where there is a paucity of new and effective antimicrobial agents. Pseudomonas aeruginosa infections are associated with increased mortality and morbidity, especially in immunocompromised and burn patients respectively. The organism is capable of developing resistance to practically most classes of antibiotics and has always been considered a difficult target for antimicrobial chemotherapy because of the ability of bacteria to form biofilm. A biofilm is a structured consortium of bacteria, embedded in a self-produced polymer matrix consisting of polysaccharide, protein and DNA. Biofilm bacteria are a major concern in the treatment of infectious diseases. The objective of this work is to evaluate the efficacy of the combination of Tetracycline with different D-amino acids such as D-Leucine, D-Methionine, D-Tyrosine, and D-Tryptophan against P.aeruginosa biofilm. Sub-inhibitory concentrations of Tetracycline (0.5 MIC) along with different D-aminoacids were tested for its anti-biofilm activity. The validations of these results were done in in vitro wound dressing and ex vivo porcine skin models which shows that tetracycline-D-tryptophan combination could reduce biofilm formation. The studies using porcine skin explant confirms the efficacy of this combination for inhibiting the biofilm formation even in biological substances. The Hemocompatibility study shows no significant hemolysis by this combination. The results established the potential therapeutic application of D-aminoacids alone or in combination with tetracycline for treating biofilm associated clinical problems caused by P.aeruginosa.

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PDF iconcombinatorial-effect-of-d-aminoacids-and-tetracycline-against-pseudomonas-aeruginosa-biofilm-21september2016.pdf

2016

Journal Article

K. Dhara, Dr. Ramachandran T., Dr. Bipin G. Nair, and Dr. Satheesh Babu T. G., “Au nanoparticles decorated reduced graphene oxide for the fabrication of disposable nonenzymatic hydrogen peroxide sensor”, Journal of Electroanalytical Chemistry, vol. 764, pp. 64-70, 2016.[Abstract]


A simple approach is followed for the fabrication of disposable nonenzymatic hydrogen peroxide (H2O2) sensor using gold nanoparticles decorated reduced graphene oxide (Au/rGO) nanocomposite. Au/rGO nanocomposite was prepared by one pot reduction of graphene oxide and Au(III) ions. The composite was characterized using various spectroscopic and microscopic techniques. The Au/rGO nanocomposite suspension was cast on the indigenously fabricated screen printed electrode (SPE). Voltammetric studies on the modified electrode showed that the Au/rGO nanocomposite modified SPE have enhanced catalytic activity towards H2O2. The sensor exhibited linear relationship in the range from 20 μM to 10 mM with a sensitivity of 1238 μA mM- 1 cm- 2 and a limit of detection 0.1 μM. The sensor also showed excellent selectivity in presence of other electroactive species such as ascorbic acid, dopamine, glucose and uric acid. © 2016 Elsevier B.V. All rights reserved.

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2016

Journal Article

Dr. Shyam Diwakar, Radhamani, R., Hemalata Sasidharakurup, Dhanush Kumar, Nizar, N., Dr. Krishnashree Achuthan, and Dr. Bipin G. Nair, “Assessing students and teachers experience on simulation and remote biotechnology virtual labs: A case study with a light microscopy experiment”, Lecture Notes of the Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering, LNICST, vol. 160, pp. 44-51, 2016.[Abstract]


With recent trends of using Information and Communication Technologies in education, virtual labs have become more prevalent in classrooms of most schools and universities, especially in South India. The purpose of this paper was to perform a comparative analysis of virtual learning components such as animations, simulations and real-time remotely controlled experiments. As a part of this study, we conducted a series of biotechnology virtual lab workshops for University-level users within India and collected feedback related to the usage of virtual labs via direct approach. The survey amongst the students and teachers suggested simulation-based labs were more preferred in enhancing teaching and learning strategy compared to graphics-mediated animations and remotely controlled experiments. This paper also reports some of the issues faced by virtual lab users. Studies indicated that even though the web-based technologies are a new venture in education, it still poses adaptability issues. © Institute for Computer Sciences, Social Informatics and Telecommunications Engineering 2016.

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PDF iconassessing-students-and-teachers-experience-on-simulation-and-remote-biotechnology-virtual-labs-a-case-study-with-a-light microscopy experiment.pdf

2016

Journal Article

Dr. Shyam Diwakar, Dhanush Kumar, Radhamani, R., Sasidharakurup, H., Nizar, N., Dr. Krishnashree Achuthan, Prof. Nedungadi, P., Raghu Raman, and Dr. Bipin G. Nair, “Complementing Education via Virtual Labs: Implementation and Deployment of Remote Laboratories and Usage Analysis in South Indian Villages”, International Journal of Online Engineering (iJOE), vol. 12, no. 03, 2016.[Abstract]


ICT-enabled virtual and remote labs have become a platform augmenting user engagement in blended education scenarios enhancing University education in rural India.
A novel trend is the use of remote laboratories as learning and teaching tools in classrooms and elsewhere. This paper reports case studies based on our deployment of 20 web-based
virtual labs with more than 170+ online experiments in Biotechnology and Biomedical engineering discipline with content for undergraduate and postgraduate education.

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PDF iconcomplementing-education-via-virtual-labs-implementation-and deployment-of-emote-laboratories-and-usage-analysis-in-south-indian-villages.pdf

2016

Journal Article

S. Kalyanavenkataraman, Pandurangan Nanjan, Dr. Asoke Banerji, Dr. Bipin G. Nair, and Geetha B Kumar, “Discovery of arjunolic acid as a novel non-zinc binding carbonic anhydrase II inhibitor”, Bioorganic chemistry, vol. 66, pp. 72–79, 2016.[Abstract]


Elevated levels of carbonic anhydrase II (CA II) have been shown to be associated with cardiac hypertrophy and heart failure. Although arjunolic acid (AA) has a diverse range of therapeutic applications including cardio-protection, there have been no reports on the effect of AA on CA II. The present study describes for the first time, the novel zinc independent inhibition of CA II by AA. The molecular docking studies of AA indicated that the hydroxyl group at C2 of the A-ring, which hydrogen bonds with the catalytic site residues (His64, Asn62 and Asn67), along with the gem-dimethyl group at C20 of the E-ring, greatly influences the inhibitory activity, independent of the catalytic zinc, unlike the inhibition observed with most CA II inhibitors. Among the triterpenoids tested viz. arjunolic acid, arjunic acid, asiatic acid, oleanolic acid and ursolic acid, AA was the most potent in inhibiting CA II in vitro with an IC50 of 9 μM. It was interesting to note, that in spite of exhibiting very little differences in their structures, these triterpenoids exhibited vast differences in their inhibitory activities, with IC50 values ranging from 9 μM to as high as 333 μM. Furthermore, AA also inhibited the cytosolic activity of CA in H9c2 cardiomyocytes, as reflected by the decrease in acidification of the intracellular pH (pHi). The decreased acidification reduced the intracellular calcium levels, which further prevented the mitochondrial membrane depolarization. Thus, these studies provide a better understanding for establishing the novel molecular mechanism involved in CA II inhibition by the non-zinc binding inhibitor AA.

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2016

Journal Article

D. Nair, Vanuopadath, M., Dr. Bipin G. Nair, Dr. Jayashree G., and Nair, S. Sadasivan, “Identification and characterization of a library of surfactins and fengycins from a marine endophytic Bacillus sp.”, Journal of basic microbiology, vol. 56, pp. 1159–1172, 2016.[Abstract]


An endophytic bacterial strain from a marine green alga,Ulva lactuca, was isolated and identified by 16S rRNA gene sequencing method. The bacterial isolate was found to secrete two major families of cyclic depsilipopeptides, surfactins, and fengycins. Sequencing of the isolated lipopeptides was carried out using the MSndata obtained from an electrospray ionization (ESI) ion trap mass spectrometer coupled to an HPLC system. The assigned sequences were confirmed by a chemical derivatization approach involving esterification followed by mass spectrometric analysis. Distinction of leucine residues from isoleucine was established through a combined electron transfer dissociation-collision-induced dissociation (ETD-CID) method. The fengycins described in this study were found to cause significant delay of growth of two plants,Vigna radiata(mung bean) andOryza sativa(rice). To the best of our knowledge, this is the first study describing identification and characterization of cyclic peptides from an endophyticBacillus sp. isolated from marine algae.

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2016

Journal Article

Dr. Satheesh Babu T. G., Stanley, J., R, J. Sree, Ramachandran, T., and Dr. Bipin G. Nair, “Vertically aligned TiO2 nanotube arrays decorated with CuO mesoclusters for the nonenzymatic sensing of glucose”, Journal of Nanoscience and Nanotechnology, vol. 16, pp. 1-8, 2016.

2016

Journal Article

Dr. Satheesh Babu T. G., Dhara, K., Stanley, J., Ramachandran, T., and Dr. Bipin G. Nair, “Cupric oxide modified screen printed electrode for the nonenzymatic glucose sensing”, Journal of Nanoscience and Nanotechnology, vol. 16, no. 8, pp. 8772-8778, 2016.

2016

Journal Article

H. Parasuram, Dr. Bipin G. Nair, D‘Angelo, E., Hines, M., Naldi, G., and Dr. Shyam Diwakar, “Computational Modeling of Single Neuron Extracellular Electric Potentials and Network Local Field Potentials using LFPsim”, Frontiers in Computational Neuroscience, p. 10, 2016.[Abstract]


Local Field Potentials (LFPs) are population signals generated by complex spatiotemporal interaction of current sources and dipoles. Mathematical computations of LFPs allow the study of circuit functions and dysfunctions via simulations. This paper introduces LFPsim, a NEURON-based tool for computing population LFP activity and single neuron extracellular potentials. LFPsim was developed to be used on existing cable compartmental neuron and network models. Point source, line source, and RC based filter approximations can be used to compute extracellular activity. As a demonstration of efficient implementation, we showcase LFPs from mathematical models of electrotonically compact cerebellum granule neurons and morphologically complex neurons of the neocortical column. LFPsim reproduced neocortical LFP at 8, 32, and 56 Hz via current injection, in vitro post-synaptic N2a, N2b waves and in vivo T-C waves in cerebellum granular layer. LFPsim also includes a simulation of multi-electrode array of LFPs in network populations to aid computational inference between biophysical activity in neural networks and corresponding multi-unit activity resulting in extracellular and evoked LFP signals.

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PDF iconcomputational-modeling-of-single-neuron-extracellular-electric-potentialsand-network-local-field-potentials-using-lfpsim.pdf

2016

Journal Article

G. Sathe, Pinto, S. M., Syed, N., Nanjappa, V., Solanki, H. S., Renuse, S., Chavan, S., Khan, A. Ahmad, Patil, A. H., Nirujogi, R. Sekhar, Dr. Bipin G. Nair, Mathur, P. Prakash, Prasad, T. S. Keshava, Gowda, H., and Chatterjee, A., “Phosphotyrosine profiling of curcumin-induced signaling.”, Clinical proteomics, vol. 13, no. 1, p. 13, 2016.[Abstract]


BACKGROUND: Curcumin, derived from the rhizome Curcuma longa, is a natural anti-cancer agent and has been shown to inhibit proliferation and survival of tumor cells. Although the anti-cancer effects of curcumin are well established, detailed understanding of the signaling pathways altered by curcumin is still lacking. In this study, we carried out SILAC-based quantitative proteomic analysis of a HNSCC cell line (CAL 27) to investigate tyrosine signaling in response to curcumin.RESULTS: Using high resolution Orbitrap Fusion Tribrid Fourier transform mass spectrometer, we identified 627 phosphotyrosine sites mapping to 359 proteins. We observed alterations in the level of phosphorylation of 304 sites corresponding to 197 proteins upon curcumin treatment. We report here for the first time, curcumin-induced alterations in the phosphorylation of several kinases including TNK2, FRK, AXL, MAPK12 and phosphatases such as PTPN6, PTPRK, and INPPL1 among others. Pathway analysis revealed that the proteins differentially phosphorylated in response to curcumin are known to be involved in focal adhesion kinase signaling and actin cytoskeleton reorganization.CONCLUSIONS: The study indicates that curcumin may regulate cellular processes such as proliferation and migration through perturbation of the focal adhesion kinase pathway. This is the first quantitative phosphoproteomics-based study demonstrating the signaling events that are altered in response to curcumin. Considering the importance of curcumin as an anti-cancer agent, this study will significantly improve the current knowledge of curcumin-mediated signaling in cancer.

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PDF iconphosphotyrosine-profiling-of-curcumin‑induced-signaling-jan2016.pdf

2016

Journal Article

M. Bhattacharjee, Balakrishnan, L., Renuse, S., Advani, J., Goel, R., Sathe, G., Prasad, T. S. Keshava, Dr. Bipin G. Nair, Jois, R., Shankar, S., and Pandey, A., “Synovial fluid proteome in rheumatoid arthritis.”, Clinical proteomics, vol. 13, no. 1, p. 1, 2016.[Abstract]


BACKGROUND: Rheumatoid arthritis (RA) is a chronic autoinflammatory disorder that affects small joints. Despite intense efforts, there are currently no definitive markers for early diagnosis of RA and for monitoring the progression of this disease, though some of the markers like anti CCP antibodies and anti vimentin antibodies are promising. We sought to catalogue the proteins present in the synovial fluid of patients with RA. It was done with the aim of identifying newer biomarkers, if any, that might prove promising in future.METHODS: To enrich the low abundance proteins, we undertook two approaches-multiple affinity removal system (MARS14) to deplete some of the most abundant proteins and lectin affinity chromatography for enrichment of glycoproteins. The peptides were analyzed by LC-MS/MS on a high resolution Fourier transform mass spectrometer.RESULTS: This effort was the first total profiling of the synovial fluid proteome in RA that led to identification of 956 proteins. From the list, we identified a number of functionally significant proteins including vascular cell adhesion molecule-1, S100 proteins, AXL receptor protein tyrosine kinase, macrophage colony stimulating factor (M-CSF), programmed cell death ligand 2 (PDCD1LG2), TNF receptor 2, (TNFRSF1B) and many novel proteins including hyaluronan-binding protein 2, semaphorin 4A (SEMA4D) and osteoclast stimulating factor 1. Overall, our findings illustrate the complex and dynamic nature of RA in which multiple pathways seems to be participating actively.CONCLUSIONS: The use of high resolution mass spectrometry thus, enabled identification of proteins which might be critical to the progression of RA.

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PDF iconsynovial-fluid-proteome-in-rheumatoid-arthritis-december2016.pdf

2016

Journal Article

A. Hollands, Corriden, R., Gysler, G., Dahesh, S., Olson, J., Ali, S. Raza, Kunkel, M. T., Lin, A. E., Forli, S., Newton, A. C., Geetha B Kumar, Dr. Bipin G. Nair, J Perry, J. P., and Nizet, V., “Natural Product Anacardic Acid from Cashew Nut Shells Stimulates Neutrophil Extracellular Trap Production and Bactericidal Activity.”, Journal of Biological Chemistry, jbc-M115., 2016.[Abstract]


Emerging antibiotic resistance among pathogenic bacteria is an issue of great clinical importance, and new approaches to therapy are urgently needed. Anacardic acid, the primary active component of cashew nut shell extract, is a natural product used in the treatment of a variety of medical conditions, including infectious abscesses. Here, we investigate the effects of this natural product on the function of human neutrophils. We find that anacardic acid stimulates the production of reactive oxygen species and neutrophil extracellular traps, two mechanisms utilized by neutrophils to kill invading bacteria. Molecular modeling and pharmacological inhibitor studies suggest anacardic acid stimulation of neutrophils occurs in a PI3K-dependent manner through activation of surface-expressed G protein-coupled sphingosine-1-phosphate receptors. Neutrophil extracellular traps produced in response to anacardic acid are bactericidal and complement select direct antimicrobial activities of the compound.

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PDF iconnatural-product-anacardic-acid-from-cashew-nut-shells-stimulates-neutrophil-extracellular-trap-production-and-bactericidal-activity-13may2016.pdf

2016

Journal Article

T. Subbannayya, Variar, P., Advani, J., Dr. Bipin G. Nair, Shankar, S., Gowda, H., Saussez, S., Chatterjee, A., and Prasad, T. S. Keshava, “An integrated signal transduction network of macrophage migration inhibitory factor.”, Journal of cell communication and signaling, vol. 10, no. 2, pp. 165-170., 2016.[Abstract]


Macrophage migration inhibitory factor (MIF) is a glycosylated multi-functional protein that acts as an enzyme as well as a cytokine. MIF mediates its actions through a cell surface class II major histocompatibility chaperone, CD74 and co-receptors such as CD44, CXCR2, CXCR4 or CXCR7. MIF has been implicated in the pathogenesis of several acute and chronic inflammatory diseases. Although MIF is a molecule of biomedical importance, a public resource of MIF signaling pathway is currently lacking. In view of this, we carried out detailed data mining and documentation of the signaling events pertaining to MIF from published literature and developed an integrated reaction map of MIF signaling. This resulted in the cataloguing of 68 molecules belonging to MIF signaling pathway, which includes 24 protein-protein interactions, 44 post-translational modifications, 11 protein translocation events and 8 activation/inhibition events. In addition, 65 gene regulation events at the mRNA levels induced by MIF signaling have also been catalogued. This signaling pathway has been integrated into NetPath ( http://www.netpath.org ), a freely available human signaling pathway resource developed previously by our group. The MIF pathway data is freely available online in various community standard data exchange formats. We expect that data on signaling events and a detailed signaling map of MIF will provide the scientific community with an improved platform to facilitate further molecular as well as biomedical investigations on MIF.

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PDF iconintegrated-signal-transduction-network-macrophage-migration-inhibitory-factor-03may2016.pdf

2016

Journal Article

K. R. Murthy, Dammalli, M., Pinto, S. M., Murthy, K. Babu, Nirujogi, R. Sekhar, Madugundu, A. K., Dey, G., Subbannayya, Y., Mishra, U. Kumar, Dr. Bipin G. Nair, Gowda, H., and Prasad, T. S. Keshava, “A Comprehensive Proteomics Analysis of the Human Iris Tissue: Ready to Embrace Postgenomics Precision Medicine in Ophthalmology?”, OMICS: A Journal of Integrative Biology, vol. 20, no. 9, pp. 510-519, 2016.[Abstract]


The annual economic burden of visual disorders in the United States was estimated at $139 billion. Ophthalmology is therefore one of the salient application fields of postgenomics biotechnologies such as proteomics in the pursuit of global precision medicine. Interestingly, the protein composition of the human iris tissue still remains largely unexplored. In this context, the uveal tract constitutes the vascular middle coat of the eye and is formed by the choroid, ciliary body, and iris. The iris forms the anterior most part of the uvea. It is a thin muscular diaphragm with a central perforation called pupil. Inflammation of the uvea is termed uveitis and causes reduced vision or blindness. However, the pathogenesis of the spectrum of diseases causing uveitis is still not very well understood. We investigated the proteome of the iris tissue harvested from healthy donor eyes that were enucleated within 6 h of death using high-resolution Fourier transform mass spectrometry. A total of 4959 nonredundant proteins were identified in the human iris, which included proteins involved in signaling, cell communication, metabolism, immune response, and transport. This study is the first attempt to comprehensively profile the global proteome of the human iris tissue and, thus, offers the potential to facilitate biomedical research into pathological diseases of the uvea such as Behcet's disease, Vogt Koyonagi Harada's disease, and juvenile rheumatoid arthritis. Finally, we make a call to the broader visual health and ophthalmology community that proteomics offers a veritable prospect to obtain a systems scale, functional, and dynamic picture of the eye tissue in health and disease. This knowledge is ultimately pertinent for precision medicine diagnostics and therapeutics innovation to address the pressing needs of the 21st century visual health.

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2016

Journal Article

Aab Pradeep, Raveendran, Jac, Dr. Ramachandran T., Dr. Bipin G. Nair, and Dr. Satheesh Babu T. G., “Computational simulation and fabrication of smooth edged passive micromixers with alternately varying diameter for efficient mixing”, Microelectronic Engineering, vol. 165, pp. 32-40, 2016.[Abstract]


To improve the efficiency of passive micromixers, microchannels of varying geometry have been widely studied. A highly efficient passive micromixer was developed by alternatively varying the cross-sectional diameter along the flow. Microfluidic channels of various geometries were designed and the fluid flow patterns were studied using COMSOL Multiphysics. The extent of mixing in the microchannels for the various designs were analyzed and the most efficient micromixer was further optimized for best mixing performance. The optimized design was fabricated using direct laser write lithography. The spin speed, exposure energy, baking temperature, baking and development time were observed to play an important role in fabrication. Experimental evaluation of the simulation results was carried out by injecting coloured solutions through the PDMS microchannels and by electrochemical studies.

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2016

Journal Article

A. Omanakuttan, Bose, C., Pandurangan, N., Kumar, G. B., Banerji, A., and Dr. Bipin G. Nair, “Nitric Oxide and ERK mediates regulation of cellular processes by Ecdysterone”, Experimental Cell Research, vol. 346, no. 2, pp. 167-175, 2016.[Abstract]


The complex process of wound healing is a major problem associated with diabetes, venous or arterial disease, old age and infection. A wide range of pharmacological effects including anabolic, anti-diabetic and hepato-protective activities have been attributed to Ecdysterone. In earlier studies, Ecdysterone has been shown to modulate eNOS and iNOS expression in diabetic animals and activate osteogenic differentiation through the Extracellular-signal-Regulated Kinase (ERK) pathway in periodontal ligament stem cells. However, in the wound healing process, Ecdysterone has only been shown to enhance granulation tissue formation in rabbits. There have been no studies to date, which elucidate the molecular mechanism underlying the complex cellular process involved in wound healing. The present study, demonstrates a novel interaction between the phytosteroid Ecdysterone and Nitric Oxide Synthase (NOS), in an Epidermal Growth Factor Receptor (EGFR)-dependent manner, thereby promoting cell proliferation, cell spreading and cell migration. These observations were further supported by the 4-amino-5-methylamino- 2′, 7′ -difluorofluorescein diacetate (DAF FM) fluorescence assay which indicated that Ecdysterone activates NOS resulting in increased Nitric Oxide (NO) production. Additionally, studies with inhibitors of both the EGFR and ERK, demonstrated that Ecdysterone activates NOS through modulation of EGFR and ERK. These results clearly demonstrate, for the first time, that Ecdysterone enhances Nitric Oxide production and modulates complex cellular processes by activating ERK1/2 through the EGF pathway. © 2016

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PDF iconnitric-oxideand-erk-mediates-regulation-of-cellular-processes-by-ecdystrone-18july2016.pdf

2016

Journal Article

Ra Radhamani, Kumar, Da, Dr. Krishnashree Achuthan, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Implementing and deploying magnetic material testing as an online laboratory”, Advances in Intelligent Systems and Computing, vol. 530, pp. 925-934, 2016.[Abstract]


Hysteresis loop tracing (HLT) experiment is an undergraduate experiment for physics and engineering students to demonstrate magnetic properties of ferrite materials. In this paper, we explore a new approach of setting- up triggered testing of magnetic hysteresis via a remotely controlled loop tracer. To aid student learners, through an experimental design, we focused on factors such as analytical expression of mathematical model and modeling of reversible changes, which were crucial for learning hysterisis components. The goal was to study the phenomena of magnetic hysteresis and to calculate the retentivity, coercivity and saturation magnetization of a material using a hybrid model including simulation and remotely controlled hysteresis loop tracer. The remotely controlled equipment allowed recording the applied magnetic field (H) from an internet-enabled computer. To analyze learning experiences using online laboratories, we evaluated usage of online experiment among engineering students (N=200) by organized hands-on workshops and direct feedback collection. We found students adapted to use simualtions and remotely controlled lab equipment augmenting laboratory skills, equipment accessibility and blended learning experiences. © Springer International Publishing AG 2016.

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PDF iconimplementing-and-deploying-magnetic-material-testing-as-an-online-laboratory.pdf

2016

Journal Article

M. Vanuopadath, Nair, D., Dr. Bipin G. Nair, and Nair, S. Sadasivan, “Post-translational Modifications of Proteins: Biomarkers and Therapeutic Targets for Diabetes Related Complications”, Current Proteomics, 2016, vol. 13, 2016.[Abstract]


Diabetes Mellitus is a chronic metabolic disorder that is often associated with various complications including micro- and macro- angiopathies. The increase in mortality rates associated with these complications is one among the major factors that compels to define proper therapeutic strategies. Protein signatures including their post-translational modifications that are modulated under various disease conditions enabled the biomarker discovery processes and thereby facilitate to predict and diagnose the disease onset at an earlier stage. The identification of the post-translationally modified proteins not only enabled the biomarker prediction associated with various disease conditions but also has a great impact in target based drug discovery process. Mass spectrometry based proteome profiling aided the identification and characterization of these site specific modifications that had a huge impact on various functional aspects in a biological context. In this review, we tried to compile and discuss the information available regarding some of the modified proteins with regard to deregulated glucose metabolism. Several commonly observed modifications including glycosylation, hydroxylation, phosphorylation, nitration, nitrosylation and carbonylation that seem to have a major role in the management of diabetes disorders are summarized. Moreover, the importance and impact of less explored post-translational modifications such as palmitoylation, carbamylation, deamidation and SUMOylation that are associated to diabetes related complications are described. More »»

2016

Journal Article

Dr. Jyotsna Nambiar, Bose, C., Meera Venugopal, Dr. Asoke Banerji, Patel, T. B., Dr. Geetha Kumar, and Dr. Bipin G. Nair, “Anacardic acid inhibits gelatinases through the regulation of Spry2, MMP-14, EMMPRIN and RECK”, Experimental Cell Research, vol. 349, pp. 139-151, 2016.[Abstract]


Earlier studies from our laboratory have identified Anacardic acid (AA) as a potent inhibitor of gelatinases (MMP-2 and 9), which are over-expressed in a wide variety of cancers (Omanakuttan et al., 2012). Disruption of the finely tuned matrix metalloproteinase (MMP) activator/inhibitor balance plays a decisive role in determining the fate of the cell. The present study demonstrates for the first time, that in addition to regulating the expression as well as activity of gelatinases, AA also inhibits the expression of its endogenous activators like MMP-14 and Extracellular Matrix MetalloProteinase Inducer (EMMPRIN) and induces the expression of its endogenous inhibitor, REversion-inducing Cysteine-rich protein with Kazal motifs (RECK). In addition to modulating gelatinases, AA also inhibits the expression of various components of the Epidermal Growth Factor (EGF) pathway like EGF, Protein Kinase B (Akt) and Mitogen-activated protein kinases (MAPK). Furthermore, AA also activates the expression of Sprouty 2 (Spry2), a negative regulator of EGF pathway, and silencing Spry2 results in up-regulation of expression of gelatinases as well as MMP-14. The present study thus elucidates a novel mechanism of action of AA and provides a strong basis for utilizing this molecule as a template for cancer therapeutics.

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PDF iconanacardic-acid-inhibits-gelatinases-through-the-regulation-of-spry-2-mmp-14-emmprin-and-reck-11october2016.pdf

2016

Journal Article

P. Malvi, Chaube, B., Singh, S. Vikram, Mohammad, N., Pandey, V., Vijayakumar, M. Vavachan, Radhakrishnan, R. Meenatheri, Vanuopadath, M., Nair, S. Sadasivan, Dr. Bipin G. Nair, and Bhat, M. Kumar, “Weight control interventions improve therapeutic efficacy of dacarbazine in melanoma by reversing obesity-induced drug resistance.”, Cancer Metab, vol. 4, p. 21, 2016.[Abstract]


BACKGROUND: Obesity-related cellular, metabolic, and molecular alterations have been shown to increase cancer risk and tumor progression and are associated with poorer therapeutic outcome in cancer patients. However, the impact of obesity and weight-control interventions on the therapeutic response in melanoma is poorly understood.
METHODS: High fat diet (HFD)-induced obese mouse model was used in this study to evaluate the outcome of dacarbazine (DTIC) therapy in melanoma. We employed LC-MS/MS to determine the quantity of the drug in tumor, and in various tissues. Unique in vitro approach was used to complement in vivo findings by culturing melanoma cells in either conditioned medium (CM) obtained from differentiated adipocytes or in serum collected from experimental mice.
RESULTS: We report that diet-induced obesity impairs the outcome of DTIC therapy and reduces overall survival in tumor-bearing mice. We provide evidence that obesity restricts the accessibility of DTIC to tumor tissue. Critically, upon curtailing adiposity, accumulation and efficacy of DTIC is significantly improved. Moreover, using appropriate in vitro approaches, we show that melanoma cells exhibit a drug-resistant phenotype when cultured in serum collected from diet-induced obese mice or in CM collected from 3T3-L1 adipocytes. The impaired therapeutic response to DTIC in obese state is mediated by fatty acid synthase (FASN), caveolin-1 (Cav-1), and P-glycoprotein (P-gp). The response to DTIC and overall survival were improved upon employing weight control interventions in the tumor-bearing HFD-fed (obese) mice.

CONCLUSIONS: This study indicates that obesity not only supports rapid melanoma progression but also impairs the outcome of chemotherapy, which can be improved upon employing weight control interventions. From clinically relevant point of view, our study exemplifies the importance of lifestyle interventions in the treatment of obesity-promoted cancers.

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PDF iconweight-control-interventions-improve-therapeutic-efficacy-of-dacarbazine-in-melanoma-by-reversing-obesity-induced-drug-resistance-2016.pdf

2015

Journal Article

Ka Dhara, Dr. Ramachandran T., Dr. Bipin G. Nair, and Dr. Satheesh Babu T. G., “Single step synthesis of Au-CuO nanoparticles decorated reduced graphene oxide for high performance disposable nonenzymatic glucose sensor”, Journal of Electroanalytical Chemistry, vol. 743, pp. 1-9, 2015.[Abstract]


A nonenzymatic electrochemical glucose sensor was fabricated using gold-copper oxide nanoparticles decorated reduced graphene oxide (Au-CuO/rGO). A novel one step chemical process was employed for the synthesis of nanocomposite. Morphology and crystal planes of the nanocomposite were characterized using high resolution scanning electron microscopy (HRSEM) and X-ray diffraction (XRD) respectively. The Au-CuO/rGO nanocomposite was dispersed in N,N-dimethyl formamide (DMF) and drop-casted on the working area of the indigenously fabricated screen printed electrode (SPE). The sensor showed good electrocatalytic activity in alkaline medium for the direct electrooxidation of glucose with linear detection range of 1 μM to 12 mM and a lower detection limit of 0.1 μM. The sensor exhibited an excellent sensitivity 2356 μA mM- 1 cm- 2. Sensor was used for the determination of serum glucose concentration and the results obtained were compared with commercially available test strips. © 2015 Elsevier B.V. All rights reserved.

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PDF iconsingle-step-synthesis-of-au-cuo-nanoparticles-decorated-reduced-graphene-oxide-for-high-performance-disposable-nonenzymatic-glucose-sensor-2015.pdf

2015

Journal Article

Dr. Suneesh P. V., Sara, V. Vidhu, Dr. Ramachandran T., Dr. Bipin G. Nair, and Dr. Satheesh Babu T. G., “Co-Cu alloy nanoparticles decorated TiO2 nanotube arrays for highly sensitive and selective nonenzymatic sensing of glucose”, Sensors and Actuators, B: Chemical, vol. 215, pp. 337-344, 2015.[Abstract]


A nonenzymatic glucose sensor was fabricated by electrodepositing cobalt rich cobalt-copper alloy nanoparticles (Co-CuNPs) on vertically aligned TiO2 nanotube (TDNT) arrays. For this, TDNT arrays with tube diameter of 60 nm were synthesized by electrochemical anodization. The composition of the electrodeposited alloy was optimized based on the electrocatalytic activity towards glucose oxidation. This is achieved by controlling the concentration of electrolyte and time of deposition. Chemical composition of the optimized Co-Cu alloy nanoparticles is determined to be Cu0.15Co2.84O4 with fcc crystalline structure. The sensor showed two linear range of detection with high sensitivity of 4651.0 μA mM-1 cm-2 up to 5 mM and 2581.70 μA mM-1 cm-2 from 5 mM to 12 mM with a lower detection limit of 0.6 μM (S/N = 3). The sensor is highly selective to glucose in the presence of various exogeneous and endogeneous interfering species and other sugars. The response of the sensor towards blood serum was in good agreement with that of commercially available glucose sensors. © 2015 Elsevier B.V.

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PDF iconco–cu-alloy-nanoparticles-decorated-tio2-nanotube-arrays-for-highlysensitive-and-selective-nonenzymatic-sensing-of-glucose-2fdecember2015.pdf

2015

Journal Article

Pandurangan Nanjan, Dr. Jyotsna Nambiar, Dr. Bipin G. Nair, and Dr. Asoke Banerji, “Synthesis and Discovery of (I-3,II-3)-Biacacetin as a Novel Non-zinc Binding Inhibitor of MMP-2 and MMP-9”, Bioorganic & Medicinal Chemistry, vol. 23, pp. 3781 - 3787, 2015.[Abstract]


Abstract Eleven biflavones (7a–b and 9a–i) were synthesised by a simple and efficient protocol and screened for MMP-2 and MMP-9 inhibitory activities. Amongst them, a natural product-like analog, (I-3,II-3)-biacacetin (9h) was found to be the most potent inhibitor. Molecular docking studies suggest that unlike most of the known inhibitors, 9h inhibits MMP-2 and MMP-9 through non-zinc binding interactions.

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PDF iconsynthesis-and-discovery-of-I-3-II-3-biacacetin-as-a-novel-non-zinc-binding-inhibitor-of-mmp-2-and-mmp-9-29march2015.pdf

2015

Journal Article

Hemalata Sasidharakurup, Radhamani, R., Dhanush Kumar, Dr. Shyam Diwakar, Nizar, N., Dr. Bipin G. Nair, and Dr. Krishnashree Achuthan, “Using Virtual Laboratories as Interactive Textbooks: Studies on Blended Learning in Biotechnology Classrooms”, EAI Endorsed Trans. e-Learning, Accept., 2015.[Abstract]


Virtual laboratories, an ICT-based initiative, is a new venture that is becoming more prevalent in universities for improving classroom education. With geographically remote and economically constrained institutes in India as the focus, we developed web-based virtual labs for virtualizing the wet-lab techniques and experiments with the aid of graphics favoured animations, mathematical simulators and remote triggered experimentations. In this paper, we analysed perceived usefulness of Biotechnology virtual labs amongst student groups and its role in improving the student’s performance when introduced as a learning tool in a blended classroom scenario. A pedagogical survey, via workshops and online feedback, was carried out among 600 university-level students and 100 remote users of various Indian universities. Comparing learning groups on usage of blended learning approach against a control group (traditional classroom methods) and an experimental group (teacher-mediated virtual labs), our studies indicate augmented academic performance among students in blended environments. Findings also indicated usage of remotely-triggered labs aided enhancing interaction-based lab education enabling anytime-anywhere student participation scenarios.

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PDF iconusing-virtual-laboratories-interactive-textbooks-studies-blended-learning-biotechnology-01july2015.pdf

2015

Journal Article

E. S. Dove, İ Barlas, Ö., Birch, K., Boehme, C., Borda-Rodriguez, A., Byne, W. M., Chaverneff, F., Coşkun, Y., Dahl, M. - L., Dereli, T., Dr. Shyam Diwakar, Elbeyli, L., Endrenyi, L., Eroğlu-Kesim, B., Ferguson, L. R., Güngör, K., Gürsoy, U., Hekim, N., Huzair, F., Kaushik, K., Kickbusch, I., Kıroğlu, O., Kolker, E., Könönen, E., Lin, B., Llerena, A., Malha, F., Dr. Bipin G. Nair, Patrinos, G. P., Şardaş, S., Sert, Ö., Srivastava, S., Steuten, L. M. G., Toraman, C., Vayena, E., Wang, W., Warnich, L., and Özdemir, V., “An Appeal to the Global Health Community for a Tripartite Innovation: An “Essential Diagnostics List,”“Health in All Policies,” and “See-Through 21st Century Science and Ethics””, Omics: a journal of integrative biology, vol. 19, pp. 435–442, 2015.[Abstract]


Diagnostics spanning a wide range of new biotechnologies, including proteomics, metabolomics, and nanotechnology, are emerging as companion tests to innovative medicines. In this Opinion, we present the rationale for promulgating an “Essential Diagnostics List.” Additionally, we explain the ways in which adopting a vision for “Health in All Policies” could link essential diagnostics with robust and timely societal outcomes such as sustainable development, human rights, gender parity, and alleviation of poverty. We do so in three ways. First, we propose the need for a new, “see through” taxonomy for knowledge-based innovation as we transition from the material industries (e.g., textiles, plastic, cement, glass) dominant in the 20th century to the anticipated knowledge industry of the 21st century. If knowledge is the currency of the present century, then it is sensible to adopt an approach that thoroughly examines scientific knowledge, starting with the production aims, methods, quality, distribution, access, and the ends it purports to serve. Second, we explain that this knowledge trajectory focus on innovation is crucial and applicable across all sectors, including public, private, or public–private partnerships, as it underscores the fact that scientific knowledge is a co-product of technology, human values, and social systems. By making the value systems embedded in scientific design and knowledge co-production transparent, we all stand to benefit from sustainable and transparent science. Third, we appeal to the global health community to consider the necessary qualities of good governance for 21st century organizations that will embark on developing essential diagnostics. These have importance not only for science and knowledge-based innovation, but also for the ways in which we can build open, healthy, and peaceful civil societies today and for future generations.

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PDF iconan-appeal-to-the-global-health-community-for-a-tripartite-innovation-an-essential-diagnostics-list-health-in-all-policies-and-see-through-21-st-century-science-and-ethics-01August2015.pdf

2015

Journal Article

K. R. Murthy, Rajagopalan, P., Pinto, S. M., Advani, J., Murthy, P. R., Goel, R., Subbannayya, Y., Balakrishnan, L., Dash, M., Anil, A. K., Dey, G., Chatterjee, A., Gowda, H., Chakravarti, S., Shankar, S., Sahasrabuddhe, N. A., Dr. Bipin G. Nair, Somani, B. Lal, Keshava, P. T. S., and Pandey, A., “Proteomics of Human Aqueous Humor”, Omics: a journal of integrative biology, vol. 19, pp. 283–293, 2015.[Abstract]


The aqueous humor is a colorless, transparent fluid that fills the anterior chamber of the eye. It plays an important role in maintaining the intraocular pressure and providing nourishment to the lens and cornea. The constitution of the aqueous humor is controlled by the blood–aqueous barrier. Though this ocular fluid has been extensively studied, its role in ocular physiology is still not completely understood. In this study, aqueous humor samples were collected from 250 patients undergoing cataract surgery, subjected to multiple fractionation strategies and analyzed on a Fourier transform LTQ-Orbitrap Velos mass spectrometer. In all, we identified 763 proteins, of which 386 have been identified for the first time in this study. Sorbitol dehydrogenase (SORD), filensin (BFSP1), and phakinin (BFSP2) are some of the proteins that have not been previously reported in the aqueous humor. Gene Ontology analysis revealed 35% of the identified proteins to be extracellular, with a majority of them involved in cell communication and signal transduction. This study comprehensively reports 386 novel proteins that have important potential as biomarker candidates for future research into personalized medicine and diagnostics aimed towards improving visual health.

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PDF iconproteomics-of-human-aqueous-humor-01may2015.pdf

2015

Journal Article

Dr. Jyotsna Nambiar, G., K., S.R., S., S.N., G., R.S., L., and Dr. Bipin G. Nair, “A Novel2-Alkoxy-3, 5-Dihydroxypyridine Mediated Regulation of Gelatinases”, International Journal of Pharma and Bio Sciences, vol. 6, pp. 779-788, 2015.

2015

Journal Article

N. Mohammad, Singh, S. Vikram, Malvi, P., Chaube, B., Athavale, D., Vanuopadath, M., Nair, S. Sadasivan, Dr. Bipin G. Nair, and Bhat, M. Kumar, “Strategy to enhance efficacy of doxorubicin in solid tumor cells by methyl-β-cyclodextrin: Involvement of p53 and Fas receptor ligand complex”, Scientific reports, vol. 5, 2015.[Abstract]


Doxorubicin (DOX) is one of the preferred drugs for treating breast and liver cancers. However, its clinical application is limited due to severe side effects and the accompanying drug resistance. In this context, we investigated the effect on therapeutic efficacy of DOX by cholesterol depleting agent methyl-β-cyclodextrin (MCD), and explored the involvement of p53. MCD sensitizes MCF-7 and Hepa1-6 cells to DOX, Combination of MCD and marginal dose of DOX reduces the cell viability, and promoted apoptosis through induction of pro-apoptotic protein, Bax, activation of caspase-8 and caspase-7, down regulation of anti-apoptotic protein Bcl-2 and finally promoting PARP cleavage. Mechanistically, sensitization to DOX by MCD was due to the induction of FasR/FasL pathway through p53 activation. Furthermore, inhibition of p53 by pharmacological inhibitor pifithrin-α (PFT-α) or its specific siRNA attenuated p53 function and down-regulated FasR/FasL, thereby preventing cell death. Animal experiments were performed using C57BL/6J mouse isografted with Hepa1-6 cells. Tumor growth was retarded and survival increased in mice administered MCD together with DOX to as compared to either agent alone. Collectively, these results suggest that MCD enhances the sensitivity to DOX for which wild type p53 is an important determinant.

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PDF iconstrategy-enhance-efficacy-doxorubicin-solid-tumor-cells-methyl-cyclodextrin-involvement-of-p-53-and-fas-receptor-ligand-complex-01july2015.pdf

2015

Journal Article

K. Dhara, Dr. Ramachandran T., Dr. Bipin G. Nair, and Dr. Satheesh Babu T. G., “Highly sensitive and wide-range nonenzymatic disposable glucose sensor based on a screen printed carbon electrode modified with reduced graphene oxide and Pd-CuO nanoparticles”, Microchimica Acta, 2015.[Abstract]


A nanocomposite consisting of reduced graphene oxide decorated with palladium-copper oxide nanoparticles (Pd-CuO/rGO) was synthesized by single-step chemical reduction. The morphology and crystal structure of the nanocomposite were characterized by field-emission scanning electron microscopy, high resolution transmission electron microscopy and X-ray diffraction analysis. A 3-electrode system was fabricated by screen printing technology and the Pd-CuO/rGO nanocomposite was dropcast on the carbon working electrode. The catalytic activity towards glucose in 0.2 M NaOH solutions was analyzed by linear sweep voltammetry and amperometry. The steady state current obtained at a constant potential of +0.6 V (vs. Ag/AgCl) showed the modified electrode to possess a wide analytical range (6 μM to 22 mM), a rather low limit of detection (30 nM), excellent sensitivity (3355 μA∙mM−1∙cm−2) and good selectivity over commonly interfering species and other sugars including fructose, sucrose and lactose. The sensor was successfully employed to the determination of glucose in blood serum. [Figure not available: see fulltext.] © 2015 Springer-Verlag Wien

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PDF iconhighly-sensitive-and-wide-range-nonenzymatic-disposable-glucose-sensor-based-screen-printed-carbon-electrode-modified-with-reduced-graphene-oxide-and-pd-cuo-nanoparticles-08july2015.pdf

2015

Journal Article

S. Ray, Dr. Shyam Diwakar, Srivastava, S., and Dr. Bipin G. Nair, “E-learning resources and virtual labs”, Nature India Special Issue, pp. 13-14., 2015.[Abstract]


India’s recent strides in information technology have propelled the growth of web-based digital learning in most disciplines of science and engineering education. Distance education and open learning endeavours offer many advantages in resource-limited developing countries, where the number of potential learners is much higher than the number of experienced teachers or advanced educational institutes1.

However, these endeavours alone have proved insufficient in providing practical skills for science experiments or analysis of scientific data. Virtual laboratories, which act as free, round-the-clock replicas of actual laboratories, could be an effective alternative. Learners in a virtual laboratory can understand scientific theories and also experience practical experimental procedures2,3. As educational budgets in developing and under-developed countries continue to shrink, e-learning and open-learning programmes are gaining popularity4.

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PDF icone-learning-resources-and-virtual-labs.pdf

2015

Journal Article

Sa Muzaffar, Bose, C., Dr. Asoke Banerji, Dr. Bipin G. Nair, and Chattoo, B. Ba, “Anacardic acid induces apoptosis-like cell death in the rice blast fungus Magnaporthe oryzae”, Applied Microbiology and Biotechnology, 2015.[Abstract]


<p>Anacardic acid (6-pentadecylsalicylic acid), extracted from cashew nut shell liquid, is a natural phenolic lipid well known for its strong antibacterial, antioxidant, and anticancer activities. Its effect has been well studied in bacterial and mammalian systems but remains largely unexplored in fungi. The present study identifies antifungal, cytotoxic, and antioxidant activities of anacardic acid in the rice blast fungus Magnaporthe oryzae. It was found that anacardic acid causes inhibition of conidial germination and mycelial growth in this ascomycetous fungus. Phosphatidylserine externalization, chromatin condensation, DNA degradation, and loss of mitochondrial membrane potential suggest that growth inhibition of fungus is mainly caused by apoptosis-like cell death. Broad-spectrum caspase inhibitor Z-VAD-FMK treatment indicated that anacardic acid induces caspase-independent apoptosis in M. oryzae. Expression of a predicted ortholog of apoptosis-inducing factor (AIF) was upregulated during the process of apoptosis, suggesting the possibility of mitochondria dependent apoptosis via activation of apoptosis-inducing factor. Anacardic acid treatment leads to decrease in reactive oxygen species rather than increase in reactive oxygen species (ROS) accumulation normally observed during apoptosis, confirming the antioxidant properties of anacardic acid as suggested by earlier reports. Our study also shows that anacardic acid renders the fungus highly sensitive to DNA damaging agents like ethyl methanesulfonate (EMS). Treatment of rice leaves with anacardic acid prevents M. oryzae from infecting the plant without affecting the leaf, suggesting that anacardic acid can be an effective antifungal agent. © 2015 Springer-Verlag Berlin Heidelberg</p>

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PDF iconanacardic-acid-induces-apoptosis-cell-death-rice-blast-fungus-magnaporthe-oryzae-3august2015.pdf

2015

Journal Article

N. M., Dr. Bipin G. Nair, S., D., C., diSerio, A., N., and R., T., “GPGPU implementation of a spiking neuronal circuit performing sparse recoding”, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 8623, pp. 285-297, 2015.[Abstract]


Modeling and simulation techniques have been used extensively to study the complexities of brain circuits. Simulations of bio-realistic networks consisting of large number of neurons require massive computational power when they are designed to provide real-time responses in millisecond scale. A network model of cerebellar granular layer was developed and simulated here on Graphic Processing Units (GPU) which delivered a high compute capacity at low cost. We used a mathematical model namely, Adaptive Exponential leaky integrate-and-fire (AdEx) equations to model the different types of neurons in the cerebellum. The hypothesis relating spatiotemporal information processing in the input layer of the cerebellum and its relations to sparse activation of cell clusters was evaluated. The main goal of this paper was to understand the computational efficiency and scalability issues while implementing a large-scale microcircuit consisting of millions of neurons and synapses. The results suggest efficient scale-up based on pleasantly parallel modes of operations allows simulations of large-scale spiking network models for cerebellum-like network circuits. © Springer International Publishing Switzerland 2015.

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2015

Journal Article

T. Subbannayya, Leal-Rojas, P., Barbhuiya, M. A., Raja, R., Renuse, S., Sathe, G., Pinto, S. M., Syed, N., Nanjappa, V., Patil, A. H., and Dr. Bipin G. Nair, “Macrophage Migration Inhibitory Factor-a Therapeutic Target in Gallbladder Cancer”, BMC cancer, vol. 15, no. 1, p. 843, 2015.[Abstract]


Background

Poor prognosis in gallbladder cancer is due to late presentation of the disease, lack of reliable biomarkers for early diagnosis and limited targeted therapies. Early diagnostic markers and novel therapeutic targets can significantly improve clinical management of gallbladder cancer.

Methods

Proteomic analysis of four gallbladder cancer cell lines based on the invasive property (non-invasive to highly invasive) was carried out using the isobaric tags for relative and absolute quantitation labeling-based quantitative proteomic approach. The expression of macrophage migration inhibitory factor was analysed in gallbladder adenocarcinoma tissues using immunohistochemistry.&nbsp;In vitro&nbsp;cellular assays were carried out in a panel of gallbladder cancer cell lines using MIF inhibitors, ISO-1 and 4-IPP or its specific siRNA.

Results

The quantitative proteomic experiment led to the identification of 3,653 proteins, among which 654 were found to be overexpressed and 387 were downregulated in the invasive cell lines (OCUG-1, NOZ and GB-d1) compared to the non-invasive cell line, TGBC24TKB. Among these, macrophage migration inhibitory factor (MIF) was observed to be highly overexpressed in two of the invasive cell lines. MIF is a pleiotropic proinflammatory cytokine that plays a causative role in multiple diseases, including cancer. MIF has been reported to play a central role in tumor cell proliferation and invasion in several cancers. Immunohistochemical labeling of tumor tissue microarrays for MIF expression revealed that it was overexpressed in 21 of 29 gallbladder adenocarcinoma cases. Silencing/inhibition of MIF using siRNA and/or MIF antagonists resulted in a significant decrease in cell viability, colony forming ability and invasive property of the gallbladder cancer cells.

Conclusions

Our findings support the role of MIF in tumor aggressiveness and suggest its potential application as a therapeutic target for gallbladder cancer.

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PDF iconmacrophage-migration-inhibitory-factor-therapeutic-target-gallbladder-cancer-2015.pdf

2015

Journal Article

A. S. H. A. R. PAI and Dr. Bipin G. Nair, “Synthesis and Characterization of a Binary Oxide ZrO2–TiO2 and its Application in Chlorophyll Dye-Sensitized Solar Cell with Reduced Graphene Oxide as Counter Electrodes”, Bulletin of Materials Science, vol. 38, no. 5, pp. 1129-1133, 2015.[Abstract]


Natural dyes have been used to sensitize TiO2 nanocrystalline solar cells, but they still require pigment purification and co-adsorption of other compounds. In this study, nanocrystalline ZrO2–TiO2 films sensitized with the bioorganic dye, chlorophyll extracted from green leaves of Chromolaena odorata were investigated. The nanocrystalline ZrO2–TiO2 films were synthesized by the precipitation synthesis. The samples were characterized using X-ray diffraction, UV–vis absorption spectroscopy, Fourier transform infrared spectroscopy and scanning electron microscopy. The photoelectrodes were prepared using ZrO2–TiO2 sensitized with the chlorophyll dye and the counter electrodes using reduced graphene oxide. The shift in the absorption wavelength of chlorophyll showed an increase of adsorption of dye. The conversion efficiency was also studied.

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PDF iconsynthesis-and-characterization-binary-oxide-zro2-tio2-and-its-application-chlorophyll-dye-sensitized-solar-cell-with-reduced-graphene-oxide-as-counter-electrodes-16april2015.pdf

2015

Journal Article

V. Nanjappa, Renuse, S., Sathe, G. J., Raja, R., Syed, N., Radhakrishnan, A., Subbannayya, T., Patil, A., Marimuthu, A., Sahasrabuddhe, N. A., and Dr. Bipin G. Nair, “Chronic Exposure to Chewing Tobacco Selects for Overexpression of Stearoyl-CoA Desaturase in Normal Oral Keratinocytes”, Cancer biology & therapy, vol. 16, no. 11, pp. 1593-1603, 2015.[Abstract]


Chewing tobacco is a common practice in certain socio-economic sections of southern Asia, particularly in the Indian subcontinent and has been well associated with head and neck squamous cell carcinoma. The molecular mechanisms of chewing tobacco which leads to malignancy remains unclear. In large majority of studies, short-term exposure to tobacco has been evaluated. From a biological perspective, however, long-term (chronic) exposure to tobacco mimics the pathogenesis of oral cancer more closely. We developed a cell line model to investigate the chronic effects of chewing tobacco. Chronic exposure to tobacco resulted in higher cellular proliferation and invasive ability of the normal oral keratinocytes (OKF6/TERT1). We carried out quantitative proteomic analysis of OKF6/TERT1 cells chronically treated with chewing tobacco compared to the untreated cells. We identified a total of 3,636 proteins among which expression of 408 proteins were found to be significantly altered. Among the overexpressed proteins, stearoyl-CoA desaturase (SCD) was found to be 2.6-fold overexpressed in the tobacco treated cells. Silencing/inhibition of SCD using its specific siRNA or inhibitor led to a decrease in cellular proliferation, invasion and colony forming ability of not only the tobacco treated cells but also in a panel of head and neck cancer cell lines. These findings suggest that chronic exposure to chewing tobacco induced carcinogenesis in non-malignant oral epithelial cells and SCD plays an essential role in this process. The current study provides evidence that SCD can act as a potential therapeutic target in head and neck squamous cell carcinoma, especially in patients who are users of tobacco.

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PDF iconchronic-exposure-chewing-tobacco-selects-overexpression-stearoyl-coa-desaturase-normal-oral-keratinocytes-01september2015.pdf

2015

Journal Article

L. Dhevi N. Selvan, Sreenivasamurthy, S. K., Kumar, S., Yelamanchi, S. D., Madugundu, A. K., Anil, A. K., Renuse, S., Dr. Bipin G. Nair, Gowda, H., Mathur, P. P., Satishchandra, P., Shankar, S. K., Mahadevan, A., and Prasad, T. S. Keshava, “Characterization of Host Response to Cryptococcus Neoformans Through Quantitative Proteomic Analysis of Cryptococcal Meningitis Co-infected with HIV”, Mol. BioSyst., vol. 11, pp. 2529-2540, 2015.[Abstract]


Cryptococcal meningitis is the most common opportunistic fungal infection causing morbidity and mortality (&gt;60%) in HIV-associated immunocompromised individuals caused by Cryptococcus neoformans. Molecular mechanisms of cryptococcal infection in brain have been studied using experimental animal models and cell lines. There are limited studies for the molecular understanding of cryptococcal meningitis in human brain. The proteins involved in the process of invasion and infection in human brain still remains obscure. To this end we carried out mass spectrometry-based quantitative proteomics of frontal lobe brain tissues from cryptococcal meningitis patients and controls to identify host proteins that are associated with the pathogenesis of cryptococcal meningitis. We identified 317 proteins to be differentially expressed ([greater-than-or-equal]2-fold) from a total of 3423 human proteins. We found proteins involved in immune response and signal transduction to be differentially expressed in response to cryptococcal infection in human brain. Immune response proteins including complement factors{,} major histocompatibility proteins{,} proteins previously known to be involved in fungal invasion to brain such as caveolin 1 and actin were identified to be differentially expressed in cryptococcal meningitis brain tissues co-infected with HIV. We also validated the expression status of 5 proteins using immunohistochemistry. Overexpression of major histocompatibility complexes{,} class I{,} B (HLA-B){,} actin alpha 2 smooth muscle aorta (ACTA2) and caveolin 1 (CAV1) and downregulation of peripheral myelin protein 2 (PMP2) and alpha crystallin B chain (CRYAB) in cryptococcal meningitis were confirmed by IHC-based validation experiments. This study provides the brain proteome profile of cryptococcal meningitis co-infected with HIV for a better understanding of the host response associated with the disease.

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2015

Journal Article

P. V. Suneesh, Vargis, V. Sara, Ramachandran, T., Dr. Bipin G. Nair, and Babu, T. G. Satheesh, “Co–Cu alloy nanoparticles decorated TiO2 nanotube arrays for highly sensitive and selective nonenzymatic sensing of glucose”, Sensors and Actuators B: Chemical, vol. 215, pp. 337 - 344, 2015.[Abstract]


A nonenzymatic glucose sensor was fabricated by electrodepositing cobalt rich cobalt–copper alloy nanoparticles (Co–CuNPs) on vertically aligned TiO2 nanotube (TDNT) arrays. For this, TDNT arrays with tube diameter of 60nm were synthesized by electrochemical anodization. The composition of the electrodeposited alloy was optimized based on the electrocatalytic activity towards glucose oxidation. This is achieved by controlling the concentration of electrolyte and time of deposition. Chemical composition of the optimized Co–Cu alloy nanoparticles is determined to be Cu0.15Co2.84O4 with fcc crystalline structure. The sensor showed two linear range of detection with high sensitivity of 4651.0μAmM−1cm−2 up to 5mM and 2581.70μAmM−1cm−2 from 5mM to 12mM with a lower detection limit of 0.6μM (S/N=3). The sensor is highly selective to glucose in the presence of various exogeneous and endogeneous interfering species and other sugars. The response of the sensor towards blood serum was in good agreement with that of commercially available glucose sensors.

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2014

Journal Article

L. Dhevi Naga Selvan, Kaviyil, J. Embekkat, Nirujogi, R. Sekhar, Muthusamy, B., Puttamallesh, V. N., Subbannayya, T., Syed, N., Radhakrishnan, A., Kelkar, D. S., Ahmad, S., and Dr. Bipin G. Nair, “Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry”, Clinical proteomics, vol. 11, no. 1, p. 1, 2014.[Abstract]


Curcumin, derived from the rhizome Curcuma longa, is a natural anti-cancer agent and has been shown to inhibit proliferation and survival of tumor cells. Although the anti-cancer effects of curcumin are well established, detailed understanding of the signaling pathways altered by curcumin is still lacking. In this study, we carried out SILAC-based quantitative proteomic analysis of a HNSCC cell line (CAL 27) to investigate tyrosine signaling in response to curcumin. More »»
PDF iconproteogenomic-analysis-of-pathogenic-yeast-cryptococcus-neoformans-using high-resolution-mass-spectrometry-2015.pdf

2014

Journal Article

J. Kurian Thomas, Kim, M. - S., Balakrishnan, L., Nanjappa, V., Raju, R., Marimuthu, A., Radhakrishnan, A., Muthusamy, B., Khan, A. Ahmad, Sakamuri, S., Dr. Bipin G. Nair, Tankala, S. Gupta, Singal, M., Sirdeshmukh, R., Chatterjee, A., Prasad, T. S. Keshava, Maitra, A., Gowda, H., Hruban, R. H., and Pandey, A., “Pancreatic Cancer Database: An integrative resource for pancreatic cancer.”, Cancer biology & therapy, vol. 15, pp. 963-967, 2014.[Abstract]


Pancreatic cancer is the fourth leading cause of cancer-related death in the world. The etiology of pancreatic cancer is heterogeneous with a wide range of alterations that have already been reported at the level of the genome, transcriptome, and proteome. The past decade has witnessed a large number of experimental studies using high-throughput technology platforms to identify genes whose expression at the transcript or protein levels is altered in pancreatic cancer. Based on expression studies, a number of molecules have also been proposed as potential biomarkers for diagnosis and prognosis of this deadly cancer. Currently, there are no repositories which provide an integrative view of multiple Omics data sets from published research on pancreatic cancer. Here, we describe the development of a web-based resource, Pancreatic Cancer Database (http://www.pancreaticcancerdatabase.org), as a unified platform for pancreatic cancer research. PCD contains manually curated information pertaining to quantitative alterations in miRNA, mRNA, and proteins obtained from small-scale as well as high-throughput studies of pancreatic cancer tissues and cell lines. We believe that PCD will serve as an integrative platform for scientific community involved in pancreatic cancer research.

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PDF iconpancreatic-cancer-database-23april2014.pdf

2014

Journal Article

S. Bab Dwivedi, Muthusamy, Bac, Kumar, Pa, Kim, M. - Sd, Nirujogi, R. Sac, Getnet, Dd, Ahiakonu, Pe, De, Gaf, Dr. Bipin G. Nair, Gowda, Ha, Prasad, T. S. Kab c f, Kumar, Ng, Pandey, Aad h, and Okulate, Me, “Brain proteomics of anopheles gambiae”, OMICS A Journal of Integrative Biology, vol. 18, pp. 421-437, 2014.[Abstract]


Anopheles gambiae has a well-adapted system for host localization, feeding, and mating behavior, which are all governed by neuronal processes in the brain. However, there are no published reports characterizing the brain proteome to elucidate neuronal signaling mechanisms in the vector. To this end, a large-scale mapping of the brain proteome of An. gambiae was carried out using high resolution tandem mass spectrometry, revealing a repertoire of >1800 proteins, of which 15% could not be assigned any function. A large proportion of the identified proteins were predicted to be involved in diverse biological processes including metabolism, transport, protein synthesis, and olfaction. This study also led to the identification of 10 GPCR classes of proteins, which could govern sensory pathways in mosquitoes. Proteins involved in metabolic and neural processes, chromatin modeling, and synaptic vesicle transport associated with neuronal transmission were predominantly expressed in the brain. Proteogenomic analysis expanded our findings with the identification of 15 novel genes and 71 cases of gene refinements, a subset of which were validated by RT-PCR and sequencing. Overall, our study offers valuable insights into the brain physiology of the vector that could possibly open avenues for intervention strategies for malaria in the future. © Copyright 2014, Mary Ann Liebert, Inc. 2014.

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PDF iconbrain-proteomics-of-anopheles-gambiae-2014.pdf

2014

Journal Article

Nab Hekim, Coşkun, Yc, Sinav, Ad, Abou-Zeid, A. He, Aǧirbaşli, Mf, Akintola, S. Og, Aynacioǧlu, Sh, Bayram, Mij, Bragazzi, N. Lk, Dandara, Cl, Dereli, Tim, Dove, E. Sn, Elbeyli, Lo, Endrenyi, Lp, Erciyas, Kq, Faris, Jr, Ferguson, L. Rst, Göǧüş, Fj, Güngör, Ku, Gürsoy, Mv, Gürsoy, U. Kv, Karaömerlioǧlu, M. Aw, Kickbusch, Ix, Kiliç, Ty, Kilinç, Mz, Kocagöz, Taa, Lin, Babac, Llerena, Aadae, Manolopoulos, V. Gaf, Dr. Bipin G. Nair, Özkan, Bah, Pang, Tai, Şardaş, Saj, Srivastava, Sak, Toraman, Cal, Üstün, Kq, Warnich, Lam, Wonkam, Al, Yakicier, M. Can, Yaşar, Uao, and Özdemir, Vcag al ap, “Translating biotechnology to knowledge-based innovation, peace, and development? Deploy a science peace corps - An open letter to world leaders”, OMICS A Journal of Integrative Biology, vol. 18, pp. 415-420, 2014.[Abstract]


Scholarship knows no geographical boundaries. This science diplomacy and biotechnology journalism article introduces an original concept and policy petition to innovate the global translational science, a Science Peace Corps. Service at the new Corps could entail volunteer work for a minimum of 6 weeks, and up to a maximum of 2 years, for translational research in any region of the world to build capacity manifestly for development and peace, instead of the narrow bench-to-bedside model of life science translation. Topics for translational research are envisioned to include all fields of life sciences and medicine, as long as they are linked to potential or concrete endpoints in development, foreign policy, conflict management, post-crisis capacity building, and/or peace scholarship domains. As a new instrument in the global science and technology governance toolbox, a Science Peace Corps could work effectively, for example, towards elucidating the emerging concept of "one health" - encompassing human, environmental, plant, microbial, ecosystem, and planet health - thus serving as an innovative crosscutting pillar of 21st century integrative biology. An interdisciplinary program of this caliber for development would link 21st century life sciences to foreign policy and peace, in ways that can benefit many nations despite their ideological differences. We note that a Science Peace Corps is timely. The Intergovernmental Panel on Climate Change (IPCC) of the United Nations released the Fifth Assessment Report on March 31, 2014. Worrisomely, the report underscores that no person or nation will remain untouched by the climate change, highlighting the shared pressing life sciences challenges for global society. To this end, we recall that President John F. Kennedy advocated for volunteer work that has enduring, transgenerational, and global impacts. This culminated in establishment of the Peace Corps in 1961. Earlier, President Abraham Lincoln aptly observed, "nearly all men can stand adversity, but if you want to test a man's character, give him power." We therefore petition President Barack Obama, other world leaders, and international development agencies in positions of power around the globe, to consider deploying a Science Peace Corps to cultivate the essential (and presently missing) ties among life sciences, foreign policy, development, and peace agendas. A Science Peace Corps requires support by a credible and independent intergovernmental organization or development agency for funding, and arbitration in the course of volunteer work when the global versus local (glocal) value-based priorities and human rights intersect in synergy or conflict. In all, Science Peace Corps is an invitation to a new pathway for competence in 21st century science that is locally productive and globally competitive. It can open up scientific institutions to broader considerations and broader inputs, and thus cultivate vital translational science in a world sorely in need of solidarity and sustainable responses to the challenges of 21st century science and society. © Copyright 2014, Mary Ann Liebert, Inc. 2014.

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PDF icontranslating-biotechnology-knowledge-based-innovation-peace-and-development-deploy-a-science-peace-corps-an-open-letter-to-world-leaders-2014.pdf

2014

Journal Article

S. Renuse, Madugundu, A. K., Kumar, P., Dr. Bipin G. Nair, Gowda, H., Prasad, T. S. Keshava, and Pandey, A., “Proteomic analysis and genome annotation of Pichia pastoris, a recombinant protein expression host”, PROTEOMICS, vol. 14, pp. 2769–2779, 2014.[Abstract]


Pichia pastoris is a widely used eukaryotic host for production of recombinant proteins. We performed a proteogenomic analysis using high resolution Fourier transform MS to characterize the proteome of the GS115 strain. Our analysis resulted in identification of 46 889 unique peptides mapping to 3914 unique protein groups, which corresponds to ∼80% of the predicted genes. In addition, our proteogenomic analysis led to the discovery of 64 novel genes and correction of 11 predicted gene models. The strategy used here demonstrates the utility of high resolution MS-derived peptide sequence data to cover near complete proteomes of organisms. Given the popularity of P. pastoris as a protein expression host, this proteome map should provide a list of contaminants derived from the host to assist in optimization of heterologous protein production. All MS data have been deposited in the ProteomeXchange with identifier PXD000627.

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PDF iconproteomic-analysis-and-genome-annotation-pichia-pastoris-recombinant-protein-expression-host-2015.pdf

2014

Journal Article

K. R. Murthy, Goel, R., Subbannayya, Y., Jacob, H. K. C., Murthy, P. R., Manda, S. Srinivas, Patil, A. H., Sharma, R., Sahasrabuddhe, N. A., Parashar, A., Dr. Bipin G. Nair, Krishna, V., Prasad, T. S. Keshava, Gowda, H., and Pandey, A., “Proteomic analysis of human vitreous humor”, Clinical Proteomics, vol. 11, 2014.[Abstract]


Background: The vitreous humor is a transparent, gelatinous mass whose main constituent is water. It plays an important role in providing metabolic nutrient requirements of the lens, coordinating eye growth and providing support to the retina. It is in close proximity to the retina and reflects many of the changes occurring in this tissue. The biochemical changes occurring in the vitreous could provide a better understanding about the pathophysiological processes that occur in vitreoretinopathy. In this study, we investigated the proteome of normal human vitreous humor using high resolution Fourier transform mass spectrometry.
Results: The vitreous humor was subjected to multiple fractionation techniques followed by LC-MS/MS analysis. We identified 1,205 proteins, 682 of which have not been described previously in the vitreous humor. Most proteins were localized to the extracellular space (24%), cytoplasm (20%) or plasma membrane (14%). Classification based on molecular function showed that 27% had catalytic activity, 10% structural activity, 10% binding activity, 4% cell and 4% transporter activity. Categorization for biological processes showed 28% participate in metabolism, 20% in cell communication and 13% in cell growth. The data have been deposited to the ProteomeXchange with identifier PXD000957.
Conclusion: This large catalog of vitreous proteins should facilitate biomedical research into pathological conditions of the eye including diabetic retinopathy, retinal detachment and cataract.

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PDF iconproteomic-analysis-of-human-vitreous-humor-2014.pdf

2014

Journal Article

Dr. Shyam Diwakar, Dr. Bipin G. Nair, Sasidharakurup, H., Radhamani, R., Sujatha, G., Shekhar, A., Achuthan, K., Prof. Nedungadi, P., and Raghu Raman, “Usage and Diffusion of Biotechnology Virtual Labs for Enhancing University education in India’s Urban and Rural Areas”, E-Learning as a Socio-Cultural System: A Multidimensional Analysis, pp. 63-83, 2014.[Abstract]


Information and Communication Technology (ICT)-enabled virtual laboratories provide an online learning experience with the aid of computer-based instructional materials (animation, simulation, and remote-trigger experiments) for improving the active learning process. The project reported on in this chapter was set up in order to enhance university and college education, which is now becoming an advanced training environment for solving the geographical, social, and economic challenges faced in the interdisciplinary field of science education, especially in India. In order to study the role of biotechnology virtual laboratories in the current education system, a pedagogical survey, via workshops and online feedback, was carried out among several student and teacher groups of different Indian universities. This chapter reports how virtual labs in biotechnology can be used to improve teaching and learning experiences in an easy and understandable way with user interaction and how such tools serve to effectively reduce the problems of laboratory education especially in remote areas. The results obtained from user-feedback analysis suggest the use of virtual labs as a recommended component in blended education in large classroom scenarios for enhancing autonomous learning process and as an alternative to enhance lab education in geographically remote and economically challenged institutes.

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PDF iconusage-and-diffusion-of-biotechnology-virtual-labs-for-enhancing-university-education-in-india-s-urban-and-rural-areas.pdf

2014

Journal Article

Dr. Shyam Diwakar, Parasuram, H., Medini, Ca, Raghu Raman, Prof. Nedungadi, P., Wiertelak, Ed, Srivastava, Se, Dr. Krishnashree Achuthan, and Dr. Bipin G. Nair, “Complementing neurophysiology education for developing countries via cost-effective virtual labs: Case studies and classroom scenarios”, Journal of Undergraduate Neuroscience Education, vol. 12, pp. A130-A139, 2014.[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. © Faculty for Undergraduate Neuroscience.

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PDF iconcomplementing-neurophysiology-education-for-developing-countries-via-cost-effective-virtual-labs-case-studies-&-classroom-scenarios.pdf

2014

Journal Article

V. Özdemir, Kolker, E., Hotez, P. J., Mohin, S., Prainsack, B., Wynne, B., Vayena, E., Coşkun, Y., Dereli, T., Huzair, F., Borda-Rodriguez, A., Bragazzi, N. L., Faris, J., Ramesar, R., Wonkam, A., Dandara, C., Dr. Bipin G. Nair, Llerena, A., Kiliç, K., Jain, R., Reddy, P. J., Gollapalli, K., Srivastava, S., and Kickbusch, I., “Ready to put metadata on the post-2015 development agenda? Linking data publications to responsible innovation and science diplomacy”, Omics: a journal of integrative biology, vol. 18, no. 1, pp. 1-9, 2014.[Abstract]


Metadata refer to descriptions about data or as some put it, "data about data." Metadata capture what happens on the backstage of science, on the trajectory from study conception, design, funding, implementation, and analysis to reporting. Definitions of metadata vary, but they can include the context information surrounding the practice of science, or data generated as one uses a technology, including transactional information about the user. As the pursuit of knowledge broadens in the 21st century from traditional "science of whats" (data) to include "science of hows" (metadata), we analyze the ways in which metadata serve as a catalyst for responsible and open innovation, and by extension, science diplomacy. In 2015, the United Nations Millennium Development Goals (MDGs) will formally come to an end. Therefore, we propose that metadata, as an ingredient of responsible innovation, can help achieve the Sustainable Development Goals (SDGs) on the post-2015 agenda. Such responsible innovation, as a collective learning process, has become a key component, for example, of the European Union's 80 billion Euro Horizon 2020 R&D Program from 2014-2020. Looking ahead, OMICS: A Journal of Integrative Biology, is launching an initiative for a multi-omics metadata checklist that is flexible yet comprehensive, and will enable more complete utilization of single and multi-omics data sets through data harmonization and greater visibility and accessibility. The generation of metadata that shed light on how omics research is carried out, by whom and under what circumstances, will create an "intervention space" for integration of science with its socio-technical context. This will go a long way to addressing responsible innovation for a fairer and more transparent society. If we believe in science, then such reflexive qualities and commitments attained by availability of omics metadata are preconditions for a robust and socially attuned science, which can then remain broadly respected, independent, and responsibly innovative. "In Sierra Leone, we have not too much electricity. The lights will come on once in a week, and the rest of the month, dark[ness]. So I made my own battery to power light in people's houses." Kelvin Doe (Global Minimum, 2012) MIT Visiting Young Innovator Cambridge, USA, and Sierra Leone "An important function of the (Global) R&D Observatory will be to provide support and training to build capacity in the collection and analysis of R&D flows, and how to link them to the product pipeline." World Health Organization (2013) Draft Working Paper on a Global Health R&D Observatory © Mary Ann Liebert, Inc.

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2014

Journal Article

K. Dhara, Stanley, J., Ramachandran, T., Dr. Bipin G. Nair, and T.G, S. Babu, “Pt-CuO nanoparticles decorated reduced graphene oxide for the fabrication of highly sensitive non-enzymatic disposable glucose sensor”, Sensors and Actuators B: Chemical, vol. 195, pp. 197–205, 2014.[Abstract]


Platinum nanocubes and copper oxide nanoflowers decorated reduced graphene oxide (rGO) obtained by one step chemical process. X-ray crystallographic analysis confirms that CuO in monoclinic form and Pt in cubic crystal form. Pt-CuO/rGO nanocomposite dispersed in N,N-dimethylformamide (DMF) was drop casted onto the working electrode of an indigenously fabricated screen printed three electrode system. Oxidation of glucose on the Pt-CuO/rGO nanocomposite modified screen printed electrode (SPE) was occurred at +0.35 V. The sensor showed a limit of detection 0.01 μM (S/N = 3) and very high sensitivity of 3577 μA mM−1 cm−2 with linear response upto 12 mM. The sensor was highly selective to glucose in the presence of commonly interfering species like ascorbic acid (AA), dopamine (DA), uric acid (UA) and acetaminophen. The sensor was employed for the testing of glucose in blood serum and the results obtained were comparable with other standard test methods.

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2013

Journal Article

Dr. Suneesh P. V., Chandhini, K., Ramachandran, T., Dr. Bipin G. Nair, and Babu, T. G. Satheesh, “Tantalum oxide honeycomb architectures for the development of a non-enzymatic glucose sensor with wide detection range”, Biosensors and Bioelectronics, vol. 50, pp. 472 - 477, 2013.[Abstract]


Abstract Tantalum oxide honeycomb nanostructures (THNS) were fabricated by electrochemical anodisation of tantalum in H2SO4–HF medium. \{XRD\} analysis showed that annealing of \{THNS\} at 400 °C improves the crystallinity. \{HRSEM\} and \{AFM\} results illustrated that nanopores with an average diameter of 30 nm were uniformly distributed and the pore size reduced to 24 nm and 18 nm during subsequent electrodeposition of Pt and CuO. Electrodeposited Pt and CuO exhibited face centered cubic (fcc) and monoclinic crystal structure respectively. Cyclic voltammetric studies revealed that, on the hybrid material electrooxidation of glucose occurs at a lower potential (0.45 V). The sensor exhibited linear response to glucose up to 31 mM, fast response time (&lt;3 s) and a low detection limit of 1 μM (S/N=3). The sensor is free of interference from ascorbic acid, uric acid, dopamine and acetaminophen. Sensor was used to analyze glucose in blood serum samples.

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2013

Journal Article

Tab Subbannayya, Balakrishnan, Lac, Sudarshan, Gc, Advani, Ja, Kumar, Sc, Mahmood, Rc, Dr. Bipin G. Nair, Sirdeshmukh, Ra, Mukherjee, K. Kd, Umathe, S. Ne, Raju, Ra, and Prasad, T. Sab Keshava, “An integrated map of corticotropin-releasing hormone signaling pathway”, Journal of Cell Communication and Signaling, vol. 7, pp. 295-300, 2013.

2013

Journal Article

Vab c Özdemir, Llerena, Ade, McKinnon, R. Af, Srivastava, Sg, Dove, E. Sch, Ferguson, L. Rij k, Masellis, Ml, Dr. Bipin G. Nair, Gurwitz, Dn, and Warnich, Lo, “CPPM 2013 onward: Building a socio-technical GPS for global personalized medicine - A welcome to editors-in-chief Adrián LLerena (Spain) and Ross A. McKinnon (Australia)”, Current Pharmacogenomics and Personalized Medicine, vol. 11, pp. 87-92, 2013.

2013

Journal Article

A. R. Pai and Dr. Bipin G. Nair, “Synthesis of Reduced Graphene Oxide Using Novel Exfoliation Technique and its Characterizations”, Journal of Nano-and electronic Physics, vol. 5, p. 02032 , 2013.[Abstract]


For processing of graphene based composite materials Graphene oxide is considered to be the main precursor. Though epitaxial growth and chemical vapor deposition techniques have been utilized to get monolayers of graphene, wet chemical process have been used for its large scale synthesis. For the extraction of graphene monolayer the chemical route relies on the weakening of the Van der Waals cohesive force upon the insertion of reactants in the inter layer space as a consequence sp2 lattice is partially degraded into a sp2-sp3 sheet that possesses a less π-π stacking stability. The method described here uses a novel chemical exfoliation technique. The graphite from the pencil lead is used as the precursor and it is treated with alcohol-ketone-surfactant mixture and mechanically and thermally agitated so as to get the golden brown colored suspension. The material was characterized by Fourier Transform Infra Red spectroscopy. The absence of 1570 cm – 1 peak clearly indicates the oxidation of C = C bonds. The SEM images confirmed the presence of the nanoplatelets of graphene oxide. The AFM analysis confirmed the sheet thickness of the graphene oxide sheets to be &lt; 5 nm. The sheet resistance of the sheets of thermally treated graphene oxide or reduced graphene oxide on Si wafer (p-type, 4-6 Ω/cm) was measured as 200-300 Ω/□. The Ellipsometric characterisations also matches with that of the thermally reduced graphene oxide films formed.&nbsp;

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2013

Journal Article

D. Malhotra, Dr. Shyam Diwakar, Ozdemir, V., Dr. Bipin G. Nair, and Srivastava, S., “BIOQUEST India: A Global Biotechnology Forum for Knowledge-Based Innovation and Sustainable Development”, Current Pharmacogenomics and Personalized Medicine (Formerly Current Pharmacogenomics), vol. 11, pp. 8–11, 2013.[Abstract]


Introduction
Biotechnology and knowledge-based innovations are sought after by countries small and large for development and societal prosperity, not to forget for advancing the standards in medicine, health systems and services of nations. Key elements to this science and technology driven development agenda are exemplified by BIOQUEST India. This global biotechnology forum draws from local and regional advances in the Asia-Pacific and integrates it with key global scientific progress in life sciences.

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2013

Journal Article

M. Bhattacharjee, Sharma, R., Goel, R., Balakrishnan, L., Renuse, S., Advani, J., Gupta, S. Tankala, Verma, R., Pinto, S. M., Sekhar, N. Raja, Dr. Bipin G. Nair, Prasad, T. S. K., Harsha, H. C., Jois, R., Shankar, S., and Pandey, A., “A multilectin affinity approach for comparative glycoprotein profiling of rheumatoid arthritis and spondyloarthropathy”, Clinical proteomics, vol. 10, no. 1, p. 1, 2013.[Abstract]


BACKGROUND: Arthritis refers to inflammation of joints and includes common disorders such as rheumatoid arthritis (RA) and spondyloarthropathies (SpAs). These diseases differ mainly in terms of their clinical manifestations and the underlying pathogenesis. Glycoproteins in synovial fluid might reflect the disease activity status in the joints affected by arthritis; yet they have not been systematically studied previously. Although markers have been described for assisting in the diagnosis of RA, there are currently no known biomarkers for SpA.

MATERIALS AND METHODS: We sought to determine the relative abundance of glycoproteins in RA and SpA by lectin affinity chromatography coupled to iTRAQ labeling and LC-MS/MS analysis. We also used ELISA to validate the overexpression of VCAM-1, one of the candidate proteins identified in this study, in synovial fluid from RA patients.

RESULTS AND DISCUSSION: We identified proteins that were previously reported to be overexpressed in RA including metalloproteinase inhibitor 1 (TIMP1), myeloperoxidase (MPO) and several S100 proteins. In addition, we discovered several novel candidates that were overexpressed in SpA including Apolipoproteins C-II and C-III and the SUN domain-containing protein 3 (SUN3). Novel molecules found overexpressed in RA included extracellular matrix protein 1 (ECM1) and lumican (LUM). We validated one of the candidate biomarkers, vascular cell adhesion molecule 1 (VCAM1), in 20 RA and SpA samples using ELISA and confirmed its overexpression in RA (p-value <0.01). Our quantitative glycoproteomic approach to study arthritic disorders should open up new avenues for additional proteomics-based discovery studies in rheumatological disorders.

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2013

Journal Article

Asha Vijayan, Chaitanya Nutakki, Chaitanya Medini, Hareesh Singanamala, Dr. Bipin G. Nair, Krishnasree Achuthan, and Dr. Shyam Diwakar, “Classifying Movement Articulation for Robotic Arms via Machine Learning”, Journal of Intelligent Computing, vol. 4, no. 3, pp. 123-134, 2013.[Abstract]


Articulation via target-oriented approaches have been commonly used in robotics. Movement of a robotic arm can involve targeting via a forward or inverse kinematics approach to reach the target. We attempted to transform the task of controlling the motor articulation to a machine learning approach. Towards this goal, we built an online robotic arm to extract articulation datasets and have used SVM and Naïve Bayes techniques to predict multi-joint articulation. For controlling the preciseness and efficiency, we developed pick and place tasks based on pre-marked positions and extracted training datasets which were then used for learning. We have used classification as a scheme to replace prediction-correction approach as usually attempted in traditional robotics. This study reports significant classification accuracy and efficiency on real and synthetic datasets generated by the device. The study also suggests SVM and Naive Bayes algorithms as alternatives for computational intensive prediction-correction learning schemes for articulator movement in laboratory environments.

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PDF iconclassifying-movement-articulation-for-robotic-arms-via-machine-learning.pdf

2012

Journal Article

Chaitanya Medini, Dr. Bipin G. Nair, Egidio D'Angelo, Naldi, G., and Dr. Shyam Diwakar, “Modeling spike-train processing in the cerebellum granular layer and changes in plasticity reveal single neuron effects in neural ensembles”, Computational intelligence and neuroscience, vol. 2012, p. 7, 2012.[Abstract]


<p>The cerebellum input stage has been known to perform combinatorial operations on input signals. In this paper, two types of mathematical models were used to reproduce the role of feed-forward inhibition and computation in the granular layer microcircuitry to investigate spike train processing. A simple spiking model and a biophysically-detailed model of the network were used to study signal recoding in the granular layer and to test observations like center-surround organization and time-window hypothesis in addition to effects of induced plasticity. Simulations suggest that simple neuron models may be used to abstract timing phenomenon in large networks, however detailed models were needed to reconstruct population coding via evoked local field potentials (LFP) and for simulating changes in synaptic plasticity. Our results also indicated that spatio-temporal code of the granular network is mainly controlled by the feed-forward inhibition from the Golgi cell synapses. Spike amplitude and total number of spikes were modulated by LTP and LTD. Reconstructing granular layer evoked-LFP suggests that granular layer propagates the nonlinearities of individual neurons. Simulations indicate that granular layer network operates a robust population code for a wide range of intervals, controlled by the Golgi cell inhibition and is regulated by the post-synaptic excitability.</p>

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PDF iconmodeling-spike-train-processing-in-the-cerebellum-granular-layer-and-changes-in-plasticity-reveal-single-neuron-effects-in-neural-ensembles.pdf

2012

Journal Article

A. Omanakuttan, Dr. Jyotsna Nambiar, Harris, R. M., Bose, C., Pandurangan Nanjan, Varghese, R. K., Kumar, G. B., Tainer, J. A., Dr. Asoke Banerji, J. Perry, J. P., and Dr. Bipin G. Nair, “Anacardic Acid Inhibits the Catalytic Activity of Matrix Metalloproteinase-2 and Matrix Metalloproteinase-9”, 2012.[Abstract]


Cashew nut shell liquid (CNSL) has been used in traditional medicine for the treatment of a wide variety of pathophysiological conditions. To further define the mechanism of CNSL action, we investigated the effect of cashew nut shell extract (CNSE) on two matrix metalloproteinases, MMP-2/gelatinase A and MMP-9/gelatinase B, which are known to have critical roles in several disease states. We observed that the major constituent of CNSE, anacardic acid, markedly inhibited the gelatinase activity of 3T3-L1 cells. Our gelatin zymography studies on these two secreted gelatinases, present in the conditioned media from 3T3-L1 cells, established that anacardic acid directly inhibited the catalytic activities of both MMP-2 and MMP-9. Our docking studies suggested that anacardic acid binds into the MMP-2/9 active site, with the carboxylate group of anacardic acid chelating the catalytic zinc ion and forming a hydrogen bond to a key catalytic glutamate side chain and the C15 aliphatic group being accommodated within the relatively large S1′ pocket of these gelatinases. In agreement with the docking results, our fluorescence-based studies on the recombinant MMP-2 catalytic core domain demonstrated that anacardic acid directly inhibits substrate peptide cleavage in a dose-dependent manner, with an IC50&nbsp;of 11.11 μM. In addition, our gelatinase zymography and fluorescence data confirmed that the cardol-cardanol mixture, salicylic acid, and aspirin, all of which lack key functional groups present in anacardic acid, are much weaker MMP-2/MMP-9 inhibitors. Our results provide the first evidence for inhibition of gelatinase catalytic activity by anacardic acid, providing a novel template for drug discovery and a molecular mechanism potentially involved in CNSL therapeutic action.

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2012

Journal Article

S. Ray, Koshy, N. R., Dr. Shyam Diwakar, Dr. Bipin G. Nair, and Srivastava, S., “Sakshat Labs: India's Virtual Proteomics Initiative”, PLoS biology, vol. 10, p. e1001353, 2012.[Abstract]


The article reports on the launch of Virtual Proteomics Lab (VPL) by India's Ministry of Human Resource Development (MHRD) as part of a comprehensive Virtual Lab Project with the goal of providing easily accessible and high-quality-education across the globe. The VPL can be found at Indian Institute of Technology (IIT) Bombay as a national project dedicated to high-throughput proteome separation and analysis techniques. The effort also aimed at making consolidated practical proteomics resource.

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2012

Journal Article

Dr. Bipin G. Nair, Krishnan, R., Nizar, N., Radhamani, R., Rajan, K., Yoosef, A., Sujatha, G., Radhamony, V., Dr. Krishnashree Achuthan, and Dr. Shyam Diwakar, “Role of ICT-enabled visualization-oriented virtual laboratories in Universities for enhancing biotechnology education – VALUE initiative: Case study and impacts”, FormaMente, vol. VII, pp. 1-2, 2012.[Abstract]


Information and Communication Technology (ICT) enabled virtual labs have been setup in order to facilitate and enhance higher education. VALUE Biotechnology virtual labs were implemented as part of an ICT initiative and tested between several students and teacher groups. In this paper, we discuss about the application of virtualizing concepts and experiments in biotechnology, one of the fundamental area of biological sciences to impart quality education to meet the necessities of students. We found virtual labs, enhanced attention and student performance in biotechnology courses. The paper reports that applying virtualization techniques, biotechnology education could be intensified in terms of student attention and virtual lab can serve as an effective teaching pedagogy. The paper shows how virtual labs in biotechnology can be exploited to improve teaching and student performance. This study analyzes the trends of user behavior towards virtual laboratories and the usability of these laboratories as a learning and curriculum material. Findings from indicated biotechnology virtual laboratories encompass all the core subjects of their curriculum materials in an easy and understandable way with user-interaction and serve to reduce the problems of laboratory education especially in economically challenged and geographically remote areas. Virtual laboratories target a user-friendly outlook to modern laboratory education, aiding as an optional evaluation component for University teachers.

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2012

Journal Article

Dr. Shyam Diwakar, Dr. Krishnashree Achuthan, Prof. Nedungadi, P., and Dr. Bipin G. Nair, “Biotechnology Virtual Labs: Facilitating Laboratory Access Anytime-Anywhere for Classroom Education”, Innovations in Biotechnology Edited by Dr. Eddy C. Agbo, 2012.[Abstract]


<p>Biotechnology is becoming more popular and well identified as a mainline industry.Students have shown greater interest in learning the techniques. As a discipline, biotechnology has led to new advancements in many areas. Criminal investigation has changed dramatically thanks to DNA fingerprinting. Significant advances in forensic medicine, anthropology and wildlife management have been noticed in the last few years. Biotechnology has brought out hundreds of medical diagnostic tests that keep the blood safe from infectious diseases such as HIV and also aid detection of other conditions early enough to be successfully treated.</p>

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PDF iconbiotechnology-virtual-labs-facilitating-laboratory-access-anytime-anywhere-for-classroom-education.pdf

2012

Journal Article

S. Ray, Koshy, N. R., Dr. Shyam Diwakar, Dr. Bipin G. Nair, and Srivastava, S., “Community Page-Sakshat Labs: India's Virtual Proteomics Initiative”, PLoS-Biology, vol. 10, p. 1306, 2012.

2012

Journal Article

Dr. Satheesh Babu T. G., Varadarajan, D., Murugan, G., Ramachandran, T., and Dr. Bipin G. Nair, “Gold Nanoparticle–Polypyrrole Composite Modified TiO2 Nanotube Array Electrode for the Amperometric Sensing of Ascorbic Acid”, Journal of Applied Electrochemistry, vol. 42, pp. 427-434, 2012.[Abstract]


<p>Titanium dioxide (TiO2) nanotubes were fabricated by anodisation of titanium foil in 0.15&nbsp;M ammonium fluoride in an aqueous solution of glycerol (90&nbsp;% v/v). Electropolymerisation of pyrrole and deposition of gold nanoparticles on to the TiO2&nbsp;nanotube array electrode were carried out by cyclic voltammetry (CV). Electrochemical characterization of the sensor was performed by CV and electrochemical impedance spectroscopy. The morphology of the electrode was studied after every step of modification using field emission scanning electron microscope and atomic force microscope. The sensor was tested for AA and other biomolecules in phosphate buffered saline solution of pH 7 using CV, differential pulse voltammetry and amperometry. The sensor exhibited very high sensitivity of 63.912&nbsp;μA&nbsp;mM−1&nbsp;cm−2&nbsp;and excellent selectivity to ascorbic acid (AA) in the presence of other biomolecules such as uric acid, dopamine, glucose and para-acetaminophen. It also showed very good linearity (<em class="a-plus-plus">R</em>&nbsp;=&nbsp;0.9995) over a wide range (1&nbsp;μM–5&nbsp;mM) of detection. The sensor was tested for AA in lemon and found its concentration to be 339&nbsp;mg&nbsp;ml−1.</p>

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2011

Journal Article

D. Sab Kelkar, Kumar, Dc, Kumar, Pa, Balakrishnan, Lad, Muthusamy, Bae, Yadav, A. Kc, Shrivastava, Pc, Marimuthu, Aaf, Anand, Sg, Sundaram, Hg, Kingsbury, Rg, Harsha, H. Ca, Dr. Bipin G. Nair, Prasad, T. S. Kae f, Chauhan, D. Sh, Katoch, Kh, Katoch, V. Mi, Kumar, Pg, Chaerkady, Raj, Ramachandran, Sc, Dash, Dc, and Pandey, Aaj, “Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry”, Molecular and Cellular Proteomics, vol. 10, 2011.[Abstract]


The genome sequencing of H37Rv strain of Mycobacterium tuberculosis was completed in 1998 followed by the whole genome sequencing of a clinical isolate, CDC1551 in 2002. Since then, the genomic sequences of a number of other strains have become available making it one of the better studied pathogenic bacterial species at the genomic level. However, annotation of its genome remains challenging because of high GC content and dissimilarity to other model prokaryotes. To this end, we carried out an in-depth proteogenomic analysis of the M. tuberculosis H37Rv strain using Fourier transform mass spectrometry with high resolution at both MS and tandem MS levels. In all, we identified 3176 proteins from Mycobacterium tuberculosis representing ∼80% of its total predicted gene count. In addition to protein database search, we carried out a genome database search, which led to identification of ∼250 novel peptides. Based on these novel genome search-specific peptides, we discovered 41 novel protein coding genes in the H37Rv genome. Using peptide evidence and alternative gene prediction tools, we also corrected 79 gene models. Finally, mass spectrometric data from N terminus-derived peptides confirmed 727 existing annotations for translational start sites while correcting those for 33 proteins. We report creation of a high confidence set of protein coding regions in Mycobacterium tuberculosis genome obtained by high resolution tandem mass-spectrometry at both precursor and fragment detection steps for the first time. This proteogenomic approach should be generally applicable to other organisms whose genomes have already been sequenced for obtaining a more accurate catalogue of protein-coding genes. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.

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2011

Journal Article

Hab c Pawar, Kashyap, M. Ka, Sahasrabuddhe, N. Aag j k, Renuse, Sah j k, Harsha, H. Ca, Kumar, Pa, Sharma, Jag, Kandasamy, Kan, Marimuthu, Aag, Dr. Bipin G. Nair, Rajagopalan, Sd, Maharudraiah, Jae, Premalatha, C. Sc, Kumar, K. V. Vf, Vijayakumar, Mf, Chaerkady, Raj k, Prasad, T. S. Kag i, Kumar, R. Vc, and Pandey, Ajk l m, “Quantitative tissue proteomics of esophageal squamous cell carcinoma for novel biomarker discovery”, Cancer Biology and Therapy, vol. 12, pp. 510-522, 2011.[Abstract]


Esophageal squamous cell carcinoma (ESCC) is among the top ten most frequent malignancies worldwide. In this study, our objective was to identify potential biomarkers for ESCC through a quantitative proteomic approach using the isobaric tags for relative and absolute quantitation (iTRaQ) approach. We compared the protein expression profiles of ESCC tumor tissues with the corresponding adjacent normal tissue from ten patients. LC-MS/MS analysis of strong cation exchange chromatography fractions was performed on an accurate Mass QTOF mass spectrometer, which led to the identification of 687 proteins. In all, 257 proteins were identified as differentially expressed in ESCC as compared with normal. We found several previously known protein biomarkers to be upregulated in ESCC including thrombospondin 1 (THBS1), periostin 1 (POSTN) and heat shock 70 kDa protein 9 (HSPA9) confirming the validity of our approach. In addition, several novel proteins that had not been reported previously were identified in our screen. These novel biomarker candidates included prosaposin (PSAP), plectin 1 (PLEC1) and protein disulfide isomerase a 4 (PDIA4) that were further validated to be overexpressed by immunohistochemical labeling using tissue microarrays. The success of our study shows that this mass spectrometric strategy can be applied to cancers in general to develop a panel of candidate biomarkers, which can then be validated by other techniques.

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2011

Journal Article

H. Parasuram, Dr. Bipin G. Nair, Naldi, G., D’Angelo, E., and Dr. Shyam Diwakar, “A modeling based study on the origin and nature of evoked post-synaptic local field potentials in granular layer”, Journal of Physiology-Paris, vol. 105, no. 1-3, pp. 71–82, 2011.[Abstract]


Understanding population activities of underlying neurons reveal emergent behavior as patterns of information flow in neural circuits. Evoked local field potentials (LFPs) arise from complex interactions of spatial distribution of current sources, time dynamics, and spatial distribution of dipoles apart underlying conductive properties of the extracellular medium. We reconstructed LFP to test and parameterize the molecular mechanisms of cellular function with network properties. The sensitivity of LFP to local excitatory and inhibitory connections was tested using two novel techniques. In the first, we used a single granule neuron as a model kernel for reconstructing population activity. The second technique consisted using a detailed network model. LTP and LTD regulating the spatiotemporal pattern of granular layer responses to mossy fiber inputs was studied. The effect of changes in synaptic release probability and modulation in intrinsic excitability of granule cell on LFP was studied. The study revealed cellular function and plasticity were represented in LFP wave revealing the activity of underlying neurons. Changes to single cell properties during LTP and LTD were reflected in the LFP wave suggesting the sparse recoding function of granule neurons as spatial pattern generators. Both modeling approaches generated LFP in vitro (Mapelli and D'Angelo, 2007) and in vivo (Roggeri et al., 2008) waveforms as reported in experiments and predict that the expression mechanisms revealed in vitro can explain the LFP changes associated with LTP and LTD in vivo.

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PDF icona-modeling-based-study-on-the-origin-and-nature-of-evoked-post-synaptic-local-field-potentials-in-granular-layer.pdf

2011

Journal Article

Dr. Shyam Diwakar, Dr. Krishnashree Achuthan, Prof. Nedungadi, P., and Dr. Bipin G. Nair, “Enhanced facilitation of biotechnology education in developing nations via virtual labs: analysis, implementation and case-studies”, International Journal of Computer Theory and Engineering, vol. 3, pp. 1–8, 2011.[Abstract]


Methods for educating students in biotechnology require intensive training in laboratory procedures. Laboratory procedures cost Universities in terms of equipment and experienced guidance which often come short in many developing countries. Universities need revitalizing approach and well-adapted curriculum especially in terms of laboratory practice. For enhanced education at the level of University-level laboratory courses such as those in biology or biotechnology, one of the key elements is the need to allow the student to familiarize laboratory techniques in par with regular theory. The Sakshat Amrita virtual biotechnology lab project focusing on virtualizing wet-lab techniques and integrating the learning experience has added a new dimension to the regular teaching courses at the University. Establishing virtual labs requires both domain knowledge and virtualizing skills via programming, animation and device-based feedback. This paper reports a cost-effective process used in virtualizing real biotechnology labs for education at Universities. The major challenge in setting up an effective knowledge dissemination for laboratory courses was not only the scientific approach of biotechnology, but included the virtualization aspects such as usage/design scalability, deliverability efficiency, network connectivity issues, security and speed of adaptability to incorporate and update changes into existing experiments. This paper also discusses an issue-specific case-study of a functional virtual lab in biotechnology and its many issues and challenges.

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PDF iconenhanced-facilitation-of-biotechnology-education-in-developing-nations-via-virtual-labs-analysis-implementation -and-case-studies.pdf

2010

Journal Article

T. S. Ka Prasad, Keerthikumar, Sab, Chaerkady, Rac, Kandasamy, Kab c, Renuse, Sac d, Marimuthu, Aae, Venugopal, A. Kab c, Thomas, J. Ka, Jacob, H. K. Cac e, Goel, Rab, Pawar, Haf, Sahasrabuddhe, N. Aac e, Krishna, Vb, Dr. Bipin G. Nair, Gucek, Mg, Cole, R. Nh, Ravikumar, Ri, Harsha, H. Cae, and Pandey, Ac, “Comparative proteomic analysis of Candida albicans and Candida glabrata”, Clinical Proteomics, vol. 6, pp. 163-173, 2010.[Abstract]


Introduction: Candida albicans and Candida glabrata are the two most common opportunistic pathogens which are part of the normal flora in humans. Clinical diagnosis of infection by these organisms is still largely based on culturing of these organisms. In order to identify species-specific protein expression patterns, we carried out a comparative proteomic analysis of C. albicans and C. glabrata. Methods: We used "isobaric tag for relative and absolute quantitation" (iTRAQ) labeling of cell homogenates of C. albicans and C. glabrata followed by LC-MS/MS analysis using a quadrupole time-of-flight mass spectrometer. The MS/MS data was searched against a protein database comprised of known and predicted proteins reported from these two organisms. Subsequently, we carried out a bioinformatics analysis to group orthologous proteins across C. albicans and C. glabrata and calculated protein abundance changes between the two species. Results and Conclusions: We identified 500 proteins from these organisms, the large majority of which corresponded to predicted transcripts. A number of proteins were observed to be significantly differentially expressed between the two species including enolase (Eno1), fructose-bisphosphate aldolase (Fba1), CCT ring complex subunit (Cct2), pyruvate kinase (Cdc19), and pyruvate carboxylase (Pyc2). This study illustrates a strategy for investigating protein expression patterns across closely related organisms by combining orthology information with quantitative proteomics.

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2010

Journal Article

Dr. Satheesh Babu T. G., Dr. Suneesh P. V., Ramachandran, T., and Dr. Bipin G. Nair, “Gold Nanoparticles Modified Titania Nanotube Arrays for Amperometric Determination of Ascorbic Acid”, Analytical Letters, vol. 43, no. 18, pp. 2809-2822, 2010.[Abstract]


Development and use of highly ordered, vertically aligned TiO2 nanotube arrays modified with gold nanoparticles for the selective detection of ascorbic acid (AA) in the presence of uric acid and glucose are reported here. Gold nanoparticles were electrodeposited on the Nanotube arrays by CV. The sensor was characterized using SEM, EDS, CV, and EIS. It showed very good performance with a sensitivity of 46.8&nbsp;μA mM−1&nbsp;cm−2, response time below 2 seconds and linearity in the range of 1&nbsp;μM to 5&nbsp;mM with a detection limit of 0.1&nbsp;μM and was tested for the AA concentration in pharmaceutical preparations.

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2010

Journal Article

Dr. Satheesh Babu T. G., Ramachandran, T., and Dr. Bipin G. Nair, “Single step modification of copper electrode for the highly sensitive and selective non-enzymatic determination of glucose”, Microchimica Acta, vol. 169, pp. 49-55, 2010.[Abstract]


A non-enzymatic sensor was developed for the determination of glucose in alkaline medium by anodisation of copper in sodium potassium tartrate solution. The morphology of the modified copper electrode was studied by scanning electron microscopy, and its electrochemical behavior by cyclic voltammetry and electrochemical impedance spectroscopy. The electrode enables direct electrocatalytic oxidation of glucose on a CuO/Cu electrode at 0.7 V in 0.1 M sodium hydroxide. At this potential, the sensor is highly selective to glucose even in the presence of ascorbic acid, uric acid, or dopamine which are common interfering species. The sensor displays a sensitivity of 761.9 μA mM−1 cm−2, a linear detection range from 2 μM to 20 mM, a response time of <1 s, and a detection limit of 1 μM (S/N = 3). It was tested for determination of glucose level in blood serum.

More »»

2009

Journal Article

S. S Mohan, J Perry, J. P., Poulose, N., Dr. Bipin G. Nair, and Anilkumar, G., “Homology modeling of GLUT4, an insulin regulated facilitated glucose transporter and docking studies with ATP and its inhibitors”, Journal of Biomolecular Structure and Dynamics, vol. 26, pp. 455–464, 2009.[Abstract]


GLUT4 is a 12 transmembrane (TM) protein belonging to the Class I facilitated glucose transporter family that transports glucose into the cells in an insulin regulated manner. GLUT4 plays a key role in the maintenance of blood glucose homeostasis and inhibition of glucose transporter activity may lead to insulin resistance, hallmark of type 2 diabetes. No crystal structure data is available for any members of the facilitated glucose transporter family. Here, in this paper, we have generated a homology model of GLUT4 based on experimental data available on GLUT1, a Class I facilitated glucose transporter and the crystal structure data obtained from the Glycerol 3-phosphate transporter. The model identified regions in GLUT4 that form a channel for the transport of glucose along with the substrate interacting residues. Docking and electrostatic potential data analysis of GLUT4 model has mapped an ATP binding region close to the binding site of cytochalasin B and genistein, two GLUT4 inhibitors, and this may explain the mechanism by which these inhibitors could potentially affect the GLUT4 function. More »»

2009

Journal Article

T. .Ramachandran and Dr. Bipin G. Nair, “A Highly Selective and Sensitive Ascorbic Acid Sensor Using Electrodeposited Gold Nanoparticles on Polyaniline Modified Titanium Dioxide Nanotube Arrays”, Journal of Physical Chemistry (communicated), 2009.

2000

Journal Article

K. A. Alvi, Dr. Bipin G. Nair, Rabenstein, J., Davis, G., and Baker, D. B., “CD45 Tyrosine Phosphatase Inhibitory Components from Aspergillus niger”, J. Antibiotics, no. 53, pp. 110-113, 2000.[Abstract]


Two inhibitors of CD45 tyrosine phosphatase, dihydrocarolic acid (1) and penitricin D (2), were isolated from a fermentation broth of the fungus Aspergillus niger and purified by HSCCC (high speed countercurrent chromatography) followed by HPLC. The structures were determined by NMR. The inhibitory activities of both compounds were specific to tyrosine phosphatases. More »»

2000

Journal Article

Dr. Bipin G. Nair, Alvi, K. A., Baker, D. B., Steinecker, V., and .Hosken, M., “Identification of Inhibitors of Inducible Nitric Oxide Synthase from Microbial Extracts”, J. Antibiotics, vol. 53, pp. 496-501, 2000.[Abstract]


A new member of the angucycline family, vineomycin C (3), together with four known metabolites saquayamycin A1 (1), A-7884 (2), rabelomycin (5) and xanthomegnin (6) were isolated from microbial extracts. The structures were determined by 1D and 2D NMR techniques and chemical degradation. Compounds 1-3 and 5 were isolated from a fermentation of Streptomyces sp., while 6 was isolated from a fungal fermentation extract. All five compounds have shown potent inhibitory activity in the inducible nitric oxide synthase (iNOS) assay. More »»

1998

Journal Article

K. A. Alvi, Casey, A., and Dr. Bipin G. Nair, “Pulchellalactam: a CD45 protein tyrosine phosphatase inhibitor from the marine fungus Corollospora pulchella”, The Journal of antibiotics, Japan Antibiotics Research Association, vol. 51, pp. 515–517, 1998.

1997

Journal Article

K. A. Alvi, Dr. Bipin G. Nair, Gallo, C., and Baker, D., “Screening of microbial extracts for tyrosine kinase inhibitors”, Journal of antibiotics, vol. 50, pp. 264–266, 1997.

1997

Journal Article

K. A. Alvi, Dr. Bipin G. Nair, Pu, H., Ursino, R., Gallo, C., and Mocek, U., “Phomacins: Three Novel Antitumor Cytochalasan Constituents Produced by a Phoma sp.”, The Journal of organic chemistry, vol. 62, pp. 2148–2151, 1997.[Abstract]


Three novel cytochalasans, phomacins A, B and C, were isolated from a fermentation broth of the fungus Phoma sp. and purified by HSCCC (high speed countercurrent chromatography) followed by HPLC. The structures were determined by 1D and 2D NMR techniques. All three compounds have shown potent inhibitory activity against the HT29 colonic adenocarcinoma cell line. More »»

1996

Journal Article

T. B. Patel, .Sun, H., .Poppleton, H., Dr. Bipin G. Nair, .M.Rashed, H., and .Yu, Y., “Epidermal growth factor mediated regulation of G-proteins and adenylyl cyclase in cardiac muscle”, Methods in Neurosci, no. 29, pp. 319-343, 1996.[Abstract]


Publisher Summary This chapter presents a number of experimental approaches that have proved to be very useful in elucidating the mechanism(s) involved in epidermal growth factor (EGF) -mediated stimulation of cardiac adenylylcyclase. However, there are several additional questions pertaining to the detailed understanding of the mechanism(s) involved in interactions between the \{EGF\} receptor and Gs interaction. Thus, the in vitro studies demonstrate the juxtamembrane region of the \{EGF\} receptor that is important for stimulation of Gs by performing mutation(s) of key residue(s) in the juxtamembrane region of the \{EGF\} receptor, to determine whether the ability of \{EGF\} to stimulate adenylylcyclase can be obliterated. Similarly, it is important to determine the region(s) of Gsα that interact with the \{EGF\} receptor. It is also determine that what elements confer specificity to the ability of \{EGF\} to stimulate adenylylcyclase. The latter goal poses a particularly important question, because \{EGF\} does not elevate cAMP content in all cells that express the \{EGF\} receptor, Gs, and adenylylcyclase. More »»

1995

Journal Article

Dr. Bipin G. Nair, Yu, Y., Rashed, H. M., Sun, H., and Patel, T. B., “Transforming growth factor- beta 1 modulates adenylyl cyclase signaling elements and epidermal growth factor signaling in cardiomyocytes”, Journal of cellular physiology, vol. 164, pp. 232–239, 1995.[Abstract]


Studies presented in this report were designed to investigate the effects of transforming growth factor-beta 1 (TGF-beta 1) on epidermal growth factor (EGF)-mediated stimulation of cAMP accumulation in cardiac myocytes and elucidate the mechanism(s) involved in this modulation. TGF-beta 1 (20 pM) treatment of cardiac myocytes, in a time-dependent manner, decreased the ability of EGF (100 nM) to increase cAMP accumulation. Significant attenuation of EGF-elicited cAMP accumulation was observed 2 h after exposure to TGF-beta 1 and 18 h after addition of TGF-beta 1, the ability of EGF to increase cAMP accumulation was completely obliterated. TGF-beta 1 neither decreased immunoprecipitable EGF receptors in membranes from cardiomyocytes nor altered the specific binding of [125I]EGF to cardiomyocyte membranes. However, TGF-beta 1 decreased the ability of EGF to phosphorylate membrane proteins on tyrosine residues. TGF-beta 1 treatment of cardiomyocytes also decreased the ability of forskolin to augment cAMP accumulation in intact cells and stimulate adenylyl cyclase activity. Similarly, in membranes of TGF-beta 1-treated cells, neither isoproterenol nor EGF stimulated adenylyl cyclase activity. Interestingly, as assessed by the ability of A1F4- to stimulate adenylyl cyclase, TGF-beta 1 did not alter the coupling between Gs and catalytic subunits. Likewise, TGF-beta 1 did not alter the functional activity of the inhibitory regulatory element of the system, Gi. Western analysis of cellular proteins revealed that TGF-beta 1 did not alter the amounts of Ga alpha, Gi alpha 2, and Gi alpha 3. We conclude that TGF-beta 1 attenuates EGF-elicited cAMP accumulation in cardiomyocytes, in part, by decreasing the EGF receptor kinase function and that TGF-beta 1-mediated alterations in the activity of adenylyl cyclase catalytic subunit also contribute toward the regulation of adenylyl cyclase by various agonists. More »»

1995

Journal Article

T. B. Patel, Dr. Bipin G. Nair, Padmini, E., Rashed, H. M., and Sun, H., “Alterations in messenger RNA encoding atrial natriuretic hormone receptor A and C subtypes during hepatic regeneration”, Hepatology, vol. 21, pp. 1682–1689, 1995.[Abstract]


Previously, we demonstrated that, 48 hours after partial hepatectomy, in the regenerating liver the number of both atrial natriuretic hormone (ANF) receptor subtypes, the guanylyl cyclase—linked and ANF-C receptors, is increased twofold. Subsequently, we demonstrated that activation of ANF-C receptors inhibits growth of hepatocytes. Therefore, studies were performed to determine whether, during hepatic regeneration, the increase in ANF receptor subtypes is accompanied by an increase in their respective transcripts. Our data demonstrate that in the normal and regenerating rat liver, the predominant guanylyl cyclase-linked ANF receptor is of the ANF-A subtype. Moreover, messenger RNA (mRNA) encoding the ANF-A and ANF-C receptors are transiently increased after surgery; the levels of mRNA encoding both receptor subtypes remain unchanged in livers of sham-operated animals. ANF-A receptor mRNA is maximally increased 12 hours after partial hepatectomy, whereas the maximal increase in ANF-C receptor mRNA is observed between 0.5 hour and 4 hours after hepatectomy. The increase in ANF-C receptor transcript is accompanied by increased expression of protein, 4 hours after hepatectomy. However, the ANF-C receptor protein is also elevated 48 hours after partial hepatectomy when ANF-C receptor mRNA levels are not different from controls. Likewise, although ANF-A receptors are increased when hepatic levels of mRNA encoding the protein are maximally elevated, the maximal increase in ANF-A receptor protein occurs at times when transcript levels are low and similar to those in sham-operated controls. These findings demonstrate differential regulation in the expression of ANF-A and ANF-C receptors and are illustrative of regulation of expression of both receptors at the translational or posttranslational levels. More »»

1993

Journal Article

Dr. Bipin G. Nair and Patel, T. B., “Regulation of cardiac adenylyl cyclase by Epidermal Growth Factor (EGF): Role of EGF receptor protein tyrosine kinase activity”, Biochemical pharmacology, vol. 46, pp. 1239–1245, 1993.[Abstract]


We have shown previously that the α subunit of the stimulatory GTP binding regulatory component of adenylyl cyclase (Gsα) mediates epidermal growth factor (EGF)-elicited stimulation of rat cardiac adenylyl cyclase (Nair et al., J Biol Chem265: 21317–21322, 1990). Employing purified protein phosphotyrosine phosphatase, and benzylidene derivatives (tyrphostins: compounds 11 and 12) that selectively inhibit EGF receptor protein tyrosine kinase (EGFRK) activity, the role of EGFRK in EGF-mediated stimulation of cardiac adenylyl cyclase was investigated. The ability of the tyrphostins to inhibit the EGFRK activity in cardiac membranes was determined by monitoring tyrosine phosphorylation of either the 170 kDa protein or immunoprecipitated EGF receptor at 0° and room temperature, respectively. Compounds 11 and 12, in a concentration-dependent manner, inhibited EGF receptor tyrosine kinase activity. In assays of adenylyl cyclase activity neither compound 11 nor compound 12 altered Gpp(NH)p- or isoproterenol-stimulated activity. However, both compounds, in a concentration-dependent manner, attenuated the ability of EGF to stimulate adenylyl cyclase activity without altering specific binding of [125I]EGF to cardiac membranes. Similarly, protein phosphotyrosine phosphatase obliterated the ability of EGF, but not isoproterenol, to stimulate adenylyl cyclase. Thus, we conclude that protein tyrosine kinase activity of the EGF receptor is essential for the stimulation of cardiac adenylyl cyclase by EGF. More »»

1993

Journal Article

Dr. Bipin G. Nair, Rashed, H. M., and Patel, T. B., “Epidermal growth factor produces inotropic and chronotropic effects in rat hearts by increasing cyclic AMP accumulation”, Growth Factors, vol. 8, pp. 41–48, 1993.[Abstract]


Previously we have shown that epidermal growth factor (EGF) stimulates cardiac adenylyl cyclase and increases cAMP accumulation in the rat heart (Nair et al., Biochem. J. 264, 563-571, 1989). Moreover, we have shown that the stimulation of adenylyl cyclase by EGF in heart is mediated via activation of the stimulatory GTP binding regulatory protein Gs alpha (Nair et al., J. Biol. Chem. 265, 21317-21322, 1990). Since cAMP increases the beating rate of hearts, studies were performed to investigate the effects of EGF on mechanical function of the heart and the role of cAMP in mediating the cardiac effects of EGF. In isolated perfused rat hearts EGF (15 nM) decreased perfusion pressure, increased ventricular contractility and heart rate in a manner similar to that observed with the beta-adrenergic receptor agonist isoproterenol (10 nM). In the presence of the adenosine A1 receptor agonist (-)-N6-(R-phenylisopropyl)-adenosine (PIA, 100 nM) which via activation of the inhibitory GTP binding protein Gi inhibits adenylyl cyclase, the effects of EGF on cAMP accumulation in the heart were markedly attenuated. PIA also decreased the ability of EGF and isoproterenol to alter cardiac contractility and beating rate. However, PIA did not attenuate the increase in heart rate and contractility induced by the alpha-adrenergic agonist phenylephrine which does not stimulate cAMP accumulation in the heart. These data suggest that EGF alters cardiac function by increasing cellular cAMP accumulation. More »»

1993

Journal Article

A. R. Amin, Swenson, C. D., Xue, B., Ishida, Y., Dr. Bipin G. Nair, Patel, T. B., Chused, T. M., and G Thorbecke, J., “Regulation of IgD-Receptor Expression on Murine T Cells: II. Upregulation of IgD Receptors Is Obtained after Activation of Various Intracellular Second-Messenger Systems; Tyrosine Kinase Activity Is Required for the Effect of IgD”, Cellular immunology, vol. 152, pp. 422–439, 1993.[Abstract]


The presence of IgD receptors (IgD-R) on T cells during a primary response to antigen causes augmented antibody production and facilitates priming for a secondary response. Cross-linked, but not monomeric IgD leads to a rapid upregulation of these receptors on T cells. As shown in the present study, the rapid upregulation of IgD-specific receptors is also induced by cross-linking of T cell surface molecules known to mediate triggering of T cell activation, such as CD3, CD2, and Thy 1. Furthermore, IgD-R are also upregulated by pharmacologically active compounds that increase intracellular cAMP and by PMA/DiOG plus ionomycin, but not by either PMA or ionomycin alone. The upregulation of IgD-R by anti-CD3 is inhibited by both calphostin C and herbimycin A, while that due to DiOG plus ionomycin is only inhibited by calphostin C. Upregulation of IgD-R by increased cAMP is blocked by HA1004, but not by low concentrations of staurosporine or herbimycin A. IgD itself does not cause an increase in intracellular cAMP, protein kinase C translocation, influx of extracellular Ca2+, or a change in membrane potential. Relatively specific inhibitors of these activation pathways, HA1004, calphostin C, and neomycin, also fail to interfere with IgD-receptor upregulation by IgD itself. However, tyrosine kinase inhibitors, including herbimycin A, tyrphostin C11, and genistein, completely prevent the effect of IgD on IgD-R expression. Although an influx of Ca2+ is apparently not involved, a role for intracellular Ca2+ in the upregulation of IgD-R by IgD on T cells is indicated by the susceptibility to inhibition by BAPTA, W7, and FK520. We conclude that activation of at least three different second-messenger systems can cause IgD-R upregulation, but that the effect of IgD itself requires tyrosine kinase activity, perhaps in an intracellular Ca(2+)-dependent manner. More »»

1992

Journal Article

Y. Yu, Dr. Bipin G. Nair, and Patel, T. B., “Epidermal growth factor stimulates cAMP accumulation in cultured rat cardiac myocytes”, Journal of cellular physiology, vol. 150, pp. 559–567, 1992.[Abstract]


We have previously shown that epidermal growth factor (EGF) augments cAMP accumulation in the heart and stimulates cardiac adenylyl cyclase via a G protein mediated mechanism (Nair et al., 1989). More recently, employing an antibody against the carboxy-terminus decapeptide of Gs alpha, we have demonstrated that Gs alpha mediates the effects of EGF on cardiac adenylyl cyclase (Nair et al., 1990). Since the heart comprises of a variety of cell types, the purpose of the studies presented here was to determine whether or not the effects of EGF on adenylyl cyclase were mediated in cardiac myocytes or noncardiomyocytes. Therefore, cultures of ventricular cardiomyocytes and noncardiomyocytes from neonatal rat hearts were established and characterized. Apart from the differences in cellular morphology, cardiomyocytes but not the noncardiomyocytes employed in our studies expressed the alpha- and beta-myosin heavy chain (MHC) mRNA and the beta-MHC protein. Additionally, as described previously, treatment of cardiomyocytes with thyroid hormone increased alpha-MHC mRNA and decreased the expression of beta-MHC mRNA, indicating that the cardiomyocytes employed in our studies were responding in a physiologically relevant manner. EGF in a time-dependent manner increased cAMP accumulation in the cardiomyocytes but not in noncardiomyocytes. Maximum and half-maximum effects were observed at 100 nM and 2 nM concentrations of EGF, respectively. As determined by the presence of immunoreactive EGF receptors and tyrosine phosphorylation of the 170 kDa protein in membranes of cardiomyocytes and noncardiomyocytes, both the cell populations contained functional EGF receptors. Therefore, the differential effects of EGF on cAMP accumulation in the two cell populations appear to be due to differential coupling of the EGF receptors to the adenylyl cyclase system rather than the absence of EGF receptors in noncardiomyocytes. Consistent with our previous findings in isolated membranes and perfused rat hearts, EGF-elicited increase in cAMP accumulation in cardiomyocytes did not involve activation of beta-adrenoreceptors and was abolished by prior treatment of cells with cholera toxin. Overall, our findings demonstrate that EGF-elicited increase in cAMP accumulation in the heart is the reflection of changes in cAMP content of cardiomyocytes and not noncardiomyocytes. More »»

1991

Journal Article

Dr. Bipin G. Nair, Steinke, L., Yu, Y. M., Rashed, H. M., Seyer, J. M., and Patel, T. B., “Increase in the number of atrial natriuretic hormone receptors in regenerating rat liver.”, Journal of Biological Chemistry, vol. 266, pp. 567–573, 1991.[Abstract]


Forty-eight hours after partial (approximately 67%) hepatectomy the activity of the particulate guanylate cyclase was increased by 2-fold in the regenerating rat liver. This increase was not an artifact of membrane isolation procedures, and as determined by 125I-labeled Tyr-28 atrial natriuretic hormone-(1-28) ANF binding, was accompanied by a 2-fold increase in the number of ANF receptors. The Kd of the receptors in membranes of regenerating livers was not significantly different from the Kd of the receptors in livers of sham-operated rats. The linear synthetic descysteine analog of ANF, analog I, which binds only to the 66-kDa receptors, displaced approximately 40% of the specifically bound 125I-ANF in liver membranes from both hepatectomized and sham-operated (control) animals. Affinity cross-linking studies with 125I-ANF confirmed the increase in the 116-kDa ANF receptor in membranes of regenerating livers. In perfused livers derived from control and hepatectomized animals, the basal rates of cGMP production were not significantly different. However, atriopeptin II-stimulated cGMP production was twice as great in regenerating livers as compared with controls. These data demonstrate that the increase in particulate guanylate cyclase activity observed during liver regeneration is due to an increase in the 116-kDa ANF receptor-associated activity. Additionally, our data demonstrate that the regenerating rat liver may be a valuable model with which to study the role of the hepatic ANF receptor/particulate guanylate cyclase. More »»

1991

Journal Article

Dr. Bipin G. Nair and Patel, T. B., “Inhibition of hepatic adenylate cyclase by NADH”, Life sciences, vol. 49, pp. 915–923, 1991.[Abstract]


Adenylate cyclase activity in isolated rat liver plasma membranes was inhibited by NADH in a concentration-dependent manner. Half-maximal inhibition of adenylate cyclase was observed at 120 microM concentration of NADH. The effect of NADH was specific since adenylate cyclase activity was not altered by NAD+, NADP+, NADPH, and nicotinic acid. The ability of NADH to inhibit adenylate cyclase was not altered when the enzyme was stimulated by activating the cyclase was not altered when the enzyme was stimulated by activating the Gs regulatory element with either glucagon or cholera toxin. Similarly, inhibition of Gi function by pertussis toxin treatment of membranes did not attenuate the ability of NADH to inhibit adenylate cyclase activity. Inhibition of adenylate cyclase activity to the same extent in the presence and absence of the Gpp (NH) p suggested that NADH directly affects the catalytic subunit. This notion was confirmed by the finding that NADH also inhibited solubilized adenylate cyclase in the absence of Gpp (NH)p. Kinetic analysis of the NADH-mediated inhibition suggested that NADH competes with ATP to inhibit adenylate cyclase; in the presence of NADH (1 mM) the Km for ATP was increased from 0.24 +/- 0.02 mM to 0.44 +/- 0.08 mM with no change in Vmax. This observation and the inability of high NADH concentrations to completely inhibit the enzyme suggest that NADH interacts at a site(s) on the enzyme to increase the Km for ATP by 2-fold and this inhibitory effect is overcome at high ATP concentrations. More »»

1991

Journal Article

E. Claro, Wallace, M. A., Fain, J. N., Dr. Bipin G. Nair, Patel, T. B., Shanker, G., and Baker, H. J., “Altered phosphoinositide-specific phospholipase C and adenylyl cyclase in brain cortical membranes of cats with GM1 and GM2 gangliosidosis”, Molecular brain research, vol. 11, pp. 265–271, 1991.[Abstract]


Phosphoinositide-specific phospholipase C and adenylyl cyclase were studied in brain cortical membranes from cats with GM1 and GM2 gangliosidosis. In contrast to brain cortical membranes from unaffected control cats, phospholipase C acting against exogenously supplied phosphoinositide substrates did not respond to stimulation by GTP gamma S, carbachol or fluoroaluminate in cortical membranes of cats with gangliosidosis. However, the enzyme was activated by calcium in membranes from affected cats to the same extent as in membranes from control cats. Basal adenylyl cyclase activity was increased 3-fold in cortical membranes of cats with GM1 and GM2 gangliosidosis, compared with unaffected sibling controls. Fluoroaluminate was equally effective in stimulating adenylyl cyclase in controls and in membranes of affected and normal cats. In addition, GppNHp was able to inhibit the forskolin-activated enzyme both in membranes from cats with gangliosidosis and sibling controls. These data suggest that the activation of phosphoinositide-specific phospholipase C in brain membranes by guanine nucleotide binding proteins is markedly impaired in GM1 and GM2 gangliosidoses. More »»

1990

Journal Article

Dr. Bipin G. Nair, Parikh, B., Milligan, G., and Patel, T. B., “Gs alpha mediates epidermal growth factor-elicited stimulation of rat cardiac adenylate cyclase.”, Journal of Biological Chemistry, vol. 265, pp. 21317–21322, 1990.[Abstract]


In an earlier study we demonstrated that epidermal growth factor (EGF) increases the cellular accumulation of cAMP in perfused rat hearts by stimulating the cardiac adenylate cyclase via a stimulatory GTP-binding protein (Nair, B. G., Rashed, H. M., and Patel, T. B. (1989) Biochem. J. 264, 563-571). Employing antiserum, CS1, generated against a synthetic decapeptide RMHLRQYELL representing the carboxyl terminus of Gs alpha, the involvement of Gs in mediating the effects of EGF on cardiac adenylate cyclase was further investigated. The CS1 antiserum specifically recognized two forms, (52 and 40 kDa) of Gs alpha in rat cardiac membranes; the 52 kDa being the predominant species. In functional assays of adenylate cyclase activity, the CS1 antiserum did not alter either aluminum fluoride- or forskolin-stimulated adenylate cyclase activity. Similarly, basal adenylate cyclase activity in the absence of guanyl-5'-yl imidodiphosphate (Gpp(NH)p) was also not altered by the CS1 antiserum. However, as compared with controls performed in the presence of non-immune serum, preincubation of cardiac membranes with the CS1 antiserum resulted in a concentration-dependent inhibition of Gpp(NH)p-, isoproterenol-, and EGF-stimulated activities. In experiments which monitored Gi function as the ability of different G(pp)NHp, (-)N6-(R-phenylisopropyl)adenosine and carbachol to inhibit forskolin-stimulated adenylate cyclase, CS1 antiserum by inhibiting Gs, increased the apparent activity of Gi. Overall, our data demonstrate that the CS1 antiserum can specifically inhibit Gs function and therefore the stimulation of adenylate cyclase by agonists whose actions are mediated by Gs. In this respect, the data presented here demonstrate that Gs is the G-protein involved in mediating EGF-elicited stimulation of cardiac adenylate cyclase. Additionally, the finding that CS1 antiserum can overcome the effects of Gpp(NH)p on Gs, but not Gi, suggests that the carboxyl-terminal region of Gs alpha is important in the interactions with GTP or its analogs. More »»

1989

Journal Article

Dr. Bipin G. Nair, Rashed, H. M., and Patel, T. B., “Epidermal growth factor stimulates rat cardiac adenylate cyclase through a GTP-binding regulatory protein.”, Biochem. J, vol. 264, pp. 563–571, 1989.[Abstract]


In isolated perfused rat hearts, epidermal growth factor (EGF; 15 nM) increased cellular cyclic AMP (cAMP) content by 9.5-fold. In rat cardiac membranes, EGF also stimulated adenylate cyclase activity in a dose-dependent manner, with maximal stimulation (35% above control) being observed at 10 nM-EGF. Half-maximal stimulation of adenylate cyclase was observed at 40 pM-EGF. Although the beta-adrenergic-receptor antagonist propranolol markedly attenuated the isoprenaline-mediated increase in cAMP content of perfused hearts and stimulation of adenylate cyclase activity, it did not alter the ability of EGF to elevate tissue cAMP content and stimulate adenylate cyclase. The involvement of a guanine-nucleotide-binding protein (G-protein) in the activation of adenylate cyclase by EGF was indicated by the following evidence. First, the EGF-mediated stimulation of adenylate cyclase required the presence of the non-hydrolysable GTP analogue, guanyl-5'-yl-imidodiphosphate (p[NH]ppG). Maximal stimulation was observed in the presence of 10 microM-p[NH]ppG. Secondly, in the presence of 10 microM-p[NH]ppG, the stable GDP analogue guanosine 5'-[beta-thio]diphosphate at a concentration of 10 microM blocked the stimulation of the adenylate cyclase by 1 nM- and 10 nM-EGF. Third, NaF + AlCl3-stimulated adenylate cyclase activity was not altered by EGF. The ability of EGF to stimulate adenylate cyclase was not affected by pertussis-toxin treatment of cardiac membranes. However, in cholera-toxin-treated cardiac membranes, when the adenylate cyclase activity was stimulated by 2-fold, EGF was ineffective. Finally, PMA by itself did not alter the activity of cardiac adenylate cyclase, but abolished the EGF-mediated stimulation of this enzyme activity. The experimental evidence in the present paper demonstrates, for the first time, that EGF stimulates adenylate cyclase in rat cardiac membranes through a stimulatory GTP-binding regulatory protein, and this effect is manifested in elevated cellular cAMP levels in perfused hearts exposed to EGF. More »»

1986

Journal Article

M. Sonavaria, Dr. Bipin G. Nair, and CHHATPAR, H. S., “Carbon starvation mediated changes in carbohydrate metabolism inNeurospora crassa”, Journal of Biosciences, vol. 10, pp. 187–192, 1986.[Abstract]


Carbon starvation conditions were found to increase the activities of gluconeogenic enzymes such as malic enzyme, cytosolic malate dehydrogenase and isocitrate lyase along with proteases and inhibition in glucose catabolic enzymes such as G6P dehydrogenase and FDP aldolase inNeurospora crassa More »»

1984

Journal Article

S. Pinge, Patel, S., Dr. Bipin G. Nair, and CHHATPAR, H. S., “Effect of chloramphenicol on some of the cytosolic enzymes from Neurospora crassa”, Indian journal of experimental biology, vol. 22, pp. 102-103, 1984.

1984

Journal Article

S. Ram, Dr. Bipin G. Nair, and CHHATPAR, H. S., “Photoregulation of some enzymes fromNeurospora crassa”, Experientia, vol. 40, pp. 1382–1384, 1984.[Abstract]


Light-grown cultures of Neurospora crassa showed photoregulation of a number of enzymes. Proteases and cytosolic malate dehydrogenase showed an increase in activity. There was a decrease in the activity of mitochondrial malate dehydrogenase, isocitrate dehydrogenase and cytosolic glucose-6P-dehydrogenase, isocitrate dehydrogenase and isocitrate lyase. More »»

1983

Journal Article

S. SAVANT, PARIKH, N., Dr. Bipin G. Nair, and CHHATPAR, H. S., “Phosphate Mediated Biochemical-Changes In Neurospora-Crassa”, Current Science, vol. 52, pp. 1070-1072, 1983.

1981

Journal Article

K. SHAH, RAO, S., Dr. Bipin G. Nair, and MODI, V. V., “Modification of Antifungal Activity of Econazole in Presence of Betamethazone”, INDIAN JOURNAL OF MEDICAL RESEARCH, vol. 73, pp. 965–969, 1981.[Abstract]


An attempt was made to find the optimal proportion of econazole to betamethasone which gives the least inhibition of antifungal activity of econazole. There was a gradual reduction in O2 consumption by Candida tropicalis (ATCC 13803) with increase in the concentration of econazole. Betamethasone stimulated the O2 consumption by C. tropicalis. The changes elicited by betamethasone in various concentrations on the antifungal activity of econazole were investigated by the Warburg manometric technique. There was no significant decrease in antifungal activity of econazole when combined with betamethasone in a 1:0.1 prooortion. The inhibition of O2 consumption was more at a 1:0.1 ratio than at 1:0.125. The minimal inhibitory concentration of econazole was found to be 0.06 .mu.g by plate assay method. It was observed by plate assay and by turbidometric assay that 1:0.075 was the optimal ratio of econazole to betamethasone, which did not give significant decrease in antifungal activity. More »»

Publication Type: Conference Paper

Year of Publication Publication Type Title

2018

Conference Paper

Dr. Shyam Diwakar, R, R., N, N., Dr. Bipin G. Nair, and Dr. Krishnashree Achuthan, “Using Learning Theory for Assessing Effectiveness of Laboratory Education Delivered via a Web-based Platform”, in International Conference on Remote Engineering and Virtual experimentation (REV 2018), Dusseldorf, Germany, 2018.

2018

Conference Paper

Dr. Shyam Diwakar, Dr. Bipin G. Nair, Manjusha Nair, D, K., M, K., L., E., R, R., and N, N., “Design and Implementation of an Open-Source Browser-based Laboratory Platform for EEG Data Analysis”, in Proceedings of the Seventh International Conference on Advances in Computing, Communications and Informatics (ICACCI-2018), Bangalore, Karnataka, India, 2018.

2018

Conference Paper

Dr. Shyam Diwakar, Dr. Bipin G. Nair, R, R., A, D., A, N., ,, G, M., N, N., and K., A., “Virtual Laboratories in Biotechnology are Significant Educational Informatics Tools”, in Proceedings of the Seventh International Conference on Advances in Computing, Communications and Informatics (ICACCI-2018), Bangalore, Karnataka, India, 2018.

2018

Conference Paper

Dr. Shyam Diwakar, C, N., S., R., and Dr. Bipin G. Nair, “Modeling Nitric Oxide Induced Neural Activity and Neurovascular Coupling in a Cerebellum Circuit”, in Proceedings of the Seventh International Conference on Advances in Computing, Communications and Informatics (ICACCI-2018), Bangalore, Karnataka, India, 2018.

2018

Conference Paper

Dr. Shyam Diwakar, Dr. Bipin G. Nair, Manjusha Nair, M, K., L, E., R, R., N, N., and D, K., “Experimental Recording and Computational Analysis of EEG signals for a Squeeze Task: Assessments and Impacts for Applications”, in Proceedings of the Seventh International Conference on Advances in Computing, Communications and Informatics (ICACCI-2018), Bangalore, Karnataka, India, 2018.

2018

Conference Paper

Dr. Shyam Diwakar, Dr. Bipin G. Nair, V, S., P, R. L., S., G., H., E., and C., N., “Torque Analysis of Male-Female Gait and Identification using Machine Learning”, in Proceedings of the Seventh International Conference on Advances in Computing, Communications and Informatics (ICACCI-2018), Bangalore, Karnataka, India, Sept 19-22, 2018 (accepted)., 2018.

2018

Conference Paper

Dr. Shyam Diwakar, Dr. Bipin G. Nair, A, R., and A, P., “Reproducing the firing properties of a cerebellum deep cerebellar nucleus with a multi compartmental morphologically realistic biophysical model”, in Proceedings of the Seventh International Conference on Advances in Computing, Communications and Informatics (ICACCI-2018), Bangalore, Karnataka, India, Sept 19-22, 2018 (accepted)., 2018.

2018

Conference Paper

R. A., A., A., D, M., J., T., S, P., Dr. Shyam Diwakar, and Dr. Bipin G. Nair, “Trajectory tracking using a Bio-inspired neural network for a low cost robotic articulator”, in Proceedings of the Seventh International Conference on Advances in Computing, Communications and Informatics (ICACCI-2018), Bangalore, Karnataka, India, Sept 19-22, 2018 (accepted). , 2018.

2018

Conference Paper

Dr. Shyam Diwakar, Dr. Bipin G. Nair, H., S., M., P., M., B., A., P., E., P., and S., K., “Modeling of Glutamate Pathway in Alzheimer's Disease using Biochemical Systems Theory”, in Proceedings of the Seventh International Conference on Advances in Computing, Communications and Informatics (ICACCI-2018), Bangalore, Karnataka, India, Sept 19-22, 2018 (accepted). , 2018.

2018

Conference Paper

Dr. Shyam Diwakar, Dr. Bipin G. Nair, H., S., C., N., A., R., P., V., M., S., L., N., and H, M., “Spectral Correlations in Speaker-Listener Behavior During a Focused Duo Conversation using EEG”, in Proceedings of the Seventh International Conference on Advances in Computing, Communications and Informatics (ICACCI-2018), Bangalore, Karnataka, India, Sept 19-22, 2018 (accepted)., 2018.

2017

Conference Paper

V. Amrutha., Prasad Megha, Lekshmija, A., Anjana, R., Aleena, S., Dr. Bipin G. Nair, Madhavan, A., and Dr. Sanjay Pal, “Effect of compost derived lytic agents against enteric bacteria in sewage”, in InnovativeStrategies for Sustainable Water Management (ISSWM-2017), Punjab, India. , 2017.

2017

Conference Paper

Pradeesh Babu, Poornendu, S. J., Amrita Salim, Madhavan, A., Dr. Bipin G. Nair, and Dr. Sanjay Pal, “Resazurin based redox dye as an indicator for monitoring wastewater biological activity”, in Innovative Strategies for Sustainable Water Management (ISSWM-2017), Punjab, India, 2017.

2017

Conference Paper

M. Sreejith, Reghu, A. P., Anandakrishnan, K., Gopika, P. J., .Kuriakose, G., Reshma, M. J., Vishnu, K., Madhavan, A., Dr. Bipin G. Nair, and Dr. Sanjay Pal, “Screening potential antimicrobial compounds by resazurin dye based viability assay”, in Innovative Strategies for Sustainable Water Management (ISSWM-2017), Punjab, India, 2017.

2017

Conference Paper

V. Prakash, H. Sreetha, Poornima, K. H., Lakshmimol, K. N., Regma, R., Fathima, H., Vishnu, T. V., Venu, S., Dr. Bipin G. Nair, and Dr. Sanjay Pal, “Antagonistic effects of bacteriocins from Lactobacillus spp. against enteric pathogens”, in Innovative Strategies for Sustainable Water Management (ISSWM-2017), Punjab, India ., 2017.

2017

Conference Paper

S. Subhash, Kuruvelil, A. B., Aswathi, P. V., Deepasree, K., Navyamol, C. D., N.P.V., D., Prasad, P., Dr. Bipin G. Nair, and Dr. Sanjay Pal, “Screening of nematicidal activities of biocontrol fungi Aspergillus niger and Penicillium oxalicum using C. elegans as model”, in Innovative Strategies for Sustainable Water Management (ISSWM-2017) , Punjab, India. , 2017.

2017

Conference Paper

D. Tharuvana, A. Sundaresh, Sreelakshmi, V. J., Das, A., Dr. Bipin G. Nair, Dr. Sanjay Pal, and Madhavan, A., “Sand and charcoal as matrices for immobilization of phages for wastewater treatment”, in Innovative Strategies for Sustainable Water Management (ISSWM-2017) , Punjab, India. , 2017.

2017

Conference Paper

A. P. Veedu, Reshma, R. N., Dr. Bipin G. Nair, Dr. Sanjay Pal, and Madhavan, A., “Activity of probiotic strains against enteric pathogens”, in Innovative Strategies for Sustainable Water Management (ISSWM-2017) , Punjab,India. , 2017.

2017

Conference Paper

A. Madhavan, Prasad Megha, Girish, S., K. Shetty, S., Dr. Bipin G. Nair, and Dr. Sanjay Pal, “Caulobacter crescentus as a novel exoelectricigen in a dual chambered Microbial Fuel Cell (MFC)”, in Technical Program Committee of the “2017 IEEE International( Biennial) Conference on Technological Advancements in Power and Energy”, TAP Energy-2017. , 2017.

2017

Conference Paper

A. Madhavan, K. Shetty, S., Anjana, G., Das, A., Athira, A. S., Hari, H., ,, Babu, S., Dr. Bipin G. Nair, and Dr. Sanjay Pal, “Pneumatophore inspired biomimetic approach to design an energy neutral aerator for application in composting”, in Technical Program Committee of the “2017 IEEE International ( Biennial) Conference on Technological Advancements in Power and Energy”, TAP Energy-2017. , 2017.

2017

Conference Paper

P. Nagarajan, Sruthy, K. S., Lal, V. P., Devan, V. P., Krishna, A., Lakshman, A., Vineetha, K. M., Dr. Bipin G. Nair, Dr. Sanjay Pal, and Madhavan, A., “Biological treatment of domestic wastewater by selected aquatic plants”, in IEEE International Conference on Technological Advancements in Power & Energy (TAP Energy 2017). , 2017.[Abstract]


Around 30 percent of the operating costs of conventional centralized wastewater treatment is required for energy to operate the machines for pump and aeration. Comparatively, constructed wetlands involving photosynthetic plants and other organisms have a lower energy requirement. The aim of the present work is to select aquatic plants which have high efficiency of removing infection in wastewater. Four plants were chosen from locally available plants growing in wastewater. They were put in raw wastewater from toilets for 24 h and were tested for their survival and growth measured by chlorophyll content. Brahmi (Bacopa monnieri) and Duckweed were found to be best compared to Azolla and Hydrilla. The efficiency of removal of enteric infections was done by culturing the treated wastewater on Eosin Methylene Blue (EMB) agar media, a selective and differential medium for enteric gram negative bacteria. The best performing plants were Brahmi and Hydrilla which reduced the load by 67-70%. But Hydrilla did not grow as well compared to Brahmi as evident from the chlorophyll content. Hence Brahmi and Duckweed can be considered as most effective for removal of infection in wastewater among the four tested plants and potentially may save energy and synthetic chemicals otherwise required for conventional treatment systems. Brahmi, famous for its high value medicinal compounds against neuronal problems, may be used for extraction of the compounds. The remaining biomass can be used as feedstock in anaerobic digester for methane/ethanol generation to be used as biofuel.

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2017

Conference Paper

N. C, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Modeling Neurovascular coupling for fMRI BOLD reconstructions”, in XXXV Annual Meeting of Indian Academy of Neurosciences (IAN), Ravenshaw University, Cuttack, Odisha, India, 2017.

2017

Conference Paper

Dr. Bipin G. Nair, Dr. Shyam Diwakar, and Rajendran, A., “Pattern Abstraction and Sensory Encoding of Auditory and Visual Stimuli in Cerebellum Granular Layer Network”, in XXXV Annual Meeting of Indian Academy of Neurosciences (IAN), Ravenshaw University, Cuttack, Odisha, India, 2017.

2017

Conference Paper

M. N, S, P., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Using Machine learning to understand data analysis- A case study of a private health care organization”, in 6th International Conference in Advances in Computing, Communications and Informatics (ICACCI-17), 2017.

2017

Conference Paper

Asha Vijayan, Gopan, V., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Comparing robotic control using a spiking model of cerebellar network and a gain adapting forward-inverse model”, in 2017 International Conference on Advances in Computing, Communications and Informatics (ICACCI), Udupi, India, 2017.[Abstract]


Internal models inspired from the functioning of cerebellum are being increasingly used to predict and control movements of anthropomorphic manipulators. A major function of cerebellum is to fine tune the body movements with precision and are comparative to capabilities of artificial neural network. Several studies have focused on encoding the real-world information to neuronal responses but temporal information was not given due importance. Spiking neural network accounts to conversion of temporal information into the adaptive learning process. In this study, cerebellum like network was reconstructed which encodes spatial information to kinematic parameters, self-optimized by learning patterns as seen in rat cerebellum. Learning rules were incorporated into our model. Performance of the model was compared to an optimal control model and have evaluated the role of bioinspired models in representing inverse kinematics through applications to a low cost robotic arm developed at the lab. Artificial neural network of Kawato was used to compare with our existing model because of their similarity to biological circuit as seen in a real brain. Kawato's paired forward inverse model has used to train for fast movement based tasks which resembles human based motor tasks. Result suggest kinematics of a 6 DOF robotic arm was internally represented and this may have potential application in neuroprosthesis.

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2017

Conference Paper

S. Bodda, Palathingal, R. K., Sankar, V., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Modeling population network activity using lfpsim, spiking neurons and neural mass models”, in 2017 International Conference on Advances in Computing, Communications and Informatics (ICACCI), Udupi, India, 2017.[Abstract]


Local Field Potentials arising (LFP) from neural circuits are crucial to understand neural ensemble activity and can act as a link between molecular, cellular and circuit neuroscience. Additionally, mathematical estimations of LFPs allow the study of circuit functions and dysfunctions. In this study, we used mathematical reconstructions of LFP in rat cerebellum Crus IIa using spiking neuronal models and mass models based on lumped parameters to reconstruct the averaged ensemble activity. Comparing experimentally validated reconstructions of evoked LFPs using detailed multi-compartmental models, spiking neurons and lumped mass models suggest variations at the translational levels of biophysical mechanisms in granular layer. With the focus of reconnecting multiple information roles, our simulations studies indicate multi-compartmental detailed models allow estimations on the role of transmembrane currents, spiking neuron models suggest contributions of action potentials while mass models reveal averaged activity behaviour underlying Crus IIa evoked LFPs.

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2017

Conference Paper

A. Rajendran, Thankamani, A., Nirmala, N., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Computational neuroscience of substantia nigra circuit and dopamine modulation during parkinson's disease”, in 2017 International Conference on Advances in Computing, Communications and Informatics (ICACCI), Udupi, India, 2017.[Abstract]


Several interconnected brain circuits such as cerebellum, cerebral cortex, thalamus and basal ganglia process motor information in many species including mammals. Interconnection between basal ganglia and cerebellum through thalamus and cortex may influence the pathways involved in basal ganglia processing. Malfunctions in the neural circuitry of basal ganglia influenced by modifications in the dopaminergic system, which are liable for an array of motor disorders and slighter cognitive issues in Parkinson's disease. Both basal ganglia and cerebellum receives input from and send output to the cerebral cortex and these structures influence motor and cognitive operations through cerebellar-thalamo-basal ganglia-cortical circuit. This interconnected circuit (basal ganglia-cerebellum) helps to understand the role of cerebellum in motor dysfunction during Parkinson's disease. To develop models of unsupervised learning as in brain circuits, we modelled sub thalamic nucleus, internal and external parts of Globus pallidus, fast spiking striatal neuron and medium spiny neuron in striatum using Adaptive Exponential Integrate and Fire model. Simulations highlight the correlation between firing of GPe and level of dopamine and the changes induced during simulated Parkinson's disease. Such models are crucial to understand the motor processing and for developing spiking based deep learning algorithms.

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2017

Conference Paper

Chaitanya Nutakki, Narayanan, J., Anchuthengil, A. Anitha, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Classifying gait features for stance and swing using machine learning”, in 2017 International Conference on Advances in Computing, Communications and Informatics (ICACCI), Udupi, India, 2017.[Abstract]


Structured gait patterns are currently used as a biometric technique to recognize individuals and in building appropriate exoskeleton technologies. In this study, the features involved in gait were extracted and analyzed. Multiple accelerometers were used to collect the data which was then used to identify gait at various axial positions form healthy volunteers with total of 60 trails. Using machine learning optimal feature sub-selection we analyze data to implicate the optimal methods for analysis of swing phase and stance phase in a closed room environment. Study reports that the accelerometer data could classify based on the accuracy and the efficiency of the learning algorithms. Through feature ranking, results suggest gait can be attributed to a combination of Brachium of arm, Antecubitis, Carpus, Coxal, Femur and Tarsus (Shoulder, Elbow, Wrist, Hip, Knee, and Ankle). This gait study may help analyzing conditions during control and movement-related disease.

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2017

Conference Paper

H. Sasidharakurup, Dash, P., Asha Vijayan, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Computational modelling of apoptosis in parkinson's disease using biochemical systems theory”, in 2017 International Conference on Advances in Computing, Communications and Informatics (ICACCI), Udupi, India, 2017.[Abstract]


In this study, we present a computational model of Parkinson's disease (PD) that includes different biological interactions that leads to neural cell death with the use of biochemical systems theory. The model incorporates a set of important pathways in PD including dopaminergic pathway, mitochondrial pathway and P53 - DNA damage pathway. Modeling signaling pathways and simulations were performed using biochemical systems theory. Initial concentrations have been taken from experimental data in literature and were used to model the changes. Results generated by dopaminergic diseased pathway show 45% decrease in dopamine, compared to normal condition. In addition, the activity of MOMP, Caspase 9 and Apoptosome expression in diseased condition within mitochondrial pathway model have been observed in the results. The expression levels of BAX and MOMP were reconstructed and simulations suggest oligomerization of BAK leads to the elevation of MOMP. An increase in oxidative stress and apoptosis level also has been observed in the PD condition, compared to the control allowing comparisons between normal and diseased conditions with these mathematical models.

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2017

Conference Paper

Manjusha Nair, Ushakumari, K., Ramakrishnan, A., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Comparing parallel simulation of single and multi-compartmental spiking neuron models using gpgpu”, in 2017 International Conference on Advances in Computing, Communications and Informatics (ICACCI), Udupi, India, 2017.[Abstract]


Characterizing neural responses and behavior require large scale simulation of brain circuits. Spatio-temporal information processing in large scale neural simulations often require compromises between computing resources and realistic details to be represented. In this work, we compared the implementations of point neuron models and biophysically detailed neuron models on serial and parallel hardware. GPGPU like architectures provide improved run time performance for multi compartmental Hodgkin-Huxley (HH) type neurons in a computationally cost effective manner. Single compartmental Adaptive Exponential Integrate and Fire (AdEx) model implementations, both in CPU and GPU outperformed embarrassingly parallel implementation of multi compartmental HH neurons. Run time gain of CPU implementation of AdEx cluster was approximately 10 fold compared to the GPU implementation of 10-compartmental HH neurons. GPU run time gain for Adex against GPU run time gain for HH was around 35 fold. The results suggested that careful selection of the neural model, capable enough to represent the level of details expected, is a significant parameter for large scale neural simulations.

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2017

Conference Paper

Manjusha Nair, Suresh, A. Puthenpeed, Manoharan, A., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Information theoretic visualization of spiking neural networks”, in 2017 International Conference on Advances in Computing, Communications and Informatics (ICACCI), Udupi, India, 2017.[Abstract]


Visualization is a flexible way to analyze simulated data and serves as a means for scientific discovery. Large scale neural simulations using high performance and distributed computing techniques produce huge amount of data for which visual analysis is generally difficult to perform. In this paper, a spiking neuron simulation environment was created to model and simulate networks of neurons of the cerebellum. Traditional visualization techniques were used to highlight relevant findings from small scale cerebellar networks. Time varying volume visualization using traditional techniques was found infeasible as network size increased. New data abstractions were required to depict the data that changes over time. With large scale cerebellar networks, Information theoretic methods were used to reduce dimensionality and to extract valuable information from data. We suggested that, information theory can be used as an efficient scientific data analysis and visualization tool to evaluate and validate computational models of cerebellar like structures.

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2017

Conference Paper

J. Alphonse, Chaitanya Medini, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “An open-source computational neuroscience virtual laboratory tool for simulating spiking neurons and circuits”, in 2017 International Conference on Advances in Computing, Communications and Informatics (ICACCI), Udupi, India, 2017.[Abstract]


Neuronal models and real-time simulations of large-scale neural networks allow hypothesis testing of physiological data and for predicting neurological disorders. Simulators using web technologies serve as educational tools in addition to allowing experimentalists make predictions on experimental hypotheses. In this paper, we have developed a web-based neuron and network simulator to model spatio-temporal computations in animal nervous systems. Neuronal models including Hodgkin-Huxley (HH), Adaptive Exponential (AdEx) integrate and fire model and Izhikevich model were incorporated. All models were implemented using JavaScript and python with visualization using HTML5. Single neuron responses and a small-scale network dynamics corresponding to experimentally-known stimuli patterns were simulated. The simulator allows configuring neuronal dynamics through the GUI and can also allow modeling complex dynamics by interfacing with BRIAN for more large-scale and complex simulations. This web technology-based simulation environment may be used by neurophysiologists to simulate experimental protocols and modeling simple circuit dynamics with or without backend programming.

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2017

Conference Paper

N. Nizar, Radhamani, R., Dhanush Kumar, Dr. Bipin G. Nair, Dr. Shyam Diwakar, and Dr. Krishnashree Achuthan, “Implementation of analog electrical neurons as virtual labs for neuroscience education”, in 2017 International Conference on Advances in Computing, Communications and Informatics (ICACCI), Udupi, India, 2017.[Abstract]


Over the last few years, research was aimed to investigate neuromorphic computing methodologies for understanding the functions and behavior of biological neurons on a real-time basis. In neuron electrical models, the principles of computational neuroscience is translated on to analog hardware and the circuits reproduces the bio-physical properties of neurons. Our aim was to implement analog neuron models based on Hodgkin-Huxley formalism, and to deploy it as an educational platform for understanding the cellular and behavioral neuroscience. We have taken multiple analog hardware models and implemented its corresponding equivalent for studying the pedagogical concepts such as spiking, bursting, effects of ion channels, effect of pharmacological agents on spiking properties. We implemented remote electrical laboratories for science and engineering education bridging computing systems and neural studies. Initial implementation of the remote labs were done with commercial software which was later replaced with Free and Open Source Software (FOSS) architecture. Pedagogical analysis indicated, effectiveness in the usage of analog neuron model as a learning material for complementing neuroscience education in universities. Post-deployment studies on students and teachers includes perceived use of remote experimentation in a blended classroom scenario.

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2016

Conference Paper

Chaitanya Nutakki, Asha Vijayan, Hemalata Sasidharakurup, Dr. Bipin G. Nair, Dr. Krishnashree Achuthan, and Dr. Shyam Diwakar, “Low-Cost Robotic Articulator as an Online Education tool: Design, Deployment and Usage”, in Proceedings of IEEE International Conference on Robotics and Automation for Humanitarian Applications, Amrita Vishwa Vidyapeetham, Kollam, Kerala, 2016.[Abstract]


Humanitarian challenges in developing nations such as low cost prosthesis for the physically challenged, have also led to substantial progress in robotics. In this paper, we implemented and deployed a low-cost remotely controlled robotic articulator, as an education tool for university students and teachers. This tool is freely available online and is being employed to generate robotic datasets for novel algorithms. Using a server-client methodology and a browser-based user interface, the online lab allows learners to access and perform basic kinematics experiments and study robotic articulation. These experiments were developed for allowing students to enhance laboratory skills in robotics and improve practical experience without concerns for equipment access restrictions or cost.

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2016

Conference Paper

A. Sridharan, Sasidharakurup, H., Kumar, D., Nizar, N., Dr. Bipin G. Nair, Dr. Krishnashree Achuthan, and Dr. Shyam Diwakar, “Implementing a Web-Based Simulator with Explicit Neuron and Synapse Models to Aid Experimental Neuroscience and Theoretical Biophysics Education”, in Proceedings of the International Conference on Signal, Networks, Computing, and Systems, New Delhi, 2016, vol. 396, pp. 57-66.[Abstract]


In this paper, we implemented a virtual laboratory of neurons and synapses via dynamical models on a web-based platform to aid neurophysiology and computational neuroscience education. Online labs are one of the best alternatives to many universities confronting socio-economic issues in maintaining infrastructure for good laboratory practice. The neural network virtual laboratory was implemented using HTML5 and JQuery, which allowed users to access the lab as a browser-based app. The simulator allows reconstructions of population code and biophysics of single neuron firing dynamics and hence will allow experimentalists to explore its use for hypothesis-based predictions. Such tools as educational aids allow an interrelationship of cognitive, social, and teaching presence. We found students could easily reproduce the common voltage and current clamp protocols on such models without significant instructor assistance and the platform was developed to allow further extensions like raster plots, network computations using extensions to code modules. With new technologies, we foresee a potential redesign of the use of such virtual labs for large-scale modeling as teaching and learning tools in blended learning environments.

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2016

Conference Paper

R. Radhamani, Nizar, N., Dhanush Kumar, Dr. Bipin G. Nair, Dr. Krishnashree Achuthan, and Dr. Shyam Diwakar, “Low cost neuro-inspired robots for sustainable laboratory education”, in International Conference on Robotics and Automation for Humanitarian Applications, RAHA 2016 - Conference Proceedings, Kollam, India, 2016.[Abstract]


Today's technological innovations accelerate the persistence of robots for humanitarian purposes. As a significant component, the emerging role of robotics and educational technologies has been growing instantly. Several attempts have been introduced in the education sector to promote robotics education, but successful implementation of learning platforms still pose challenges. This paper highlights deployment studies based on a low cost bio-inspired robotics laboratory. The experiments were developed as part of a National Mission on Education through ICT, and provided free access to users all over the world. The present study seeks to examine the role of low cost remotely controlled neuro-inspired robotics labs as an educational tool. Our goal was to analyze the diffusion of remotely controlled robotics labs as a new pedagogy for augmenting laboratory education, by enhancing skill training among students, aiding as a teaching element and promoting distant education thereby bringing a sustainable development in robotics based education. Feedback data was collected from 100 science and engineering students, 50 university professors and 100 online users from distant locations to analyze remote robotics labs as an adaptable tool in education. The study suggested perceived usefulness of low cost robotics platform as a supplementary learning and teaching tool for enhancing robotics education. The study also promotes the perceived usage of robotics for vocational skills and as a technology education platform for learners. © 2016 IEEE.

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2016

Conference Paper

A. Madhavan, Nandakumar, V., K. Shetty, S., Dr. Bipin G. Nair, and Dr. Sanjay Pal, “Optimization of microbial fuel cell (MFC) operated with waste water as substrate”, in Electrical, Electronics, and Optimization Techniques (ICEEOT), International Conference on, Chennai, India, 2016.[Abstract]


In the present study bioelectricity generation from waste water was evaluated in a double chambered microbial fuel cell (MFC). Waste water and potassium permanganate solution (0.3%) was loaded in the anodic and the cathodic chamber respectively. The performance of MFC was studied with two different electrodes (aluminum and carbon as anodes and copper as cathode). Current and voltage measurements were carried out using Keithley source meter (2420) and multimeter respectively. The Voltammetric analysis was done to study the anodic oxidation rate. The resistance of the system was found to be low (0.466 Ω for the aluminum anode and 0.673 Ω carbon anode) which were deduced from the power density curves. The system showed a COD removal of 77% over a period of a week ofk operation.

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2016

Conference Paper

Dhanush Kumar, Dr. Krishnashree Achuthan, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Online bio-robotics labs: Open hardware models and architecture”, in 2016 International Conference on Robotics and Automation for Humanitarian Applications (RAHA), Kollam, India, 2016.[Abstract]


This paper is on free and open source software architecture (FOSS) for remote labs in order to address the affordability and scalability of robotic education technology for sustainable deployments. The proposed Raspberry Pi-Arduino-based model architecture ensures lower cost while allowing some scalability, interoperability, portability and interchangeability to the low-cost online laboratory. Remotely controlled lab provides training skills in bio-inspired robotics. Our previous studies had shown that the implementation of remotely controlled online labs in the curriculum improved active learning among students, collaboration, and augmented problem solving skills. The preliminary implementation involved proprietary software, as the remote experiment accessibility platform, which was later replaced with FOSS technology. The advantages with FOSS included a significantly lower cost and scalability for concurrent usage. The paper also reports on usage analysis and common issues in both cases of implementations.

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2016

Conference Paper

N. C, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Computational Reconstruction of fMRI BOLD from Cerebellar Input Layer”, in XXXIV Annual Meeting of Indian Academy of Neurosciences (IAN), National Brain Research Center, Manesar, India, 2016.

2016

Conference Paper

B. S, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Mathematical Modelling of Post Synaptic Evoked Local Field Potential Using Neural Mass Model”, in XXXIV Annual Meeting of Indian Academy of Neurosciences (IAN), National Brain Research Center, Manesar, India, 2016.

2016

Conference Paper

R. A, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Modeling and Parallelization of Cerebellar Microcircuit for Combinatorial Operation”, in XXXIV Annual Meeting of Indian Academy of Neurosciences (IAN), 2016.

2016

Conference Paper

S. H, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Modeling of Biochemical Pathways in Parkinson's Disease”, in XXXIV Annual Meeting of Indian Academy of Neurosciences (IAN), National Brain Research Center, Manesar, India, 2016.

2016

Conference Paper

Chaitanya Nutakki, Nair, A., Chaitanya Medini, Manjusha Nair, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Computational reconstruction of fMRI-BOLD from neural activity”, in 2016 International Conference on Advances in Computing, Communications and Informatics (ICACCI), Jaipur, India, 2016.[Abstract]


In this paper, we model function magnetic resonance imaging signals generated by neural activity (fMRI). fMRI measures changes in metabolic oxygen in blood in brain circuits based on changes in biophysical factors like concentration of total cerebral blood flow, oxy-hemoglobin and deoxy-hemoglobin content. A modified version of the Windkessel model by incorporating compliance has been used with a balloon model to generate cerebellar granular layer and visual cortex blood oxygen-level dependent (BOLD) responses. Spike raster patterns were adapted from a biophysical granular layer model as input. The model fits volume changes in blood flow to predict the BOLD responses in the cerebellum granular layer and in visual cortex. As a comparison, we tested the balloon model and the modified Windkessel model with the mathematically reconstructed BOLD response under the same input condition. Delayed compliance contributed to BOLD signal and reconstructed signals were compared to experimental measurements indicating the usability of the approach. The current study allows to correlate dynamic changes of flow and oxygenation during brain activation which connects single neuron and network activity to clinical measurements.

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2016

Conference Paper

B. S, H, P., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Computing LFP From Biophysical Models of Neurons and Neural Microcircuits”, in Proceedings of 2016 International Conference on Advances in Computing, Communications and Informatics (ICACCI 2016), Jaipur, India, 2016.

2016

Conference Paper

Chaitanya Medini, Rajendran, A. G., Jijibai, A., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Computational characterization of cerebellum granule neuron responses to auditory and visual inputs”, in 2016 International Conference on Advances in Computing, Communications and Informatics (ICACCI), Jaipur, India, 2016.[Abstract]


The multimodal nature of sensory and tactile inputs to cerebellum is of significance for understanding brain function. Granule neuron properties in modifying auditory and visual stimuli was mathematically modeled in this study. Cerebellum granule neuron is a small electrotonically compact neuron and is among the largest number of neurons in the cerebellum. Granule neurons receives four excitatory inputs from four different mossy fibers. We mathematically reconstructed the firing patterns of both auditory and visual responses and decode the mossy fiber input patterns from both modalities. A detailed multicompartment biophysical model of granule neuron was used and in vivo behavior was modeled with short and long bursts. The cable compartmental model could reproduce input-output behavior as seen in real neurons to specific inputs. The response patterns reveal how auditory and visual patterns are encoded by the mossy fiber-granule cell relay and how multiple information modalities are processed by cerebellum granule neuron as responses of auditory and visual stimuli.

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2016

Conference Paper

Chaitanya Medini, Thekkekuriyadi, A., Thayyilekandi, S., Manjusha Nair, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Modeling basal ganglia microcircuits using spiking neurons”, in 2016 International Conference on Advances in Computing, Communications and Informatics (ICACCI), Jaipur, India, 2016.[Abstract]


Basal ganglia and cerebellum have been implicated in critical roles related to control of voluntary motor movements for action selection and cognition. Basal ganglia primarily receive inputs from cortical areas as well as thalamic regions, and their functional architecture is parallel in nature which link several brain regions like cortex and thalamus. Striatum, substantia nigra, pallidum form different neuronal populations in basal ganglia circuit which were functionally distinct supporting sensorimotor, cognitive and emotional-motivational brain functions. In this paper, we have modelled and simulated basal ganglia neurons as well as basal ganglia circuit using integrate and fire neurons. Firing behaviour of subthalamic nucleus and global pallidus externa show how they modulate spike transmission in the circuit and could be used to model circuit dysfunctions in Parkinson's disease.

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2016

Conference Paper

R. Radhamani, Dhanush Kumar, Dr. Krishnashree Achuthan, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Implementing and deploying magnetic material testing as an online laboratory”, in Intelligent Systems Technologies and Applications 2016, Cham, 2016.[Abstract]


Hysteresis loop tracing (HLT) experiment is an undergraduate experiment for physics and engineering students to demonstrate magnetic properties of ferrite materials. In this paper, we explore a new approach of setting- up triggered testing of magnetic hysteresis via a remotely controlled loop tracer. To aid student learners, through an experimental design, we focused on factors such as analytical expression of mathematical model and modeling of reversible changes, which were crucial for learning hysteresis components. The goal was to study the phenomena of magnetic hysteresis and to calculate the retentivity, coercivity and saturation magnetization of a material using a hybrid model including simulation and remotely controlled hysteresis loop tracer. The remotely controlled equipment allowed recording the applied magnetic field (H) from an internet-enabled computer. To analyze learning experiences using online laboratories, we evaluated usage of online experiment among engineering students (N=200) by organized hands-on workshops and direct feedback collection. We found students adapted to use simulations and remotely controlled lab equipment augmenting laboratory skills, equipment accessibility and blended learning experiences.

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2016

Conference Paper

Sandeep Bodda, Chandranpillai, H., Viswam, P., Krishna, S., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Categorizing imagined right and left motor imagery BCI tasks for low-cost robotic neuroprosthesis”, in 2016 International Conference on Electrical, Electronics, and Optimization Techniques (ICEEOT), Chennai, India, 2016.[Abstract]


Focusing on low-cost articulation control for neuroprosthesis, electroencephalography (EEG)-based brain computer interfaces require rapid and reliable discrimination of EEG patterns associated with motor imagery generated via imagined or real movement. The objective of this study was to characterize EEG signals of two different motor imagery tasks used to control a robotic articulator. With one-sided hand movement imagination resulting in EEG changes located contra and ipsilateral areas, time-courses of two different imagery tasks were investigated via instantaneous band power changes. We compared the features extracted from the EEG patterns with standard machine learning algorithms. We report frequency-based categorization of visualized imagery more relevant than machine learning methods.

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2016

Conference Paper

P. Chellaiah, Sandeep Bodda, Lal, R., Madhu, C., Zamare, V., Dr. Bipin G. Nair, Dr. Shyam Diwakar, and Dr. Krishnashree Achuthan, “EEG-based assessment of image sequence-based user authentication in computer network security”, in 2016 International Conference on Electrical, Electronics, and Optimization Techniques (ICEEOT), Chennai, India, 2016.[Abstract]


User authentication is crucial in security systems. Although, there are many complex and secure passkey-based authentication mechanisms, majority of users prefer employing simple passwords that are viable to rubber-hose attacks. Image sequence based passwords were introduced to overcome some of the issues with textual passwords. The objective of this work was to evaluate cognitive and memory performance in image-based user authentication systems. Via EEG recordings during image sequence training task, we observed increased activity of α rhythms in F3 and FC5 channel bins and augmented levels of β rhythms in F3 and O1 channels, suggesting users personalized authentication more than in alpha-numeric password-based logins, linking potential roles of implicit and explicit sequence learning in improving human user authentication.

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2015

Conference Paper

Hemalata Sasidharakurup, Dhanush Kumar, Radhamani, R., Nizar, N., Dr. Bipin G. Nair, Dr. Krishnashree Achuthan, and Dr. Shyam Diwakar, “Role of ICT enabled Virtual Laboratories in Biotechnology Education: Case studies on blended and remote learning”, in Proceedings of 18th International Conference on Interactive Collaborative Learning, Florence, Italy, 2015.[Abstract]


Virtual labs are popularized as a visual education tool that offers diverse analysis of experiments through different components like graphics mediated animations, mathematically modeled simulations, user-interactive emulations, remote-triggered experiments and the use of augmented perception haptic devices. With the advances in ICT-based education, virtual labs have become a novel platform that helps users to engage in their proactive learning process. Our goal was to analyze the effective role of biotechnology virtual labs in improving academic performance of students and complementing classroom education. We tested the adaptability, perceived usefulness and ease of use of biotechnology virtual labs on different user groups in sciences and engineering. This study focuses mainly on the student and teacher groups from different universities across India. Feedback data was collected via a direct approach using organized workshops conducted in the year 2014-2015. 85% of participants suggested perceived usefulness of biotechnology virtual labs helped them to improve their academic performance compared to a traditional classroom scenario. Most users indicated the learning materials provided by virtual lab system were easy to understand, thus suggesting the better adaptability of ICT-enabled techniques amongst different users. This augments the role of virtual labs for remote learners all over the world. For India, such learning methods have helped overcome limitations seen in classroom-based education such as equipment accessibility, location and other economic issues. Through these studies, we construe the usage of virtual labs as a next-gen interactive textbook and as a media-rich learning source of distance and blended education.

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2015

Conference Paper

Dr. Bipin G. Nair, Hemalata Sasidharakurup, Radhamani, R., Dhanush Kumar, Nizar, N., Dr. Krishnashree Achuthan, and Dr. Shyam Diwakar, “Assessing Students and Teachers Experience on Simulation and Remote Biotechnology Virtual labs: A Case Study with a Light Microscopy Experiment”, in Proceedings of 2nd International Conference on e-Learning e-Education and Online Training (eLEOT 2015), Novedrate, Italy, 2015.[Abstract]


With recent trends of using Information and Communication Technologies in education, virtual labs have become more prevalent in classrooms of most schools and universities, especially in South India. The purpose of this paper was to perform a comparative analysis of virtual learning components such as animations, simulations and real-time remotely controlled experiments. As a part of this study, we conducted a series of biotechnology virtual lab workshops for University-level users within India and collected feedback related to the usage of virtual labs via direct approach. The survey amongst the students and teachers suggested simulation-based labs were more preferred in enhancing teaching and learning strategy compared to graphics-mediated animations and remotely controlled experiments. This paper also reports some of the issues faced by virtual lab users. Studies indicated that even though the web-based technologies are a new venture in education, it still poses adaptability issues. © Institute for Computer Sciences, Social Informatics and Telecommunications Engineering 2016.

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PDF iconassessing-students-and-teachers-experience-on-simulation-and-remote-biotechnology-virtual-labs.pdf

2015

Conference Paper

Asha Vijayan, Chaitanya Medini, Anjana Palolithazhe, Bhagyalakshmi Muralidharan, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Modeling Pattern Abstraction in Cerebellum and Estimation of Optimal Storage Capacity”, in Proceedings of the Fourth International Conference on Advances in Computing, Communications and Informatics (ICACCI-2015), Kochi, India, 2015.[Abstract]


Precise fine-tuning of motor movements has been known to be a vital function of cerebellum, which is critical for maintaining posture and balance. Purkinje cell (PC) plays a prominent role in this fine-tuning through association of inputs and output alongside learning through error correction. Several classical studies showed that PC follows perceptron like behavior, which can be used to develop cerebellum like neural circuits to address the association and learning. With respect to the input, the PC learns the motor movement through update of synaptic weights. In order to understand how cerebellar circuits associate spiking information during learning, we developed a spiking neural network using adaptive exponential integrate and fire neuron model (AdEx) based on cerebellar molecular layer perceptron-like architecture and estimated the maximal storage capacity at parallel fiber-PC synapse. In this study, we explored information storage in cerebellar microcircuits using this abstraction. Our simulations suggest that perceptron mimicking PC behavior was capable of learning the output through modification via finite precision algorithm. The study evaluates the pattern processing in cerebellar Purkinje neurons via a mathematical model estimating the storage capacity based on input patterns and indicates the role of sparse encoding of granular layer neurons in such circuits. © 2015 IEEE.

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2015

Conference Paper

Chaitanya Medini, Asha Vijayan, Ritu Maria Zacharia, Lekshmi Priya Rajagopal, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Spike Encoding for Pattern Recognition: Comparing Cerebellum Granular Layer Encoding and BSA algorithms”, in Proceedings of the Fourth International Conference on Advances in Computing, Communications and Informatics (ICACCI-2015), Kochi, India, 2015.[Abstract]


Spiking neural encoding models allow classification of real world tasks to suit for brain-machine interfaces in addition to serving as internal models. We developed a new spike encoding model inspired from cerebellum granular layer and tested different classification techniques like SVM, Naïve Bayes, MLP for training spiking neural networks to perform pattern recognition tasks on encoded datasets. As a precursor to spiking network-based pattern recognition, in this study, real world datasets were encoded into spike trains. The objective of this study was to encode information from datasets into spiking neuron patterns that were relevant for spiking neural networks and for conventional machine learning algorithms. In this initial study, we present a new approach similar to cerebellum granular layer encoding and compared it with BSA encoding techniques. We have also compared the efficiency of the encoded dataset with different datasets and with standard machine learning algorithms. © 2015 IEEE.

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PDF iconspike-encoding-for-pattern-recognition-comparing-cerebellum-granular-layer-encoding.pdf

2015

Conference Paper

N. Melethadathil, Chellaiah, P., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Classification and Clustering for Neuroinformatics: Assessing the efficacy on reverse-mapped NeuroNLP data using standard ML techniques”, in Proceedings of the Fourth International Conference on Advances in Computing, Communications and Informatics (ICACCI-2015), Kochi, India, 2015.[Abstract]


NeuroinformaticsNatural Language Processing (NeuroNLP) relies on clustering and classification for information categorization of biologically relevant extraction targets and for interconnections to knowledge-related patterns in event and text mined datasets. The accuracy of machine learning algorithms depended on quality of text-mined data while efficacy relied on the context of the choice of techniques. Although developments of automated keyword extraction methods have made differences in the quality of data selection, the efficacy of the Natural Language Processing (NLP) methods using verified keywords remain a challenge. In this paper, we studied the role of text classification and document clustering algorithms on datasets, where features were obtained by mapping to manually verified MESH terms published by National Library of Medicine (NLM). In this study, NLP data classification involved comparing 8techniques and unsupervised learning was performed with 6 clustering algorithms. Most classification techniques except meta-based algorithms namely stacking and vote, allowed 90% or higher training accuracy. Test accuracy was high (=>95%) probably due to limited test dataset. Logistic Model Trees had 30-fold higher runtime compared to other classification algorithms including Naive Bayes, AdaBoost, Hoeffding Tree. Grouped error rate in clustering was 0-4%. Runtime-wise, clustering was faster than classification algorithms on MESH-mapped NLP data suggesting clustering methods as adequate towards Medline-related datasets and text-mining big data analytic systems. © 2015 IEEE.

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PDF iconclassification-and-clustering-for-neuroinformatics-assessing-the-efficacy-on-reverse-mapped-neuronlp-data-using-standard-ml-techniques.pdf

2015

Conference Paper

J. H, Kumar, G., and Dr. Bipin G. Nair, “Antibiofilm Activity of Biosurfactants from Bacterial Strains Isolated from Oil Contaminated Soil and Sewage.”, in International conference-NHBT 2015, 2015.[Abstract]


<p>Biosurfactants are surface active molecules produced by various organisms, which have beneficial in structural diversity, low toxicity and biodegradability. These properties makes these compounds for a variety of potential applications, including cosmetics– pharmaceutical formulations, agricultural, food industry, oil recovery and environment protection technology. Furthermore, the biological properties of biosurfactants have also augment interest of industrial application. Biosurfactants are grouped into three categories of origin: microbial derived, animal-derived and plant-derived biosurfactants. In this study it is possible to isolate two bacterial strains which produce biosurfactants, from two very cheaper resources - oil contaminated soil and sewage water. The bacterial strains were tested for the ability to produce biosurfactants and screened for biosurfactant activity by oil displacement method. The highest biosurfactant producing strains were selected and identified by microscopic appearance and biochemical activities. The extracted biosurfactant’s emulsification activities were compared with synthetic surfactants. Simultaneously the biosurfactant produced by these strains were tested for its antibiofilm activity against various pathogenic microbes and found to have significant antibiofilm activity. The beneficial property of&nbsp; biosurfactant production&nbsp; make the strains an efficient bioremediation tool for various environmental application and represent greater significance in future biomedical applications.</p>

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2015

Conference Paper

Dr. Jyotsna Nambiar, Kumar, G. B., Pandurangan Nanjan, Dr. Asoke Banerji, and Dr. Bipin G. Nair, “Regulation of Gelatinases by (I-3,II-3)-Biacacetin, a Novel Non-zinc Binding Inhibitor of MMP-2 and MMP-9”, in The XXXIX All India Cell Biology Conference, 2015.[Abstract]


Gelatinases (MMP-2 and MMP-9) play a significant role in cancer progression by cleaving the major components of the extracellular matrix thereby promoting the migration of tumor cells. Majority of the MMP inhibitors reported are zinc chelating compounds which bind to the catalytic zinc via hydroxamate, carboxylate, thiol or phosphonic acid moieties. The extensive homology between catalytic domains of the MMPs makes these effective zinc binding inhibitors non-selective and toxic. To overcome such non selective toxicity, novel non-zinc binding MMP inhibitors have been developed.(I-3,II-3)-Biflavones form a small group of dimeric flavonoids which have not been extensively studied due to their limited occurrence. Among several differently substituted biflavones having hydroxy, methoxy, furano and cinnamyl moieties,(I-3,II-3)-biacacetin showed maximum inhibition of gelatinases without interfering with the zinc in the catalytic site.This novel non-zinc binding interaction of (I-3,II-3)-biacacetin was further confirmed by treating the cells with ZnCl2 along with(I-3,II-3)-biacacetin and showing that the inhibition remained unaffected even in the presence of ZnCl2.(I-3,II-3)-biacacetin showed significant reduction in migration of highly metastatic fibrosarcoma cell line, HT1080. The mechanism of (I-3,II-3)-biacacetinmediated modulation of cell migration through inhibition of gelatinases was further established by treating the cells with phorbol myristate acetate (PMA)along with (I-3,II-3)-biacacetinand using the same conditioned media for the migration assay. (I-3,II-3)-biacacetininhibitedPMA-stimulated gelatinase activity as well as migration of HT1080 cells in a concentration-dependent manner.These results suggests the use of (I-3,II-3)-biacacetin as a novel template for design and synthesis of analogswith improved potency and selectivity.

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2015

Conference Paper

D. G., Ashokan, L., Dr. Jyotsna Nambiar, Shaji, S. K., S, L., Kumar, G. B., and Dr. Bipin G. Nair, “In Vitro Culture of Primary Cells from Cancer Patients- Screening for Potent MMP-9 Inhibitors”, in The XXXIX All India Cell Biology Conference , 2015.[Abstract]


Breast cancer is the most prevalent form of cancer among women worldwide. Established cancer cell lines generated over years have been used for studying the biology of breast cancer. These cell lines which have been passaged innumerable times creates genetic drift which makes the observations biologically less relevant. In vitro culture of primary cells from fresh surgical specimens provides a more accurate means for understanding the behavior of cancer cells and the adjacent normal cells. We have developed a simple and rapid method for isolating primary cultures from breast tumor and normal cells. Two different methods were employed for isolating primary cultures- one involving enzymatic digestion and the other using explant culture which is independent of enzymatic treatment and feeder cells. The primary cells obtained were further characterized by immunocytochemistry staining for Vimentin and Cytokeratin 18. The cells stained positive for Vimentin and negative for Cytokeratin 18 which indicated that they are of mesenchymal origin. Since gelatinases play a prominent role in promoting breast cancer metastasis, the primary cells were assessed for gelatinase activity. Our observations clearly show that the cancer cells had up-regulated gelatinases activity compared to the adjacent normal cells. These cells when treated with several natural products showed a dose-dependent inhibition of gelatinase activity. The results obtained were consistent in all the primary cell lines generated from different patient samples. These studies with the primary cell lines will therefore help in obtaining biological responses that more accurately mimics the tumor/cancer micro environment.

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2015

Conference Paper

S. K. Shaji, Kumar, D. Sunil, G, D., Dr. Bipin G. Nair, and Kumar, G. B., “MicroRNA-491 Functions to Down Regulate Gelatinase B and Inhibit Cell Migration in MDA-MB-231 Triple Negative Breast Cancer Cells”, in The XXXIX All India Cell Biology Conference , 2015.[Abstract]


Breast cancer is one of the most prevalent malignancies among women worldwide. There is no targeted therapy currently available for the treatment of patients with triple negative breast cancer (TNBC). Metastasis is the primary cause of death in cancer patients. Gelatinase B (MMP-9) plays a central role in invasion and metastasis of breast cancer cells. Here we show that, in triple negative MDA-MB-231 breast cancer cell line, hsa-mir-491 directly down regulate MMP-9 expression. Bioinformatics tool analysis showed that hsa-mir-491 may target MMP-9 and has binding sites in its 3’ UTR. Luciferase reporter assay confirms the direct regulation of MMP-9 by hsa-miR-491. miRNA over expressing stable cell lines were established by lentiviral transduction of MDA-MB-231 cells with hsa-mir-491 lenti-viral vector construct. qRT-PCR studies showed down regulation of MMP-9 mRNA in miRNA over expressing cells lines compared to the normal MDA-MB-231 cells. Even though the miRNA did not have any effect on cell cycle profiles, hsa-miR-491 over expressing stable cell line showed significantly low migratory potential in assays indicating the therapeutic potential of this micorRNA as a novel means of controlling breast cancer metastasis. Our results provide the first evidence for inhibition of MMP-9 by hsa-mir-491 in breast cancer cells.

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2015

Conference Paper

A. Omanakuttan, Dr. Geetha Kumar, and Dr. Bipin G. Nair, “Ecdysterone Mediates Wound Healing in a Nitric Oxide Dependent Manner in 3T3L1 Fibroblasts.”, in The XXXIX All India Cell Biology Conference , 2015.[Abstract]


Ecdysteroids are insect moulting hormones which are structurally different from mammalian steroids, but have been shown to have several beneficial effects in mammals. Ecdysterone is known to enhance wound healing in rabbits by a faster granulation tissue formation and epithelial cell proliferation. In this study, we focused our efforts on elucidating the molecular mechanism involved in Ecdysterone mediated wound healing. In order to achieve this, we employed an in vitro wound healing assay using 3T3L1 cells treated with Ecdysterone, isolated from Sesuvium portulacastrum. The assay demonstrated that Ecdysterone enhanced in vitro wound healing activity in a dose dependent manner. Further studies demonstrated that Ecdysterone enhanced cell proliferation and cell migration in a nitric oxide dependent manner. Additionally, fluorescence studies with DAF FM diacetate, a specific indicator for nitric oxide, demonstrated that Ecdysterone enhances nitric oxide (NO) production in a dose dependent manner through activation of Nitric oxide Synthase (NOS). These results demonstrate that Ecdysterone can enhance the wound healing process in a nitric oxide (NO) dependent manner

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2015

Conference Paper

D. Sunil Kumar, Bose, C., Shaji, S. K., Dr. Asoke Banerji, Kumar, G. B., and Dr. Bipin G. Nair, “Cocos Nucifera Shell Extract Down Regulates MMP-2, MMP-9 and Cell Migration in A375 Cells”, in The XXXIX All India Cell Biology Conference , 2015.[Abstract]


Melanoma is the least common but most fatal form of skin cancer. An essential step in melanoma cell migration, invasion, and metastasis is the degradation of basement membranes and extracellular matrix. Matrix metalloproteinases (MMPs) and their tissue inhibitors play a crucial role in these complex multistep processes. We investigated the effect of extract from coconut (Cocos nucifera) shell on human melanoma cell line A375. The coconut shell extract was fractionated and the bioactivity screening was carried out. The ethyl methyl ketone (EMK) extract, which was identified as being most potent was further purified to yield two main subfractions (F1 and F2). Comparative studies with gelatin zymography demonstrated that the ‘F1’ significantly down regulated the gelatinolytic activity of MMP-2 and MMP-9. Similarly ,the gene expression studies with ‘F1’ showed down regulation of MMP-2, MMP-9, VEGF and COX-2 all of which play key roles in metastasis, angiogenesis and tumor promoting inflammation. Further, studies confirmed that ‘F1’ inhibited migration and caused arrest at G2/M phase of the cell cycle. Susequently, the structural characterization by LC-MS/MS and NMR studies determined the active fraction, ‘F1’to be oxyresveratrol, a stilbenoid. Thus, we report for the first time the isolation and characterization of the compound, oxyresveratrol from coconut shell and also show its regulation of MMPs in human melanoma which suggests its therapeutic potential in cancer.

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2015

Conference Paper

C. Nutakki, Asha Vijayan, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Implementing Cerebellar Biophysics for Trajectory planning in Robotic arms”, in Proceedings of the International symposium on Translational Neuroscience & XXXIII Annual Conference of the Indian Academy of Neurosciences, Panjab University, Chandigarh , India, 2015.

2015

Conference Paper

Manjusha Nair, Madhu, P., Mohan, V., Rajendran, A. G., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “GPGPU implementation of information theoretic algorithms for the analysis of granular layer neurons”, in 2015 International Conference on Computing and Network Communications (CoCoNet), IEEE, 2015.[Abstract]


Methods originally developed for communication systems are widely used in computational neuroscience to understand the information representation and processing performed by neurons and neural circuits in the brain. Information theoretic quantities Entropy and Mutual Information (MI) have been used in neuroscience as a metric to estimate the efficiency of information representation by neurons. These quantities are used here to measure the stimulus discrimination reliability of the cerebellar granule neurons using simulated response trains produced by a multi-compartmental model of Wistar rat neuron. With &nbsp;1011 granule neurons in the cerebellum, understanding spatio-temporal processing in such structures demands efficient, fast algorithms. Since the serial version of the algorithm had multiple estimation loops which increased the process time considerably with the problem size, we re-implemented the MI algorithm in GPGPU hardware as an efficient way of parallelizing the MI computations. Task-level parallelism and GPU optimizations were used to improve the process time. Estimates on GPGPUs showed 15X time efficiency compared to the CPU version of the algorithm. In order to understand learning inside the cerebellar circuit, synaptic plasticity conditions were simulated in the neuron model. We were able to quantify the stimulus discrimination reliability of granule neurons under control, LTP and LTD conditions and the analysis revealed that stimulus discrimination capability of the neuron was increased during high plasticity state.

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2015

Conference Paper

Manjusha Nair, Surya, S., Kumar, R. S., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Efficient simulations of spiking neurons on parallel and distributed platforms: Towards large-scale modeling in computational neuroscience”, in 2015 IEEE Recent Advances in Intelligent Computational Systems (RAICS), Trivandrum, India, 2015.[Abstract]


Human brain communicates information by means of electro-chemical reactions and processes it in a parallel, distributed manner. Computational models of neurons at different levels of details are used in order to make predictions for physiological dysfunctions. Advances in the field of brain simulations and brain computer interfaces have increased the complexity of this modeling process. With a focus to build large-scale detailed networks, we used high performance computing techniques to model and simulate the granular layer of the cerebellum. Neuronal firing patterns of cerebellar granule neurons were modeled using two mathematical models Hodgkin-Huxley (HH) and Adaptive Exponential Leaky Integrate and Fire (AdEx). The performance efficiency of these modeled neurons was tested against a detailed multi-compartmental model of the granule cell. We compared different schemes suitable for large scale simulations of cerebellar networks. Large networks of neurons were constructed and simulated. Graphic Processing Units (GPU) was employed in the pleasantly parallel implementation while Message Passing Interface (MPI) was used in the distributed computing approach. This allowed to explore constraints of different parallel architectures and to efficiently load balance the tasks by maximally utilizing the available resources. For small scale networks, the observed absolute speedup was 6X in an MPI based approach with 32 processors while GPUs gave 10X performance gain compared to a single CPU implementation. In large networks, GPUs gave approximately 5X performance gain in processing time compared to the MPI implementation. The results enabled us to choose parallelization schemes suitable for large-scale simulations of cerebellar circuits. We are currently extending the network model based on large scale simulations evaluated in this paper and using a hybrid - heterogeneous MPI based multi-GPU architecture for incorporating millions of cerebellar neurons for assessing physiolo- ical disorders in such circuits.

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2015

Conference Paper

Dhanush Kumar, Sasidharakurup, H., Radhamani, R., Nizar, N., Dr. Bipin G. Nair, Dr. Shyam Diwakar, and Dr. Krishnashree Achuthan, “Mobile Learning and Biotechnology Education via Remote Labs: Deployment-based study on Real Time Shared Resources”, in 9th International Conference on Interactive Mobile and Communication Technologies and Learning 2015, Mediterranean Palace Hotel, Thessaloniki, Greece., 2015.[Abstract]


With recent advances in ICT, virtual and remote laboratories have become ubiquitous as a complementary tool allowing student users to access a mobile platform and utilize real-time shared equipment over the internet. In this paper, we explore the role of biotechnology remotely controlled labs in augmenting student education via allowing real time shared resources. We deployed 23 virtual laboratories with 218 virtual experiments in biotechnology to provide an online laboratory experience that allowed students and teachers to share and augment conceptual and practical knowledge. Student users reported high usability and repeatability of experimental process and suggested virtual labs as complementing tool for augmenting student’s perception in an active learning scenario. Hybrid approaches in mobile learning indicated student users preferred a blended learning role via classrooms. We also observed that performance in examinations improved with those students using remote labs. We also evaluated the role of virtual labs as a teaching tool for university teachers.

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2015

Conference Paper

R. Radhamani, Sasidharakurup, H., Dhanush Kumar, Nizar, N., Dr. Krishnashree Achuthan, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Role of Biotechnology simulation and remotely triggered virtual labs in complementing university education”, in 2015 International Conference on Interactive Mobile Communication Technologies and Learning (IMCL), Thessaloniki, Greece, 2015.[Abstract]


Blended learning has been popularized in many universities in the last decade due to the rapid advances in computer technologies and relative increase in the usage of internet connectivity. A major constraint in providing high quality laboratory resources in some universities and in economically challenged countries is high costs, training personnel, training time and maintenance-related issues. Virtual and remote labs complement the real laboratory resources with virtually defined techniques including simulations, animations, remote triggering of the actual equipment and videos that facilitate user interactions. Our goal was to analyze the effectiveness of biotechnology virtual labs in integrating learning process among school and university students of ages 12-15 years and 17-24 years respectively within India. These labs were developed as part of a National mission on Education through ICT. We also focused on the use of virtual and remote labs as a new pedagogy for distance and mobile learning courses and the context of usage outside scheduled classroom timings. The evaluation of biotechnology virtual labs was performed via surveys, including online and manual feedback reports for analyzing the learning process of various student groups. Studies amongst students of different age groups suggested that virtualization helped their active learning in a traditional classroom scenario. Feedback from student users also indicated virtual and remote labs aided, mobile learning by improving their academic performance, after using virtual and remote labs (post usage) as education platform. Feedback statistics showed 90% of students used biotechnology virtual lab techniques and that helped them to get an actual feel of the experiment. All participants scored more than 70% in the post-test, improving the class average from the pre-test scenario. 91% of teachers who participated in the workshops indicated that they could use virtual and remote labs in their daily teaching pro- ess as teaching material thereby reducing their lecture preparation time. Feedback analysis also indicated improved student performance enhancing laboratory education.

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2015

Conference Paper

S. Bodda, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “EEG-Based Assessment and Categorisation for Imagery Based Movement and Mental Tasks”, in Proceedings of the International symposium on Translational Neuroscience & XXXIII Annual Conference of the Indian Academy of Neurosciences,, Panjab University, Chandigarh , India, 2015.[Abstract]


Focusing on rapid and reliable discrimination of EEG patterns associated with motor imagery and to evaluate the cognitive and memory performance of human user authentication in image-based password systems. This study presents a methodology which uses a nonlinear pattern recognition to study the spatial distribution of EEG patterns accompanying higher cortical functions. The multivariate decision rules associate EEG patterns differentiating performance of motor and mental tasks. These patterns discriminate between the tasks are consistent with, and extend the results of, univariate analysis of spectral intensities. Commercial EEG setup (Lievesley et al., 2011) was used to extract EEG patterns from 14 electrodes. Raw EEG signals were pre-processed using Surface Laplacian filter, Band pass filter (Babiloni et al., 2000; Blanchard and Blankertz, 2004; Cincotti et al., 2001; Dornhege et al., 2003). Fast Fourier Transform, power spectrum density and independent component analysis to extract features (Hosni et al., 2007; Olesen, 2012). The main focus have been discrimination of α and β rhythms for mental and motor imagery tasks. In this study we used EEG recordings of motor task and image based password authentication system to evaluate cognitive and memory performance of human user authentication in image-based password systems. Also we characterized the EEG signals of two different motor imagery tasks for applying as brain-based control of a robotic articulator. Time courses of two different imagery and mental tasks were investigated by the calculation of instantaneous band power changes and patterns and compared whether the quantification of these features could be classified using machine learning classifiers. We observed the variance change of 4.28 and 3.05 % allowing discrimination α - β components. We also found machine learning was not significantly reliable to discriminate both movement imagery data and image-based authentication tasks unlike α -β categorisation

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2015

Conference Paper

A. G. Rajendran, Manjusha Nair, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Analyzing Mutual Information and Synaptic Efficacy at Mossy Fiber –Granule Cell Relay in Rat Cerebellum”, in Proceedings of the International symposium on Translational Neuroscience & XXXIII Annual Conference of the Indian Academy of Neurosciences, Panjab University, Chandigarh , 2015.

2015

Conference Paper

Chaitanya Medini, Naldi, G., Dr. Bipin G. Nair, Egidio D'Angelo, and Dr. Shyam Diwakar, “Reconstructing fMRI BOLD signals arising from cerebellar granule neurons - comparing GLM and balloon models”, in 2015 International Joint Conference on Neural Networks (IJCNN), Killarney, Ireland, 2015.[Abstract]


Understanding the relationship between fMRI BOLD and underlying neuronal activity has been crucial to connect circuit behavior to cognitive functions. In this paper, we modeled fMRI BOLD reconstructions with general linear model and balloon modeling using biophysical models of rat cerebellum granular layer and stimuli spike trains of various response times. Linear convolution of the hemodynamic response function with the known spiking information reconstructed activity similar to experimental BOLD-like signals with the limitation of short stimuli trains. Balloon model through Volterra kernels gave seemingly similar results to that of general linear model. Our main goal in this study was to understand the activity role of densely populated clusters through BOLD-like reconstructions given neuronal responses and by varying response times for the whole stimulus duration.

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2015

Conference Paper

H. Parasuram, Dr. Bipin G. Nair, Naldi, G., Egidio D'Angelo, and Dr. Shyam Diwakar, “Exploiting point source approximation on detailed neuronal models to reconstruct single neuron electric field and population LFP”, in 2015 International Joint Conference on Neural Networks (IJCNN), Killarney, Ireland, 2015.[Abstract]


Extracellular electrodes record local field potential as an average response from the neurons within the vicinity of the electrode. Here, we used neuronal models and point source approximation techniques to study the compartmental contribution of single neuron LFP and the attenuation properties of extracellular medium. Cable compartmental contribution of single neuron LFP was estimated by computing electric potential generated by localized ion channels. We simulated the electric potential generated from axon-hillock region contributed significantly to the single neuron extracellular field. Models of cerebellar granule neuron and L5 pyramidal neuron were used to study single neuron extracellular field potentials. Attenuation properties of the extracellular medium were studied via the granule cell model. A computational model of a rat Crus-IIa cerebellar granular layer, built with detailed anatomical and physiological properties allowed reconstructing population LFP. As with single neurons, the same technique was able to reconstruct the T and C waves of evoked postsynaptic in vivo LFP trace. In addition to role of attenuation on the width of signals, plasticity was simulated via modifications of intrinsic properties of underlying neurons and population LFP validated experimental data correlating network function to underlying single neuron activity.

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2015

Conference Paper

M. C., B., B., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Comparing Firing Properties of Two Interconnected Circuits to Understand Information Processing at Afferent Pathways”, in Proceedings of the Integrated Systems Neuroscience (ISN) workshop, University of Manchester, UK, 2015.

2014

Conference Paper

P. Aarathi, Jeethu, R., Dr. Bipin G. Nair, and Dr. Satheesh Babu T. G., “Design, Simulation and fabrication of Microfluidic Channels for Lab-on-a-Chip applications”, in International Conference on Biomaterials-2014 , Asian Polymers Association, New Delhi, 2014.

2014

Conference Paper

T. S. Sethu Parvathy, Keerthy, D., Dr. Bipin G. Nair, and Dr. Satheesh Babu T. G., “Activated Screen Printed Electrode For Highly Sensitive Ascorbic Acid Sensing”, in International Conference on Biomaterials-2014, Asian Polymers Association, New Delhi, 2014.

2014

Conference Paper

Chaitanya Medini, Asha Vijayan, Egidio D'Angelo, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Computationally Efficient Bio-realistic Reconstructions of Cerebellar Neuron Spiking Patterns”, in Proceedings of the 2014 International Conference on Interdisciplinary Advances in Applied Computing, Amrita Vishwa Vidyapeetham, Coimbatore, India, 2014.[Abstract]


Simple spiking models have been known to replicate detailed mathematical models firing properties with reliable accuracy in spike timing. We modified the adaptive exponential integrate and fire mathematical model to reconstruct different cerebellar neuronal firing patterns. We were able to reconstruct the firing dynamics of various types of cerebellar neurons and validated with previously published experimental studies. To model the neurons, we exploited particle swarm optimization to fit the parameters. The study showcases the match of electroresponsiveness of the neuronal models to data from biological neurons. Results suggest that models are close reconstructions of the biological data since frequency and spike-timing closely matched known values and were similar to those in previously published detailed computationally intensive biophysical models. Such spiking models have a number of applications including design of large-scale circuit models in order to understand physiological dysfunction and for various computational advantages.

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PDF iconcomputationally-efficient-bio-realistic-reconstructions-of-cerebellar-neuron-spiking-patterns.pdf

2014

Conference Paper

Dr. Shyam Diwakar, Sandeep Bodda, Chaitanya Nutakki, Asha Vijayan, Dr. Krishnashree Achuthan, and Dr. Bipin G. Nair, “Neural Control using EEG as a BCI Technique for Low Cost Prosthetic Arms”, in In Proceedings of the International Conference on Neural Computation Theory and Applications (NCTA-2014), Rome, Italy, 2014.[Abstract]


There have been significant advancements in brain computer interface (BCI) techniques using EEG-like methods. EEG can serve as non-invasive BMI technique, to control devices like wheelchairs, cursors and robotic arm. In this paper, we discuss the use of EEG recordings to control low-cost robotic arms by extracting motor task patterns and indicate where such control algorithms may show promise towards the humanitarian challenge. Studies have shown robotic arm movement solutions using kinematics and machine learning methods. With iterative processes for trajectory making, EEG signals have been known to be used to control robotic arms. The paper also showcases a case-study developed towards this challenge in order to test such algorithmic approaches. Non-traditional approaches using neuro-inspired processing techniques without implicit kinematics have also shown potential applications. Use of EEG to resolve temporal information may, indeed, help understand movement coordination in robotic arm.

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PDF iconneural-control-using-eeg-as-a-bci-technique-for-low-cost-prosthetic-arms.pdf

2014

Conference Paper

Manjusha Nair, Subramanyan, K., Dr. Shyam Diwakar, and Dr. Bipin G. Nair, “Parameter optimization and nonlinear fitting for computational models in neuroscience on GPGPUs”, in International Conference on High Performance Computing and Applications (ICHPCA), 2014 , C. V. Raman College of Engineering, Bhubaneswar, 2014.[Abstract]


One of the main challenges in computational modeling of neurons is to reproduce the realistic behaviour of the neurons of the brain under different behavioural conditions. Fitting electrophysiological data to computational models is required to validate model function and test predictions. Various tools and algorithms exist to fit the spike train recorded from neurons to computational models. All these require huge computational power and time to produce biologically feasible results. Large network models rely on the single neuron models to reproduce population activity. A stochastic optimization technique called Particle Swam Optimisation (PSO) was used here to fit spiking neuron model called Adaptive Exponential Leaky Integrate and Fire (AdEx) model to the firing patterns of different types of neurons in the granular layer of the cerebellum. Tuning a network of different types of spiking neurons is computationally intensive, and hence we used Graphic Processing Units (GPU) to run the parameter optimisation of AdEx using PSO. Using the basic principles of swam intelligence, we could optimize the n-dimensional space search of the parameters of the spiking neuron model. The results were significant and we observed a 15X performance in GPU when compared to CPU. We analysed the accuracy of the optimization process with the increase in width of the search space and tuned the PSO algorithm to suit the particular problem domain. This work has promising roles towards applied modeling and can be extended to many other disciplines of model-based predictions.

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PDF iconparameter-optimization-and-nonlinear-fitting-for-computational-models-in-neuroscience-on-gpgpus.pdf

2014

Conference Paper

R. Radhamani, Sasidharakurup, H., Kumar, D., Nizar, N., Dr. Bipin G. Nair, Dr. Krishnashree Achuthan, and Dr. Shyam Diwakar, “Explicit Interactions by Users Form a Critical Element in Virtual Labs Aiding Enhanced Education – A Case Study from Biotechnology Virtual Labs”, in Technology for Education (T4E), 2014 IEEE Sixth International Conference on, 2014.[Abstract]


Virtual laboratories are ICT tools that are becoming more prevalent in classroom education complementing the lack of resources or tutors while enabling anytime-anywhere student participation scenarios. Specifically disciplines such as biotechnology, which are interaction rich, have seen several types of virtual labs. In this paper, we explore an analysis of student feedback post virtual labs sessions suggesting virtual labs improve teaching and learning experiences via user-interactions. Feedback was collected from undergraduate and postgraduate level students belonging to biotechnology programs. We look at two objectives namely perceived usefulness and the role of interactions on the virtual platform and simulators, in addition to animations. Most data were collected using direct approach via organized workshops. This approach allowed us to extract useful information without concerns of sparseness and unsolicited data compared to remote feedback. Our studies on feedback analysis indicate that student users interpret results in animation based virtual labs. However, a larger percentage of users suggest student usage and performance improved only with interactive simulators rather than animations. Although further tests are being performed, our preliminary studies on 200 participants suggest novel virtual labs models must include a simulation or emulations of lab environment in order to enhance student laboratory skills.

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PDF iconexplicit-interactions-by-users-form-a-critical-element-in-virtual-labs-aiding-enhanced-education-a-case-study-from-biotechnology-virtual-labs.pdf

2014

Conference Paper

D. Kumar, Hareesh Singanamala, Dr. Krishnashree Achuthan, Srivastava, S., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Implementing a Remote-Triggered Light Microscope: Enabling Lab Access via VALUE Virtual Labs”, in Proceedings of the 2014 International Conference on Interdisciplinary Advances in Applied Computing, New York, NY, USA, 2014.[Abstract]


Biotechnology and biology education has been known to show declining student interest due to classroom environments and instructor teaching styles, hence we introduced virtual labs as an interactive self-learning material in a blended environment. With ICT-based education becoming ubiquitous, virtual and remote triggered labs have become a novel platform that helps users to engage in a proactive learning process. A promisingly new trend in virtual labs-based education is the development of remote laboratories that are available over the internet and can be accessed by students and teachers. We implemented and deployed a low-cost light microscope using a simple front-end to enable users to have any time-anywhere access. This paper reports the implementation, deployment and user-case studies on the learning and usage based on the remote-triggered virtual lab. This study also focuses on the analysis of using remote-triggered experiments as supplementary laboratory resources for overcoming the problems faced in a traditional lab environment. The study used online feedback surveys for evaluating the learning outcome and the flexibility of user-interactions with the remote labs and reports the status of usage of remote triggered techniques in biology courses. The statistical analysis suggests that remote labs are an easy learning and interactive platform for users from different places.

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PDF iconimplementing-a-remote-triggered-light-microscope-enabling-lab-access-via-value-virtual-labs.pdf

2014

Conference Paper

A. Yoosef, Parasuram, H., Chaitanya Medini, Solinas, S., Egidio D'Angelo, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Parallelization of a Computational Model of a Biophysical Neuronal Circuitry of Rat Cerebellum”, in Proceedings of the 2014 International Conference on Interdisciplinary Advances in Applied Computing, New York, NY, USA, 2014.[Abstract]


Rapid progress in biophysical neural network modelling has been observed in the last years as a focus within computational neuroscience. Detailed multi-compartmental neuron models that were built to simulate physiological aspects of cerebellar neurons and microcircuits involve hundreds of equations. Simulating several hundreds of neurons is computationally expensive. Storage of data and run-time evaluations also prove to be major challenges in this kind of scenario, which limits the researchers.

In this paper, we use detailed models of neurons reconstructing the biophysics of cable properties and action ion channel models to generate a neural micro circuitry of cerebellum input layer. We report the process of adapting and profiling a parallel, MPI-based version of the network model on NEURON for large-scale simulations. Using multi-split and distributed approaches, our model was parallelized on multi-core, multi-processor systems. A spatio-temporal activation pattern, called the centre-surround was elicited in the model validating the biophysical role of synaptic inhibition modulating excitatory activation, usually observed during sensory or tactile stimulation. Performance tests were carried out on two heterogeneous computing clusters. We see a significant reduction of computational cost in terms of power and time while simulating parallelized code although the most apt method depended on network size and nature of synaptic connections. We find 'embarrassingly parallel' method augmented efficiency in terms of processor core usage and also decreased simulation time.

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PDF iconparallelization-of-a-computational-model-of-a-biophysical-neuronal-Circuitry-of-Rat-Cerebellum.pdf

2014

Conference Paper

R. Radhamani, Sasidharakurup, H., Sujatha, G., Dr. Bipin G. Nair, Dr. Krishnashree Achuthan, and Dr. Shyam Diwakar, “Virtual Labs Improve Student's Performance in a Classroom”, in E-Learning, E-Education, and Online Training, 2014, vol. 138, pp. 138-146.[Abstract]


With the world wide acceptance of virtual educational technologies, it has been shown that they play a vital role in the scientific arena. The purpose of this paper was to analyze the role of Biotechnology virtual laboratories in integrating student’s learning ability and introducing it as an effective instructional tool in biotechnology courses. A post-usage survey was conducted among the users and included questions about perceptions of virtual laboratories, its role in virtualization of sophisticated instruments. The survey suggested virtual labs usage enhanced autonomous and guided educational methods. Comparing groups on usage of virtual labs against a control (traditional lab), our studies suggest improved performance in students using virtual labs. Usage analysis and surveys indicated that biotechnology virtual labs are significant elements in adaptive learning process in blended classroom environment.

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PDF iconvirtual-labs-improve-students-performance.pdf

2014

Conference Paper

P. H., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Studying cerebellar dysfunction at single neuron and circuit level”, in Proceedings of the International Conference on Recent Advances in Cognition and Health, Banaras Hindu University, Varanasi, India, 2014.

2014

Conference Paper

M. C., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Blood Oxygenation Level Dependent (BOLD) Signal Reconstructions on Large Scale Cerebellar Microcircuits to Predict Neuronal Dysfunction”, in Proceedings of the International Conference on Recent Advances in Cognition and Health, Banaras Hindu University, Varanasi, India, 2014.

2014

Conference Paper

B. S., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Using surface EEG to explore computer brain interactions for robotic manipulation”, in Proceedings of the International Conference on Recent Advances in Cognition and Health, Banaras Hindu University, Varanasi, India, 2014.

2014

Conference Paper

N. C., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Robotic arm controlling using spiking neuron network models”, in Proceedings of the International Conference on Recent Advances in Cognition and Health, Banaras Hindu University, Varanasi, 2014.

2014

Conference Paper

B. S., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Extracting motor imagery for computer -brain interactions: Using F4 F3 channels for robotic manipulation”, in Proceedings of the International symposium on Translational Neuroscience & XXXII Annual Conference of the Indian Academy of Neurosciences, NIMHANS, Bangalore , India, 2014.

2014

Conference Paper

C. Nutakki, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Modelling of robotic arm kinematics using cerebellum based internal model”, in Proceedings of the International symposium on Translational Neuroscience & XXXII Annual Conference of the Indian Academy of Neurosciences, NIMHANS, Bangalore , India, 2014.

2014

Conference Paper

A. Yoosef, Rajendran, A. G., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Parallelization of Cerebellar Granular Layer Circuitry Model for Physiological Predictions”, in Proceedings of the International symposium on Translational Neuroscience & XXXII Annual Conference of the Indian Academy of Neurosciences, NIMHANS, Bangalore , India, 2014.

2014

Conference Paper

Manjusha Nair, G., R. A., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Analysis and Quantification of Neural Information Processing during Cerebellar Plasticity”, in Proceedings of the International symposium on Translational Neuroscience & XXXII Annual Conference of the Indian Academy of Neurosciences, NIMHANS, Bangalore , India, 2014.

2014

Conference Paper

S. H., R., R., N., N., Dr. Bipin G. Nair, Dr. Shyam Diwakar, and Dr. Krishnashree Achuthan, “Neuroscience Virtual Lab decreases teaching time and improves students’ perception in blended learning environment”, in Proceedings of the International symposium on Translational Neuroscience & XXXII Annual Conference of the Indian Academy of Neurosciences, NIMHANS, Bangalore , India, 2014.

2014

Conference Paper

D. Kumar, Dr. Bipin G. Nair, Dr. Shyam Diwakar, and Dr. Krishnashree Achuthan, “Deploying realistic neuron analogues for patch clamp technique education”, in Proceedings of the International symposium on Translational Neuroscience & XXXII Annual Conference of the Indian Academy of Neurosciences, NIMHANS, Bangalore , India, 2014.

2014

Conference Paper

M. N., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Facilitating Neuroscience Surveys using a Meta Path based Neuroinformatics Text-Mining Platform”, in Proceedings of the International symposium on Translational Neuroscience & XXXII Annual Conference of the Indian Academy of Neurosciences, NIMHANS, Bangalore , India, 2014.

2014

Conference Paper

Manjusha Nair, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Large-Scale Simulations of Cerebellar Microcircuit Relays using Spiking Neuron on GPUs.”, in Proceedings of the Eleventh International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, University of Cambridge, Cambridge, UK, 2014.[Abstract]


This paper uses scientific computing techniques in understanding cerebellar networks and attempts to model functional behavior of circuits via computational neuroscience. Since highly parallel programmable processors like Graphic Processing Units (GPUs) deliver a high compute capacity at low cost, we modeled granular layer neurons of the rat cerebellum on GPUs and reconstructed a network microcircuit of granular layer for predicting computational properties in such circuits. The main objective of this work was to reconstruct models apt for large scale simulations, involving thousands of neurons while maintaining an acceptable degree of biological details. The hypothesis relating to spatio-temporal information processing in the input layer of the cerebellum has been tested using mathematical modeling. The role of mossy fiber excitation and the modulatory role of Golgi cell inhibition on the granule cells were analyzed. A scalable network consisting of up to 2 million neurons were simulated in millisecond time-scale and the performance efficiency of GPUs over CPUs was compared. The main goal was to understand the scalability issues while implementing such large scale networks and to optimize shared memory access. In GPUs, multi-core parallelization allowed efficient management of computational overheads imposed by synaptic dynamics. We also briefly investigated the performance improvements focusing on decreasing memory access times and the role of optimization techniques. This work is a proof-of-concept implementation apt for densely-packed microcircuits of electrotonically compact neurons with targets to optimize real-time performance and scalability.

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2013

Conference Paper

Asha Vijayan, Chaitanya Medini, Hareesh Singanamala, Chaitanya Nutakki, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Classification of robotic arm movement using SVM and Naïve Bayes classifiers”, in Proceedings of Third International Conference on Innovative Computing Technology (INTECH 2013), London, 2013.[Abstract]


Target-oriented approaches have been commonly used in robotics. In 3D space, movement of a robotic arm depends on the target position which can either follow a forward or inverse kinematics approach to reach the target. Predicting the movement of a robotic arm requires prior learning through methods such as transformation matrices or other machine learning techniques. In this paper, we built an online robotic arm to extract movement datasets and have used machine learning algorithms to predict robotic arm articulation. For efficient training, small training datasets were used for learning purpose. Classification is used as a scheme to replace prediction-correction approach and to test whether the method can function as a replacement of usual forward kinematics schemes or predictor-corrector methods in directing a remotely controlled robotic articulator. This study reports significant classification accuracy and efficiency on real and synthetic datasets generated by the device. The study also suggests linear SVM and Naïve Bayes algorithms as alternatives for computational intensive learning schemes while predicting articulator movement in laboratory environments.

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PDF iconclassification-of-robotic-arm-movement-using-svm-and-naïve-bayes-classifiers.pdf

2013

Conference Paper

C. Umesh, M., A. A., Stanley, J., Dr. Bipin G. Nair, and Dr. Satheesh Babu T. G., “Multiple Signal Amplification Platform for Immunosensing”, in Amrita Bioquest, Amrita Vishwa Vidyapeetham, Amritapuri Campus, 2013.

2013

Conference Paper

T. Jyotsna, Dhivyalakshmi, J., Jyothi, S., Vidhusara, V., Dr. Bipin G. Nair, and Dr. Satheesh Babu T. G., “Fabrication of NiO-Pt Nanoparticles Modified Disposable Screen Printed Electrode for the Determination of Blood Glucose”, in Amrita Bioquest, Amrita Vishwa Vidyapeetham, Amritapuri Campus, 2013.

2013

Conference Paper

S. R. Shrinidhi, Aarathi, P., T., R., Dr. Bipin G. Nair, and Dr. Satheesh Babu T. G., “Fabrication of Highly Sensitive and Selective Non-enzymatic Glucose Sensor”, in Amrita Bioquest, Amrita Vishwa Vidyapeetham, Amritapuri Campus, 2013.

2013

Conference Paper

S. John, Ramyakrishnan, S., Vineeth, R. S., Dr. Bipin G. Nair, and Dr. Satheesh Babu T. G., “Development of a Non-enzymatic Glucose Biosensor using Copper Oxide Nanoparticle Modified TiO2 Nanotube Arrays”, in Amrita Bioquest, Amrita Vishwa Vidyapeetham, Amritapuri Campus,, 2013.

2013

Conference Paper

R. Jeethu, T, R., Dr. Bipin G. Nair, and Dr. Satheesh Babu T. G., “Non-enzymatic Electrochemical Sensor for the Detection of Creatinine”, in Amrita Bioquest, Amrita Vishwa Vidyapeetham, Amritapuri Campus, 2013.

2013

Conference Paper

S. John, T., R., Dr. Bipin G. Nair, and Dr. Satheesh Babu T. G., “Pt-Pd Decorated TiO2 Nanotube Array for the Non-enzymatic Determination of Glucose in Neutral Medium”, in Amrita Bioquest, Amrita Vishwa Vidyapeetham, Amritapuri Campus, 2013.

2013

Conference Paper

S. Vargis Vidhu, Jyothi, S. R., Ramachandran, T., Dr. Bipin G. Nair, and Dr. Satheesh Babu T. G., “Au Nanoparticles-Polyaniline Nanocomposites Modified TiO2 Nanotube Array for Amperometric Determination of Ascorbic Acid”, in Amrita Bioquest, Amrita Vishwa Vidyapeetham, Amritapuri Campus, 2013.

2013

Conference Paper

D. Keerthy, Dr. Bipin G. Nair, Ramachandran, T., and Dr. Satheesh Babu T. G., “Pt-CuO-Graphene Nanocomposite for Non-enzymatic Amperometric Glucose Detection”, in Amrita Bioquest, Amrita Vishwa Vidyapeetham, Amritapuri Campus, 2013.

2013

Conference Paper

H. Parasuram, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Implications of algorithms on LFP reconstruction in cerebellar granular layer”, in International Conference on Biotechnology for innovative applications, Amrita Vishwa Vidyapeetham, Kerala, 2013.

2013

Conference Paper

K. Chaitanya Medini, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Integrating spiking models for BOLD Reconstruction”, in Proceedings of International workshop on Hippocampus: From synapses to behaviour, INCF workshop – IISER, Pune, India, 2013.

2013

Conference Paper

Asha Vijayan, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “A cerebellum-like approach for neuromorphic hardware based on bio-realistic model of cerebellar microcircuitry”, in Proceedings of International workshop on Hippocampus: From synapses to behaviour, INCF workshop - IISER, Pune, India, 2013.

2013

Conference Paper

H. Parasuram, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Studying plasticity effects in cerebellum granular layer micro circuitry using local field potential reconstruction”, in Proceedings of International symposium on Neurosciences & XXXI Annual Conference of Indian Academy of Neurosciences, University of Allahabad, Allahabad, 2013.

2013

Conference Paper

B. S, Dr. Shyam Diwakar, and Dr. Bipin G. Nair, “Analysis of Motor Tasks from EEG for Robotic Arm Control”, in International Conference on Biotechnology for innovative applications, Amrita Vishwa Vidyapeetham, Kerala, 2013.

2013

Conference Paper

N. C, H, S., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Forward Kinematics and Inverse Kinematics Algorithms for Controlling Bio Inspired Robotic Articulators”, in International Conference on Biotechnology for innovative applications, Amrita Vishwa Vidyapeetham, Kerala, 2013.

2013

Conference Paper

K. Chaitanya Medini, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Modelling hemodynamic response function (HRF) to predict BOLD response of cerebellum granular layer using simple spiking models”, in International Conference on Biotechnology for innovative applications, Amrita Vishwa Vidyapeetham, Kerala, 2013.

2013

Conference Paper

Manjusha Nair, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Small Scale Modeling of Cerebellar Networks Using GPUs”, in International Conference on Biotechnology for innovative applications, Amrita Vishwa Vidyapeetham, Kerala, 2013.

2013

Conference Paper

Dhanush Kumar, Parangan, M., Hareesh Singanamala, Dr. Shyam Diwakar, Dr. Bipin G. Nair, and Dr. Krishnashree Achuthan, “Remote Triggered Biotechnology Labs: Implementation Issues and Challenges”, in International Conference on Biotechnology for innovative applications, Amrita Vishwa Vidyapeetham, Kerala, 2013.

2013

Conference Paper

Hareesh Singanamala, Dhanush Kumar, Parangan, M., Dr. Bipin G. Nair, Dr. Shyam Diwakar, and Dr. Krishnashree Achuthan, “Remote Laboratory: Controlling a Robotic Articulator”, in International Conference on Biotechnology for innovative applications, Amrita Vishwa Vidyapeetham, Kerala, 2013.

2013

Conference Paper

M. Parangan, Dhanush Kumar, Hareesh Singanamala, Dr. Shyam Diwakar, Dr. Bipin G. Nair, and Dr. Krishnashree Achuthan, “Setting a Low-Cost Remote-triggered Biotechnology Laboratory: Case Study on Light Microscopy”, in International Conference on Biotechnology for innovative applications, Amrita Vishwa Vidyapeetham, Kerala, 2013.

2013

Conference Paper

R. R, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Biotechnology Virtual Labs: Usage Case Studies”, in International Conference on Biotechnology for innovative applications, Amrita Vishwa Vidyapeetham, Kerala, 2013.

2013

Conference Paper

S. G, Dr. Shyam Diwakar, and Dr. Bipin G. Nair, “Exploring Molecular Biology Education through Virtual Labs”, in International Conference on Biotechnology for innovative applications, Amrita Vishwa Vidyapeetham, Kerala, 2013.

2013

Conference Paper

A. Shekar, Sasidharakurup, H., Dr. Bipin G. Nair, Dr. Shyam Diwakar, and Dr. Krishnashree Achuthan, “Bioinformatics Virtual Lab: Analysis of Student – Content Interaction”, in International Conference on Biotechnology for innovative applications, Amrita Vishwa Vidyapeetham, Kerala, 2013.

2013

Conference Paper

R. Krishnan, Dr. Bipin G. Nair, Dr. Shyam Diwakar, and Dr. Krishnashree Achuthan, “Impacts of Virtual Cell Biology Experiments on Non-Biotechnology Users”, in International Conference on Biotechnology for innovative applications, Amrita Vishwa Vidyapeetham, Kerala, 2013.

2013

Conference Paper

V. Radhamony, Dr. Bipin G. Nair, Dr. Shyam Diwakar, and Dr. Krishnashree Achuthan, “Biochemistry Virtual Lab: For Complementing Lab Practicals”, in International Conference on Biotechnology for innovative applications, Amrita Vishwa Vidyapeetham, Kerala, 2013.

2011

Conference Paper

Dr. Shyam Diwakar, Dr. Krishnashree Achuthan, Prof. Nedungadi, P., and Dr. Bipin G. Nair, “VirtualLabs: Pervasive education & scenes from an ICT perspective”, in Proceedings of the 5TH GUIDE INTERNATIONAL CONFERENCE 2011, Rome, 2011.

2011

Conference Paper

P. H, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Using detailed biophysical models to reconstruct cerebellar post-synaptic evoked local field potential reveals single neuron effects in population code”, in Proceedings of the International symposium on `Recent Trends in Neurosciences & XXIX Annual Conference of Indian Academy of Neurosciences, 2011.

2011

Conference Paper

M. N, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Neuroinformatics database for multi-level physiological mapping based on sematic clustering”, in Proceedings of the International symposium on `Recent Trends in Neurosciences & XXIX Annual Conference of Indian Academy of Neurosciences, 2011.

2011

Conference Paper

W. A, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Electroresponsiveness of cerebellar granule neuron and regulation of spatio-temporal processing in the cerebellar granular layer”, in Proceedings of the International symposium on `Recent Trends in Neurosciences & XXIX Annual Conference of Indian Academy of Neurosciences, 2011.

2011

Conference Paper

Manjusha Nair, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Information Coding in Single Granule Neuron of the Cerebellum”, in Proceedings of the International symposium on `Recent Trends in Neurosciences & XXIX Annual Conference of Indian Academy of Neurosciences, 2011.

2011

Conference Paper

Dr. Bipin G. Nair, Dr. Shyam Diwakar, H, P., C, M., Manjusha Nair, N, M., G, N., and E, D. ’A., “Modeling evoked local field potentials in the cerebellum granular layer and plasticity changes reveal single neuron effects in neural ensembles”, in Acta Physiologica, 2011.

2010

Conference Paper

H. Parasuraman, Abdulmanaph, N., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Reconstructing extracellular local field potential in cerebellar granular layer networks”, in Proceedings 2010 IEEE 5th International Conference on Bio-Inspired Computing: Theories and Applications, BIC-TA 2010, Changsha, 2010, pp. 1504-1509.[Abstract]


Local field potentials (LFPs) arise from complex interactions of spatial distribution of current sources, time dynamics, spatial distribution of dipoles apart underlying conductive properties of the extracellular medium. We reconstruct LFP in order to test and parameterize the molecular mechanisms of cellular function with network properties. The sensitivity of LFP to local excitatory and inhibitory connections was tested using two novel approaches. In the first, we used a single granule neuron as a model kernel for reconstructing population activity. The second approach consisted using a detailed network model. L TP and LTD could regulate the spatiotemporal pattern of granular layer responses to mossy fiber inputs. The effect of changes in synaptic release probability and modulation in intrinsic excitability of granule cell on LFP was studied. The study revealed cellular function was represented in LFP wave revealing the activity of underlying neurons. Changes to cell during L TP and LTD were reflected by LFP wave as an indicator of the function of granule neurons as spatial pattern generators. Both modeling approaches generated LFP in vitro [16] and in vivo [17] waveforms as reported in experiments. © 2010 IEEE.

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PDF iconreconstructing-extracellular-local-field-potential-in-cerebellar-granular-layer.pdf

2010

Conference Paper

C. Medini, Subramaniyam, S., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Modeling cerebellar granular layer excitability and combinatorial computation with spikes”, in Proceedings 2010 IEEE 5th International Conference on Bio-Inspired Computing: Theories and Applications, BIC-TA 2010, Changsha, 2010, pp. 1495-1503.[Abstract]


The cerebellum input stage has been known to perform combinatorial operations [1] [3] on input signals. In this paper, we developed a model to study information transmission and signal recoding in the cerebellar granular layer and to test observations like center-surround organization and time-window hypothesis [1] [2]. We also developed simple neuron models for abstracting timing phenomena in large networks. Detailed biophysical models were used to study synaptic plasticity and its effect in generation and modulation of spikes in the granular layer network. Our results indicated that spatio-temporal information transfer through the granular network is controlled by synaptic inhibition [1]. Spike amplitude and number of spikes were modulated by L TP and LTD. Both in vitro and in vivo simulations indicated that inhibitory input via Golgi cells acts as a modulator and regulates the post synaptic excitability. © 2010 IEEE.

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PDF iconmodeling-cerebellar-granular-layer-excitability-and-combinatorial-computation-with-spikes.pdf

2010

Conference Paper

N. Abdulmanaph, James, P., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Characterizing information transmission in cerebellar granule neuron”, in Proceedings 2010 IEEE 5th International Conference on Bio-Inspired Computing: Theories and Applications, BIC-TA 2010, Changsha, 2010, pp. 1487-1494.[Abstract]


At the cellular scale, single-neurons process information mainly through spikes or action potentials [1]. Although the types of synaptic plasticity and the range of times cales over which they operate suggest that synapses have a more active role in information processing, the parameter space still remains unexplored. We used a mathematical model of cerebellar granule cell to explore information transmission in mossy fibre - granule cell synapse of the cerebellum. The impact of plasticity changes in excitatory synaptic release probability and variation in intrinsic excitability of granule cell was studied combining the modulatory effects of inhibition. We explore the changes in pre and post synaptic factors and report their influence on first spike latency and spike amplitude, revealing the indicators of information encoding in individual neurons [2]. © 2010 IEEE.

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PDF iconcharacterizing-information-transmission-in-cerebellar-granule-neuron.pdf

2010

Conference Paper

Dr. Manitha B. Nair, Melethadathil, N., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Information processing via post-synaptic EPSP-spike complex and model-based predictions of induced changes during plasticity in cerebellar granular neuron”, in Proceedings of the 1st Amrita ACM-W Celebration of Women in Computing in India, A2CWiC'10, Coimbatore, 2010.[Abstract]


Understanding functional role of spike bursts in the brain circuits is vital in analyzing coding of sensory information. Information coding in neurons or brain cells happen as spikes or action potentials and excitatory post-synaptic potentials (EPSPs). Information transmission at the Mossy fiber- Granule cell synaptic relay is crucial to understand mechanisms of signal coding in the cerebellum. We analyzed spiking in granule cells via a detailed computational model and computed the spiking-potentiation contributing to signal recoding in granular layer. Plasticity is simulated in the granule cell model by changing the intrinsic excitability and release probability of the cells. Excitatory post synaptic potentials and spikes on varying Golgi cell (GoC) inhibition and Mossy fiber(MF) excitation were analyzed simultaneously with the effect of induced plasticity changes based on the timing and amplitude of the postsynaptic signals. It is found that a set of EPSPs reaching maximum threshold amplitude are converted to less number of high amplitude EPSPs or spikes. Exploring the EPSP-spike complex in granular neurons reveal possible mechanisms and quantification of information encoding in individual neurons of the cerebellar granular layer. Therefore, our study is potentially an important estimation of cerebellar function. © 2010 ACM.

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PDF iconinformation-processing-via-post-synaptic-epsp-spike-complex-and-model-based-predictions-of-induced-changes-during-plasticity-in-cerebellar-granular-neuron.pdf

2010

Conference Paper

N. Abdulmanaph, Parasuraman, H., Dr. Bipin G. Nair, Dr. Shyam Diwakar, and , “Modeling granular layer local field potential using single neuron and network based approaches to predict LTP/LTD in extracellular recordings”, in Cinquième conférence plénière française de Neurosciences Computationnelles,'Neurocomp'10', 2010.[Abstract]


Local field potentials (LFPs) are recorded as waveforms of extracellular activity that arise from complex interactions of spatial distribution of current sources, time dynamics, spatial distribution of dipoles apart underlying conductive properties of the extracellular medium. We reconstructed granular layer post-synaptic LFP by two different approaches in order to test and parameterize the molecular mechanisms of cellular function with network properties. In the first, we used a single granule neuron as a model kernel for reconstructing population activity. The second approach consisted using a detailed network model. LTP and LTD could regulate the spatiotemporal pattern of granular layer responses to mossy fibre inputs. The effect of changes in synaptic release probability and modulation in intrinsic excitability of granule cell on LFP was studied. The study revealed cellular function was represented in LFP wave revealing the activity of underlying neurons. Changes to cell during LTP and LTD were reflected by LFP wave as an indicator of the function of granule neurons as spatial pattern generators. Both modeling approaches generated LFP in vitro [16] and in vivo [17] waveforms as reported in experiments.

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PDF iconmodeling-granular-layer-local-field-potential-using-single-neuron-and-network-based-approaches-to-predict-ltpltd-in-extracellular-recordings.pdf

2010

Conference Paper

S. Subramaniyam, Chaitanya Medini, Dr. Bipin G. Nair, Dr. Shyam Diwakar, and , “Modeling spatio-temporal processing in cerebellar granular layer and effects of controlled inhibition on plasticity”, in Cinquième conférence plénière française de Neurosciences Computationnelles,'Neurocomp'10', 2010.[Abstract]


The cerebellum input stage has been known to perform spatio-temporal transformations and combinatorial operations [1] [2] on input signals. In this paper, we developed a model to study information transmission and signal recoding in the cerebellar granular layer and to test observations like center-surround organization and time-window hypothesis [1] [3]. Detailed biophysical models were used to study synaptic plasticity and its effect in generation and modulation of spikes in the granular layer network. Our results indicated that spatio-temporal information transfer through the granular network is controlled by synaptic inhibition [1]. Spike amplitude and number of spikes were modulated by LTP and LTD. Both in vitro and in vivo simulations indicated that inhibitory input via Golgi cells acts as a modulator and regulates the post synaptic excitability.

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PDF iconmodeling-spatio-temporal-processing-in-cerebellar-granular-layer-and-effects-of-controlled-inhibition.pdf

2010

Conference Paper

P. James, Abdulmanaph, N., Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Exploring input-output characteristics of the cerebellar granule neuron: role of synaptic inhibition, spike timing and plasticity”, in Proceedings of Neurocomp (Lyon, France), 2010.

2010

Conference Paper

M. Parangan, Asok, C., Parasuraman, H., Dr. Krishnashree Achuthan, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Modeling Action Potentials and Bursting Phenomena using Analog Electrical Neurons”, in Proceedings of ACM A2CWIC (in press), 2010.

2009

Conference Paper

Asha Vijayan, Bessey Elen Skariah, Dr. Bipin G. Nair, Gerald H Lushington, Shabarinath Subramaniam, and Mahesh Visvanathan, “PathMapper-an integrative approach for oncogene pathway identification”, in IEEE International Conference on Bioinformatics and Biomedicine Workshop, 2009. BIBMW 2009., Washington, DC, 2009.[Abstract]


Although generation of high-throughput expression data is becoming customary, the fast, easy, and methodical presentation and analysis of these data in a biological context is still an obstruction. To tackle this necessity we have developed PathMapper, a standalone application which maps expression profiles of genes or proteins concurrently onto major, currently available regulatory, metabolic and cellular pathways. PathMapper automatically predicts protein functions directly from genes and can systematically identify differences between metabolic pathways and map genes onto pathways. MYSQL database is used to store, query, and manipulate the large amounts of data that are involved. PathMapper allows its users to (i) upload microarray data into a database; (ii) integrate gene expression with enzymes of the pathways; (iii) generate pathway diagrams (iv) visualize gene expression for each pathway. A graphical pathway represe- ntation permits the visualization of the expressed genes in a functional context. Based on publicly available pathway databases, PathMapper can be adapted to any organism and is currently available for human, mouse and rat genome arrays. About 20% of the probe sets of each array have been assigned to EC numbers by homology relationship and linked to its corresponding metabolic pathways. This tool can be downloaded and evaluated using the following Web link : (http://parasakti.amrita.ac.in/~amm07bi008/PathMapper). More »»

Publication Type: Conference Proceedings

Year of Publication Publication Type Title

2018

Conference Proceedings

Dr. Shyam Diwakar, ,, ,, Sandeep Bodda, and Dr. Bipin G. Nair, “Experimental Recording and Assessing Gait Phases Using Mobile Phone Sensors and EEG”, Proceedings of the Seventh International Conference on Advances in Computing, Communications and Informatics (ICACCI-2018), Bangalore, Karnataka, India. 2018.

2016

Conference Proceedings

J. Raveendran, Pradeep, A., Dr. Ramachandran T., Dr. Satheesh Babu T. G., and Dr. Bipin G. Nair, “Design and Fabrication of Three Layered Lab-on-a-chip for Electrochemical Detection of Multiple Analytes”, International Conference on Advanced Materials, SCICON’16,. 2016.

2015

Conference Proceedings

S. Subhash, J Anupama, N., Sanalkumar, A., Krishna, D. L., Das, G. S., Ajith, S., Kumar, S. S., and Dr. Bipin G. Nair, “Inhibitory effect of plant extracts on siderophores production by Klebsiella pneumoniae”, Proceedings of 27 Kerala Science Congress. p. 34, 2015.

2014

Conference Proceedings

Dr. Shyam Diwakar, Chellaiah, P., Dr. Bipin G. Nair, and Dr. Krishnashree Achuthan, “Theme Interception Sequence Learning: Deflecting Rubber-Hose Attacks Using Implicit Learning”, In Proceedings of the 3rd International Conference on Frontiers of Intelligent Computing: Theory and Applications (FICTA) Springer International Publishing. Springer International Publishing, Switzerland, pp. 495-502, 2014.[Abstract]


Existing cryptographic systems use strong passwords but several techniques are vulnerable to rubber-hose attacks, wherein the user is forced to reveal the secret key. This paper specifies a defence technique against rubber-hose attacks by taking advantage of image sequence-based theme selection, dependent on a user’s personal construct and active implicit learning. In this paper, an attempt to allow the human brain to generate the password via a computer task of arranging themed images through which the user learns a password without any conscious knowledge of the learned pattern. Although used in authentication, users cannot be coerced into revealing the secret key since the user has no direct knowledge on the choice of the learned secret. We also show that theme interception sequence learning tool works significantly well with mixed user age groups and can be used as a secondary layer of security where human user authentication remains a priority.

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PDF icontheme-interception-sequence-learning-deflecting-rubber-hose-attacks-using-implicit-learning.pdf

2014

Conference Proceedings

D. Nair, Vanuopadath, M., Dr. Bipin G. Nair, G, J., and S, S., “Isolation and Characterisation of Lipopeptides from a Bacillus subtilis sp. Strain, a marime algal endophyte”, Fourth International Seminar on Sustainable Utilisation of Tropical Plant Biomass- Ayur informatics. pp. 89-91, 2014.

2014

Conference Proceedings

L. Ramakrishnan, Aarathi Krishna, Asha Vijayan, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Implementing cerebellar neural network in FPGA”, International symposium on Translational Neuroscience & XXXII Annual Conference of the Indian Academy of Neurosciences. NIMHANS, Bangalore, India, 2014.

2013

Conference Proceedings

S. Subhash, .A, A., .P, A., Nair, D., Poulouse, P., V.J, P., and Dr. Bipin G. Nair, “Studies on the effect of fungal enzymes on Klebsiella Biofilm inhibition”, Amrita Bioquest 2013. Elsevier publications, Amrita School of Engineering, p. 489, 2013.

2013

Conference Proceedings

Asha Vijayan, Dr. Bipin G. Nair, and Dr. Shyam Diwakar, “Inverse Kinematics with cerebellar spiking neurons”, Amrita Bioquest . 2013.

2011

Conference Proceedings

Ha Parasuram, Dr. Bipin G. Nair, Dr. Krishnashree Achuthan, and Dr. Shyam Diwakar, “Taking project tiger to the classroom: A virtual lab case study”, Communications in Computer and Information Science, vol. 191 CCIS. Kochi, pp. 337-348, 2011.[Abstract]


Understanding how population dynamics change over time is critical to many practical problems as pest control, endangered species protection etc. Teaching population ecology is not easy since data is usually collected over a very long period. This paper discusses a specific tiger population case study relating to growth rate predictions using an online virtual lab. Studying tiger populations and introduction of such data in classrooms help in creating awareness and support new pedagogies to estimate animal population dynamics. We have used online virtual labs which are ready-made tools to perform simple experiments and analysis. An important and usually complex case of population analysis as in tiger populations in India is studied in this paper. Although some major parameters like food, transient movement, and ecosystem details have been ignored, predicted data for tiger population follows closely to actual data for previous years and even predicts the growth rate with a small standard deviation of 10%. Our results with tiger populations come close to the actual census values. We propose the use of simple mathematical models to make assessment of transient animal populations such as tigers, and sharks. Also use of such ready-made pro-academic online tools encourages new studies and an enhanced pedagogy to population ecology for mathematicians, biotechnologists, wildlife institute personnel among many other cross-disciplinary scientists. © 2011 Springer-Verlag.

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PDF icontaking-project-tiger-to-the-classroom-a-virtual-lab case study.pdf

Publication Type: Book Chapter

Year of Publication Publication Type Title

2018

Book Chapter

S. Diwakar, Nutakki, C., Bodda, S., Rajendran, A., Vijayan, A., and Dr. Bipin G. Nair, “Mathematical Modelling of Cerebellar Granular Layer Neurons and Network Activity: Information Estimation, Population Behaviour and Robotic Abstractions”, in Mathematical and Theoretical Neuroscience: Cell, Network and Data Analysis, G. Naldi and Nieus, T. Cham: Springer International Publishing, 2018, pp. 61–85.[Abstract]


Recent studies show cerebellum having a crucial role in motor coordination and cognition, and it has been observed that in patients with movement disorders and other neurological conditions cerebellar circuits are known to be affected. Simulations allow insight on how cerebellar granular layer processes spike information and to understand afferent information divergence in the cerebellar cortex. With excitation-inhibition ratios adapted from in vitro experimental data in the cerebellum granular layer, the model allows reconstructing spatial recoding of sensory and tactile patterns in cerebellum. Granular layer population activity reconstruction was performed with biophysical modeling of fMRI BOLD signals and evoked local field potentials from single neuron and network models implemented in NEURON environment. In this chapter, evoked local field potentials have been reconstructed using biophysical and neuronal mass models interpreting averaged activity and constraining population behavior as observed in experiments. Using neuronal activity and correlating blood flow using the balloon and modified Windkessel model, generated cerebellar granular layer BOLD response. With the focus of relating neural activity to clinical correlations such models help constraining network models and predicting activity-dependent emergent behavior and manifestations. To reverse engineering brain function, cerebellar circuit functions were abstracted into a spiking network based trajectory control model for robotic articulation.

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2017

Book Chapter

Dr. Shyam Diwakar, Medini, C., Nair, M., Parasuram, H., Asha Vijayan, and Dr. Bipin G. Nair, “Computational Neuroscience of Timing, Plasticity and Function in Cerebellum Microcircuits”, in Computational Neurology and Psychiatry, vol. 6, Springer Series in Bio-/Neuroinformatics, 2017, pp. 343–371.[Abstract]


Cerebellum has been known to show homogeneity in circuit organization and hence the “modules” or various circuits in the cerebellum are attributed to the diversity of functions such as timing, pattern recognition, movement planning and dysfunctions such as ataxia related to the cerebellum. Ataxia-like conditions, induced by intrinsic excitability changes, disable spiking or bursts and thereby limit the quanta of downstream information. Understanding timing, plasticity and functional roles of cerebellum involve large-scale and microcircuit reconstructions validating molecular mechanisms in population activity. Using mathematical modelling, we attempted to reconstruct information transmission at the granular layer of the cerebellum, a circuit whose role in dysfunctions remain yet to be fully explored. We have employed spiking models to reconstruct timing roles and detailed biophysical models for extracellular activity and local field population response. The roles of inhibition, induced plasticity and their implications in information transmission were evaluated. Modulatory roles of Golgi inhibition and pattern abstraction via optimal storage were estimated. An abstraction of the granular and Purkinje layer circuit for neurorobotic roles such as pattern recognition and spike encoding via two new methods was developed. Simulations suggest plasticity at cerebellar relays may be an important element of tremendous storage capacity reliable in the learning of coordination of actions, sensorimotor or cognitive, in which the cerebellum participates. More »»

2016

Book Chapter

S. Ray, Srivastava, S., Diwakar, S., Dr. Bipin G. Nair, and Ozdemir, V., “Delivering on the Promise of Bioeconomy in the Developing World: Link It with Social Innovation and Education”, in Biomarker Discovery in the Developing World: Dissecting the Pipeline for Meeting the Challenges, S. Srivastava New Delhi: Springer India, 2016, pp. 73–81.[Abstract]


In developing countries where numerous factors such as rapid population growth and entrenched social problems hinder equitable economic growth and education, research and development (R{&amp;}D) are often neglected as well. But the importance of R{&amp;}D extends beyond science. The capacity to generate and advance their scientific scholarship is important for all countries – for such independent scientific thinking skills might also empower the citizens' capacity and will to think democratically in a global interdependent world. Social innovation is explained here as a form of responsible innovation that brings together funders, scientists, and knowledge user communities to address long-standing and/or entrenched societal problems. Moreover, in social innovation, the user communities such as citizens can also contribute to the scientific design and funding beyond a passive role to merely adopt innovations developed by scientific experts. The overall success of developing nations thus rests on building successful linkages of the education ecosystem with social innovation and bioeconomy. To this end, E-learning endeavors and the virtual biotechnology labs are novel initiatives that are rapidly transforming society in the developing world. Distance education and E-learning and open learning endeavors are certainly advantageous for the resource-limited developing countries, where the numbers of potential learners are much higher than the number of well-experienced teachers and educational institutes capable of providing the required infrastructures for basic and advanced scientific education. India, in particular, has had strikingly innovative and forward-looking investments in biotechnology distributed learning practices that can illuminate the global society of scientists and citizens. In this chapter we will highlight the fundamental need and present scenario of virtual laboratories in advanced sophisticated life science education in the developing world.

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2013

Book Chapter

N. Ajayakumar, Schrenk, W., Dr. Bipin G. Nair, and Dr. Sudarslal S., “Mass Spectrometric Characterization of a Novel Antimicrobial Peptide Isolated from Clitoria Ternatea”, in Prospects in Bioscience: Addressing the Issues, A. Sabu and Augustine, A. Springer India, 2013, pp. 251-256.[Abstract]


Increasing microbial resistance to common antibiotics has become a serious threat in maintaining public health. Due to their distinctive features, antimicrobial peptides have become attractive molecules as novel antibiotics. Plants are constantly exposed to attack from a large range of pathogens, and under such conditions, they synthesize antimicrobial peptides as part of their innate defense mechanism. In an effort to identify potential antimicrobial peptides, we have isolated and characterized a novel eight-residue linear peptide from Clitoria ternatea, a perennial plant which belongs to Fabaceae family. Liquid chromatography-electrospray ionization mass spectrometry (LC-ESI-MS) shows a UV-absorbing fraction at 230 nm with a measured molecular mass of 787.4 Da. The sequence of the peptide, QAANSVAK, was derived through de novo approach using tandem mass spectrometric (MS/MS) data obtained after collision-induced dissociation (CID). The sequence was further confirmed through chemical derivatization and proteolysis followed by data-dependent MS/MS analysis. Antimicrobial studies of the nearly homogenous peptide fraction after solid-phase extraction (SPE) show activity against Bacillus subtilis. The peptide bears no sequence similarity with any of the linear peptides isolated thus far from other organisms.

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1996

Book Chapter

T. B. Patel, Sun, H., Poppleton, H., Dr. Bipin G. Nair, Rashed, H. M., and Yu, Y. - M., “[21] Epidermal Growth Factor-mediated Regulation of G Proteins and Adenylylcyclase in Cardiac Muscle”, in G Proteins, vol. 29, P. C. Roche Academic Press, 1996, pp. 319 - 343.[Abstract]


Publisher Summary This chapter presents a number of experimental approaches that have proved to be very useful in elucidating the mechanism(s) involved in epidermal growth factor (EGF) -mediated stimulation of cardiac adenylylcyclase. However, there are several additional questions pertaining to the detailed understanding of the mechanism(s) involved in interactions between the EGF receptor and Gs interaction. Thus, the in vitro studies demonstrate the juxtamembrane region of the EGF receptor that is important for stimulation of Gs by performing mutation(s) of key residue(s) in the juxtamembrane region of the EGF receptor, to determine whether the ability of EGF to stimulate adenylylcyclase can be obliterated. Similarly, it is important to determine the region(s) of Gsα that interact with the EGF receptor. It is also determine that what elements confer specificity to the ability of EGF to stimulate adenylylcyclase. The latter goal poses a particularly important question, because EGF does not elevate cAMP content in all cells that express the EGF receptor, Gs, and adenylylcyclase.

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Publication Type: Patent

Year of Publication Publication Type Title

2018

Patent

S. V. Nair, Chandran, P., and Dr. Bipin G. Nair, “Detergent compatible assay for protein estimation”, U.S. Patent 2018410128522018.

2018

Patent

S. Pal, Dr. Bipin G. Nair, Madhavan, A., Pradeesh Babu, Amrita Salim, P., C., Stanely, J., and Babu, S., “Methods and devices for detecting antimicrobial resistant bacteria using bacteriophages”, U.S. Patent 2017410206692018.

2017

Patent

E. Schaefer, Dr. Bipin G. Nair, and Guruvayoorappa, K., “Cartridge connection method for precise delivery of liquid”, 2017.[Abstract]


A mobile medical pump has a tubular cartridge unit with a first end having an interface to an infusion line and a second, open end having a first engagement interface, with a piston inserted in the cartridge and engaging an inner diameter of the cartridge, such that translation of the piston within the cartridge will draw in or expel liquid to or from the cartridge, a case housing having an opening for inserting the cartridge and an internal second engagement interface at a depth that, with a cartridge fully inserted and the first and second engagement interfaces joined, an infusion line may be connected to the first end external to the case, and a piston rod within the case housing, the piston rod having a permanent magnet at a first end with a planar surface orthogonal to a longitudinal axis of the piston rod, and a threaded opening at an opposite end engaging a rotatable translation screw driven by a translation drive system including an electric motor. With the piston rod set at a preprogrammed position, inserting a charged cartridge into the case to engage the first and second engagement interfaces, causes the magnet end of the piston rod to securely contact a steel plate embedded in the piston, such that translation of the piston rod by the translation drive system will expel liquid from the cartridge, and holding the piston rod motionless will hold the piston motionless, preventing any discharge of liquid from the cartridge.

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2017

Patent

Dr. Bipin G. Nair, T.G, S. Babu, and T, R., “Non- Enzymatic Glucose Sensor.”, 2017.

2017

Patent

Dr. Bipin G. Nair, “Dual Microcontroller-based Liquid Infusion Device”, 2017.

2017

Patent

S. Babu Thekkedath, Thiagarajan, R., and Dr. Bipin G. Nair, “Non-enzymatic glucose sensor”, U.S. Patent 15/431,8012017.

2017

Patent

S. Babu Thekkedath, Pradeep, A., Dr. Bipin G. Nair, Raveendran, J., Raj, V., and Stanley, J., “Lab-on-a-chip glucose sensor array device with integrated non-enzymatic sensors”, U.S. Patent 2017410396572017.

2016

Patent

S. Babu Thekkedath, Thiagarajan, R., and Dr. Bipin G. Nair, “Non-enzymatic glucose sensor”, U.S. Patent 3697/CHE/20122016.

2014

Patent

A. R. Pai and Dr. Bipin G. Nair, “Method of preparing reduced graphene oxide”, U.S. Patent 626/CHE/20142014.

2014

Patent

E. Schaefer, Guruvayurappan, K., and Dr. Bipin G. Nair, “Cartridge connection method for precise delivery of liquid”, U.S. Patent 1888/CHE/20112014.

2012

Patent

E. Schaefer, Dr. Bipin G. Nair, and Dr. Geetha Kumar, “Key pad for Medical Devices”, 2012.

2012

Patent

Dr. Bipin G. Nair, Kumar, G., Eastman, C., and Schäfer, E., “Medical device keypad interface”, U.S. Patent US 29/420,8812012.[Abstract]


A portion of the disclosure of this patent document may contain material to which a claim for copyright and trademark is made. The copyright and trademark owner has no objection to the reproduction of the patent document or the patent disclosure, as it appears in the U.S. Patent Office records, but reserves all other copyright and trademark rights whatsoever.

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2011

Patent

Dr. Bipin G. Nair, Guruvayoorappan, K., and Kumar, H., “Dual Microcontroller Based Liquid Infusion System”, U.S. Patent US 11/942,6102011.[Abstract]


A highly reliable and robust functioning liquid infusion system for use in biomedical applications comprises a dual microcontroller system where the first microcontroller is configured to administer the liquid and the second microcontroller is configured to monitor the accurate functioning of the system and various performance parameters such as flow rate of liquid, presence of leaks or blocks in the liquid passage, level of drug in the cartridge and battery condition. The liquid injection portion comprises a cylindrical airtight liquid holder or drug cartridge with a movable internal piston that is in contact with a movable stem, and a micromotor, which controls the drug delivery. The system is programmable with a dosing system stored into the driver/monitor microcontrollers. A low power LCD module is used to display the operating parameters with multiple language interface and alarm conditions, if any. The system is also equipped with a system of sensors that trigger an alarm to indicate abnormal conditions.

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Patents:

Year Title
2017 Eckherd Schaefer, Bipin G Nair, K Guruvayoorappan. Cartridge connection method for precise delivery of liquid . Patent no. US9533093 B2, Jan.3, 2017.
2017 Satheesh Babu T.G, Ramachandran T, Bipin G Nair. Non- Enzymatic Glucose Sensor. Patent No. US 9,606,080 B2, Mar.28, 2017
2017 Bipin G Nair. Dual microcontroller-based liquid infusion device. Indian patent No. 281908, Mar 28, 2017..
2012 Eckherd Schaefer, Geetha Kumar, Bipin Nair. Key pad for Medical Devices. The Patent Office, Government of India_ Certificate of Registration of Design, Design No. 244105, March 26, 2012
2012 Bipin G Nair, Geetha Kumar, Crystal Eastman, Eckhard Schafer. Medical device keypad interface. US Patent No. 29/420,881, May 14, 2012.
2011 Bipin G Nair, K Guruvayoorappan, Harish Kumar. Dual Microcontroller Based Liquid Infusion System. US Patent No. US 8,034,019 B2, October 2011.

PATENTS FILED

Year Title
2018 Sobha V Nair, Prakash Chandran, Bipin Nair. Detergent compatible assay for protein estimation. Application 201841012852, Date of filing of Application: April 4, 2018.
2018 Sanjay Pal, Bipin Nair, Ajith Madhavan, Pradeesh Babu, Amrita Salim, Chandni P., John Stanely, Satheesh Babu. Methods and devices for detecting antimicrobial resistant bacteria using bacteriophages. Application 201741020669, Date of filing of application: June 13, 2018.
2017 Satheesh Babu Thekkedath, Ramachandran Thiagarajan, Bipin Nair. Non-enzymatic glucose sensor. Application 15/431,801, Date of filing of application: February 14, 2017.
2017 Satheesh Babu Thekkedath, Arathi Pradeep, Bipin Nair, Jeethu Raveendran, Vineeth Raj, John Stanley. Lab-on-a-chip glucose sensor array device with integrated non-enzymatic sensors. Application 201741039657, Date of filing of application: November 7, 2017.
2016 Satheesh Babu Thekkedath, Ramachandran Thiagarajan, Bipin Nair. Non-enzymatic glucose sensor. Application 3697/CHE/2012, Date of filing of application: April 8, 2016.
2014 Asha R Pai, Bipin Nair. Method of preparing reduced graphene oxide. Application No.626/CHE/2014 A, Date of filing of Application: November 2, 2014
2014 Eckhard Schaefer, K. Guruvayurappan, Bipin Nair. Cartridge connection method for precise delivery of liquid. Application 1888/CHE/2011, Date of filing of application: June 2, 2014.
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