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Search Results: 1 - 10 of 130566 matches for " Vasaikar Suhas V "
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NeuroDNet - an open source platform for constructing and analyzing neurodegenerative disease networks
Vasaikar Suhas V,Padhi Aditya K,Jayaram Bhyravabhotla,Gomes James
BMC Neuroscience , 2013, DOI: 10.1186/1471-2202-14-3
Abstract: Background Genetic networks control cellular functions. Aberrations in normal cellular function are caused by mutations in genes that disrupt the fine tuning of genetic networks and cause disease or disorder. However, the large number of signalling molecules, genes and proteins that constitute such networks, and the consequent complexity of interactions, has restrained progress in research elucidating disease mechanisms. Hence, carrying out a systematic analysis of how diseases alter the character of these networks is important. We illustrate this through our work on neurodegenerative disease networks. We created a database, NeuroDNet, which brings together relevant information about signalling molecules, genes and proteins, and their interactions, for constructing neurodegenerative disease networks. Description NeuroDNet is a database with interactive tools that enables the creation of interaction networks for twelve neurodegenerative diseases under one portal for interrogation and analyses. It is the first of its kind, which enables the construction and analysis of neurodegenerative diseases through protein interaction networks, regulatory networks and Boolean networks. The database has a three-tier architecture - foundation, function and interface. The foundation tier contains the human genome data with 23857 protein-coding genes linked to more than 300 genes reported in clinical studies of neurodegenerative diseases. The database architecture was designed to retrieve neurodegenerative disease information seamlessly through the interface tier using specific functional information. Features of this database enable users to extract, analyze and display information related to a disease in many different ways. Conclusions The application of NeuroDNet was illustrated using three case studies. Through these case studies, the construction and analyses of a PPI network for angiogenin protein in amyotrophic lateral sclerosis, a signal-gene-protein interaction network for presenilin protein in Alzheimer's disease and a Boolean network for a mammalian cell cycle was demonstrated. NeuroDNet is accessible at http://bioschool.iitd.ac.in/NeuroDNet/.
Mechanisms of Loss of Functions of Human Angiogenin Variants Implicated in Amyotrophic Lateral Sclerosis
Aditya K. Padhi, Hirdesh Kumar, Suhas V. Vasaikar, Bhyravabhotla Jayaram, James Gomes
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0032479
Abstract: Background Mutations in the coding region of angiogenin (ANG) gene have been found in patients suffering from Amyotrophic Lateral Sclerosis (ALS). Neurodegeneration results from the loss of angiogenic ability of ANG (protein coded by ANG). In this work, we performed extensive molecular dynamics (MD) simulations of wild-type ANG and disease associated ANG variants to elucidate the mechanism behind the loss of ribonucleolytic activity and nuclear translocation activity, functions needed for angiogenesis. Methodology/Principal Findings MD simulations were carried out to study the structural and dynamic differences in the catalytic site and nuclear localization signal residues between WT-ANG (Wild-type ANG) and six mutants. Variants K17I, S28N, P112L and V113I have confirmed association with ALS, while T195C and A238G single nucleotide polymorphisms (SNPs) encoding L35P and K60E mutants respectively, have not been associated with ALS. Our results show that loss of ribonucleolytic activity in K17I is caused by conformational switching of the catalytic residue His114 by 99°. The loss of nuclear translocation activity of S28N and P112L is caused by changes in the folding of the residues 31RRR33 that result in the reduction in solvent accessible surface area (SASA). Consequently, we predict that V113I will exhibit loss of angiogenic properties by loss of nuclear translocation activity and L35P by loss of both ribonucleolytic activity and nuclear translocation activity. No functional loss was inferred for K60E. The MD simulation results were supported by hydrogen bond interaction analyses and molecular docking studies. Conclusions/Significance Conformational switching of catalytic residue His114 seems to be the mechanism causing loss of ribonucleolytic activity and reduction in SASA of nuclear localization signal residues 31RRR33 results in loss of nuclear translocation activity in ANG mutants. Therefore, we predict that L35P mutant, would exhibit loss of angiogenic functions, and hence would correlate with ALS while K60E would not show any loss.
Modulation of Neuronal Proteome Profile in Response to Japanese Encephalitis Virus Infection
Nabonita Sengupta, Sourish Ghosh, Suhas V. Vasaikar, James Gomes, Anirban Basu
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0090211
Abstract: In this study we have reported the in vivo proteomic changes during Japanese Encephalitis Virus (JEV) infection in combination with in vitro studies which will help in the comprehensive characterization of the modifications in the host metabolism in response to JEV infection. We performed a 2-DE based quantitative proteomic study of JEV-infected mouse brain as well as mouse neuroblastoma (Neuro2a) cells to analyze the host response to this lethal virus. 56 host proteins were found to be differentially expressed post JEV infection (defined as exhibiting ≥1.5-fold change in protein abundance upon JEV infection). Bioinformatics analyses were used to generate JEV-regulated host response networks which reported that the identified proteins were found to be associated with various cellular processes ranging from intracellular protein transport, cellular metabolism and ER stress associated unfolded protein response. JEV was found to invade the host protein folding machinery to sustain its survival and replication inside the host thereby generating a vigorous unfolded protein response, subsequently triggering a number of pathways responsible for the JEV associated pathologies. The results were also validated using a human cell line to correlate them to the human response to JEV. The present investigation is the first report on JEV-host interactome in in vivo model and will be of potential interest for future antiviral research in this field.
Bilateral transtentorial herniation and isolated fourth ventricle: A scientific note
Udayakumaran Suhas
Neurology India , 2011,
Abstract:
WiMAX or LTE: Which Technology to Adopt? A Comprehensive Comparative Study
Suhas Raut
Communications of the IBIMA , 2009,
Abstract: The industry landscape in telecommunications is changing rapidly at the moment. Services are increasingly shifting from voice to data and from circuit-switched to packet-switched ones. LTE and WiMAX are the two technologies poised to dominate next generation mobile networks. Battle between LTE & WiMAX technologies is already heating up with WiMAX being ahead due to availability of standards through IEEE 802.16 and is up and running but lacks in substantial roll out plans due to cost. On the contrary, LTE upgrades from 3G networks are rumored to be as simple as slotting in a new card in the rack. Researchers and business community is divided over the choice of LTE and WiMAX. Few researchers feel that 3G LTE can bring substantial technologies and economical benefits to operators deploying mobile networks beyond 3G. This paper presents a comprehensive comparative study to help arrive at the choice between LTE and WiMAX.
Management Framework for Globally Distributed Teams in IT Industry
Suhas Raut
Communications of the IBIMA , 2008,
Abstract: Software development is a highly creative and collaborative endeavor in which success requires a fine degree of coordination between many people from many different disciplines, often working across different geographies and time zones and sometimes across cultural borders. When implementing software development in a global environment, a popular strategy is the establishment of globally distributed teams.Project management owes its existence as a management discipline to the complex, high technology undertakings. Projects are complex endeavors and project outcomes are far from being certain. Software development teams are plagued by management problems that result in missed deadlines, budget overruns, and canceled projects, and effective management remains an open problem. The management aspect becomes further challenging and complicated while dealing ethical, time zone, cross cultural issues inherent to a globally distributed team. In this paper we have presented an adept management framework for globally distributed teams.
Atomic Batteries: Energy from Radioactivity
Suhas Kumar
Physics , 2015,
Abstract: With alternate, sustainable, natural sources of energy being sought after, there is new interest in energy from radioactivity, including natural and waste radioactive materials. A study of various atomic batteries is presented with perspectives of development and comparisons of performance parameters and cost. We discuss radioisotope thermal generators, indirect conversion batteries, direct conversion batteries, and direct charge batteries. We qualitatively describe their principles of operation and their applications. We project possible market trends through our comparative cost analysis. We also explore a future direction for certain atomic batteries by using nanomaterials to improve their performance.
Fundamental Limits to Moore's Law
Suhas Kumar
Physics , 2015,
Abstract: The theoretical and practical aspects of the fundamental, ultimate, physical limits to scaling, or Moore-s law, is presented.
The Complex of Non-separating embedded spheres
Suhas Pandit
Mathematics , 2012,
Abstract: For n >2, we shall show that the group Aut(NS(M)) of simplicial automorphisms of the complex NS(M) of non-separating embedded spheres in the manifold M,connected sum of n copies of S^2 X S^1, isomorphic to the group Out(F_n) of outer automorphisms of the free group F_n, where $F_n$ is identified with the fundamental group of M up to conjugacy of the base point in M.
Comparative bioequivalence studies of tramadol hydrochloride sustained-release 200 mg tablets
Suhas S Khandave, Satish V Sawant, Santosh S Joshi, et al
Drug Design, Development and Therapy , 2010, DOI: http://dx.doi.org/10.2147/DDDT.S15133
Abstract: mparative bioequivalence studies of tramadol hydrochloride sustained-release 200 mg tablets Original Research (8629) Total Article Views Authors: Suhas S Khandave, Satish V Sawant, Santosh S Joshi, et al Published Date November 2010 Volume 2010:4 Pages 367 - 374 DOI: http://dx.doi.org/10.2147/DDDT.S15133 Suhas S Khandave1, Satish V Sawant1, Santosh S Joshi1, Yatish K Bansal2, Sonal S Kadam2 1Accutest Research Laboratories (I) Private Limited, Koparkhirne, Navi Mumbai, Maharashtra, India; 2Ipca Laboratories Limited, Kandivli Mumbai, Maharashtra, India Background: Tramadol hydrochloride is available as 50 mg immediate-release (IR) and 100 mg, 200 mg, and 300 mg sustained-release (SR) tablets. The recommended dose of tramadol is 50–100 mg IR tablets every 4–6 hours. The tramadol SR 200 mg tablet is a better therapeutic option, with a reduced frequency of dosing, and improved patient compliance and quality of life. The present study evaluated the bioequivalence of a generic tramadol SR 200 mg tablet. Methods: A comparative in vitro dissolution study was performed on the test and reference products, followed by two separate single-dose bioequivalence studies under fasting and fed conditions and one multiple-dose bioequivalence study under fasting conditions. These bioequivalence studies were conducted in healthy human subjects using an open-label, randomized, two-treatment, two-period, two-sequence, crossover design. The oral administration of the test and reference products was done on day 1 for both the single-dose studies and on days 1–5 for the multiple-dose study in each study period as per the randomization code. Serial blood samples were collected at predefined time points in all the studies. Analysis of plasma concentrations of tramadol and O-desmethyltramadol (the M1 metabolite) was done by a validated liquid chromatography-mass spectrometry analytical method. The standard acceptance criterion of bioequivalence was applied on log-transformed pharmacokinetic parameters for tramadol and its M1 metabolite. Results: The ratios for geometric least-square means and 90% confidence intervals were within the acceptance range of 80%–125% for log-transformed primary pharmacokinetic parameters for tramadol and its M1 metabolite in all the three studies. Conclusion: The test product is bioequivalent to the reference product in terms of rate and extent of absorption, as evident from the single-dose and multiple-dose studies. Both the treatments were well tolerated.
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