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K N Srinivasan

Publications and source records attributed to K N Srinivasan.

13 recordsLinked to original sources
PubMed2005

Accurate prediction of scorpion toxin functional properties from primary structures.

Scorpion toxins are common experimental tools for studies of biochemical and pharmacological properties of ion channels. The number of functionally annotated scorpion toxins is steadily growing, but the number of identified toxin sequences is increasing at much faster pace. With an estimated 100,000 different variants, bioinformatic analysis of scorpion toxins is becoming a necessary tool for their systematic functional analysis. Here, we report a bioinformatics-driven system involving scorpion toxin structural classification, functional annotation, database technology, sequence comparison, nearest neighbour analysis, and decision rules which produces highly accurate predictions of scorpion toxin functional properties.

Algorithms↗
PubMed2004

Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens.

MOTIVATION: Processing and presentation of major histocompatibility complex class I antigens to cytotoxic T-lymphocytes is crucial for immune surveillance against intracellular bacteria, parasites, viruses and tumors. Identification of antigenic regions on pathogen proteins will play a pivotal role in designer vaccine immunotherapy. We have developed a system that not only identifies high binding T-cell antigenic epitopes, but also class I T-cell antigenic clusters termed immunological hot spots. METHODS: MULTIPRED, a computational system for promiscuous prediction of HLA class I binders, uses artificial neural networks (ANN) and hidden Markov models (HMM) as predictive engines. The models were rigorously trained, tested and validated using experimentally identified HLA class I T-cell epitopes from human melanoma related proteins and human papillomavirus proteins E6 and E7. We have developed a scoring scheme for identification of immunological hot spots for HLA class I molecules, which is the sum of the highest four predictions within a window of 30 amino acids. RESULTS: Our predictions against experimental data from four melanoma-related proteins showed that MULTIPRED ANN and HMM models could predict T-cell epitopes with high accuracy. The analysis of proteins E6 and E7 showed that ANN models appear to be more accurate for prediction of HLA-A3 hot spots and HMM models for HLA-A2 predictions. For illustration of its utility we applied MULTIPRED for prediction of promiscuous T-cell epitopes in all four SARS coronavirus structural proteins. MULTIPRED predicted HLA-A2 and HLA-A3 hot spots in each of these proteins.

Algorithms↗
PubMed2004

Potential effects of tetrodotoxin exposure to human glial cells postulated using microarray approach.

Sodium channels play an important role in many neurological disorders and also in prostate cancer. Tetrodotoxin (TTX), a blocker of voltage-gated sodium channels has been chiefly used as a molecular probe for the study and characterization of these channels. The regulation of gene expression in response for the exposure of TTX to glial cells which are reported to be involved in neurodegenerative process is poorly understood. Therefore, the present study aims to develop a repository of genes and map it on a few pivotal neurodegenerative pathways to speculate the effect of TTX. Using Affymetrix GeneChip (HG-U133A), we have selected a subset of 692 differentially expressed genes, several of which are-cullin 4A (CUL4A), ubiquitin carrier protein (E2-EPF), proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional protease 7) (PSMB8), protein tyrosine phosphatase type IVA (PTP4A1), intercellular adhesion molecule 1 (ICAM1), prostaglandin-endoperoxide synthase 2 (PTGS2), and caspase 1 (CASP1). These genes, which facilitate some of the neurodegenerative pathways, such as ubiquitin, proteasome, inflammation and kinases, were identified to be up- or down-regulated for the TTX treatment. Thus, the selected genes were further examined on ubiquitin-proteasome mediated inflammatory responses pathway as ample evidence for the role of glial cell-mediated inflammation in the neurodegenerative process are available. In summary, our result provides a basic understanding of the differentially expressed genes along with one of the possible pathway which may have been modulated by the exposure of TTX.

Cell Survival↗
PubMed2002

Plasma melatonin, pinealocyte morphology, and surface receptors/antigen expression on macrophages/microglia in the pineal gland following a high-altitude exposure.

The present study examined the effects of high-altitude exposure on the pineal gland, the main source of production of melatonin. It was surmised that hypoxia experienced at high altitude, caused by decreased oxygen tension in the ambient air, might lead to some structural alterations in the pineal gland and, hence, affect its melatonin production. Adult Wistar rats were exposed to an altitude of 8,000 m for 2 hr in an altitude chamber and then sacrificed at various time intervals after the exposure. Normal rats kept at ground level were used as controls. Blood samples were collected at various time intervals for measurement of plasma melatonin level, and the pineal glands from both groups were processed for electron microscopy and immunohistochemistry. The plasma melatonin level showed a steady increase following altitude exposure peaking at 7 days and returned to control levels thereafter. Between 1 and 4 days after altitude exposure, the mitochondrial number and lipid droplets in the pinealocytes appeared to be reduced compared with those in control rats. At 7 days, however, the mitochondrial numbers and lipid droplets were noticeably increased. At the same time interval, the expression of complement type 3 receptors and major histocompatibility class II antigens as detected with the antibodies OX-42 and OX-6, respectively, in macrophages/microglia was up-regulated compared with that in the control rats and those killed at earlier times. This was attributed to the increased serum melatonin after the altitude exposure. By 14 and 21 days, the ultrastructure of pinealocytes and immunoreactivity of macrophages/microglia were comparable with those in the control rats. We conclude from this study that an altitude exposure in rats leads to an increase in melatonin production, which returned to control levels with passage of time.

Altitude Sickness↗
PubMed2002

SCORPION, a molecular database of scorpion toxins.

Increasing interest in the studies of toxins and the requirements for better structural and functional annotations have created a need for improved data management in the field of toxins. The molecular database, SCORPION, contains more than 200 entries of fully referenced scorpion toxin data including primary sequences, three-dimensional structures, structural and functional annotations of scorpion toxins along with relevant literature references. SCORPION has a set of search tools that allow users to extract data and perform specific queries. These entries have been compiled from public databases and literature, cleaned of errors and enriched with additional structural and functional information. The grouping of scorpion toxins provides a basis for extending and clarifying the existing structural and functional classifications. The bioinformatics modules in SCORPION facilitate analyses aimed at classification of scorpion toxins and identification of sequence patterns associated with specific structural or functional properties of scorpion toxins. The SCORPION database is accessible via the Internet at sdmc.krdl.org.sg:8080/scorpion.

Animals↗
PubMed2001

Functional site of bukatoxin, an alpha-type sodium channel neurotoxin from the Chinese scorpion (Buthus martensi Karsch) venom: probable role of the (52)PDKVP(56) loop.

Alpha-toxins from scorpion venoms prolong the action potential of excitable cells by blocking sodium channel inactivation. We have purified bukatoxin, an alpha-toxin from scorpion (Buthus martensi Karsch) venom, to homogeneity. Bukatoxin produced marked relaxant responses in the carbachol-precontracted rat anococcygeus muscle (ACM), which were mediated through the L-arginine-nitric oxide synthase-nitric oxide pathway, consequent to a neuronal release of nitric oxide. Based on the presence of proline residues in the flanking segments of protein-protein interaction sites, we predicted the site between (52)PP(56) to be the potential interaction site of bukatoxin. A homology model of bukatoxin indicated the presence of this site on the surface. Buka11, a synthetic peptide designed based on this predicted site, produced a concentration-dependent nitric oxide-mediated relaxant response in ACM. Using alanine-substituted peptides, we have shown the importance (53)DKV(55) flanked by proline residues in the functional site of bukatoxin.

Amino Acid Motifs↗
PubMed2000

Effect of occupation on lipid peroxidation and antioxidants' status in masons.

Effect of occupation on haematological factors, lipid peroxidation and antioxidants' status was studied in masons and compared with normal subjects. Red blood corpuscles (RBC), haemoglobin (Hb), Vitamin C, Vitamin E, beta-carotene levels and glutathione peroxidase (GSHPx), superoxide dismutase (SOD) and catalase (CAT) activities decreased. Thiobarbituric acid reacting substances (TBARS) level increased. Occupational exposure to cement increased lipid peroxidation but decreased antioxidants' levels in masons. Increased lipid peroxidation seems to be responsible for the reduction in RBC and Hb.

Adult↗
PubMed2000

Effect of excessive intake of thermally oxidized sesame oil on lipids, lipid peroxidation and antioxidants' status in rats.

Fresh and thermally oxidized sesame, groundnut and coconut oils were fed to different groups of rats, as high fat diet (20%). Feeding fresh and thermally oxidized oils increased the levels of total cholesterol, low density lipoprotein cholesterol (LDL-C), and phospholipids but high density lipoprotein cholesterol (HDL-C) decreased in all the experimental animals. The levels of very low density lipoproteincholesterol (VLDL-C) and triacylglycerol increased only in groundnut and coconut oils-fed groups and decreased in sesame oil-fed group when compared with the control. When fresh and the corresponding thermally oxidized oils-fed groups were compared with the control, total cholesterol and LDL-cholesterol alone increased while triacylglycerol, VLDL-cholesterol, HDL-cholesterol, HDL/LDL ratio and phospholipids decreased. Thiobarbituric acid reacting substances increased in all the experimental animals and more so in corresponding thermally oxidized oils. It was less pronounced in sesame oil-fed groups when compared with the corresponding other oils-fed groups. Feeding of thermally oxidized oils decreased the levels of vitamin E, vitamin C and reduced glutathione when compared with fresh oils. Among the three thermally oxidized edible oils, sesame oil exhibited lesser risk for hyperlipidemic disorders.

Animals↗