Showing papers by "Kuvempu University published in 2009"

Human Protein Reference Database—2009 update

Abstract: Human Protein Reference Database (HPRD--http://www.hprd.org/), initially described in 2003, is a database of curated proteomic information pertaining to human proteins. We have recently added a number of new features in HPRD. These include PhosphoMotif Finder, which allows users to find the presence of over 320 experimentally verified phosphorylation motifs in proteins of interest. Another new feature is a protein distributed annotation system--Human Proteinpedia (http://www.humanproteinpedia.org/)--through which laboratories can submit their data, which is mapped onto protein entries in HPRD. Over 75 laboratories involved in proteomics research have already participated in this effort by submitting data for over 15,000 human proteins. The submitted data includes mass spectrometry and protein microarray-derived data, among other data types. Finally, HPRD is also linked to a compendium of human signaling pathways developed by our group, NetPath (http://www.netpath.org/), which currently contains annotations for several cancer and immune signaling pathways. Since the last update, more than 5500 new protein sequences have been added, making HPRD a comprehensive resource for studying the human proteome.

Genomewide mRNA profiling of esophageal squamous cell carcinoma for identification of cancer biomarkers.

Abstract: Cancer of the esophagus is of two main types, each with distinct etiological and pathological characteristics. Esophageal squamous cell carcinoma (ESCC) is predominant type of esophageal cancers worldwide comprising almost 95% of cases. While ESCC is prevalent in the developing world, esophageal adenocarcinoma is commonly seen in the developed country, usually in association with Barrett's esophagus. In spite of its higher prevalence, ESCC has not been studied as intensively as esophageal adenocarcinoma. ESCC and esophageal adenocarcinoma are common cancers worldwide with poor survival rate among patients mainly because both of these cancers lack early biomarkers of identification. Molecular mechanisms contributing to initiation and progression of esophageal squamous cell carcinoma are still poorly understood. Development of DNA microarray technology allows high-throughput identification of gene expression profiles in cancers. In order to identify molecules as candidates for early diagnosis and/or as therapeutic targets, we analyzed the mRNA expression profiles of 20 cases of ESCC using whole genome DNA microarrays. A total of 2,235 genes were differentially regulated in the tumors as compared to the corresponding adjacent normal epithelium of which 881 were significantly upregulated. We validated two molecules that were not previously reported to be overexpressed in ESCC, oral cancer overexpressed 2 (ORAOV2) and fibroblast activation protein (FAP), by immunohistochemical labeling of tissue microarrays and archival tissue sections and found that they were overexpressed in 98% (116/118) and 68% (79/116) of cases, respectively. By gene enrichment analysis, we identified significant downregulation of several genes in the arachidonic acid metabolic pathway. Overall, using this approach we have identified a number of promising novel candidates that can be validated further for their potential to serve as biomarkers for ESCC.

Human Proteinpedia: a unified discovery resource for proteomics research

Abstract: Sharing proteomic data with the biomedical community through a unified proteomic resource, especially in the context of individual proteins, is a challenging prospect. We have developed a community portal, designated as Human Proteinpedia (http://www.humanproteinpedia.org/), for sharing both unpublished and published human proteomic data through the use of a distributed annotation system designed specifically for this purpose. This system allows laboratories to contribute and maintain protein annotations, which are also mapped to the corresponding proteins through the Human Protein Reference Database (HPRD; http://www.hprd.org/). Thus, it is possible to visualize data pertaining to experimentally validated posttranslational modifications (PTMs), protein isoforms, protein–protein interactions (PPIs), tissue expression, expression in cell lines, subcellular localization and enzyme substrates in the context of individual proteins. With enthusiastic participation of the proteomics community, the past 15 months have witnessed data contributions from more than 75 labs around the world including 2710 distinct experiments, >1.9 million peptides, >4.8 million MS/MS spectra, 150 368 protein expression annotations, 17 410 PTMs, 34 624 PPIs and 2906 subcellular localization annotations. Human Proteinpedia should serve as an integrated platform to store, integrate and disseminate such proteomic data and is inching towards evolving into a unified human proteomics resource.

Diversity of phytoplanktons in a waste stabilization pond at Shimoga Town, Karnataka State, India.

Abstract: To understand the diversity of phytoplanktons in waste stabilization pond effluents the hitherto study is undertaken. Species diversity indices of Shannon-Wiener and Simpson were applied to phytoplanktons. The diversity indices are of mathematical function to explain the abundance of each species. The total numbers of algae identified were 71 species belonging to Cyanophyceae, Chlorophyceae, Euglenophyceae, Bacillariophyceace and Desmidaceae. Chlorella and Scenedesmus were the dominant forms among the algal genera throughout the study period. Phytoplanktons play a vital role in improving the water quality of wastewater in waste stabilization ponds. Diversity indices provide important information about rarity and commonness of species in a community. The diversity indices of all the species explained the water was moderately polluted with less diversity level and highest possible equal number of different species of phytoplanktons. Greater impact of pollution leads to the lesser diversity of phytoplanktons.

Detection of Uric Acid in the Presence of Dopamine and High Concentration of Ascorbic Acid Using PDDA Modified Graphite Electrode

Abstract: The properties of graphite electrode (Gr) modified with poly(diallyl dimethyl ammonium chloride) (PDDA) for the detection of uric acid (UA) in the presence of dopamine (DA) and high concentration of ascorbic acid (AA) have been investigated by cyclic voltammetry, differential pulse voltammetry and chronoamperometry. The polymer modified graphite electrode was prepared by a very simple method just by immersing the graphite electrode in PDDA solution for 20 minutes. The PDDA/Gr modified electrode displayed excellent electrocatalytic activity towards the oxidation of UA, DA and AA compared to that at the bare graphite electrode. The electrochemical oxidation signals of UA, DA and AA are well resolved into three distinct peaks with peak potential separations of 220 mV, 168 mV and 387 mV between AA-DA, DA-UA and AA-UA respectively in cyclic voltammetry studies and the corresponding peak potential separations are 230 mV, 130 mV and 354 mV respectively in differential pulse voltammetry. The lowest detection limits obtained for UA, DA and AA were 1×10−7 M, 2×10−7 M and 800×10−9 M respectively. The PDDA/Gr electrode efficiently eliminated the interference of DA and a high concentration of AA in the determination of UA with good selectivity, sensitivity and reproducibility. The modified electrode was also successfully applied for simultaneous determination of UA, DA and AA in their ternary mixture.

RAPID: Resource of Asian Primary Immunodeficiency Diseases

Abstract: Availability of a freely accessible, dynamic and integrated database for primary immunodeficiency diseases (PID) is important both for researchers as well as clinicians. To build a PID informational platform and also as a part of action to initiate a network of PID research in Asia, we have constructed a web-based compendium of molecular alterations in PID, named Resource of Asian Primary Immunodeficiency Diseases ( RAPID), which is available as a worldwide web resource at http://rapid.rcai.riken.jp/. It hosts information on sequence variations and expression at the mRNA and protein levels of all genes reported to be involved in PID patients. The main objective of this database is to provide detailed information pertaining to genes and proteins involved in primary immunodeficiency diseases along with other relevant information about protein-protein interactions, mouse studies and microarray gene-expression profiles in various organs and cells of the immune system. RAPID also hosts a tool, mutation viewer, to predict deleterious and novel mutations and also to obtain mutation-based 3D structures for PID genes. Thus, information contained in this database should help physicians and other biomedical investigators to further investigate the role of these molecules in PID.

Mafic and ultramafic magmatism and associated mineralization in the Dharwar craton, southern India

Abstract: Evidence of mafic and ultramafic magmatism exists in many parts of the Dharwar craton which is divided into two blocks, the West Dharwar Craton (WDC) and the East Dharwar Craton (EDC). The mafic-ultramafic rocks occur in supracrustal/greenstone belts and in numerous enclaves and slivers in the WDC. The oldest recorded maficultramafic rocks, which are mainly komatiitic in nature, are preserved in the Sargur Group which is more than 3.3–3.4 Ga old, the youngest being manifested by 63–76 Ma old mafic dyke magmatism, possibly related to Deccan volcanism.

PathBuilder—open source software for annotating and developing pathway resources

Abstract: Summary: We have developed PathBuilder, an open-source web application to annotate biological information pertaining to signaling pathways and to create web-based pathway resources. PathBuilder enables annotation of molecular events including protein–protein interactions, enzyme–substrate relationships and protein translocation events either manually or through automated importing of data from other databases. Salient features of PathBuilder include automatic validation of data formats, built-in modules for visualization of pathways, automated import of data from other pathway resources, export of data in several standard data exchange formats and an application programming interface for retrieving existing pathway datasets. Availability: PathBuilder is freely available for download at http://pathbuilder.sourceforge.net/ under the terms of GNU lesser general public license (LGPL: http://www.gnu.org/copyleft/lesser.html). The software is platform independent and has been tested on Windows and Linux platforms. Contact: ude.imhj@yednap Supplementary information: Supplementary data are available at Bioinformatics online.

Potential Benefits of Flaxseed in Health and Disease - A Perspective

Abstract: Flaxseed has been known since the Stone Ages. Originating in Mesopotamia, it has long history of use in India and was a commonly used food before World War II. Flaxseed cultivation and popularity declined after the fall of Rome and gradually forgotten until 1990s. Flaxseed oil, lignan precursors and its mucilage have many potential uses in the prevention or treatment of disease as a nutraceutical (drug). Due to several health benefits dietary flaxseed is a valuable strategy to limit several life-style diseases including hormone-responsive tumor, cholesterol-induced atherogenesis as well as abnormalities in endothelialdependent vasorelaxation. As this insightful rediscovery shows, current nutritional understanding provides an excellent opportunity to reintroduce this important food to the world.

Preparation and Evaluation of Nimesulide-loaded Ethylcellulose and Methylcellulose Nanoparticles and Microparticles for Oral Delivery:

Abstract: The present study was designed to assess and compare with a range of surfactant-coated, nimesulide-free, and nimesulide-loaded ethylcellulose/methylcellulose (EC/MC) nanoparticles that were prepared by varying drug concentration (ED/MD), polymer concentration (EP/MP), and surfactant concentration (ES/MS). EC/MC nanoparticles prepared by desolvation method produced discrete particles and they were characterized by SEM, AFM, and FTIR studies. The particles mean size diameter (nm) ranged from 244 to 1056 nm and 1065 to 1710 nm for EC and MC nanoparticles, respectively. Studies on drug: polymer ratio showed a linear relationship between drug concentration and percentage of loading in nanoparticles. The encapsulation efficiency decreased with the increase of nimesulide concentration with respect to polymer concentration. Encapsulation efficiency of drug-loaded nanoparticles was varied between 32.8% and 64.9%. The in vitro release of drug-loaded nanoparticles was found to be a first order. This was significantly increased in EC nanoparticles (95.50%) in comparison with MC nanoparticles (95.12%) after 12 h in 24 h long study. Nimesulide release from EC nanoparticles was much slower at slightly alkaline pH 7.4. The in vitro hemolysis tests of nanoparticles were carried out to ascertain the hemocompatibility and shown to be insignificant for EC nanoparticles. In comparison, ES4 from EC formulations with nimesulide was found to be promising with slow and sustained drug release.

Electrochemical studies of Zn–Ni alloy coatings from acid chloride bath

Abstract: The electrodeposition of Zn–Ni alloy from chloride bath was carried out in presence of condensation product (CP) formed between vanillin and hexamine. The investigation of electrodeposition and nucleation process was carried out on glassy carbon electrode using cyclic voltammetric and chronoamperometric techniques. During the anodic scan of cyclic voltammetry, three anodic peaks were observed corresponding to the dissolution of zinc and nickel from different phases of Zn–Ni alloy. The model of Scharifker and Hills was used to analyze the current transients and it revealed that Zn–Ni electrocrystallization process in the presence of CP, under the studied conditions, is governed by three-dimensional nucleation process controlled by diffusion. In presence of CP, the results indicated that nucleation process changes from progressive to instantaneous when the deposition potential becomes more negative. The phase structure and surface morphology of the deposits were characterized by means of X-ray diffraction analysis and Scanning electron microscopy, respectively.

Carmine and fast green as corrosion inhibitors for mild steel in hydrochloric acid solution

Abstract: The inhibition action of carmine and fast green dyes on corrosion of mild steel in 0.5 M HCl was investigated using mass loss, polarization and electrochemical impedance (EIS) methods at 300 K. The inhibition efficiency was found to increase with increasing concentration of the inhibitors. The inhibition efficiency of fast green (%η - 98) is higher than that of carmine (%η - 92) and found to be maximum in 1 × 10-3 M solution. The inhibitors act as mixed type with predominant cathodic effect. The inhibitors were adsorbed on the mild steel surface according to the Temkin adsorption isotherm. The surface morphology of the mild steel specimens was evaluated using SEM images.

Studies on synthesis and pharmacological activities of 1,2,4-triazolo[3,4-b]1,3,4-thiadiazoles and their dihydro analogues.

Abstract: 4-Amino-5-substituted aryl-3-mercapto-1,2,4-triazoles are versatile synthons for constructing various biologically active heterocycles. Starting from 4-amino-5-substituted aryl-3-mercapto-1,2,4-triazole 3a-c, a series of new 3,5-disubstituted-1,2,4-triazolo-[3,4-b]1,3,4-thiadiazoles and their 5,6-dihydrotriazolothiadiazoles were prepared. The structures of all the newly synthesized compounds have been confirmed by elemental analysis, IR,( 1)H-NMR, (13)C-NMR, and mass spectra. The antimicrobial effects of the synthesized compounds were investigated using the paper disc method. Anti-inflammatory and analgesic activities of the synthesized compounds were assessed by carrageenan-induced rat paw oedema method and by Eddy's hot plate method, respectively. Some of the compounds exhibited promising antimicrobial activities as well as moderate to good anti-inflammatory activity and analgesic activity.

1,2,3-Triazole Fused Quinoline-Peptidomimetics: Studies on Synthesis, DNA Binding and Photonuclease Activity

Abstract: We present, simple approach for the accession of 1,2,3-triazole fused quinoline peptide analogues from 3-(azidomethyl)-2-chloroquinoline in a three-step mechanistic pathway. The UV–Visible absorbance plot shows dynamic interaction of parent triazole derivative with CT DNA as efficient DNA intercalator (K b = 4.6 × 10−4 M−1). Finally, the efficient DNA damage was observed on photo-irradiation at 360 nm in the presence of 2-(9H-Fluoren-9-ylmethoxycarbonylamino)-propionic acid 1-(2-chloro-quinolin-3-ylmethyl)-1H-[1,2,3]triazole-4-ylmethyl ester (6a). We present, simple approach for the accession of 1,2,3-triazole fused quinoline peptide analogues from 3-(azidomethyl)-2-chloroquinoline in a three-step mechanistic pathway. The UV–Visible absorbance plot shows dynamic interaction of parent triazole derivative with CT DNA as efficient DNA intercalator (K b = 4.6 × 10−4). Finally, the efficient DNA damage was observed on photo-irradiation at 360 nm in the presence of 2-(9H-Fluoren-9-ylmethoxycarbonylamino)-propionic acid 1-(2-chloro-quinolin-3-ylmethyl)-1H-[1,2,3]triazole-4-ylmethyl ester (6a).

Prediction of Candidate Primary Immunodeficiency Disease Genes Using a Support Vector Machine Learning Approach

Abstract: Screening and early identification of primary immunodeficiency disease (PID) genes is a major challenge for physicians. Many resources have catalogued molecular alterations in known PID genes along with their associated clinical and immunological phenotypes. However, these resources do not assist in identifying candidate PID genes. We have recently developed a platform designated Resource of Asian PDIs, which hosts information pertaining to molecular alterations, protein-protein interaction networks, mouse studies and microarray gene expression profiling of all known PID genes. Using this resource as a discovery tool, we describe the development of an algorithm for prediction of candidate PID genes. Using a support vector machine learning approach, we have predicted 1442 candidate PID genes using 69 binary features of 148 known PID genes and 3162 non-PID genes as a training data set. The power of this approach is illustrated by the fact that six of the predicted genes have recently been experimentally confirmed to be PID genes. The remaining genes in this predicted data set represent attractive candidates for testing in patients where the etiology cannot be ascribed to any of the known PID genes.

Controlled release of theophylline through semi-interpenetrating network microspheres of chitosan-(dextran-g-acrylamide)

Abstract: Semi-interpenetrating network microspheres of chitosan-(dextran-g-acrylamide) were prepared by emulsion-crosslinking method using glutaraldehyde (GA) as a crosslinking agent. Graft copolymerization of dextran with acrylamide (Dx-g-AAm) was carried out by aqueous free-radical polymerization using ceric ammonium nitrate (CAN) as initiator. The grafting efficiency was found to be 92%. Theophylline (TH), antiasthmatic drug, was successfully encapsulated into semi-INP microspheres by varying the ratio of Dx-g-AAm and amount of GA. The laser light scattering technique shows that the particles size increased with increasing amount of graft copolymer and decrease with increasing amount of GA. The % encapsulation efficiency was found to vary between 50 and 78. MPs were characterized by FTIR spectroscopy and differential scanning calorimetry (DSC) techniques to confirm the graft copolymer, formation of semi-IPN structure of MPs and molecular distribution of the drug molecules in the polymer matrix. In vitro release studies of TH from these matrices have been investigated at Ph 1.2 and 7.4 media and the slow release were extended up to 18 h at 37°C. The release rates were fitted to an empirical equation to estimate the diffusion exponent n, which indicated that the release from the MPs follows non-Fickian type.