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Dinesh Gupta

Publications and source records attributed to Dinesh Gupta.

8 recordsLinked to original sources
PubMed2006

ProtRepeatsDB: a database of amino acid repeats in genomes.

BACKGROUND: Genome wide and cross species comparisons of amino acid repeats is an intriguing problem in biology mainly due to the highly polymorphic nature and diverse functions of amino acid repeats. Innate protein repeats constitute vital functional and structural regions in proteins. Repeats are of great consequence in evolution of proteins, as evident from analysis of repeats in different organisms. In the post genomic era, availability of protein sequences encoded in different genomes provides a unique opportunity to perform large scale comparative studies of amino acid repeats. ProtRepeatsDB http://bioinfo.icgeb.res.in/repeats/ is a relational database of perfect and mismatch repeats, access to which is designed as a resource and collection of tools for detection and cross species comparisons of different types of amino acid repeats. DESCRIPTION: ProtRepeatsDB (v1.2) consists of perfect as well as mismatch amino acid repeats in the protein sequences of 141 organisms, the genomes of which are now available. The web interface of ProtRepeatsDB consists of different tools to perform repeat s; based on protein IDs, organism name, repeat sequences, and keywords as in FASTA headers, size, frequency, gene ontology (GO) annotation IDs and regular expressions (REGEXP) describing repeats. These tools also allow formulation of a variety of simple, complex and logical queries to facilitate mining and large-scale cross-species comparisons of amino acid repeats. In addition to this, the database also contains sequence analysis tools to determine repeats in user input sequences. CONCLUSION: ProtRepeatsDB is a multi-organism database of different types of amino acid repeats present in proteins. It integrates useful tools to perform genome wide queries for rapid screening and identification of amino acid repeats and facilitates comparative and evolutionary studies of the repeats. The database is useful for identification of species or organism specific repeat markers, interspecies variations and polymorphism.

Amino Acid Sequence↗
PubMed2006

Does pretreatment human papillomavirus (HPV) titers predict radiation response and survival outcomes in cancer cervix?--a pilot study.

OBJECTIVE: To evaluate if pretreatment HPV titers in cancer cervix could predict radiation response and survival outcomes. METHODS: Twenty-one patients of cancer cervix were treated by radiotherapy (RT) alone. HPV titers were estimated using DNA Hybrid Capture II test. Loco-regional response at 1 month of RT--complete or partial response (CR and PR respectively) and survival outcomes--local disease-free (LDFS), disease-free (DFS) and overall (OS) survivals were evaluated against pre- and posttreatment HPV titers. RESULTS: Pretreatment HPV titers ranged from 0.81 to 3966.10 RLU/cut off (mean +/- SD: 1264.39 +/- 1148.22, median: 1129.98). Of the demographic features evaluated, mean HPV titers were significantly different only for patients achieving CR or PR at completion of RT (mean +/- SD for CR vs. PR: 1616.31 +/- 1146.86 vs. 384.57 +/- 538.80, P = 0.022). HPV titers at end of RT ranged from 0.12 to 487.42 RLU/cut off (mean +/- SD: 37.31 +/- 108.60, median: 2.33). Patients with higher pretreatment HPV titers (>1000 RLU/cutoff) had a higher CR (P = 0.022) and better survival compared to those with < or =1000 RLU/cutoff (LDFS, P = 0.004; DFS, P = 0.005; OS, P = 0.012). At completion of RT, those having > or =99.5% fall in HPV had superior survival outcomes than those with <99.5% reduction (LDFS, P = 0.002; DFS, P = 0.002; OS, P = 0.004). CONCLUSIONS: Higher pretreatment HPV titers (>1000 RLU/cutoff) could be considered as a predictor of radiotherapy response and survival in cancer cervix. A reduction in these titers to 99.5% of their baseline values at end of radiotherapy is also associated with better survival outcomes.

Brachytherapy↗
PubMed2004

Distribution of proline-rich (PxxP) motifs in distinct proteomes: functional and therapeutic implications for malaria and tuberculosis.

We have conducted a survey of proline-rich (PxxP) motifs in the proteomes of human, mouse, yeast, Mycobacterium tuberculosis and Plasmodium falciparum. Our analyses reveal a strikingly high occurrence of these motifs in each organism, suggesting a wide dependence on protein-protein interaction networks in cellular systems. All proteomes considered have an abundance of PxxP motifs which can potentially participate in binding to SH3 domain-containing proteins. A large fraction of these motifs can be assigned to structurally conserved types of class I and class II sequences. We propose that while maintaining the primary biochemical function, many proteins are likely to participate in additional interactions involving molecular cross-talk with other proteins using proline-rich and other motifs. We have also identified PxxP-containing motifs that are unique to P.falciparum and M.tuberculosis. These sequences may serve as leads for the development of peptidomimics that specifically target these organisms. We propose a novel drug target selection strategy where shared PxxP-containing motifs can be used to direct the development of inhibitors that focus on multiple targets in the cell. Screening for such unique PxxP-containing motifs in the P.falciparum proteome yielded highly conserved sequences in the variant surface antigen family that can be used to initiate design of peptidomimics that may potentially abrogate parasite cytoadherence during malaria infections.

Amino Acid Motifs↗
PubMed2003

PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data.

PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates the recently completed P. falciparum genome sequence and annotation, as well as draft sequence and annotation emerging from other Plasmodium sequencing projects. PlasmoDB currently houses information from five parasite species and provides tools for intra- and inter-species comparisons. Sequence information is integrated with other genomic-scale data emerging from the Plasmodium research community, including gene expression analysis from EST, SAGE and microarray projects and proteomics studies. The relational schema used to build PlasmoDB, GUS (Genomics Unified Schema) employs a highly structured format to accommodate the diverse data types generated by sequence and expression projects. A variety of tools allow researchers to formulate complex, biologically-based, queries of the database. A stand-alone version of the database is also available on CD-ROM (P. falciparum GenePlot), facilitating access to the data in situations where internet access is difficult (e.g. by malaria researchers working in the field). The goal of PlasmoDB is to facilitate utilization of the vast quantities of genomic-scale data produced by the global malaria research community. The software used to develop PlasmoDB has been used to create a second Apicomplexan parasite genome database, ToxoDB (http://ToxoDB.org).

Animals↗
PubMed2002

Is the mitral valve area flow-dependent in mitral stenosis? A dobutamine stress echocardiographic study.

OBJECTIVES: The purpose of this study was to compare the effect of changes in flow rate on the mitral valve area (MVA) derived from two-dimensional echocardiographic planimetry and Doppler pressure half-time (PHT) methods in patients with mitral stenosis (MS). BACKGROUND: Dobutamine stress echocardiography has been proposed as a means of assessing the severity of MS. However, data regarding the effect of an increase in flow rate on MVA are limited. If MVA is indeed flow-dependent, this has important implications for the assessment of the severity of MS, particularly in the setting of reduced cardiac output (CO). METHODS: Dobutamine echocardiography was performed in 57 patients with isolated MS who were in sinus rhythm. The MVA was determined by planimetry and Doppler PHT methods. RESULTS: Cardiac output increased by > or =50% in 27 patients (group I) and by <50% in 30 patients (group II). In group I, the MVA by planimetry increased by only 10.6 +/- 2% and the MVA by PHT increased by 21.9 +/- 4.8%. These changes were similar to those observed in group II (10.7 +/- 3% and 14.8 +/- 4%, respectively; p = NS), despite a much smaller increase in CO. A clinically important change (from the severe to mild category) occurred in only one patient when using the PHT method and in none by planimetry. CONCLUSIONS: Changes in flow rate result in small but clinically insignificant changes in echocardiographic MVA measurement. These methods provide an accurate assessment of MS severity in a majority of patients, independent of changes in flow rate.

Adolescent↗
PubMed2002

PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished).

PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates finished and draft genome sequence data and annotation emerging from Plasmodium sequencing projects. PlasmoDB currently houses information from five parasite species and provides tools for cross-species comparisons. Sequence information is also integrated with other genomic-scale data emerging from the Plasmodium research community, including gene expression analysis from EST, SAGE and microarray projects. The relational schemas used to build PlasmoDB [Genomics Unified Schema (GUS) and RNA Abundance Database (RAD)] employ a highly structured format to accommodate the diverse data types generated by sequence and expression projects. A variety of tools allow researchers to formulate complex, biologically based queries of the database. A version of the database is also available on CD-ROM (Plasmodium GenePlot), facilitating access to the data in situations where Internet access is difficult (e.g. by malaria researchers working in the field). The goal of PlasmoDB is to enhance utilization of the vast quantities of data emerging from genome-scale projects by the global malaria research community.

Animals↗
PubMedDate not supplied

Cholangiocarcinoma presenting with severe gastroparesis and pseudoachalasia.

Tumor-associated gastroparesis, though reported in association with various malignancies, is rare in patients with cholangiocarcinoma. We report a 55-year-old woman who presented with dysphagia and recurrent vomiting. Esophagogastroduodenoscopy revealed dilated stomach and excess residue without organic obstruction. 99mTc sulfur colloid solid gastric emptying study, radio-opaque marker gut transit study, and esophageal manometry showed features suggestive of gastroparesis and achalasia cardia; electrogastrography revealed bradygastria. Cholangiocarcinoma was detected on CT scan performed after the patient developed jaundice two months later. The lesion was deemed surgically unresectable. She died four months later.

Bile Duct Neoplasms↗