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Biomedical subjects

M Biswas

Publications and source records attributed to M Biswas.

At least 19 recordsLinked to original sources
PubMed2001

The InterPro database, an integrated documentation resource for protein families, domains and functional sites.

Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Each InterPro entry includes a functional description, annotation, literature references and links back to the relevant member database(s). Release 2.0 of InterPro (October 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification encoded by a total of 6804 different regular expressions, profiles, fingerprints and Hidden Markov Models. Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1,000,000 hits from 462,500 proteins in SWISS-PROT and TrEMBL). The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. Questions can be emailed to interhelp@ebi.ac.uk.

Databases, Factual↗
PubMed2001

Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes.

The SWISS-PROT group at EBI has developed the Proteome Analysis Database utilising existing resources and providing comparative analysis of the predicted protein coding sequences of the complete genomes of bacteria, archaea and eukaryotes (http://www.ebi.ac. uk/proteome/). The two main projects used, InterPro and CluSTr, give a new perspective on families, domains and sites and cover 31-67% (InterPro statistics) of the proteins from each of the complete genomes. CluSTr covers the three complete eukaryotic genomes and the incomplete human genome data. The Proteome Analysis Database is accompanied by a program that has been designed to carry out InterPro proteome comparisons for any one proteome against any other one or more of the proteomes in the database.

Animals↗
PubMed2000

Focus group discussions in medical research.

Qualitative research methods have recently started to gain popularity in social and health sciences for determining a more holistic view of peoples' perceptions about health. Focus group discussions are frequently used to obtain perspectives and attitudes of people about issues, seek explanations for behavior, triangulate data obtained through other qualitative methods and generate hypotheses. To facilitate clinicians to comprehend the use of focus group methodology in the clinical field, the meaning, purpose, advantages, limitations and quality assurance measures of focus group discussions are described. The general requirements and the method for conducting focus groups are briefly explained. In addition, key issues that could be addressed by focus group methodology have also been highlighted.

Focus Groups↗
PubMed2000

Quantitative vs qualitative research methods.

Quantitative methods have been widely used because of the fact that things that can be measured or counted gain scientific credibility over the unmeasurable. But the extent of biological abnormality, severity, consequences and the impact of illness cannot be satisfactorily captured and answered by the quantitative research alone. In such situations qualitative methods take a holistic perspective preserving the complexities of human behavior by addressing the "why" and "how" questions. In this paper an attempt has been made to highlight the strengths and weaknesses of both the methods and also that a balanced mix of both qualitative as well as quantitative methods yield the most valid and reliable results.

Data Collection↗
PubMed2000

InterPro--an integrated documentation resource for protein families, domains and functional sites.

MOTIVATION: InterPro is a new integrated documentation resource for protein families, domains and functional sites, developed initially as a means of rationalising the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. RESULTS: Merged annotations from PRINTS, PROSITE and Pfam form the InterPro core. Each combined InterPro entry includes functional descriptions and literature references, and links are made back to the relevant parent database(s), allowing users to see at a glance whether a particular family or domain has associated patterns, profiles, fingerprints, etc. Merged and individual entries (i.e. those that have no counterpart in the companion resources) are assigned unique accession numbers. Release 1.2 of InterPro (June 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification (PTMs) encoded by 6581 different regular expressions, profiles, fingerprints and Hidden Markov Models (HMMs). Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1000000 hits from 264333 different proteins out of 384572 in SWISS-PROT and TrEMBL).

Computational Biology↗
PubMed1999

Prognostic role of serum prostatic acid phosphatase for 103Pd-based radiation for prostatic carcinoma.

PURPOSE: To establish the prognostic role of serum enzymatic prostatic acid phosphatase (PAP) in patients treated with palladium (103Pd) and supplemental external beam irradiation (EBRT) for clinically localized, high-risk prostate carcinoma. METHODS AND MATERIALS: One hundred twenty-four consecutive patients with Stage T2a-T3 prostatic carcinoma were treated from 1992 through 1995. Each patient had at least one of the following risk factors for extracapsular disease extension: Stage T2b or greater (100 patients), Gleason score 7-10 (40 patients), pretreatment prostate specific antigen (PSA) >15 ng/ml (32 patients), or elevated serum PAP (25 patients). Patients received 41 Gy conformal EBRT to a limited pelvic field, followed 4 weeks later by a 103Pd boost (prescription dose 80 Gy). Biochemical failure was defined as a PSA greater than 1 ng/ml (normal <4 ng/ml). RESULTS: The overall, actuarial freedom from biochemical failure at 4 years after treatment was 79%. In Cox-proportional hazard multivariate analysis, the strongest predictor of failure was elevated pretreatment acid phosphatase (p = 0.02), followed by Gleason score (p = 0.1), and PSA (p = 0.14). CONCLUSION: PAP was the strongest predictor of long-term biochemical failure. It may be a more accurate indicator of micrometastatic disease than PSA, and as such, we suggest that it be reconsidered for general use in radiation-treated patients.

Acid Phosphatase↗
PubMed1999

A database analysis of potential glycosylating Asn-X-Ser/Thr consensus sequences.

An analysis of the frequency of occurrence of various residues at position X was carried out on the consensus glycosylating sequence Asn-X-Ser/Thr using the PDB three-dimensional database. 488 non-homologous proteins bearing 696 Asn-X-Ser/Thr (X not equal Pro) sequences were analysed. More than 65% of Asn residues, when they occur as part of the consensus sequence, lie on the surface of the protein, implying a potentiality for glycosylation. A deviation parameter (DP) was calculated as a measure of preferential (positive) or non-preferential (negative) selection. At the X position in the consensus-sequence segment, the amino acids Gly, Asn and Phe have statistically significant positive DP values. The high value of DP for Asn is a consequence of the preferential occurrence of homodoublets, while for Phe it may be a consequence of the stacking interaction of the aromatic ring with the glycan. Gly at the X position in the consensus glycosylating sequence may be functionally significant owing to its preference and its high percentage of occurrence in proteins. The Ramachandran (Phi,Psi) angles around Gly in the consensus sequence show clustering in the region which is disallowed for non-glycyl residues. In this region, a hydrogen bond between the side chain of Asn and the peptide backbone/side chain of Ser/Thr is possible, reflecting a positional as well as a conformational role in the consensus glycosylating sequence. For the 44 confirmed N-glycosylating sequences, an in-depth analysis of the (Psi(N), Phi(X), Psi(X), Phi(S/T)) dihedral angles, which position the side chains of Asn and Ser/Thr, shows that these can be grouped into nine conformational states. In most cases, a direct or water-mediated hydrogen bond between OD1 of Asn and OG of Ser/Thr is possible, reflecting the possible importance of this hydrogen bonding in the glycosylation process.

Amino Acid Sequence↗
PubMed1995

Rapid detection of Vibrio cholerae 0139 in faecal specimens by coagglutination.

We compared the conventional culture method with the coagglutination (CoA) test for detecting V. cholerae 0139 antigen in a 4 h faecal enrichment culture. The CoA test reacted positively in all 13 culture positive stool specimens from patients with clinical cholera and negatively in all 23 culture negative specimens from non-diarrhoeal healthy controls. The test also did not show cross reaction with V. cholerae 01 antigen or with any of the enterobacterial antigens of the coliforms. The CoA test was found to be technically simple, rapid and reliable in diagnosing V. cholerae 0139 infection.

Agglutination Tests↗
PubMed1994

Changing bacteriological profile of cholera in Nagpur, 1991-93.

In Nagpur (Maharashtra) during the period 1991-93, Vibrio cholerae serogroup 01 predominated in 1991 (94.7%) and 1992 (86.4%) but significantly declined in 1993 (10.7%). Serogroups 02-0138 were infrequently encountered. A new strain V. cholerae serogroup 0139 emerged in 1993 and accounted for 89.3 per cent of the total vibrios isolated in the year. Replacement of the endemic 01 strain by the new 0139 strain was observed.

Cholera↗
PubMed1993

Atypical desmoid tumor of the abdomen: a case report.

Desmoids are rare lesions that are histologically benign but locally aggressive. These lesions should be considered in patients who present with abdominal masses, particularly if there is a prior history of familial polyposis. This case report describes a patient with an abdominal desmoid that demonstrated atypical features on computed tomography and correlative magnetic resonance images.

Abdominal Neoplasms↗
PubMed1992

Effect of bioamines on uptake of promastigotes of Leishmania donovani by hamster peritoneal macrophages.

Epinephrine and norepinephrine inhibit attachment of Leishmania donovani promastigotes to cultured hamster peritoneal macrophages. The inhibition was significant at catecholamine concentrations of 10(-4) and 10(-5) M and occurred when they were added to the cell mixtures, or after pre-treatment of either macrophages or parasites. Inhibition of attachment after pre-treatment was less marked than when the catecholamines were added to parasite-cell mixtures. Similar results were obtained with dibutyryl cyclic AMP, cholera toxin, theophylline, and cadaverine which raise intracellular cyclic AMP (cAMP). Pretreatment of parasites or macrophages with the bioamines elevated the intracellular cAMP concentration. It is suggested that the inhibitory effect on the host-parasite interaction is mediated through cAMP.

Animals↗
PubMed1991

Quantitation of insulin injection by high-performance liquid chromatography and high-performance capillary electrophoresis.

High-performance capillary electrophoresis (HPCE) was evaluated as a potential technique for the regulatory analysis of commercial dosage forms of insulin. A comparison was made to a liquid chromatographic analysis presently being proposed as an official monograph in the United States Pharmacopeia. The salient points of this comparison were accuracy, precision and ease of use. Both authentic (i.e. single blind, spiked) samples and commercial pharmaceutical formulations (injections) were examined. Chromatographic analyses of both commercial formulations and authentic samples were characterized by good precision, with accuracy being supported by results from authentic (spiked) samples. Conventional HPCE (by which is meant a non-micellar electrolyte used with an uncoated, unmodified fused-silica capillary) achieved reasonable accuracy, but less than impressive precision, when applied to authentic samples. When used for commercial formulations, this type of HPCE did not produce a level of accuracy suitable for regulatory purposes, even with the use of an internal standard.

Animals↗
PubMed1991

Isolation of a phosphoryl choline-binding protein from the hemolymph of the snail, Achatina fulica.

A phosphorylcholine-binding protein from the hemolymph of the snail Achatina fulica was purified to near homogeneity using a Sepharose phenylphosphorylcholine affinity column. The protein bound to the affinity column was eluted with 5 mM phosphorylcholine as a single symmetrical peak. The purified protein (400 Kda) contained 35-40% carbohydrate. On SDS-PAGE the protein separated into two bands of 20 and 24 Kda, and had a pI of 5.9. On immunodiffusion, antiserum to the snail phosphorylcholine binding protein did not cross-react against other phosphorylcholine binding proteins, like rat serum phosphorylcholine-binding protein (PCBP), limulus C-reactive protein (CRP), or human CRP. On pretreatment of the snail hemolymph with this antiserum, the hemagglutination titer of the hemolymph was markedly decreased. The purified snail phosphorylcholine binding protein agglutinated rabbit erythrocytes in the absence of divalent cation (Ca+2) but trace amount of Ca+2 increased its binding. The strongest inhibitor of the agglutination reaction was lactose, followed by melibiose and 2-deoxygalactose. The relationships of the snail phosphorylcholine binding protein to other hemolymph agglutinins and to CRPs are discussed in light of common phylogeny.

Animals↗
PubMed1990

Total serum glycosylated proteins in detection and monitoring of gestational diabetes.

The goal of this study was to determine whether serum glycosylated protein levels (i.e., fructosamine) can reliably screen for gestational diabetes and whether these levels are valid markers of short-term glycemic control in the third trimester of pregnancy. Ninety-seven pregnant women at 26-28 wk gestation were evaluated over 9 mo. HbA1c and serum glycosylated protein (serum fructosamine) were determined at the baseline venipuncture of the 100-g oral glucose tolerance test performed to detect gestational diabetes. Of the 97 women studied, 13 tested positive for gestational diabetes (National Diabetes Data Group criteria). There were significant differences in the fasting and 1-, 2-, and 3-h glucose values between nondiabetic and diabetic patients (P less than 0.005 at each time point). No difference was noted in the baseline serum glycosylated protein level (2.02 +/- 0.08 vs. 1.98 +/- 0.02 mM, NS) or HbA1c level (4.42 +/- 0.2 vs. 4.6 +/- 0.3%, NS) between gestational and nondiabetic patients. Diabetic patients were followed at 2-wk intervals, with serum glycosylated protein analysis, HbA1c, fasting glucose, and mean glucose determined by outpatient monitoring. Serum glycosylated protein correlated significantly to fasting blood glucose (r = 0.81, P less than 0.001) and mean outpatient glucose (r = 0.62, P less than 0.001) at the 2-wk follow-up visits. No correlation was found between HbA1c and fasting blood glucose (r = 0.11, NS) or mean outpatient glucose (r = -0.12, NS) during the follow-up period. The serum glycosylated protein level (serum fructosamine) is not a useful screening test for gestational diabetes. However, this assay shows potential as an objective marker of short-term control in evaluating the maternal glycemic state.

Adolescent↗
PubMed1987

The conformation of glycans of the oligo-D-mannosidic type, and their interaction with concanavalin A: a computer-modelling study.

The favored conformations of glycans of the oligo-D-mannosidic type have been determined by using empirical energy calculations. An interesting aspect is that the alpha-(1----3)-linked terminal D-mannose residue of the outer trimannosidic core fragment, in all the conformations which fall within 5 kcal.mol-1 of the global minimum, always lies close to the chitobiose core. These models are in general agreement with the available n.m.r. data. The probable modes of binding of these glycans to concanavalin A (Con A) were determined, by using a computer-modelling technique which identifies the positions for the different conformers of the carbohydrate in the binding site of Con A, based on stereochemical considerations. These studies showed that Con A can bind only to two of the three terminal D-mannose residues in these glycans, because the D-mannose residue which lies close to the chitobiose core is inaccessible for the binding of Con A. Of these two terminal D-mannose residues, the alpha-(1----6)-linked D-mannose may bind the more strongly. Furthermore, it is shown that the internal D-mannose residue will, at best, interact very weakly with the carbohydrate-binding site of Con A. These results rationalize well the available data on the binding affinity of these glycans to Con A. They further support the conclusion that the binding affinity of a glycan to Con A does not depend on the number in the glycan, of D-mannose residues which possess free 3-, 4-, and 6-hydroxyl groups, but, rather, on the accessibility of these residues to Con A.

Carbohydrate Conformation↗
PubMed1987

Effect of lapachol, a naphthaquinone isolated from Tectona grandis, on experimental peptic ulcer and gastric secretion.

Lapachol, a naphthaquinone isolated from the roots of Tectona grandis given at a dose of 5 mg kg-1 p.o. twice daily for 3 days was found to have an anti-ulcerogenic effect on subsequently induced experimental gastric and duodenal ulcers in rats and guinea-pigs. Its action appears to be associated with an effect on the protein content of gastric juice, and it reversed aspirin-induced changes in peptic activity, protein and sialic acid.

Animals↗