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Biomedical subjects

S Sujatha

Publications and source records attributed to S Sujatha.

At least 19 recordsLinked to original sources
PubMed2003

Co-infection with hepatitis C virus and human immunodeficiency virus among patients with sexually transmitted diseases in Pondicherry, South India.

Hepatitis C virus (HCV), which is usually transmitted by blood and blood products is emerging as an important agent in the list of sexually transmitted diseases (STDs). The present study was undertaken to document the burden of HCV infection in individuals with STDs in this tertiary care hospital in South India. One hundred serum samples collected from individuals with STDs were tested for antibodies to HCV by a third generation ELISA. All the samples were also screened for HIV infection. Six out of 100 individuals were found to possess antibodies against HCV (95% confidence interval [CI=1.3-10.7%). Fourteen out of 100 samples were positive for HIV (95% CI=7-20.9%). The seroprevalence of HCV in HIV positive individuals was 21.4% (3/14) whereas the corresponding figure for HIV negative individuals was only 3.5% (3/86). The difference was found to be statistically significant (p<0.01).

Adolescent↗
PubMed2002

SUPFAM--a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes.

Members of a superfamily of proteins could result from divergent evolution of homologues with insignificant similarity in the amino acid sequences. A superfamily relationship is detected commonly after the three-dimensional structures of the proteins are determined using X-ray analysis or NMR. The SUPFAM database described here relates two homologous protein families in a multiple sequence alignment database of either known or unknown structure. The present release (1.1), which is the first version of the SUPFAM database, has been derived by analysing Pfam, which is one of the commonly used databases of multiple sequence alignments of homologous proteins. The first step in establishing SUPFAM is to relate Pfam families with the families in PALI, which is an alignment database of homologous proteins of known structure that is derived largely from SCOP. The second step involves relating Pfam families which could not be associated reliably with a protein superfamily of known structure. The profile matching procedure, IMPALA, has been used in these steps. The first step resulted in identification of 1280 Pfam families (out of 2697, i.e. 47%) which are related, either by close homologous connection to a SCOP family or by distant relationship to a SCOP family, potentially forming new superfamily connections. Using the profiles of 1417 Pfam families with apparently no structural information, an all-against-all comparison involving a sequence-profile match using IMPALA resulted in clustering of 67 homologous protein families of Pfam into 28 potential new superfamilies. Expansion of groups of related proteins of yet unknown structural information, as proposed in SUPFAM, should help in identifying 'priority proteins' for structure determination in structural genomics initiatives to expand the coverage of structural information in the protein sequence space. For example, we could assign 858 distinct Pfam domains in 2203 of the gene products in the genome of Mycobacterium tubercolosis. Fifty-one of these Pfam families of unknown structure could be clustered into 17 potentially new superfamilies forming good targets for structural genomics. SUPFAM database can be accessed at http://pauling.mbu.iisc.ernet.in/~supfam.

Animals↗
PubMed2001

PALI-a database of Phylogeny and ALIgnment of homologous protein structures.

PALI (release 1.2) contains three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of homologous protein domains in various families. The data set of homologous protein structures has been derived by consulting the SCOP database (release 1.50) and the data set comprises 604 families of homologous proteins involving 2739 protein domain structures with each family made up of at least two members. Each member in a family has been structurally aligned with every other member in the same family (pairwise alignment) and all the members in the family are also aligned using simultaneous super-position (multiple alignment). The structural alignments are performed largely automatically, with manual interventions especially in the cases of distantly related proteins, using the program STAMP (version 4.2). Every family is also associated with two dendrograms, calculated using PHYLIP (version 3.5), one based on a structural dissimilarity metric defined for every pairwise alignment and the other based on similarity of topologically equivalent residues. These dendrograms enable easy comparison of sequence and structure-based relationships among the members in a family. Structure-based alignments with the details of structural and sequence similarities, superposed coordinate sets and dendrograms can be accessed conveniently using a web interface. The database can be queried for protein pairs with sequence or structural similarities falling within a specified range. Thus PALI forms a useful resource to help in analysing the relationship between sequence and structure variation at a given level of sequence similarity. PALI also contains over 653 'orphans' (single member families). Using the web interface involving PSI_BLAST and PHYLIP it is possible to associate the sequence of a new protein with one of the families in PALI and generate a phylogenetic tree combining the query sequence and proteins of known 3-D structure. The database with the web interfaced search and dendrogram generation tools can be accessed at http://pauling.mbu.iisc.ernet. in/ approximately pali.

Databases, Factual↗
PubMed2001

Functional complementation between mutations at two distant positions in Escherichia coli RNA polymerase as revealed by second-site suppression.

Subunit-subunit interactions are critical for the assembly of the core of Escherichia coli RNA polymerase. The mutant alpha-subunit C131A is unable to complement the temperature-sensitive alpha-R45C mutant strain, which is defective for binding of the beta-subunit. In vitro reconstitution experiments, however, indicate that the alpha-C131A variant is able to form the intermediate alpha2beta, but is defective in contacting the beta'-subunit. We used this alpha-C131A mutant to isolate a suppressor mutation in the beta'-subunit. Genetic and biochemical characterization of the beta' suppressor indicates the allele-specific nature of its effect. Sequence analysis of the suppressor revealed a single substitution of Gly at position 333, an evolutionarily conserved position in the conserved region C of the beta'-subunit, by Asp. However, the crystal structure of the bacterial RNA polymerase indicates that the primary mutation (alpha-C131A) and its suppressor lie far apart. Thus, we propose that long-range interactions, as in this case, may play an important role in the functional assembly of E. coli RNA polymerase.

Amino Acid Sequence↗
PubMed2001

PALI: a database of alignments and phylogeny of homologous protein structures.

PALI is a database of structure-based sequence alignments and phylogenetic relationships derived on the basis of three-dimensional structures of homologous proteins. This database enables grouping of pairs of homologous protein structures on the basis of their sequence identity calculated from the structure-based alignment and PALI also enables association of a new sequence to a family and automatic generation of a dendrogram combining the query sequence and homologous protein structures.

Databases, Factual↗
PubMed2001

Molecular modelling of epitope presentation using membrane protein OmpC.

Three-dimensional models of the chimeric S. typhi OmpC protein carrying an epitope from rotavirus VP4 capsid protein on either of two exposed loops (fourth and sixth) were constructed separately, using computer-aided homology modelling. The theoretical model of S. typhi OmpC was used as a template. The monomers were initially energy minimized. The trimers were generated for both the chimeric S. typhi OmpC proteins and the structures were optimized after several cycles of minimization. The surface accessibility calculations for the resulting models show that epitope recognition should be more effective in the fourth loop than in the sixth loop, in accordance with the experimental results on the immunogenic nature of the rotaviral epitope inserted into the two putative loops of S. typhi OmpC.

Amino Acid Sequence↗
PubMed1999

Detection of putative Zn(II) binding sites within Escherichia coli RNA polymerase: inconsistency between sequence-based prediction and 65Zn blotting.

The availability of repeating 'Cys' and/or 'His' units in a particular order prompts the prediction of Zn(II) finger motifs in a protein. Escherichia coli RNA polymerase has two tightly bound Zn(II) per molecule of the enzyme as detected by atomic absorption spectroscopy. One Zn(II) was identified to be at the beta subunit, whereas the other putative Zn(II) binding site has recently been predicted to be at the N-terminal half of the beta' subunit, from primary sequence analysis. We show here that the beta' subunit has no ability to bind 65Zn(II). On the other hand, the N-terminal domain of the alpha subunit has strong Zn(II) binding ability with no obvious functional implications.

Amino Acid Sequence↗
PubMed1998

Corneal endothelial specular microscopy following deep lamellar keratoplasty with lyophilised tissue.

PURPOSE: To assess the corneal endothelial cell density following deep lamellar keratoplasty (DLK) carried out by air dissection and with the transplantation of lyophilised tissue. METHOD: Contact endothelial specular microscopy was carried out on a series of patients who had undergone DLK with a minimum of 1 year post-operative follow-up. RESULTS: Twenty eyes of 18 patients were examined at follow-up times ranging from 1 to 8 years post-operatively (mean 3 years). Indications for surgery were: keratoconus (n = 12), herpes simplex virus (HSV) keratitis (n = 1), herpes zoster ophthalmicus (HZO) keratitis (n = 1), lipid keratopathy (n = 2), lattice dystrophy (n = 1) and corneal scarring (n = 3). Overall, mean post-operative cell density was 2417 cells/mm2 (range 928-3656 cells/mm2). In eyes with pathological conditions not likely to have affected the endothelial cell density, such as keratoconus or lattice degeneration, the mean cell density was 2837 cells/mm2 (range 1030-3656 cells/mm2). CONCLUSIONS: In patients undergoing DLK for conditions such as keratoconus the post-operative cell density was at a normal level in the majority of cases. Cell loss through this surgical intervention thus appears generally to be small. The prospect for long-term survival of these grafts is good.

Adolescent↗
PubMed1988

Effect of cobra and viper venoms on alpha 2-macroglobulin activity in human, bovine, and goat sera.

Incubation of human serum with cobra or viper venoms (10 micrograms/0.1 ml serum) caused negligible decrease in total protease inhibitory activity whereas alpha 2-macroglobulin activity was reduced by 67.0-82.0% in 16 hr. The action of venoms on MG activity was time dependent. Human alpha 2-macroglobulin activity was reduced to a much greater extent than goat or bovine factors by the venoms. While 25 micrograms venoms/0.1 ml serum caused 60-100% inhibition of human alpha 2-macroglobulin activity, the bovine factor was not affected under similar conditions. Goat alpha 2-macroglobulin was affected to the extent of 0-20%. Evidence is provided to show that venom proteases generate endogenous proteases in situ in human plasma or serum which in turn bind to alpha 2-macroglobulin. The venom-mediated action was abolished by prior dialysis of the serum or its dilution. Ethylenediaminetetraacetate at 10(-3) M concentration also blocked the reaction. While phenylmethylsulfonyl fluoride had no effect, pepstatin in the concentration range 10(-2) to 10(-3) M caused partial inhibition of the venom-mediated inhibition of alpha 2-macroglobulin activity in human serum.

Animals↗
PubMedDate not supplied

An outbreak of typhoid due to multidrug resistant Salmonella typhi in Pondicherry.

An outbreak of typhoid due to multi-drug resistant Salmonella typhi is reported from Pondicherry, India. While the average prevalence of drug resistant strains in 1980-1988 had been 11.7%, it increased to 52% in 1989-1990. The majority of strains (80.8%) were resistant to chloramphenicol, streptomycin, tetracycline and ampicillin; 40% were resistant to co-trimoxazole. Minimum inhibitory concentrations to 8 antibiotics for 17 representative strains were more than 10-fold greater than those of 13 sensitive strains. The multi-resistance was shown to be plasmid mediated in direct conjugation experiments and the strains belonged to Viphage type O, biotype II.

Chloramphenicol Resistance↗