Self-organizing maps: A tool to ascertain taxonomic relatedness based on features derived from 16S rDNA sequence.

Exploitation of microbial wealth, of which almost 95% or more is still unexplored, is a growing need. The taxonomic placements of a new isolate based on phenotypic characteristics are now being supported by information preserved in the 16S rRNA gene. However, the analysis of 16S rDNA sequences retrieved from metagenome, by the available bioinformatics tools, is subject to limitations. In this study, the occurrences of nucleotide features in 16S rDNA sequences have been used to ascertain the taxonomic placement of organisms. The tetra- and penta-nucleotide features were extracted from the training data set of the 16S rDNA sequence, and was subjected to an artifi cial neural network (ANN) based tool known as self-organizing map (SOM), which helped in visualization of unsupervised classifi cation. For selection of signifi cant features, principal component analysis (PCA) or curvilinear component analysis (CCA) was applied. The SOM along with these techniques could discriminate the sample sequences with more than 90% accuracy, highlighting the relevance of features. To ascertain the confi dence level in the developed classifi cation approach, the test data set was specifi cally evaluated for Thiobacillus, with Acidiphilium, Paracocus and Starkeya, which are taxonomically reassigned. The evaluation proved the excellent generalization capability of the developed tool. The topology of genera in SOM supported the conventional chemo-biochemical classifi cation reported in the Bergey manual.

Evaluation of BioFM liquid medium for culture of cerebrospinal fluid in tuberculous meningitis to identify Mycobacterium tuberculosis.

The present study was designed to evaluate the sensitivity and specificity of liquid culture medium (BioFM broth) for the diagnosis of tuberculous meningitis (TBM) in cerebrospinal fluid (CSF). CSF samples from 200 patients (TBM group = 150 and non-TBM group = 50) were tested for culture of Mycobacterium tuberculosis in BioFM liquid culture medium. Out of 150 TBM cases, 120 were found to be culture positive, indicating a sensitivity of 80% in BioFM broth within 2-3 weeks of inoculation. Positive cultures were also observed for CSF from 32 (64%) out of 50 non-TBM patients in BioFM liquid culture medium within 4 days of sample inoculation. Therefore, according to our study, BioFM broth system yielded 80% sensitivity [95% confidence interval (CI): 67-93%] and 36% specificity (95% CI: 57-98%) for TBM diagnosis. Our results indicate that although BioFM broth allows the detection of positive cultures within a shorter time, it has a high potential for contamination or for the coexistence of M. tuberculosis and non-tuberculous meningitis (NTM). This coexistence may go undetected or potentially lead to erroneous reporting of results.

Demonstration of IgG antibodies to 30 Kd protein antigen in CSF for diagnosis of tuberculous meningitis by antibody-capturing ELISA.

OBJECTIVE: A simple and rapid immunological assay method has been developed to demonstrate the presence of IgG antibodies to 30Kd protein antigen (30Kdpa) and culture filtrate protein (CFP) in the CSF of patients with Tuberculous meningitis (TBM). METHOD: Antibody capturing Enzyme Linked Immunosorbent Assay (ELISA) was standardized with CFP antigen of MTB. The IgG antibodies were assayed in CSF sample from TBM and non-TBM patients against 30 Kdpa. RESULTS: The sensitivity and specificity of IgG antibodies for the diagnosis of suspected patients of TBM using 30 Kdpa was 80% and 91% respectively and the corresponding figures for CFP were 85% and 94% respectively. The sensitivity and specificity in two confirmed cases of TBM was 100%. CONCLUSION: The presence of this 30Kdpa in the CSF of suspected cases of TBM consistently would indicate that the selected protein band carries the candidate protein marker antigen, which is specific to M. tuberculosis and could be considered as a diagnostic marker for TBM.

Synergistic effect of ayurvedic pearl preparation on enhancing effectiveness of antibiotics.

Studies were carried out with ayurvedic preparations derived from pearl, which include preparations bhasma and pishti. The synergistic effect to reduce the dose of antibiotic was tested against E. coli the test bacterium with ampicillin antibiotic by bore well and disks diffusion methods. It was observed that pearl preparations do not show any antibacterial activity but when used at 200 microg/ml concentration with antibiotics, then even at sub-lethal dose, the antibiotic has effectively shown the results with reduced contact time. The protocol was also tested with the other bacteria like, Pseudomonas aeruginosa. Vibrio cholarae, Salmonella typhi, and Staphylococcus aureus and has shown similar results. The pearl bhasma synergistic effect was also tested with other antibiotics such as erythromycin, kanamycin, and ampicillin.

Cerebellar granule cell membranes and glutamate mediates transactivation of glutamine synthetase promoter.

Potential region of glutamine synthetase promoter driving astrocyte-specific transactivation, mediated by cerebellar granule cell membrane and glutamate has been identified by deletion analysis of promoter and transient transfection. The promoter region from -420 to -765 was found to be potentially important for this transactivation. These results provided further evidence for importance of neuronal-glial and glutamate-glial interactions in regulation of glial gene expression.