A5085789773- Tuberculosis Research and Epidemiology
- Computational Drug Discovery Methods
- Bioinformatics and Genomic Networks
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Mycobacterium research and diagnosis
- Biochemical and Molecular Research
- Enzyme Structure and Function
- vaccines and immunoinformatics approaches
- Microbial Metabolic Engineering and Bioproduction
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Gene Regulatory Network Analysis
- Bacterial Genetics and Biotechnology
- Glycosylation and Glycoproteins Research
- Immunotherapy and Immune Responses
- Monoclonal and Polyclonal Antibodies Research
- Bacteriophages and microbial interactions
- Carbohydrate Chemistry and Synthesis
- Antibiotic Resistance in Bacteria
- Biochemical and Structural Characterization
- Toxin Mechanisms and Immunotoxins
- Epigenetics and DNA Methylation
- T-cell and B-cell Immunology
- Cancer therapeutics and mechanisms
Indian Institute of Science Bangalore
2015-2024
All India Institute of Medical Sciences
2024
Areté Associates (United States)
2023
Bangalore University
2015-2018
Weatherford College
2009
Sify Technologies (India)
2006
University of Madras
2006
Indian Institute of Technology Madras
2001
University of Leicester
1999
University of Bath
1999
Systems level modelling and simulations of biological processes are proving to be invaluable in obtaining a quantitative dynamic perspective various aspects cellular function. In particular, constraint-based analyses metabolic networks have gained considerable popularity for simulating metabolism, which flux balance analysis (FBA), is most widely used. Unlike mechanistic that depend on accurate kinetic data, scarcely available, FBA based the principle conservation mass network, utilizes...
Abstract Background Tuberculosis still remains one of the largest killer infectious diseases, warranting identification newer targets and drugs. Identification validation appropriate for designing drugs are critical steps in drug discovery, which at present major bottle-necks. A majority current clinical use many diseases have been designed without knowledge targets, perhaps because standard methodologies to identify such a high-throughput fashion do not really exist. With different kinds...
Recognizing similarities and deriving relationships among protein molecules is a fundamental requirement in present-day biology. Similarities can be present at various levels which detected through comparison of sequences or their structural folds. In some cases obscure these could merely the substructures binding sites. Inferring functional between by comparing sites still largely exploratory not as yet routine protocol. One main reasons for this limitation choice appropriate analytical...
There is a pressing need for new therapeutics to combat multidrug- and carbapenem-resistant bacterial pathogens. This challenge prompted us use long short-term memory (LSTM) language model understand the underlying grammar, i.e. arrangement frequencies of amino acid residues, in known antimicrobial peptide sequences. According output our LSTM network, we synthesized 10 peptides tested them against All these displayed broad-spectrum activity, validating LSTM-based design approach. Our two...
Ω76 is a promising drug with remarkably low toxicity, which may be used in the future for treating highly resistant infections.
Moxifloxacin is central to treatment of multidrug-resistant tuberculosis. Effects moxifloxacin on the Mycobacterium tuberculosis redox state were explored identify strategies for increasing lethality and reducing prevalence extensively resistant A noninvasive biosensor a reactive oxygen species (ROS)-sensitive dye revealed that induces oxidative stress correlated with M. death. was mitigated by supplementing bacterial cultures an ROS scavenger (thiourea), iron chelator (bipyridyl), and,...
Mycobacterium tuberculosis is the focus of several investigations for design newer drugs, as remains a major epidemic despite availability drugs and vaccine. Mycobacteria owe many their unique qualities to mycolic acids, which are known be important growth, survival, pathogenicity. Mycolic acid biosynthesis has therefore been number biochemical genetic studies. It also turns out pathway inhibited by front-line anti-tubercular such isoniazid ethionamide. Recent years have seen emergence...
Emergence of drug resistant varieties tuberculosis is posing a major threat to global eradication programmes. Although several approaches have been explored counter resistance, there has limited success due lack understanding how resistance emerges in bacteria upon treatment. A systems level analysis the proteins involved essential gain insights into routes required for emergence resistance. We derive genome-scale protein-protein interaction network Mycobacterium H37Rv from STRING database,...
Understanding channel structures that lead to active sites or traverse the molecule is important in study of molecular functions such as ion, ligand, and small transport. Efficient methods for extracting, storing, analyzing protein channels are required support studies. Further, there a need an integrated framework supports computation channels, interactive exploration their structure, detailed visual analysis properties. We describe method extraction based on alpha complex representation....
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We report the whole genome sequences of a Mycobacterium smegmatis laboratory wild-type strain (MC(2) 155) and mutants (4XR1, 4XR2) resistant to isoniazid. Compared MC(2) 155 (NC_008596), widely used in experiments, 155, 4XR1, 4XR2 strains are 60, 128 93 bp longer, respectively.
We isolated an 8 kDa mycobacterial hypothetical protein, Rv3423.1, from the chromatin of human macrophages infected with Mycobacterium tuberculosis H37Rv. Bioinformatics predictions followed by in vitro biochemical assays purified recombinant protein showed that Rv3423.1 is a novel histone acetyltransferase acetylates H3 at K9/K14 positions. Transient transfection containing GFP ‐tagged H1 RFP revealed co‐localizes nucleus. Co‐immunoprecipitation confirmed Rv3423.1–histone interaction...
Tuberculosis remains a major global health challenge worldwide, causing more than million deaths annually. To determine newer methods for detecting and combating the disease, it is necessary to characterise host responses infection. Several high throughput omics studies have provided rich resource including list of several genes differentially regulated in tuberculosis. An integrated analysis these identify unified response Such data integration met with challenges owing platform dependency,...
Lectins are known to be important for many biological processes, due their ability recognize cell surface carbohydrates with high specificity. Plant lectins have been model systems study protein–carbohydrate recognition, because individually they exhibit sensitivity and as a group large diversity in recognizing carbohydrate structures. Although extensive studies carried out legume that led interesting insights into the sequence determinants of sugar recognition them, frameworks such specific...
In the post-genomic era where sequences are being determined at a rapid rate, we highly reliant on computational methods for their tentative biochemical characterization. The Pfam database currently contains 3,786 families corresponding to "Domains of Unknown Function" (DUF) or "Uncharacterized Protein Family" (UPF), which 3,087 have no reported three-dimensional structure, constituting almost one-fourth known protein in search both structure and function.We applied 'computational structural...
The prokaryotic ubiquitous Toxin-antitoxin (TA) modules encodes for a stable toxin and an unstable antitoxin. VapBC subfamily is the most abundant Type II TA system in M. tuberculosis genome. However, exact physiological role of these systems are still unknown. Here, we have comprehensively characterized VapBC21 locus from tuberculosis. overexpression VapC21 inhibited mycobacterial growth bacteriostatic manner as expected, inhibition was abrogated upon co-expression cognate antitoxin,...