Allam Appa Rao

Gene expression profile in obesity and type 2 diabetes mellitus

Obesity is an important component of metabolic syndrome X and predisposes to the development of type 2 diabetes mellitus. The incidence of obesity, type 2 diabetes mellitus and metabolic syndrome X is increasing, and the cause(s) for this increasing incidence is not clear. Although genetics could play an important role in the higher prevalence of these diseases, it is not clear how genetic factors interact with environmental and dietary factors to increase their incidence. We performed gene expression profile in subjects with obesity and type 2 diabetes mellitus with and without family history of these diseases. It was noted that genes involved in carbohydrate, lipid and amino acid metabolism pathways, glycan of biosynthesis, metabolism of cofactors and vitamin pathways, ubiquitin mediated proteolysis, signal transduction pathways, neuroactive ligand-receptor interaction, nervous system pathways, neurodegenerative disorders pathways are upregulated in obesity compared to healthy subjects. In contrast genes involved in cell adhesion molecules, cytokine-cytokine receptor interaction, insulin signaling and immune system pathways are downregulated in obese. Genes involved in signal transduction, regulation of actin cytoskeleton, antigen processing and presentation, complement and coagulation cascades, axon guidance and neurodegenerative disorders pathways are upregulated in subjects with type 2 diabetes with family history of diabetes compared to those who are diabetic but with no family history. Genes involved in oxidative phosphorylation, immune, nervous system, and metabolic disorders pathways are upregulated in those with diabetes with family history of diabetes compared to those with diabetes but with no family history. In contrast, genes involved in lipid and amino acid pathways, ubiquitin mediated proteolysis, signal transduction, insulin signaling and PPAR signaling pathways are downregulated in subjects with diabetes with family history of diabetes. It was noted that genes involved in inflammatory pathway are differentially expressed both in obesity and type 2 diabetes. These results suggest that genes concerned with carbohydrate, lipid and amino acid metabolic pathways, neuronal function and inflammation play a significant role in the pathobiology of obesity and type 2 diabetes.

Techniques for integrating -omics data.

The challenge for -omics research is to tackle the problem of fragmentation of knowledge by integrating several sources of heterogeneous information into a coherent entity. It is widely recognized that successful data integration is one of the keys to improve productivity for stored data. Through proper data integration tools and algorithms, researchers may correlate relationships that enable them to make better and faster decisions. The need for data integration is essential for present ‐omics community, because ‐omics data is currently spread world wide in wide variety of formats. These formats can be integrated and migrated across platforms through different techniques and one of the important techniques often used is XML. XML is used to provide a document markup language that is easier to learn, retrieve, store and transmit. It is semantically richer than HTML. Here, we describe bio warehousing, database federation, controlled vocabularies and highlighting the XML application to store, migrate and validate -omics data.

Views and opinion on BDNF as a target for diabetic cognitive dysfunction

Type 2 diabetes mellitus (T2DM) is a known cause of cognitive dysfunction and involves increased risk of dementia. Brain-derived neurotrophic factor (BDNF) is a member of neurotrophic family of nerve growth factors, a key protein in promoting memory, growth and survival of neurons. BDNF is recognized as a metabotrophic factor, a molecule that is involved in Alzheimer’s disease (AD) as well as in other neurological disorders. It provides cellular and local regulatory mechanisms for mediating synaptic plasticity. Impaired BDNF signaling can compromise many aspects of brain functions. Studies investigating the relationship between diabetes and BDNF in adults demonstrate that BDNF levels are decreased in T2DM and are regulated in response to plasma levels of glucose. BDNF could serve as biomarker in predicting the development of obesity and T2DM. Thirty-two cavities were predicted to locate the active sites of BDNF for the ligands to bind. The shape of the site was identified by extracting the cavity volume surfaces enclosing regions with highest probability. Different ligands can be chosen for interaction of active sites of BDNF and can be targeted for drug discovery. This review focuses on computational exploitation selectively to deliver BDNF as a drug to appropriate hypothalamic neurons, which can serve as a novel approach in diabetic encephalopathy treatment.

Quality of care: assessment

To translate science into clinical practice we must first assess the quality of care that is being delivered. The resulting information about qualitative and quantitative parameters can then be assessed. Ultimately insights can be obtained into improving the quality of care in diabetes mellitus. The Diabetes Quality Improvement Programme in USA has shown such an exercise is feasible. A similar exercise in India is necessary to improve the quality of diabetes care.

Enhanced Butyrylcholinesterase Activity may be the Common Link in Triggering Low-Grade Systemic Inflammation and Decrease in Cognitive Function in Diabetes Mellitus and Alzheimers disease

There is increasing evidence that diabetes mellitus and Alzheimers disease occur more often than by chance. Recently, we proposed that increase in the activity of the enzyme butyrylcholinesterase could be a common link between these two conditions. Acetylcholine is an anti-inflammatory molecule. Butyrylcholinesterase by inactivating acetylcholine may enhance inflammation and induce decline in cognitive function. In the present study, it was noted that streptozotocin- induced diabetic animals showed dyslipidemia, increase in plasma lipid peroxides, decrease in circulating plasma superoxide dismutase activity, decline in cognitive function as assessed by the Morris water maze method, and a significant increase in serum butyrylcholinesterase activity. These results suggest that increased plasma and, possibly, tissue concentrations of butyrylcholinesterase lead to decrease in acetylcholine levels, an anti-inflammatory molecule, which may trigger low-grade systemic inflammation in diabetes mellitus and Alzheimers disease that could account for decline in cognitive function.

G-IMEx: A comprehensive software tool for detection of microsatellites from genome sequences.

Microsatellites are ubiquitous short tandem repeats found in all known genomes and are known to play a very important role in various studies and fields including DNA fingerprinting, paternity studies, evolutionary studies, virulence and adaptation of certain bacteria and viruses etc. Due to the sequencing of several genomes and the availability of enormous amounts of sequence data during the past few years, computational studies of microsatellites are of interest for many researchers. In this context, we developed a software tool called Imperfect Microsatellite Extractor (IMEx), to extract perfect, imperfect and compound microsatellites from genome sequences along with their complete statistics. Recently we developed a user-friendly graphical-interface using JAVA for IMEx to be used as a stand-alone software named G-IMEx. G-IMEx takes a nucleotide sequence as an input and the results are produced in both html and text formats. The Linux version of G-IMEx can be downloaded for free from http://www.cdfd.org.in/imex

Agonistic approach of omega-3, omega-6 and its metabolites with BDNF: An in-silico study.

Brain derived neurotrophic factor (BDNF) is a member of neurotrophic family of growth factors, mainly found in the hippocampus and cerebral cortex of brain. Studies have shown that there is a link between BDNF and cognitive dysfunction, as well as there is a relationship between the PUFAs intake and their effect on BDNF production. Intake of PUFAs, mainly omega-3 and omega-6 has show increase in production of BDNF in brain. In our study we performed docking studies on PUFAs and their metabolites with BDNF using MVD (Molegro Virtual Docker), this has shown that the metabolites of the PUFAs mainly LXA_4, NPD1, HDHA have shown more binding affinity towards BDNF. These metabolites of PUFAs are responsible for modulation of BDNF activity.

Comparative analysis of microsatellite detecting software: a significant variation in results and influence of parameters

Microsatellites are a unique type of repeat patterns found in genome sequences of all known organisms including bacteria and viruses. These repeats play an important role in genome evolution, are associated with various diseases, have been used as molecular markers in DNA Fingerprinting, Population Genetics etc. Various bioinformatics tools have been developed for extraction of microsatellites from DNA sequences. However, not all tools can identify microsatellites with similar sensitivities and hence studies on microsatellites can suffer from significant biases in results and interpretations depending on the type of tool used. In order to get a clear idea on inherent limitations and biases with regard to extraction of microsatellites especially under the influence of varying threshold values of program parameters we carried out a comparative analysis of performance of some of the widely used tools using some test DNA sequences. We extracted imperfect microsatellites from three different sequences (E. coli bacterial genome, C. elegans Chromosome I and Drosophila Chromosome X) using the commonly used microsatellite extraction tools TRF, Sputnik, SciRoKoCo and IMEx with varying parameters and analyzed the results. We observed a significant variation in the number of microsatellites extracted by these tools even when used with default / suggested parameters. Relaxation of parameter values lead to an increase in the number of repeats detected but still the differences among the results persist. In TRF, Sputnik and SciRoKoCo it was observed that the number of mismatches increases with the increase in the tract length of the repeat indicating the level of imperfection is not uniform throughout the repeats. The four tools investigated in this study differ in their algorithms, in the parameters they use and hence in the number of microsatellites detected. The score based programs identify more number of divergent penta and hexa nucleotide repeats than IMEx. We therefore suggest that it is prudent to alter parameters appropriately to detect as many microsatellites as possible as a means not to miss any genuine repeat tracts or to use more than one tool as a means to get a good consensus. We also made a detailed survey of the available features of all microsatellite extraction tools. Apart from differences in their algorithm, efficiency and parameters, the tools also differ largely in terms of the features and flexibility.

Development and Validation of LC Method for the Determination of Famciclovir in Pharmaceutical Formulation Using an Experimental Design

A rapid and sensitive RP-HPLC method with UV detection (242 nm) for routine analysis of famciclovir in pharmaceutical formulations was developed. Chromatography was performed with mobile phase containing a mixture of methanol and phosphate buffer (50:50, v/v) with flow rate 1.0 mL min−1. Quantitation was accomplished with internal standard method. The procedure was validated for linearity (correlation coefficient =0.9999), accuracy, robustness and intermediate precision. Experimental design was used for validation of robustness and intermediate precision. To test robustness, three factors were considered; percentage v/v of methanol in mobile phase, flow rate and pH; flow rate, the percentage of organic modifier and pH have considerable important effect on the response. For intermediate precision measure the variables considered were: analyst, equipment and number of days. The RSD value (0.86%, n=24) indicated an acceptable precision of the analytical method. The proposed method was simple, sensitive, precise, accurate and quick and useful for routine quality control.

Proteomic Analysis in Diabetic Cardiomyopathy using Bioinformatics Approach

Diabetic cardiomyopathy is a distinct clinical entity that produces asymptomatic heart failure in diabetic patients without evidence of coronary artery disease and hypertension. Abnormalities in diabetic cardiomyopathy include: myocardial hypertrophy, impairment of contractile proteins, accumulation of extracellular matrix proteins, formation of advanced glycation end products, and decreased left ventricular compliance. These abnormalities lead to the most common clinical presentation of diabetic cardiomyopathy in the form of diastolic dysfunction. We evaluated the role of various proteins that are likely to be involved in diabetic cardiomyopathy by employing multiple sequence alignment using ClustalW tool and constructed a Phylogenetic tree using functional protein sequences extracted from NCBI. Phylogenetic tree was constructed using Neighbour—Joining Algorithm in bioinformatics approach. These results suggest a causal relationship between altered calcium homeostasis and diabetic cardiomyopathy that implies that efforts directed to normalize calcium homeostasis could form a novel therapeutic approach.