SNP genotyping by the 5'-nuclease reaction: advances in high-throughput genotyping with nonmodel organisms.

Population genetics studies play an increasingly important role in the management and conservation of nonmodel organisms. Unlike studies with model organisms, a typical population genetics study of a nonmodel organism may be conducted by analyzing thousands or hundreds of thousands of individuals for several dozen single nucleotide polymorphisms (SNPs). The use of robust, robotically mediated TaqMan reactions provides substantial advantages in these types of studies.

Characterization of Cdk9 T-loop phosphorylation in resting and activated CD4(+) T lymphocytes.

The cellular kinase complex P-TEFb is composed of Cdk9 and cyclin T, and it is required for expression of most protein-coding genes by RNAP II. Cdk9 has been shown recently to be activated in cis by autophosphorylation of Thr186 in its T-loop. Using a phosphospecific Cdk9 antibody, we examined the level of Cdk9 T-loop phosphorylation in resting and activated CD4(+) T lymphocytes.

Estimating the burden of disease and the economic cost attributable to chikungunya, Andhra Pradesh, India, 2005-2006.

To estimate the burden and cost of chikungunya in India, we searched for cases of fever and joint pain in the village of Mallela, Andhra Pradesh, and collected information on the demography, signs, symptoms, healthcare utilization and expenditure associated with the disease. We estimated the burden of the disease using disability-adjusted life years (DALYs). We estimated direct and indirect costs and made projections for the district and state using surveillance data corrected for under-reporting.

Cholera outbreak secondary to contaminated pipe water in an urban area, West Bengal, India, 2006.

Outbreaks of cholera are common in West Bengal. In April 2006, Garulia municipality reported a cluster of diarrhea cases. We investigated this cluster to identify the etiological agent, source of transmission and propose control measures.

Measures of postprandial lipoproteins are not associated with coronary artery disease in patients with type 2 diabetes mellitus.

Individuals with type 2 diabetes mellitus (DM) characteristically have elevated fasting and postprandial (PP) plasma triglycerides (TG). Previous case-control studies indicated that PPTG levels predict the presence of coronary artery disease (CAD) in people without DM; however, the data for patients with DM are conflicting. Therefore, we conducted a case-control study in DM individuals, 84 with (+) and 80 without (-) CAD.

Molecular events in the activation of B cells and macrophages by a non-microbial TLR4 agonist, G1-4A from Tinospora cordifolia.

G1-4A, a polysaccharide from an Indian medicinal plant Tinospora cordifolia, was recently shown to protect mice against septic shock by modulating the proinflammatory cytokines. G1-4A also activated B cells polyclonally. The present report describes in detail the molecular events associated with G1-4A-induced immunomodulation in vitro and in vivo.

A typhoid fever outbreak in a slum of South Dumdum municipality, West Bengal, India, 2007: evidence for foodborne and waterborne transmission.

Background: In April 2007, a slum of South Dumdum municipality, West Bengal reported an increase in fever cases. We investigated to identify the agent, the source and to propose recommendations.

Methods: We defined a suspected case of typhoid fever as occurrence of fever for > or = one week among residents of ward 1 of South Dumdum during February - May 2007.

Risk factors for typhoid in Darjeeling, West Bengal, India: evidence for practical action.

Objective: To identify risk factors for typhoid and propose prevention measures.

Methods: Case-control study; we compared hospital-based typhoid cases defined as fever>38 degrees C for >or=3 days with four-fold rise in 'O' antibodies on paired sera (Widal) with community, age and neighbourhood matched controls. We obtained information on drinking water, fruits, vegetables, milk products and sanitation; and calculated matched odds ratios (MOR) and attributable fractions in the population (AFP) for the risk factors or failure to use prevention measures.

Specific loss of brain ABCA1 increases brain cholesterol uptake and influences neuronal structure and function.

The expression of the cholesterol transporter ATP-binding cassette transporter A1 (ABCA1) in the brain and its role in the lipidation of apolipoproteins indicate that ABCA1 may play a critical role in brain cholesterol metabolism. To investigate the role of ABCA1 in brain cholesterol homeostasis and trafficking, we characterized mice that specifically lacked ABCA1 in the CNS, generated using the Cre/loxP recombination system. These mice showed reduced plasma high-density lipoprotein (HDL) cholesterol levels associated with decreased brain cholesterol content and enhanced brain uptake of esterified cholesterol from plasma HDL.

Scrub typhus in Darjeeling, India: opportunities for simple, practical prevention measures.

To identify risk factors for scrub typhus in Darjeeling, India, we compared 62 scrub typhus cases (acute fever with eschar and specific IgM) with 62 neighbourhood controls. Cases were more likely to live close to bushes [matched odds ratio (MOR) 10; 95% CI 2.3-63] and wood piles (MOR 3.

Differential HIV-1 integration targets more actively transcribed host genes in neonatal than adult blood mononuclear cells.

We have recently shown an increased HIV-1 replication and gene expression in neonatal (cord) blood mononuclear cells compared with adult cells, which could be due to HIV-1 integration as it targets active host genes. Here we have characterized 468 HIV-1 integration sites within cord and adult blood T-lymphocytes and monocyte-derived macrophages (MDM) from five donors. Several functional classes of genes were identified by gene ontology to be over represented, including genes for cellular components, maintenance of intracellular environment, enzyme regulation, cellular metabolism, catalytic activity and cation transport.

Na-K-Cl Cotransporter-1 in the mechanism of ammonia-induced astrocyte swelling.

Brain edema and the consequent increase in intracranial pressure and brain herniation are major complications of acute liver failure (fulminant hepatic failure) and a major cause of death in this condition. Ammonia has been strongly implicated as an important factor, and astrocyte swelling appears to be primarily responsible for the edema. Ammonia is known to cause cell swelling in cultured astrocytes, although the means by which this occurs has not been fully elucidated.

Phosphatase PPM1A regulates phosphorylation of Thr-186 in the Cdk9 T-loop.

Cdk9 is the catalytic subunit of a general RNA polymerase II elongation factor known as positive transcription elongation factor b (P-TEFb). The kinase function of P-TEFb requires phosphorylation of Thr-186 in the T-loop of Cdk9 to allow substrates to access the catalytic core of the enzyme. To identify human phosphatases that dephosphorylate the T-loop of Cdk9, we used a Thr-186-phosphospecific antiserum to screen a phosphatase expression library.

Increasing incidence of malaria in Kurseong, Darjeeling District, West Bengal, India, 2000-2004.

In Kurseong, Darjeeling District, India, malaria caused concern but insufficient information was available. We analysed surveillance data to estimate the burden of malaria and to examine trends. Confirmed malaria reports were reviewed and climatic records were collected.

Cyclin T1-dependent genes in activated CD4 T and macrophage cell lines appear enriched in HIV-1 co-factors.

HIV-1 is dependent upon cellular co-factors to mediate its replication cycle in CD4(+) T cells and macrophages, the two major cell types infected by the virus in vivo. One critical co-factor is Cyclin T1, a subunit of a general RNA polymerase II elongation factor known as P-TEFb. Cyclin T1 is targeted directly by the viral Tat protein to activate proviral transcription.

Regulation of protein kinases and coregulatory interplay of S-100beta and serotonin transporter on serotonin levels in diabetic rat brain.

Protein kinases are critical component in the regulation of signal transduction pathways, including neurotransmitters. Our previous studies have shown that serotonin (5-HT) altered under diabetic condition was accompanied by alterations of protein kinase C-alpha (PKC-alpha) and CaMKII, and those alterations were reversed after insulin administration. The current study showed that alloxan-induced diabetic animals revealed hyperglycemia and was associated with an increase in the content of 5-HT, PKC-alpha expression and PKC activity (P < 0.

Studying copy number variations using a nanofluidic platform.

Copy number variations (CNVs) in the human genome are conventionally detected using high-throughput scanning technologies, such as comparative genomic hybridization and high-density single nucleotide polymorphism (SNP) microarrays, or relatively low-throughput techniques, such as quantitative polymerase chain reaction (PCR). All these approaches are limited in resolution and can at best distinguish a twofold (or 50%) difference in copy number. We have developed a new technology to study copy numbers using a platform known as the digital array, a nanofluidic biochip capable of accurately quantitating genes of interest in DNA samples.

Mathematical analysis of copy number variation in a DNA sample using digital PCR on a nanofluidic device.

Copy Number Variations (CNVs) of regions of the human genome have been associated with multiple diseases. We present an algorithm which is mathematically sound and computationally efficient to accurately analyze CNV in a DNA sample utilizing a nanofluidic device, known as the digital array. This numerical algorithm is utilized to compute copy number variation and the associated statistical confidence interval and is based on results from probability theory and statistics.

Using mass measurements in tracer studies--a systematic approach to efficient modeling.

Tracer enrichment data are fitted by multicompartmental models to estimate rate constants and fluxes or transport rates. In apolipoprotein turnover studies, mass measurements are also available, for example, apolipoprotein B levels in very low-density lipoprotein, intermediate-density lipoprotein, and low-density lipoprotein, and are often essential to calculate some of the rate constants. The usual method to use mass measurements is to estimate pool masses along with rate constants.