Type 2 diabetes in non-obese Indian subjects is associated with reduced leptin levels: Study from Mumbai, Western India

Objective: Asian Indian subjects have a high tendency to develop Type 2 diabetes even though obesity is relatively uncommon. We evaluated the serum leptin levels in a group of non-obese Type 2 diabetic patients from Mumbai, Western India.Design: Cross sectional study.Methods: A total of 104 subjects consisting of 28 with Type 2 diabetes, 16 with impaired glucose tolerance and 60 age and sex-matched control subjects were given 75 g oral glucose tolerance test. Fasting serum leptin (IRMA), insulin and C-peptide were measured along with fasting and 2 h plasma glucose. The relation between these variables was studied by univariate and multiple regression analysis.Results: Type 2 diabetes was associated with marked (50–60%) reduction in serum leptin levels, in both men and women. Women, but not men, with impaired glucose tolerance exhibited 60% lower leptin. Serum leptin levels were positively correlated to body mass index (BMI; r = 0.501, p = 0.001) and calculated body fat percent (r = 0.525, p = 0.001) in all the study subjects with a better correlation in the normal subjects (r = 0.562 for BMI and 0.735 for body fat). On the other hand, serum leptin showed significant correlation to serum insulin (r = 0.362, p = 0.008) only in subjects with diabetes or IGT. In the multiple regression model, BMI was the only independent predictor of leptin, in all the subjects. However, in subjects with diabetes or impaired glucose tolerance, waist circumference (p = 0.003), gender (p = 0.007) and body fat (p = 0.009) were significant predictors of leptin, besides BMI. Gender-specific multiple regression revealed serum insulin as an independent predictor of leptin in men (p = 0.026). Therefore, lower serum leptin levels in diabetes is partly due to increased waist circumference, decreased BMI and male sex. These observations are consistent with the view that leptin levels in this cohort of non-obese Indians from Mumbai exhibit gender-specific relationship partly attributed to changes in serum insulin and waist circumference in men and to changes in BMI, in women.     

Crystal structures of an NAD kinase from Archaeoglobus fulgidus in complex with ATP, NAD, or NADP

NAD kinase is a ubiquitous enzyme that catalyzes the phosphorylation of NAD to NADP using ATP or inorganic polyphosphate (poly(P)) as phosphate donor, and is regarded as the only enzyme responsible for the synthesis of NADP. We present here the crystal structures of an NAD kinase from the archaeal organism Archaeoglobus fulgidus in complex with its phosphate donor ATP at 1.7 A resolution, with its substrate NAD at 3.05 A resolution, and with the product NADP in two different crystal forms at 2.45 A and 2.0 A resolution, respectively. In the ATP bound structure, the AMP portion of the ATP molecule is found to use the same binding site as the nicotinamide ribose portion of NAD/NADP in the NAD/NADP bound structures. A magnesium ion is found to be coordinated to the phosphate tail of ATP as well as to a pyrophosphate group. The conserved GGDG loop forms hydrogen bonds with the pyrophosphate group in the ATP-bound structure and the 2' phosphate group of the NADP in the NADP-bound structures. A possible phosphate transfer mechanism is proposed on the basis of the structures presented.     

Crystal structure of TM1457 from Thermotoga maritima

The crystal structure of a hypothetical protein, TM1457, from Thermotoga maritima has been determined at 2.0A resolution. TM1457 belongs to the DUF464 family (57 members) for which there is no known function. The structure shows that it is composed of two helices in contact with one side of a five-stranded beta-sheet. Two identical monomers form a pseudo-dimer in the asymmetric unit. There is a large cleft between the first alpha-helix and the second beta-strand. This cleft may be functionally important, since the two highly conserved motifs, GHA and VCAXV(S/T), are located around the cleft. A structural comparison of TM1457 with known protein structures shows the best hit with another hypothetical protein, Ybl001C from Saccharomyces cerevisiae, though they share low structural similarity. Therefore, TM1457 still retains a unique topology and reveals a novel fold.     

Design of a data model for developing laboratory information management and analysis systems for protein production

Data management has emerged as one of the central issues in the high-throughput processes of taking a protein target sequence through to a protein sample. To simplify this task, and following extensive consultation with the international structural genomics community, we describe here a model of the data related to protein production. The model is suitable for both large and small facilities for use in tracking samples, experiments, and results through the many procedures involved. The model is described in Unified Modeling Language (UML). In addition, we present relational database schemas derived from the UML. These relational schemas are already in use in a number of data management projects.     

Genetic analysis of the maximum drinks phenotype

Using data provided by the Collaborative Study on the Genetics of Alcoholism we studied the genetics of a quantitative trait: the maximum number of drinks consumed in a 24-hour period. A two-stage method was used. First, linkage analysis was performed, followed by association analysis in regions where linkage was detected. Additionally, the extent of linkage disequilibrium among single-nucleotide polymorphisms (SNP) associated with the phenotype was assessed. Linkage to chromosomes 2 and 7 was detected, and follow-up association analysis found multiple trait-associated SNPs in the chromosome 7 linkage region. Chromosome 4, which has been implicated in previous studies of the maximum drinks phenotype, did not pass our threshold for linkage evidence in stage 1, but secondary analyses of this chromosome indicated modest evidence for both linkage and association. The evidence suggests that chromosome 7 may harbor an additional locus influencing the maximum drinks consumption phenotype.     

Rain forest provides pollinating beetles for atemoya crops

Small beetles, usually species of Nitidulidae, are the natural pollinators of atemoya (Annona squamosa L. x A. cherimola Mill. hybrids; custard apple) flowers but commercial atemoya growers often need to carry out labor-intensive hand pollination to produce enough high-quality fruit. Because Australian rain forest has plant species in the same family as atemoya (Annonaceae) and because many rain forest plants are beetle pollinated, we set out to discover whether tropical rain forest in far north Queensland harbors beetles that could provide this ecosystem service for atemoya crops. Orchards were chosen along a gradient of increasing distance from tropical rain forest (0.1-24 km). We sampled 100 flowers from each of nine atemoya orchards and determined the identity and abundance of insects within each flower. To assess the amount of pollination due to insects, we bagged six flowers per tree and left another six flowers per tree accessible to insects on 10 trees at an orchard near rain forest. Results indicated that atemoya orchards < or = 0.5 km from rain forest were predominantly visited by five previously unrecognized native beetle pollinators that are likely to originate in tropical rain forest. These native beetles occurred reliably enough in crops near rain forest to have a positive effect on the quantity of fruit produced but their contribution was not great enough to satisfy commercial production needs. Management changes, aimed at increasing native beetle abundance in crops, are required before these beetles could eliminate the need for growers to hand pollinate atemoya flowers. Appreciation of the value of this resource is necessary if we are to develop landscapes that both conserve native biodiversity and support agricultural production.     

Transferable antibiotic resistance elements in Haemophilus influenzae share a common evolutionary origin with a diverse family of syntenic genomic islands

Transferable antibiotic resistance in Haemophilus influenzae was first detected in the early 1970s. After this, resistance spread rapidly worldwide and was shown to be transferred by a large 40- to 60-kb conjugative element. Bioinformatics analysis of the complete sequence of a typical H. influenzae conjugative resistance element, ICEHin1056, revealed the shared evolutionary origin of this element. ICEHin1056 has homology to 20 contiguous sequences in the National Center for Biotechnology Information database. Systematic comparison of these homologous sequences resulted in identification of a conserved syntenic genomic island consisting of up to 33 core genes in 16 beta- and gamma-Proteobacteria. These diverse genomic islands shared a common evolutionary origin, insert into tRNA genes, and have diverged widely, with G+C contents ranging from 40 to 70% and amino acid homologies as low as 20 to 25% for shared core genes. These core genes are likely to account for the conjugative transfer of the genomic islands and may even encode autonomous replication. Accessory gene clusters were nestled among the core genes and encode the following diverse major attributes: antibiotic, metal, and antiseptic resistance; degradation of chemicals; type IV secretion systems; two-component signaling systems; Vi antigen capsule synthesis; toxin production; and a wide range of metabolic functions. These related genomic islands include the following well-characterized structures: SPI-7, found in Salmonella enterica serovar Typhi; PAP1 or pKLC102, found in Pseudomonas aeruginosa; and the clc element, found in Pseudomonas sp. strain B13. This is the first report of a diverse family of related syntenic genomic islands with a deep evolutionary origin, and our findings challenge the view that genomic islands consist only of independently evolving modules.     

Relative and absolute quantitative expression profiling of cytochromes P450 using isotope-coded affinity tags

The development of a novel method for absolute quantification of proteins based on isotope-coded affinity tagging using ICAT reagents is described. The method exploits synthetic peptide standards to determine protein content at the femtomole level in biological samples. The approach is generally applicable to any subset of proteins, but is particularly appropriate for quantitative analysis of multiple, closely related isoforms, and for hydrophobic proteins that are poorly represented in 2-D gels. Relative and absolute quantification techniques are applied to an important group of microsomal metabolic enzymes, the cytochromes P450 (P450), which are critical in determining the disposition, safety and efficacy of drugs in man. Measurement of the P450 induction profile in response to chemicals is a fundamental aspect of drug safety evaluation and is currently achieved by low-throughput methods employing poorly discriminatory antibodies or substrates. Tagging technology is shown to supersede conventional methods for P450 profiling in terms of discriminatory power and throughput, exemplified by the simultaneous detection of distinct induction profiles for cyp2c subfamily members in response to phenobarbitone: cyp2c29 expression, but not cyp2c40 or cyp2c50, was induced threefold by treatment. This technology should abbreviate the drug development pathway, and provide a widely applicable, rapid means of quantifying proteins.