Association of <Emphasis Type="Italic">ADAM33</Emphasis> gene polymorphisms with adult-onset asthma and its severity in an Indian adult population

ADAM33, a member of the ADAM (a disintegrin and metalloprotease) gene family, is an asthma susceptibility gene originally identified by positional cloning. In the present study, we investigated the possible association of five single-nucleotide polymorphisms (SNPs) in the ADAM33 (rs511898, rs528557, rs44707, rs597980 and rs2787094) with adult-onset asthma in an Indian population. The study included 175 patients with mild intermittent (n = 44), mild persistent (n = 108) or moderate persistent (n = 23) subgroups of asthma, and 253 nonasthmatic control individuals. SNPs were genotyped with the help of restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR) method, and data were analysed using chi-square test and logistic regression model. Bonferroni’s correction for multiple comparisons was applied for each hypothesis. Genotypes and allele frequencies of SNPs rs511898 and rs528557 were significantly associated with adult-onset asthma (P = 0.010-<0.001). A significant association of the homozygous mutant genotype and mutant alleles of SNPs rs2787094, rs44707 and rs597980 with the asthma was also observed (P = 0.020-<0.001). A positive association between asthma and haplotypes AGCCT, GGCCT, AGACT, GCAGT, GGACT, ACCCC and AGACC were also found (P = 0.036-<0.001, OR = 2.07–8.49). Haplotypes AGCGT, GCAGC, ACAGC, ACAGT, GGAGC and GGCGT appear to protect against asthma (P = 0.013-<0.0001, OR = 0.34–0.10). Our data suggest that ADAM33 gene polymorphisms serve as genetic risk factors for asthma in Indian adult population.     

VKORC1 pharmacogenetics and pharmacoproteomics in patients on warfarin anticoagulant therapy: transthyretin precursor as a potential biomarker

BACKGROUND: Recognizing specific protein changes in response to drug administration in humans has the potential for the development of personalized medicine. Such changes can be identified by pharmacoproteomics approach based on proteomic technologies. It can also be helpful in matching a particular target-based therapy to a particular marker in a subgroup of patients, in addition to the profile of genetic polymorphism. Warfarin is a commonly prescribed oral anticoagulant in patients with prosthetic valve disease, venous thromboembolism and stroke. METHODS AND FINDING: We used a combined pharmacogenetics and iTRAQ-coupled LC-MS/MS pharmacoproteomics approach to analyze plasma protein profiles of 53 patients, and identified significantly upregulated level of transthyretin precursor in patients receiving low dose of warfarin but not in those on high dose of warfarin. In addition, real-time RT-PCR, western blotting, human IL-6 ELISA assay were done for the results validation. CONCLUSION: This combined pharmacogenomics and pharmacoproteomics approach may be applied for other target-based therapies, in matching a particular marker in a subgroup of patients, in addition to the profile of genetic polymorphism.     

Control of Vertebrate Skeletal Mineralization by Polyphosphates

Background

Skeletons are formed in a wide variety of shapes, sizes, and compositions of organic and mineral components. Many invertebrate skeletons are constructed from carbonate or silicate minerals, whereas vertebrate skeletons are instead composed of a calcium phosphate mineral known as apatite. No one yet knows why the dynamic vertebrate skeleton, which is continually rebuilt, repaired, and resorbed during growth and normal remodeling, is composed of apatite. Nor is the control of bone and calcifying cartilage mineralization well understood, though it is thought to be associated with phosphate-cleaving proteins. Researchers have assumed that skeletal mineralization is also associated with non-crystalline, calcium- and phosphate-containing electron-dense granules that have been detected in vertebrate skeletal tissue prepared under non-aqueous conditions. Again, however, the role of these granules remains poorly understood. Here, we review bone and growth plate mineralization before showing that polymers of phosphate ions (polyphosphates: (PO₃⁻)_n) are co-located with mineralizing cartilage and resorbing bone. We propose that the electron-dense granules contain polyphosphates, and explain how these polyphosphates may play an important role in apatite biomineralization.

Principal Findings/Methodology

The enzymatic formation (condensation) and destruction (hydrolytic degradation) of polyphosphates offers a simple mechanism for enzymatic control of phosphate accumulation and the relative saturation of apatite. Under circumstances in which apatite mineral formation is undesirable, such as within cartilage tissue or during bone resorption, the production of polyphosphates reduces the free orthophosphate (PO₄³⁻) concentration while permitting the accumulation of a high total PO₄³⁻ concentration. Sequestering calcium into amorphous calcium polyphosphate complexes can reduce the concentration of free calcium. The resulting reduction of both free PO₄³⁻ and free calcium lowers the relative apatite saturation, preventing formation of apatite crystals. Identified in situ within resorbing bone and mineralizing cartilage by the fluorescent reporter DAPI (4′,6-diamidino-2-phenylindole), polyphosphate formation prevents apatite crystal precipitation while accumulating high local concentrations of total calcium and phosphate. When mineralization is required, tissue non-specific alkaline phosphatase, an enzyme associated with skeletal and cartilage mineralization, cleaves orthophosphates from polyphosphates. The hydrolytic degradation of polyphosphates in the calcium-polyphosphate complex increases orthophosphate and calcium concentrations and thereby favors apatite mineral formation. The correlation of alkaline phosphatase with this process may be explained by the destruction of polyphosphates in calcifying cartilage and areas of bone formation.

Conclusions/Significance

We hypothesize that polyphosphate formation and hydrolytic degradation constitute a simple mechanism for phosphate accumulation and enzymatic control of biological apatite saturation. This enzymatic control of calcified tissue mineralization may have permitted the development of a phosphate-based, mineralized endoskeleton that can be continually remodeled.     

A collaborative GIS method for integrating local and technical knowledge in establishing biodiversity conservation priorities

Methods for establishing biodiversity conservation priorities are urgently required, as the number of species and habitats that are threatened increases relative to the material resources available for their conservation. The identification of priority areas demands the integration of biophysical data on ecosystems together with social data on human pressures and planning opportunities. But comprehensive and reliable data are rarely available to demarcate where the need for action is most urgent and where the benefits of conservation strategies can be maximized. Strategic conservation initiatives cannot wait for the creation of comprehensive databases. In order to fill the missing data gaps, the combined knowledge of local and technical experts can be used. This study presents a collaborative geographic information system (GIS) method for integrating the knowledge of local and technical experts with existing spatial environmental data to establish priority areas for biodiversity conservation. Procedures for structuring and framing the discussions, establishing assessment criteria, integrating knowledge with data, and building consensus are incorporated into the method. The method provides a novel cooperative mechanism to aid spatial knowledge management and inclusive biodiversity planning.     

Stress and development phenotyping of Hsp101 and diverse other Hsp mutants of Arabidopsis thaliana

Heat shock proteins or Hsps are critical in mounting plant resistance against heat stress. The complex Hsp spectrum of Arabidopsis thaliana plant contains over two hundred proteins belonging to six different families namely Hsp20, Hsp40, Hsp60, Hsp70, Hsp90 and Hsp100. Importantly, the cellular function(s) of most Hsps remains to be established. We aimed at phenotyping of stress and development response of the selected, homozygous hsp mutant lines produced by T-DNA insertional mutagenesis method. The heat stress phenotype was assessed for basal and acquired heat stress response at seed and seedling stages. Distinct phenotype was noted for the hot1-3 mutant (knockout mutant of Hsp101 gene) showing higher heat sensitivity and for the salk_087844 mutant (knockout mutant of Hsc70-2 gene) showing higher heat tolerance than the wild type seedlings. The homozygous cs808162 mutant (mutant of ClpB-p gene encoding for the chloroplast-localized form of Hsp101) did not survive even under unstressed, control condition. salk_064887C mutant (mutant of cpn60β4 gene) showed accelerated development cycling. The hot1-3 mutant apart from showing different heat response, exhibited development lesions like bigger size of seeds, buds, siliques, and pollen compared to the wild type plants. In response to controlled deterioration treatment of seeds, hot1-3 seeds showed higher accumulation of reactive oxygen species molecules, higher rates of protein and lipid oxidation and a faster decline in germination rate as compared to wild type seeds. Our findings show that Hsps perform diverse metabolic functions in plant response to stress, growth, and development.

     

Apolipoprotein E polymorphism in Northern Indian patients with coronary heart disease: Phenotype distribution and relation to serum lipids and lipoproteins

Apolipoprotein E (apo E), a genetic determinant of plasma lipid levels and coronary heart disease (CHD) needs to be investigated in Asian Indians since they have a propensity to develop dyslipidemia and accelerated atherosclerosis. We studied apo E phenotypes and plasma lipid levels in 52 Northern Indian male patients (aged 38–71 years) with angiographically proven CHD, and compared them to 50 healthy blood donors taken as the control group. High levels of Lp(a), (p < 0.05), and a definite trend towards lower levels of HDL-C (p < 0.05), was observed in the CHD patients as compared to the control subjects. The frequency of apo E allele 3 was 0.86 and 0.862, and 4 allele was 0.12 and 0.08 in the patients and controls, respectively. However, a lower frequency of the E2 allele was observed in the patient group (2 = 0.02) as compared to the controls (2 = 0.06) (p = ns). In individuals with apo E3/E3 phenotype, significantly lower HDL-C levels was observed in the CHD patients as compared to the control subjects (p < 0.05). A positive correlation was observed between apo E phenotypes and Lp(a) levels in the CHD subjects as compared to the controls (p < 0.05), the level being significantly high in CHD subjects with at least one E4 allele. To conclude, in this sample of Northern Indian subjects with CHD, there is a significant correlation between apo E3/E3 phenotype and low levels of HDL-C as compared to the control subjects. Further, apo E phenotype is positively correlated with high Lp(a) levels in the CHD subjects having at least one E4 allele. However, these relationships need to be explored in a larger sample of subjects.