HLA class II SNP interactions and the association with type 1 diabetes mellitus in Bengali speaking patients of Eastern India

Background

Several studies have demonstrated a fundamental role for the HLA in the susceptibility of, or protection to, type 1 diabetes mellitus (T1DM). However, this has not been adequately studied in Asian Indian populations. To assess the frequency of HLA class II (DPA1, DPB1, DQA1, DQB1 and DRB1) associated to susceptibility or protection toT1DM in a Bengali population of India with diabetes.

Results

Single nucleotide polymorphism study. The HLA genotyping was performed by a polymerase chain reaction followed by their HLA-DP, DQ, and DRB1 genotypes and haplotypes by sequencing method. The results are studied by Plink software. The χ² tests were used for the inferential statistics. To our knowledge, this study is the first of a kind which has attempted to check the HLA association with T1DM by SNPs analysis. The study recruited 151 patients with T1DM and same number of ethno-linguistic, sex matched non-diabetic controls. The present study found a significant SNP rs7990 of HLA-DQA1 (p = 0.009) negative correlation, again indicating that risk from HLA is considerably more with T1DM.

Conclusions

This study demonstrates that the HLA class-II alleles play a major role in genetic basis of T1DM.     

Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA

Background

Past work on asthmatic African American families revealed a strong linkage peak with modest evidence of association on chromosome 11q. Here, we perform tests of association for asthma and a panel of 609 SNPs in African American subjects using a sliding window approach. While efficient in screening a region of dense genotyping, this approach does create some problems: high numbers of tests, assimilating thousands of results, and questions about setting priorities on regions with association signals.

Results

We present a newly developed tool, Graphical Assessment of Sliding P-values or GrASP, which uses color display to indicate the width of the sliding windows, significance of individual tests, density of SNP coverage and location of known genes that simplifies some of these issues, and use it to identify regions of interest in these data.

Conclusion

We demonstrate that GrASP makes it easier to visualize, summarize and prioritize regions of interest from sliding window haplotype analysis, based jointly on the p-value from all the tests from these windows and the building of haplotypes of significance in the region. Using this approach, five regions yielded strong evidence for linkage and association with asthma, including the prior peak linkage region.     

CYP1A1 genotypes and haplotypes and risk of oral cancer: A case-control study in South Indians

The CYP1A1 gene encodes for the enzyme, aryl hydrocarbon hydroxylase, which is involved in the biotransformation of various aromatic tobacco precarcinogens. In the present study, the association between CYP1A1 gene polymorphisms (IVS1-728G > A, Thr461Asn and Ile462Val), and the risk of oral cancer, was examined among 157 patients with oral cancer and 132 age-matched controls, in a south Indian population. The strength of the association between CYP1A1 variants and oral cancer was estimated by logistic regression. It was found that Thr461Asn was not polymorphic. Both IVS1-728G > A and Ile462Val frequencies were consistent with Hardy-Weinberg equilibrium in the control group. There were no significant differences in genotype or haplotype frequencies between controls and cases with oral cancer. Hence, CYP1A1 SNPs can be considered as not being associated with oral cancer at either the genotype or haplotype levels in the population studied.     

Analysis of propagation of <Emphasis Type="Italic">Bacopa monnieri</Emphasis> (L.) from hairy roots,elicitation and Bacoside A contents of Ri transformed plants

Agrobacterium rhizogenes mediated transformation has been experimented in leaf explants of the memory herb Bacopa monnieri in order to assess the regeneration potential of hairy roots (HR) followed by the elicitation of transformed plants for increased Bacoside A production. Out of the four strains tested, A4 and MTCC 532 derived HR exhibited regrowth in MS basal medium while MTCC 2364 derived HR showed regeneration in MS medium supplemented with suitable phyto hormones. R1000 derived HR possessed no regeneration potential. Comparable to A4, MTCC 532 derived HR displayed maximum regrowth frequency of about 85.71 ± 1.84 % with an increase in biomass to threefold. Therefore, five HR plant lines (MTCC 532 derived) were generated and maintained in MS basal liquid medium in which HR3 topped the others in producing a huge biomass of about 67.09 ± 0.66 g FW. PCR amplification and southern hybridization analysis of rol A gene (280 bp) has been performed in order to confirm the transformation process. Moreover, HR3 plant line has accumulated highest total phenolic content of about 165.68 ± 0.82 mg GAE/g DW and highest total flavonoid content of about 497.78 ± 0.57 mg QRE/g DW when compared to other lines and untransformed controls. In addition, HR3 plant extract showed 85.58 ± 0.14 % of DPPH (2, 2-diphenyl-1-picryl hydrazyl) inhibition displaying its reliable anti oxidant potential. Further on elicitation with 10 mg/L chitosan for 2 weeks, HR3 has produced 5.83 % of Bacoside A which is fivefold and threefold increased production when compared to untransformed and transformed unelicited controls respectively. This is the first report on eliciting HR plants for increased metabolite accumulation in B. monnieri.     

Improved <Emphasis Type="Italic">Agrobacterium</Emphasis>-mediated transformation and direct plant regeneration in four cultivars of finger millet (<Emphasis Type="Italic">Eleusine coracana</Emphasis> (L.) Gaertn.)

We have developed an improved Agrobacterium-mediated transformation and rapid regeneration system for four cultivars (‘CO(Ra)-14’, ‘PR-202’, ‘Try-1’ and ‘Paiyur-2’) of finger millet using optimized transformation and direct plant regeneration conditions. The shoot apical meristems (SAMs) were used as explants in this study. Agrobacterium strain EHA105 carrying binary vector pCAMBIA1301 was used to optimize the transformation conditions. Concentration of hygromycin, the optical density of the culture, infection time, age of the explants, co-cultivation period, the concentrations of acetosyringone and antibiotics were optimized to improve the transformation frequency. The highest frequency of mean transient gus expression (85.1%) was achieved in cultivar ‘CO(Ra)-14’. The entire transformation procedure, from initiating SAMs to planting putative transgenic plantlets in the greenhouse, was completed within 45 days with the highest stable transformation frequency of 11.8% for ‘CO(Ra)-14’. PCR, gus staining and Southern blot analyses were performed in T₀ and T₁ generations to confirm the gene integration. Six events from T₀ had a single copy of the transgene and showed a normal Mendelian pattern of segregation. To our knowledge, this is the first report on the high frequency transformation of finger millet by Agrobacterium and subsequent recovery of transgenic plants via direct plant regeneration without a callus phase, in short duration (45 days). The proposed protocol could be supportive in breaking through the bottleneck in transformation and regeneration of finger millet cultivars.     

Rice bran stabilization and rice bran oil extraction using ohmic heating

Ohmic heating has been shown to increase the extraction yields of sucrose from sugar beets, apple juice from apples, beet dye from beet root, and soymilk from soybeans. Rice bran is a byproduct of the rice milling process that has economic potential by virtue of highly nutritious rice bran oil contained within the bran. In this study, ohmic heating was used to stabilize rice bran and to improve rice bran oil extraction yield as compared to microwave heating and a control (no heating). Results showed that ohmic heating is an effective method for rice bran stabilization with moisture addition. Free fatty acid concentration increased more slowly than the control for raw bran samples subjected to ohmic heating with no corresponding temperature rise, indicating that electricity has a non-thermal effect on lipase activity. Ohmic heating increased the total percent of lipids extracted from rice bran to a maximum of 92%, while 53% of total lipids were extracted from the control samples. Lowering the frequency of alternating current significantly increased the amount of oil extracted, probably due to electroporation. Ohmic heating was successfully applied to rice bran despite its high oil content. This could have important implications for the enhanced extraction of non-polar constituents.     

Association Between the M268T Polymorphism in the Angiotensinogen Gene and Essential Hypertension in a South Indian Population

Essential hypertension is a complex multifactorial disease caused by interactions between genetic and environmental factors. It is an independent determinant of cardiovascular risk. The main aim of this study was to investigate the possible influence of angiotensinogen M268T polymorphisms on hypertension in two endogamous caste populations of South India. Systolic and diastolic blood pressure, anthropometric variables, and lipid profiles were assessed. Direct sequencing of PCR products was adopted for genotyping. This polymorphism was found to be in Hardy-Weinberg equilibrium in the patients and controls of both populations. Binary odds ratios showed significant association between the M268T polymorphism and hypertension in both populations. Multivariate analysis revealed significant differences in body mass index, chest girth, calf circumference, skinfold measurements, total cholesterol, and triglyceride levels between these genotypes in the Gavara and Vaishya populations. These data further support the hypothesis that hypertension is influenced by the AGT M268T polymorphism.     

Transposable elements in plants: Recent advancements,tools and prospects

Transposable elements (TEs) have long been considered junk DNA; however, the availability of genome sequences and the growth of omics databases have accelerated the study of TEs, and they are now considered evolutionary signatures. TEs, essential genetic elements in plant genomes, can move around the genome by either “cut-paste” (DNA transposons) or “copypaste” mechanisms (RNA transposons). TEs often affect host genome size and interact with host genes, resulting in altered gene expression and regulatory networks. Several genes have been identified to be influenced/modified by the action of TEs. TEs have diverse structures and functions. Plants are capable of using TEs as promoters and enhancers to drive epigenetic mechanisms in a tissue-specific manner. However, our knowledge about TEs remains poor despite extensive research in plants. Plant physiological functions associated with TEs have been challenging to analyse due to a lack of focused research. Another limitation is the lack of sufficient genetic information. The different functions displayed by plant genomes are genetically regulated, which opens up opportunities in areas such as genomic evolution and epigenetic modification. Indeed, understanding the contribution of TEs in the plant genome is indispensable to assess the diversity of evolutionary adaptability in plant taxa. In this study, we review the applications of TEs and discuss the value of genetic information in the plant genome. Genomic information about TEs has a significant value in high throughput research, including forward and reverse genetics. We discuss current strategies in using TEs for the genetic dissection of plant genomes. This review covers opportunities to use different TEs databases to increase the productivity of economically important plants for sustainable development