Physical interaction of RTBV ORFI with D1 protein of Oryza sativa and Fe/Zn homeostasis play a key role in symptoms development during rice tungro disease to facilitate the insect mediated virus transmission.

Rice tungro disease is caused by the combined action of Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV). The RTBV is involved in the development of symptoms while RTSV is essential for virus transmission. We attempted to study the mode of action of RTBV in the development of symptoms. The tungro disease symptoms were attributed to viral interference in chlorophyll and carotenoids biosynthesis, photosynthesis machinery, iron/zinc homeostasis, and the genes encoding the enzymes associated with these biological processes of rice. The adverse effects of virus infection in photosystem II (PSII) activity was demonstrated by analyzing the Fv/Fm ratio, expression of psbA and cab1R genes, and direct interaction of RTBV ORF I protein with the D1 protein of rice. Since ORF I function is not yet known in the RTBV life cycle, this is the first report showing its involvement in regulating host photosynthesis process and symptoms development.

Heterozygosity of stromelysin-1 (rs3025058) promoter polymorphism is associated with gastric cancer.

BACKGROUND: Gastric cancer (GC) is the third most common cancer in India and is mediated by multiple genetic, epigenetic and environmental risk factors. A single nucleotide polymorphism rs3025058 at -1171 of the stromelysin-1 (matrix metalloproteinase [MMP]-3) promoter is resulting due to insertion/deletion of adenine thought to have an impact on increasing the risk for tumor formation. AIM: This study is aimed to understand the role of stromelysin-1 rs3025058 (-1171, 5A/6A) promoter polymorphism in the etiology of GC in Indian population. MATERIALS AND METHODS: Genomic DNA was isolated from blood samples of the GC patients and controls. The genotyping of stromelysin-1 rs3025058 (-1171, 5A/6A) promoter polymorphism was carried out by amplification refractory mutation system-polymerase chain reaction method followed by agarose gel electrophoresis. RESULTS: The frequency of 5A/5A, 5A/6A, and 6A/6A genotypes in GC patients were 7.69%, 76.92%, and 15.38%, while in controls were 5.31%, 86.73%, and 7.96%, respectively. There was a significant difference in the distribution of 5A/6A genotype in patients compared to the controls (P < 0.05). CONCLUSION: This study showed an increased frequency of heterozygotes for stromelysin-1 rs3025058 and thought to be involved in the etiology of GC.

The complete genome sequence of a south Indian isolate of Rice tungro spherical virus reveals evidence of genetic recombination between distinct isolates.

In this study, complete genome of a south Indian isolate of Rice tungro spherical virus (RTSV) from Andhra Pradesh (AP) was sequenced, and the predicted amino acid sequence was analysed. The RTSV RNA genome consists of 12,171 nt without the poly(A) tail, encoding a putative typical polyprotein of 3,470 amino acids. Furthermore, cleavage sites and sequence motifs of the polyprotein were predicted. Multiple alignment with other RTSV isolates showed a nucleotide sequence identity of 95% to east Indian isolates and 90% to Philippines isolates. A phylogenetic tree based on complete genome sequence showed that Indian isolates clustered together, while Vt6 and PhilA isolates of Philippines formed two separate clusters. Twelve recombination events were detected in RNA genome of RTSV using the Recombination Detection Program version 3. Recombination analysis suggested significant role of 5' end and central region of genome in virus evolution. Further, AP and Odisha isolates appeared as important RTSV isolates involved in diversification of this virus in India through recombination phenomenon. The new addition of complete genome of first south Indian isolate provided an opportunity to establish the molecular evolution of RTSV through recombination analysis and phylogenetic relationship.

The molecular diversity and evolution of Rice tungro bacilliform virus from Indian perspective.

Rice tungro disease is caused by a combination of two viruses: Rice tungro spherical virus and Rice tungro bacilliform virus (RTBV). This study was performed with the objective to decipher the molecular variability and evolution of RTBV isolates present in the tungro-affected states of Indian subcontinent. Phylogenetic analysis based on ORF-I, ORF-II, and ORF-IV sequences showed distinct divergence of Indian RTBV isolates into two groups; one consisted isolates from Hyderabad (Andhra Pradesh), Cuttack (Orissa), and Puducherry and another from West Bengal, Chinsura West Bengal, and Kanyakumari (Tamil Nadu). The results obtained from phylogenetic analysis were further supported with the single nucleotide polymorphisms (SNPs), insertion and deletion (INDELs) and evolutionary distance analysis. In addition, sequence difference count matrix revealed a maximum of 56 (ORF-I), 13 (ORF-II) and 73 (ORF-IV) nucleotides differences among all the Indian RTBV isolates taken in this study. However, at the protein level these differences were not significant as revealed by K (a)/K (s) ratio calculation. Sequence identity at nucleotide and amino acid level was 92-100 % (ORF-I), 96-100 % (ORF-II), 94-100 % (ORF-IV) and 86-100 % (ORF-I), 98-100 % (ORF-II) and 95-100 % (ORF-IV), respectively, among Indian isolates of RTBV. The divergence of RTBV isolates into two independent clusters of Indian and non-Indian was shown with the help of the data obtained from phylogeny, SNPs, and INDELs, evolutionary distance analysis, and conserved motifs analysis. The important role of ORF-I and ORF-IV in RTBV diversification and adaptation to different rice growing regions is also discussed.

Genetic variation of coat protein gene among the isolates of Rice tungro spherical virus from tungro-endemic states of the India.

Rice tungro disease, one of the major constraints to rice production in South and Southeast Asia, is caused by a combination of two viruses: Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus (RTBV). The present study was undertaken to determine the genetic variation of RTSV population present in tungro endemic states of Indian subcontinent. Phylogenetic analysis based on coat protein sequences showed distinct divergence of Indian RTSV isolates into two groups; one consisted isolates from Hyderabad (Andhra Pradesh), Cuttack (Orissa), and Puducherry and another from West Bengal, Coimbatore (Tamil Nadu), and Kanyakumari (Tamil Nadu). The results obtained from phylogenetic study were further supported with the SNPs (single nucleotide polymorphism), INDELs (insertion and deletion) and evolutionary distance analysis. In addition, sequence difference count matrix revealed 2-68 nucleotides differences among all the Indian RTSV isolates taken in this study. However, at the protein level these differences were not significant as revealed by Ka/Ks ratio calculation. Sequence identity at nucleotide and amino acid level was 92-100% and 97-100%, respectively, among Indian isolates of RTSV. Understanding of the population structure of RTSV from tungro endemic regions of India would potentially provide insights into the molecular diversification of this virus.

MMP 9 Gene Promoter Polymorphism in Gastric Cancer.

Matrix metalloproteinase-9 (gelatinase B) plays a key role in cancer invasion and metastasis by degrading the extracellular matrix and basement membrane barriers. A cytosine (C) > thymidine (T) single nucleotide polymorphism (SNP) at position -1562 in the MMP-9 promoter is reported to influence the expression of the gene. Genotyping of MMP-9 -1562 C→T promoter polymorphism in 140 gastric cancer patients and 132 healthy control subjects was carried out in order to evaluate its association with progression and development of gastric cancer. The SNP was genotyped by tetra-primer amplification refractory mutation system-polymerase chain reaction followed by agarose gel electrophoresis. Statistical methods were adopted to test for the significance of the results. Risk factor profile of the patients revealed age above 50 years, smoking, alcoholism as the factors associated with the disease. The distribution of genotype frequencies in gastric cancer patients were 28.7 % of CC, 45.5 % of CT and 25.7 % of TT, whereas in control subjects 31.8 % of CC, 53.03 % of CT and 15.15 % of TT, respectively. The allelic frequencies were 51.51 % of C and 48.48 % of T in patient group and 58.33 % of C and 41.66 % of T in controls respectively. The present study shows the possible association of epidemiological risk factors with gastric cancer. There is an increased frequency of T allele in the disease compared to control subjects. However, there is no association of the MMP-9 -1562 C→T promoter polymorphism in the development of gastric cancer.

Role of matrix metalloproteinase 3 gene promoter polymorphism in chronic pancreatitis.

AIM: To study the role of 5A/6A polymorphism of matrix metalloproteinase (MMP-3) and their levels in the pathogenesis of chronic pancreatitis (CP). METHODS: One hundred and twenty CP patients and an equal number of age and sex-matched healthy controls were included in the study. Genotypes were determined for 5A/6A allele of MMP-3 gene by allele specific PCR (AS-PCR). The serum MMP-3 levels were estimated using sandwich ELISA method. RESULTS: The distribution of the genotypes of the 5A/6A polymorphism in both control and study patients was similar (p = 0.523). Within the disease group, patients with older age, early onset of the disease, and addictions such as smoking and alcohol consumption had higher levels as compared to those who did not have these features. CONCLUSION: We conclude that functional polymorphism of MMP-3 (5A/6A) is not associated with CP. However, the higher levels within the disease group indicate its possible role in the disease process.

Helicobacter pylori infection in relation to gastric cancer progression.

Gastric cancer is a major cause of cancer death worldwide, especially in developing countries. The incidence of gastric cancer varies from country to country, probably as a result of genetic, epigenetic, and environmental factors. H. pylori infection is considered as a major risk factor in the development of gastric cancer. However, the scenario varies in Asian countries, exhibiting a higher rate of H. pylori infection and low incidence of gastric cancer, which could be attributed to strain-specific virulence factors and host genetic makeup. In this review, we discuss the various virulence factors expressed by this bacterium and their interaction with the host factors, to influence pathogenesis.

Role of Plasma MMP 9 levels in the Pathogenesis of Chronic Pancreatitis.

Pancreatic fibrosis is a key pathological feature in the etiology of chronic pancreatitis that leads to obliteration of exocrine and endocrine pancreatic tissues and its replacement by fibrous tissue resulting in clinical manifestations. Matrix metalloproteinase 9 is a member of the MMP family that is also known as gelatinase B, degrades type IV collagen of extracellular matrix and basal membrane. The present study is aimed at evaluating the clinical significance of plasma concentration of MMP-9 in chronic pancreatitis. The samples were obtained from 112 chronic pancreatitis patients and an equal number of age and sex matched healthy controls. MMP-9 levels were quantitatively measured by ELISA assay. Statistical analysis was applied to test the significance of results. The present study revealed a significant increase of plasma MMP 9 levels in chronic pancreatitis patients compared to control subjects. Elevated levels were also observed in all the patient groups compared to control subjects with regard to sex, age, addictions etc. MMP-9 degrades the type IV collagens in normal basement membrane, which in turn activates the pancreatic stellate cells which promote the development of pancreatitic fibrosis. Thus, elevated plasma levels of MMP-9 may act as a susceptibility factor for the development of chronic pancreatitis.

Genetic Diversity within the Population of Xanthomonas oryzae pv. oryzae in India.

ABSTRACT Xanthomonas oryzae pathovar oryzae causes a serious disease of rice in India and is endemic in all of the major rice-growing areas of the country. Sixty-seven X. oryzae pv. oryzae strains, collected mostly in 1994 and 1995, from 18 locations in India were analyzed by DNA fingerprinting methods using two separate repeat element probes from the X. oryzae pv. oryzae genome. These results show that strains belonging to a single pathogen lineage can be isolated from 16 of the 18 locations sampled; many of these locations are separated from each other by hundreds of kilometers and represent ecologically diverse rice-growing areas. Pathotyping analysis indicated that the strains in this lineage belong to pathotype 1b of X. oryzae pv. oryzae.