Sushil Kumar

Evidences showing association of interleukin-1B polymorphisms with increased risk of gastric cancer in an Indian population

Helicobacter pylori infection is strongly associated with gastric cancer. In the present study, the relationship between interleukin-1B (IL-1B) polymorphism, H. pylori infection, and prevalence of gastric cancer (GC) in patients of North India was evaluated using genomic DNA directly extracted from biopsy tissues for performing PCR-RFLP. A total of 136 GC cases and 110 healthy controls were included for studying polymorphisms in the genotypes of IL-1B-511, -31, +3954 and IL-1RN both in the presence and absence of H. pylori active infection. Results showed that the frequency of IL-1RN 2/2 was significantly higher in GC cases (21.32%) than the controls (9.09%) with an odds ratio (OR) of 4.391 (95% CI 1.093-10.131). The risk of GC was also found higher in other genotypes of IL-1B namely, -511 TT (chi(2)=18.975, p<0.001), -31CC (chi(2)=21.219, p<0.001), +3954 CT (chi(2)=21.082, p<0.001) and IL-1RN 1/2 (chi(2)=30.543, p<0.001) with active infection of H. pylori. Our findings indicate that the IL-1B and IL-1RN polymorphisms are associated with the development of GC and H. pylori infection markedly increases the risk of GC in North Indian population. Additionally, IL-1B-511 C/C and IL-RN 2/2 polymorphisms seem to be involved in the development of GC in H. pylori uninfected patients.

SENSITIVITY MODULATION OF SURFACE PLASMON RESONANCE SENSOR CONFIGURATIONS IN OPTICAL FIBER WAVEGUIDE

The re∞ectivity of three layer and four layer optical flber based surface plasmon resonance sensors having silica material substrate and chalcogenide material substrate is plotted and studied. Using the transfer matrix method, the re∞ection coe-cient for p- polarized incident lights at various wavelengths is obtained. It is observed that the sensitivity, detection accuracy and quality parameters of the sensor having silica substrates are much larger than the chalcogenide substrates. These parameters can also be increased by introducing an additional thin layer of silica/chalcogenide material on the metallic surface. Also, these sensor parameters are highly afiected by the thickness of the additional thin layer.

Diversity in the cag pathogenicity island of Helicobacter pylori isolates in populations from North and South India.

The cag pathogenicity island (cagPAI) has been reported to be the major virulence determinant in Helicobacter pylori-related diseases. In the present study, the diversity of the cagA gene and the integrity of the cagPAI in 158 H. pylori strains from Varanasi (North India) and Hyderabad (South India) were studied by amplifying the cagA gene (approximately 3.5 kb), followed by PCR-RFLP analysis. The results revealed significant differences in the cagA gene and the integrity of the cagPAI between North and South Indian isolates. Of 158 isolates, 40 (34.8 %) from Varanasi and 20 (46.5 %) from Hyderabad were found to carry an intact cagPAI. A partially deleted cagPAI was present in 75 (65.2 %) isolates from Varanasi and 23 (53.5 %) from Hyderabad. None of the isolates showed complete deletion of the cagPAI. Differences in the cagA 5 and 3 regions were also noted, and 11 isolates (8 from Varanasi and 3 from Hyderabad) that were cagA negative with primers for the 5 region turned out to be cagA positive with primers for the 3 variable region. It is tentatively concluded that the 3 variable region may be a better marker for cagA typing. The results also showed that the majority of the isolates harboured the Western-type EPIYA motif. PCR-RFLP analysis of the cagA gene showed 29 distinguishable digestion patterns, and cluster analysis of RFLP types from a random selection of 32 isolates placed all of the isolates into 5 groups. These results demonstrate that significant differences in the cagPAI occur among isolates from North and South India, and that RFLP of cagA could be employed for elucidating genetic variations among various isolates of H. pylori.

Direct detection and analysis of vacA genotypes and cagA gene of Helicobacter pylori from gastric biopsies by a novel multiplex polymerase chain reaction assay

Several tests/methods for the infection, detection, and genotyping of Helicobacter pylori have been developed in the past; all these differ in specificity and sensitivity and thereby could not be routinely used in clinical study especially in resource-poor developing countries. In the present study, a novel method based on multiplex polymerase chain reaction (PCR) assay was developed to detect H. pylori in patients suffering from gastrointestinal diseases. This method does not require steps of sonication, boiling, or centrifugation for obtaining DNA from biopsy samples, which are otherwise prerequisite in detecting H. pylori by PCR assay. Two hundred seventy-six patients were examined, of which 182 cases (excluding 36 patients having multiple H. pylori strain infection and 8 showing amplification of 16S rDNA only) were H. pylori positive. The dominant vacA genotype was s1 and m1 being present in 168 (92.3%) and 106 (58.2%) patients, respectively, followed by m2 (41.7%), and the lowest being s2 (7.7%). Detection of H. pylori by this method seems rapid, simpler, and suitable for both types 1 and 2 bacteria. Furthermore, genotyping of vacA and cagA genes could also be routinely performed in a large number of patients for diagnostic purposes.

Genetic diversity in strains of Helicobacter pylori from India and their relatedness to strains from other parts of the world

Helicobacter pylori is predominantly transmitted within families and infection occurs mostly in early childhood, frequently leading to persistent infection lifelong. In the present study, genetic diversity of Helicobacter pylori among North and South Indian isolates was evaluated. 16S rDNA, cagA, vacA and iceA genes were amplified followed by sequencing of respective amplicons for diversity analysis. Result of PCR assay showed that status of pathogenicity genes varied among strains from Varanasi and Hyderabad. Phylogenetic analysis based on 16S rDNA sequences showed clustering of Hyderabad and Varanasi strains in separate groups, pointing to significant diversity. Additionally, phylogenetic analysis revealed that most of the Varanasi strains shared homology with the strains from Taiwan except for two isolates which matched with an isolate from Brazil. On the other hand majority of the Hyderabad strains showed relatedness with strains from Brazil except one which showed homology with one strain from Taiwan. In conclusion our results show that genetic diversity among H. pylori isolates is widely prevalent regardless of the region from which they are isolated. More interestingly, phylogenetic analysis suggests that the Indian strains of H. pylori show close homology to those from Taiwan and/or Brazil.