Ashok Kumar Jain

Diagnosis of Helicobacter pylori: What should be the gold standard?

Since the discovery of Helicobacter pylori (H. pylori) in 1983, numerous detection methods for the presence of the bacterium have been developed. Each one of them has been associated with advantages and disadvantages. Noninvasive tests such as serology, (13)C urea breath test (UBT) and stool antigen tests are usually preferred by the clinicians. Serology has its own limitation especially in endemic areas while (13)C UBT is technically very demanding. The stool antigen detection method, although specific, is usually associated with poor sensitivity. The (13)C UBT is believed to be specific, but with present revelation of the fact that stomach is colonized by many other urease producing bacteria makes it questionable. Histology, culture, rapid urease test and polymerase chain reaction (PCR) are the tests which are carried out on antral biopsies collected by invasive means. Histology has been proposed to be very sensitive and specific but the question is how by simply looking the morphology of the bacteria in the microscope, one can claim that the curved bacterium is exclusively H. pylori. Rapid urease test (RUT), the doctors test, is also challenged because the presence of other urease producing bacteria in the stomach cannot be denied. Moreover, RUT has been reported with poor sensitivity specially, when density of the bacterium is low. Isolation of H. pylori is essential to investigate its growth requirements, antibiotic susceptibility testing, studying virulence factor to develop vaccine and many more explorations. It has also got several disadvantages i.e., special condition for transporting, media, incubation and few days waiting for the colonies to appear, apart from the speed essentially needed to process the specimens. Till date, majority of the microbiological laboratories in the world are not equipped and trained to isolate such fastidious bacterium. The option left is PCR methods to detect H. pyloris DNA in gastric mucosa, gastric juice, saliva, dental plaques and environmental specimens. There are speculations for false positivity due to detection of non-pylori Helicobacters due to genetic sharing; and false negativity due to low bacterial counts and presence of PCR inhibitors. However, specimen collection, transportation and processing do not require speed and special conditions. PCR based diagnosis may be considered as gold standard by designing primers extremely specific to H. pylori and targeting at least more than one conserved genes. Similarly specificity of PCR may be improved by use of internal Primers. Further, nested PCR will take care of false negatives by countering the effect of PCR inhibitors and low bacterial counts. Therefore, nested PCR based methods if performed properly, may be proposed as gold standard test.

The mechanism of signature inversion in odd-odd rotational bands

Abstract The signature inversion in the rotational bands belonging to high- j configurations of odd-odd deformed nuclei is analysed within the framework of an axially symmetric rotor plus two-particle model. The signature inversion seen in 160 Ho is reproduced very well, and the mechanism for it is pointed out. While a similar mechanism is seen to operate in 152 Eu and 156 Tb, it has not been possible to reproduce the inversion in these two cases.

Pseudomonas fluorescens-like bacteria from the stomach: A microbiological and molecular study

AIM To characterize oxidase- and urease-producing bacterial isolates, grown aerobically, that originated from antral biopsies of patients suffering from acid peptic diseases. METHODS A total of 258 antral biopsy specimens were subjected to isolation of bacteria followed by tests for oxidase and urease production, acid tolerance and aerobic growth. The selected isolates were further characterized by molecular techniques viz. amplifications for 16S rRNA using universal eubacterial and HSP60 gene specific primers. The amplicons were subjected to restriction analysis and partial sequencing. A phylogenetic tree was generated using unweighted pair group method with arithmetic mean (UPGMA) from evolutionary distance computed with bootstrap test of phylogeny. Assessment of acidity tolerance of bacteria isolated from antrum was performed using hydrochloric acid from 10(-7) mol/L to 10(-1) mol/L. RESULTS Of the 258 antral biopsy specimens collected from patients, 179 (69.4%) were positive for urease production by rapid urease test and 31% (80/258) yielded typical Helicobacter pylori (H. pylori) after 5-7 d of incubation under a microaerophilic environment. A total of 240 (93%) antral biopsies yielded homogeneous semi-translucent and small colonies after overnight incubation. The partial 16S rRNA sequences revealed that the isolates had 99% similarity with Pseudomonas species. A phylogenetic tree on the basis of 16S rRNA sequences denoted that JQ927226 and JQ927227 were likely to be related to Pseudomonas fluorescens (P. fluorescens). On the basis of HSP60 sequences applied to the UPGMA phylogenetic tree, it was observed that isolated strains in an aerobic environment were likely to be P. fluorescens, and HSP60 sequences had more discriminatory potential rather than 16S rRNA sequences. Interestingly, this bacterium was acid tolerant for hours at low pH. Further, a total of 250 (96.9%) genomic DNA samples of 258 biopsy specimens and DNA from 240 bacterial isolates were positive for the 613 bp amplicons by targeting P. fluorescens-specific conserved putative outer membrane protein gene sequences. CONCLUSION This study indicates that bacterial isolates from antral biopsies grown aerobically were P. fluorescens, and thus acid-tolerant bacteria other than H. pylori can also colonize the stomach and may be implicated in pathogenesis/protection.

IMPACT OF SERC'S FUNDING ON RESEARCH IN CHEMICAL SCIENCES

The paper assesses impact of Science and Engineering Research Council (SERC) funding in chemical sciences during 1976–1989 using scientometric techniques. Other indicators like awards won, fellowship to prestigious academies, membership to editorial boards received by the project investigators, Ph.D. degrees awarded, collaborations established and new courses introduced due to SERC funding have also been analyzed. The study indicates that activity index of research out put in various frontier areas of chemical sciences have gone up despite a decrease in Indian activity index in these areas. The growth pattern of papers for “Organometallic and Organometalloidal Compounds” are similar for India and world. Contribution of SERCs project investigators in high impact factor (≥2) journals and the citations received by the papers published by them are higher than Indian contributions in chemical sciences. The SERC funding has resulted in a three fold increase in the number of Ph.D. degrees awarded in chemical sciences and SERC project investigators have won many prestigious awards, fellowship to academies and membership of the editorial board of the journals. The SERC funded research has also resulted in new courses at various universities.

Odd-even staggering in the K = 1, 2, 3 and 4 rotational bands of deformed odd-odd nuclei

Abstract An analysis of the rotational structure of the K = |Ω p − Ω n | bands in the odd-odd nuclei from the rare earth region reveals an odd-even staggering in the level energies. Such an odd-even effect is present, sometimes very prominently, in almost all the K − bands with K values ranging from 1 to 4. We find that complete Coriolis coupling calculations are able to explain most of the staggering in the four nuclei studied. However, the K = 2 + and K = 4 − bands in 182 Re cannot be explained satisfactory.

Low-energy electron-SiH4 collisions using a parameter-free spherical optical potential

The authors investigate low-energy (0.1-30 eV) electron -SiH4 scattering by employing a parameter-free optical potential which is a sum of three spherical terms, namely the static, exchange and polarisation forces. The authors demonstrate that the qualitative features of the scattering parameters (such as a Ramsauer-Townsend minimum below 1 eV and a shape resonance structure around 2-3 eV) observed in recent experiments, can be very well reproduced in the present simple model. Quantitatively, the authors results (below 10 eV) are very close to the recent close-coupling calculations of Jain and Thompson (1982) and Gianturco et al (1987) using a similar kind of (but non-spherical) model optical potential. Above 10 eV, the present results are in fair agreement with experiments and are better than the earlier calculations.

Role of Proinflammatory Cytokines (Interferon Gamma) and Anti-Inflammatory Cytokine (Interleukin-10) Gene Polymorphisms in Chronic Hepatitis B Infection: An Indian Scenario

Immune-mediated mechanisms have been found to play an important role in the progression of hepatitis B virus (HBV) infection. The outcomes of infection do not appear to be determined by viral strains. Instead, allelic variants in human genome are likely to affect the disease progression. Allelic variation of proinflammatory cytokines such as interferon gamma (IFN-γ) participates in the elimination of HBV, and interleukin-10 (IL-10) helps in inhibition of Th1 effector mechanisms for host defense. The aim of this study was to determine the influence of host genetic factors in chronic HBV infection and gene promoter polymorphism or single-nucleotide polymorphism analysis of IFN-γ+874 and IL-10 (-1082, -592, and -819) on disease progression and persistence. A total of 232 patients along with 76 healthy controls were included. Allele-specific primers for IFN-γ and restriction fragment length polymorphism for IL-10 were used. The study indicated that low IFN-γ expression probably impairs host immune response to HBV, rendering these subjects more prone to HBV infection. No significant differences were detected between the 2 groups in the distributions of IL-10 genotype at the -1082, -819, and -592 positions. Odds ratio indicated that heterozygosity of genotypes -819 CT and -592 AC was more strongly associated with liver chronicity. Significantly, AA homozygous genotype was dominant in chronic hepatitis B cases in IFN-γ+874 and IL-10 (-1082 and -592) and is associated with increased risk of persistent infection.

Helicobacter pylori Is Not Eradicated after Triple Therapy: A Nested PCR Based Study

Detection of Helicobacter pylori after triple therapy is usually carried out by either rapid urease test (RUT), urea breath test (UBT), histology, bacterial isolation, and single round PCR or serological tests. In this study, antral biopsy specimens from 25 patients were tested for H. pylori by RUT, culture, histology, and nested PCR in their antral biopsy specimens before and after treatment. Three genes, namely, heat shock protein (hsp60), phosphoglucosamine mutase (ureC), and flagellar export ATP synthase (fliI) of H. pylori were targeted. Of the 25 antral biopsy specimens, the RUT, culture, histology, and nested PCR positivity dropped from 81.8% to 12%, 31% to 0%, 100 to 84%, and 100% to 92%, respectively, before and after therapy. Further, hsp60 specific amplicons from 23 out of 25 patients gave identical restriction pattern, while 6 fliI and 1 ureC specific amplicon produced different restriction pattern. Furthermore, variations in fliI gene sequences in H. pylori after treatment were also confirmed by sequencing and compared in silico. Nested PCR based detection of H. pylori is more sensitive method to detect H. pylori after therapy than culture, RUT, and histology. Further, this study suggests that H. pylori is not eradicated completely after triple therapy.

Mucosal IgA & IL-1β in Helicobacter pylori Infection.

Helicobacter pylori infection stimulates strong local inflammatory and specific IgA antibody production. The influence of antibodies on the bacterial colonization is not clear. Here, we have analysed the association between the mucosal IgA level and IL-1β in various manifestations of the infection seen endoscopically. Antral biopsies of 57 dyspeptic patients were taken for culture, histology and estimation of mucosal levels of anti-H. pylori IgA and IL-1β. Mean mucosal IgA level was higher in patients with normal mucosa compared to all other groups and lower IgA level was associated with higher bacterial density. IL-1β was higher in ulcer patients and suspicious malignancy group as compared to normal group and higher level of IL-1β was associated with higher grades of metaplasia. Present study indicates that local immunity seems to have a protective role against H. pylori infection and higher level of IL-1β induced by the pathogen may be associated with metaplasia and carcinogenesis.

Strongly coupled bands as “effectively” decoupled bands

We present experimental evidence which suggests that almost all the strongly coupled bands in the rare-earth region may also be treated as “effectively” decoupled bands. In contrast to the usual decoupled bands, the strongly coupled bands seem to arise from a system where a particle carrying an “effective” angular momentumj′ is aligned to an even-even core having an “effective” rotational angular momentumR′ which is not necessarily zero for the band head but may even haveR′=2 or, 4 or, 6⋯etc. We attempt to explain these observations in a simple physical picture whereinJR, the projection ofj, the particle angular momentum, on the rotation axis, is taken as the effectively aligned spin of the last particle. Preliminary results from schematic bandmixing calculations forh9/2 andf5/2 orbitals with the Fermi energy lying near the highK single particle levels indeed reveal the existence of “effectively” decoupled bands which seem to agree with this physical picture.