A comparative whole genome analysis of Helicobacter pylori from a human dense South Asian setting

Helicobacter pylori, a Gram-negative bacterium, is associated with a wide range of gastric diseases such as gastritis, duodenal ulcer, and gastric cancer. The prevalence of H pylori and risk of disease vary in different parts of the world based on the prevailing bacterial lineage. Here, we present a contextual and comparative genomics analysis of 20 clinical isolates of H pylori from patients in Bangladesh. Despite a uniform host ethnicity (Bengali), isolates were classified as being part of the HpAsia2 (50%) or HpEurope (50%) population. Out of twenty isolates, eighteen isolates were cagA positive, with two HpEurope isolates being cagA negative, three EPIYA motif patterns (AB, AB-C, and ABC-C) were observed among the cagA-positive isolates. Three vacA genotypes were observed with the s1m1i1dic1 genotype observed in 75% of isolates; the s1m2i1d1c2 and s2m2i2d2c2 genotypes were found to be 15% and 10% of isolates, respectively. The non-virulent genotypes s2m2i2d2c2 was only observed in HpEurope population isolates. Genotypic analysis of oipA gene, present in all isolates, revealed five different patterns of the CT repeat; all HpAsia2 isolates were in “ON” while 20% of HpEurope isolates were genotypically “OFF.” The three blood group antigen binding adhesins encoded genes (bab genes) examined and we observed that the most common genotype was (babA/babB/-) found in eight isolates, notably six were HpAsia2 isolates. The babA gene was found in all HpAsia2 isolates but present in only half of the HpEurope isolates. In silico antibiotic susceptibility analysis revealed that 40% of the strains were multi-drug resistant. Mutations associated with resistance to metronidazole, fluoroquinolone, and clarithromycin were detected 90%, 45%, and 5%, respectively, in H pylori strain. In conclusion, it is evident that two populations of H pylori with similar antibiotic profiles are predominant in Bangladesh, and it appears that genotypically the HpAisa2 isolates are potentially more virulent than the HpEurope isolates.     

Potential health benefits of anthocyanins in oxidative stress related disorders

Phytochemistry Reviews - Anthocyanins are naturally occurring water-soluble plant pigments belonging to the flavonoids chemical class. The red, blue and purple colours of leaves, flowers and fruits...     

Trophic functioning and nutrient flux in a highly productive tropical lagoon

Chiku Lagoon is a highly productive tropical lagoon with high fishery yields. Trophic networks and stoichiometrically linked water-salt-nutrient budgets were constructed to relate the functioning of the food web to nonconservative behavior of nutrients in the lagoon. Network analysis showed that the lagoon is more dependent on phytoplankton than detritus and periphyton to generate food sources for consumers. Nevertheless, detritivory is more important than herbivory in the food web. Transfer efficiency is high at low trophic levels, but declines at higher levels due to the high fishery pressure. Thus, only a small fraction of organic matter (15%) is recycled, and this all through detrital pathways, most of which involve only two compartments. Summation of individual rate measurements for primary production and respiration yielded an estimate of +249 g C m^-2 year^-1, suggesting an autotrophic ecosystem. An alternative biogeochemical approach demonstrated that the lagoon is a large sink for total dissolved nitrogen and phosphorus, and the net system metabolism was calculated to be +144 g C m^-2 year^-1, thus providing a biogeochemical explanation for the high productivity of Chiku Lagoon. Our results suggest that the high fishery yield in Chiku Lagoon can be attributed to high planktonic productivity induced by the high rate of nutrient loading, and the straight-through pathways of the food web.     

Comparative study on the inactivation of MS2 and M13 bacteriophages using energetic femtosecond lasers

Femtosecond (fs) laser irradiation techniques are emerging tools for inactivating viruses that do not involve ionizing radiation. In this work, the inactivation of two bacteriophages representing protective capsids with different geometric constraints, that is, the near‐spherical MS2 (with a diameter of 27 nm) and the filamentous M13 (with a length of 880 nm) is compared using energetic visible and near‐infrared fs laser pulses with various energies, pulse durations, and exposure times. Intriguingly, the results show that inactivation using 400 nm lasers is substantially more efficient for MS2 compared to M13. In contrast, using 800 nm lasers, M13 was slightly more efficiently inactivated. For both viruses, the genome was exposed to a harmful environment upon fs‐laser irradiation. However, in addition to the protection of the genome, the metastable capsids differ in many properties required for stepwise cell entry that may explain their dissimilar behavior after (partial) disassembly. For MS2, the dominant mechanism of fs‐laser inactivation was the aggregation of the viral capsid proteins, whereas aggregation did not affect M13 inactivation, suggesting that the dominant mechanism of M13 inactivation was related to breaking of secondary protein links.     

The world distribution of the electrophoretic variants of the red cell enzyme esterase D.

The phenotypic variation in the esterase D phenotypes among 2,405 individuals in 14 samples from populations in Europe, Africa and Asia are reported. There exists a marked difference in esterase D allele frequencies in different continental regions. Comparison of the world population data so far available show that esterase D is another useful genetic parameter for the study of population diversity.     

Screening for natural inhibitors of human topoisomerases from medicinal plants with bio-affinity ultrafiltration and LC–MS

Phytochemistry Reviews - The continuing rise in cancer morbidity and mortality all over the world makes cancer the No. 2 cause of death in humans, posing a major public health challenge. Currently,...