Isolation and identification of phosphate solubilizing bacteria able to enhance the growth and aloin-A biosynthesis of Aloe barbadensis Miller

The effect of four phosphate solubilizing bacteria (PSB) was studied on growth and aloin-A content of Aloe barbadensis in soil containing tricalcium phosphate (TCP). PSB were identified based on 16S rRNA gene sequencing as Pseudomonas synxantha, Burkholderia gladioli, Enterobacter hormaechei and Serratia marcescens. These PSB solubilized 25-340 μg ml(-1) of TCP into the liquid phase. The treatment of plants with individual PSB or mixture of these increased soil available P, P uptake in plants and plant growth. The increase in aloin-A content due to higher plant biomass and unit biomass production was 673%, 294%, 276%, 119% and 108% in plants treated with a PSB consortium, P. synxantha, S. marcescens, B. gladioli, and E. hormaechei in TCP amended soil, respectively.     

A genetic discontinuity in root-nodulating bacteria of cultivated pea in the Indian trans-Himalayas

Evolutionary relationships of 120 root‐nodulating bacteria isolated from the nodules of Pisum sativum cultivated at 22 different locations of the trans‐Himalayan valleys of Lahaul and Spiti in the state of Himachal Pradesh of India were studied using 16S rRNA gene PCR‐RFLP, ERIC‐PCR, sequencing of 16S rRNA, atpD, recA, nodC and nifH genes, carbon‐source utilization pattern (BIOLOG?), and whole‐cell fatty acid profiling. The results demonstrated that all isolates belonged to Rhizobium leguminosarum symbiovar viciae (Rlv). Isolates from the two valleys were clearly separated on the basis of ERIC fingerprints, carbon‐source utilization pattern, and whole‐cell fatty acid methyl esters. Phylogenetic analysis of atpD, recA, nodC and nifH genes revealed a common Rlv sublineage in Spiti valley. Lahaul valley isolates were represented by three sequence types of atpD and recA genes, and four sequence types of nodC and nifH genes. Genotypes from the two valleys were completely distinct, except for two Lahaul isolates that shared nodC and nifH sequences with Spiti isolates but were otherwise more similar to other Lahaul isolates. Isolates from the two highest Spiti valley sites (above 4000 m) had a distinctive whole‐cell fatty acid profile. Spiti valley isolates are closely related to Rlv sublineages from Xinjiang and Shanxi provinces in China, while Lahaul valley isolates resemble cosmopolitan strains of the western world. The high mountain pass between these valleys represents a boundary between two distinct microbial populations.     

A biochemically active MCM-like helicase in Bacillus cereus

The mini-chromosome maintenance (MCM) proteins serve as the replicative helicases in archaea and eukaryotes. Interestingly, an MCM homolog was identified, by BLAST analysis, within a phage integrated in the bacterium Bacillus cereus (Bc). BcMCM is only related to the AAA region of MCM-helicases; the typical amino-terminus is missing and is replaced by a segment with weak homology to primases. We show that BcMCM displays 3′→5′ helicase and ssDNA-stimulated ATPase activity, properties that arise from its conserved AAA domain. Isolated BcMCM is a monomer in solution but likely forms the functional oligomer in vivo. We found that the BcMCM amino-terminus can bind ssDNA and harbors a zinc atom, both hallmarks of the typical MCM amino-terminus. No BcMCM-catalyzed primase activity could be detected. We propose that the divergent amino-terminus of BcMCM is a paralog of the corresponding region of MCM-helicases. A divergent amino terminus makes BcMCM a useful model for typical MCM-helicases since it accomplishes the same function using an apparently unrelated structure.     

Can human papillomavirus DNA testing of self-collected vaginal samples compare with physician-collected cervical samples and cytology for cervical cancer screening in developing countries?

Background: To determine human papillomavirus (HPV) types by polymerase chain reaction (PCR)-reverse line blot assay and examine the concordance between HPV by Hybrid Capture 2 (HC2) and PCR on self-collected vaginal and physician-collected cervical samples and cytology. Methods: This was a cross-sectional study of 546 sexually active women aged ≥30 years with persistent vaginal discharge, intermenstrual or postcoital bleeding or an unhealthy cervix. Participants self-collected vaginal samples (HPV-S) and physicians collected cervical samples for conventional Pap smear and HPV DNA (HPV-P) testing and performed colposcopy, with directed biopsy, if indicated. HPV testing and genotyping was done by HC2 and PCR reverse line blot assay. Concordance between HC2 and PCR results of self- and physician-collected samples was determined using a Kappa statistic (κ) and Chi-square test. Results: Complete data were available for 512 sets with 98% of women providing a satisfactory self-sample. PCR detected oncogenic HPV in 12.3% of self- and 13.0% of physician-collected samples. Overall, there was 93.8% agreement between physician-collected and self-samples (κ = 76.31%, 95% confidence interval [CI]: 64.97–82.29%, p = 0.04)—complete concordance in 473 cases (57 positive, 416 negative), partial concordance in seven pairs and discordance in 32 pairs. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of self-sampling for detection of cervical intraepithelial neoplasia (CIN)2+ disease were 82.5%, 93.6%, 52.4% and 98.4%, respectively; for physician-sampling they were 87.5%, 93.2%, 52.2% and 98.9%, respectively; and for cytology they were 77.5%, 87.3%, 34.1% and 97.9%, respectively. Concordance between HC2 and PCR was 90.9% for self-samples (κ = 63.7%, 95% CI: 55.2–72.2%) and 95.3% for physician-collected samples (κ = 80.4%, 95% CI: 71.8–89.0%). Conclusions: Self-HPV sampling compares favourably with physician-sampling and cytology. A rapid, affordable, HPV self-test kit can be used as the primary method of cervical cancer screening in low-resource situations.     

Catechin and Catechin Fractions as Biochemical Markers to Study the Diversity of Indian Tea (Camellia sinensis (L.) O. Kuntze) Germplasm

The heterogeneous Indian tea germplasm includes ‘China’, ‘Assam’, ‘Cambod’, and their hybrids which were evaluated using biochemical markers viz., total catechin and their fractions, for varietal identification and characterization. Principal component analysis (PCA) of biochemical characters showed that the total catechin and trihydroxylated catechin has higher eigenvalues. The first two principal components (PCs) could differentiate more than 90% of the clones studied. This grouping based on first two principal component matrices differentiated ‘China’, and their hybrids with ‘Assam’ and ‘Cambod’ variety. Morphologically indistinct large‐leaved ‘Cambod’ variety and ‘Assam’ varieties could not be differentiated using biochemical markers, since both varietal types taxonomically belong to a single species. Clones of ‘China’ type showed low total catechin content and catechin ratio which are distinctly grouped. The ‘China–Assam’ and ‘China–Cambod’ hybrids formed intermediate groups between ‘China’ PC group and ‘Cambod’/‘Assam’ PC groups, providing evidence for genetic control of catechin ratio variation. Tea clones which are differentially positioned in the PC group could be explained based on the genetic contribution by other varietal type as parents. This biochemical characterization will be a useful tool in the development of quality‐tea clones with different proportion of total catechin and their fractions.     

Some generalizations based on stratification and vertical mixing in meromictic Lake Shira,Russia, in the period 2002–2009

In a brackish, temperate, 24-m-deep Lake Shira, the profiles of salinity, temperature, oxygen and sulfide concentrations were measured on a seasonal basis from 2002 to 2009. The lake was shown to be meromictic with autumnal overturn restricted to mixolimnion. The depth of mixolimnion and position of oxic–anoxic interface varied annually. The spring mixing processes contribute to the formation of mixolimnion in autumn. The exceptionally windy spring of 2007 caused the deepening of mixolimnion in the winter of 2008. The winter position of oxic–anoxic interface was affected by the position of lower boundary of mixolimnion in all winters. The salinity in the winter mixolimnion increased compared with the autumn because of freezing out of salts from the upper water layers meters during ice formation and their dissolution in water below. The profiles of salinity and temperature were simulated by the mathematical 1-D model of temperature and salinity conditions taking into account ice formation. The simulated profiles generally coincided with the measured ones. The coincidence implies that simplified one-dimensional model can be applied to roughly describe salinity and density profiles and mixing behavior of Lake Shira.     

Prevalence of human papillomavirus infection among young women in North India

Background: The number of women infected with human papillomavirus (HPV) and the distribution of the HPV genotypes vary across populations and with age. Objective: To determine the prevalence and genotype distribution of HPV in young married women aged 16–24 years. Methods: 1300 women residing in an urban slum in Delhi donated samples of exfoliated cervical cells that were collected by the Digene^® kit and tested for the presence of HPV DNA by two techniques in parallel, i.e., PCR using PGMY consensus primers for all HPV types and the Digene HPV test (Hybrid Capture 2 (HC2) Probe B for high-risk (hr) types. Genotyping was done on all HPV positive samples using the Roche reverse line blot assay. Results: HPV infection was detected in 91/1300 (7%) samples by PCR and 110/1300 (8.4%) samples by HC2. Genotyping identified 20 high-risk and 11 low-risk types. HPV16 was the commonest high-risk type (3%) followed by HPV52 (1.2%) and HPV51 (0.8%). Among low-risk types, HPV62 was the commonest (0.8%), followed by HPV84 and HPV89 (0.5% each). Multiple infections were found in 3% of the HPV positive samples. Conclusion: A wide spectrum of HPV genotypes is seen in this young population. Knowledge about HPV types prevalent in communities in different regions of India would be useful in devising the optimum strategy for cervical cancer prevention.