Characterisation of downy mildew resistant and susceptible pearl millet (Pennisetum glaucum (L.) R.Br.) genotypes using isozyme,protein, randomly amplified polymorphic DNA and inter-simple sequence repeat markers

In the present investigation, downy mildew resistant and susceptible pearl millet genotypes were characterised using seed protein and isozymes at pre- [45 days after sowing (DAS)] and post-infection (57 DAS, i.e. 7 days after infection) stage, as well as molecular markers at seedling stage without infection. Native polyacrylamide gel electrophoreis (PAGE) isozyme banding pattern of superoxide dismutase (SOD), peroxidase (POX), catalase (CAT), ascorbate peroxidase (APX) and esterase showed some inducible band(s) due to disease infection and differentiated resistant and susceptible genotypes. Total seed protein profiling revealed the presence of two unique protein of ～97 and ～100 kDa in resistant genotypes. Randomly amplified polymorphic DNA (RAPD) analysis did not show any specific marker for disease resistant and susceptible genotypes. However, inter-simple sequence repeat (ISSR) markers showed six markers in resistant genotypes viz., UBC-825 (900 bp), UBC-827 (900 bp), UBC-857 (1000 bp, 700 bp, 375 bp and 200 bp). Moreover, a single unique band UBC-857 (400 bp) was present in only susceptible genotypes. Overall pooled analysis of isozymes, protein profiling, RAPD and ISSR data showed two distinct clusters of resistant and susceptible genotypes. These results suggested that seed protein profiling and ISSR markers may be used for large scale screening of germplasm for disease reaction trait.     

Fast calculation of the quartet distance between trees of arbitrary degrees

Background  

A number of algorithms have been developed for calculating the quartet distance between two evolutionary trees on the same set of species. The quartet distance is the number of quartets – sub-trees induced by four leaves – that differs between the trees. Mostly, these algorithms are restricted to work on binary trees, but recently we have developed algorithms that work on trees of arbitrary degree.     

Chemical modification of alpha-chymotrypsin for obtaining high transesterification activity in low water organic media

Alpha-chymotrypsin was made more hydrophilic by modifying 11 (out of 16) ε-amino groups with pyromellitic dianhydride. The hydrophilic preparation was precipitated with n-propanol. This preparation gave significantly higher initial rates at the optimum a_w (127.51 nmol mg^?1 min^?1 in n-octane and 21.30 nmol mg^?1 min^?1 in acetonitrile at a_w=0.33) compared with the lyophilized preparation (53.50 nmol mg^?1 min^?1 in n-octane and 0.26 nmol mg^?1 min^?1 in acetonitrile at a_w=0.97). FT-IR showed that the precipitate of modified alpha-chymotrypsin has a higher content of alpha-helices and beta-sheets compared to the lyophilized powder.     

Microsatellite diversity among the primitive tribes of India

The present study was undertaken to determine the extent of diversity at 12 microsatellite short tandem repeat (STR) loci in seven primitive tribal populations of India with diverse linguistic and geographic backgrounds. DNA samples of 160 unrelated individuals were analyzed for 12 STR loci by multiplex polymerase chain reaction (PCR). Gene diversity analysis suggested that the average heterozygosity was uniformly high ( >0.7) in these groups and varied from 0.705 to 0.794. The Hardy-Weinberg equilibrium analysis revealed that these populations were in genetic equilibrium at almost all the loci. The overall G(ST) value was high (G(ST) = 0.051; range between 0.026 and 0.098 among the loci), reflecting the degree of differentiation/heterogeneity of seven populations studied for these loci. The cluster analysis and multidimensional scaling of genetic distances reveal two broad clusters of populations, besides Moolu Kurumba maintaining their distinct genetic identity vis-à-vis other populations. The genetic affinity for the three tribes of the Indo-European family could be explained based on geography and Language but not for the four Dravidian tribes as reflected by the NJT and MDS plots. For the overall data, the insignificant MANTEL correlations between genetic, linguistic and geographic distances suggest that the genetic variation among these tribes is not patterned along geographic and/or linguistic lines.     

Microbial Inoculants with Multifaceted Traits Suppress Rhizoctonia Populations and Promote Plant Growth in Cotton

The suppressive effects of microbial inoculants on cotton seedling mortality were assessed in Rhizoctonia solani‐infested soil. Per cent mortality ranged from 16 to 32 (60–120 days after sowing, DAS) and significant differences were recorded at 120 DAS, especially after drenching with compost tea of Azotobacter sp. and Anabaena torulosa—Trichoderma viride‐biofilmed formulations. The activity of hydrolytic enzymes was reduced in diseased root tissues due to a majority of the microbially inoculated treatments, compared with healthy root tissues. Per cent changes in the amounts of glomalin‐related soil proteins (GRSPs) were 2 to 85% greater than those of the uninoculated experimental controls. These microbial inoculants altered the rhizosphere bacterial communities as evident from the Denaturing gradient gel electrophoresis (DGGE) banding patterns and, also reduced the population of R. solani. While the copy numbers of the internal transcribed spacer (ITS) gene of R. solani in the uninoculated (infested soil) were approximately 1.47 × 10¹¹ per g soil, they were 1.34–1.42 × 10⁵ per g soil after the application of A. torulosa, Anabaena laxa and A. torulosa–Bacillus sp. Increases in yield (ranging from 3 to 23%) due to various microbial inoculants relative to uninoculated controls illustrated their promise as plant growth‐promoting and disease‐suppressing agents. This study illustrates the modulation of rhizosphere ecology through microbial inoculants as a mechanism of disease suppression and sustaining plant growth.     

FANCA Gene Mutations with 8 Novel Molecular Changes in Indian Fanconi Anemia Patients

Fanconi anemia (FA), a rare heterogeneous genetic disorder, is known to be associated with 19 genes and a spectrum of clinical features. We studied FANCA molecular changes in 34 unrelated and 2 siblings of Indian patients with FA and have identified 26 different molecular changes of FANCA gene, of which 8 were novel mutations (a small deletion c.2500delC, 4 non-sense mutations c.2182C>T, c.2630C>G, c.3677C>G, c.3189G>A; and 3 missense mutations; c.1273G>C, c.3679 G>C, and c.3992 T>C). Among these only 16 patients could be assigned FA-A complementation group, because we could not confirm single exon deletions detected by MLPA or cDNA amplification by secondary confirmation method and due to presence of heterozygous non-pathogenic variations or heterozygous pathogenic mutations. An effective molecular screening strategy should be developed for confirmation of these mutations and determining the breakpoints for single exon deletions.     

Has introduction of rapid drug susceptibility testing at diagnosis impacted treatment outcomes among previously treated tuberculosis patients in Gujarat,India?

Background

Revised National TB Control Programme (RNTCP) in India recommends that all previously-treated TB (PT) patients are offered drug susceptibility testing (DST) at diagnosis, using rapid diagnostics and screened out for rifampicin resistance before being treated with standardized, eight-month, retreatment regimen. This is intended to improve the early diagnosis of rifampicin resistance and its appropriate management and improve the treatment outcomes among the rest of the patients. In this state-wide study from Gujarat, India, we assess proportion of PT patients underwent rapid DST at diagnosis and the impact of this intervention on their treatment outcomes.

Methods

This is a retrospective cohort study involving review of electronic patient-records maintained routinely under RNTCP. All PT patients registered for treatment in Gujarat during January-June 2013 were included. Information on DST and treatment outcomes were extracted from ''presumptive DR-TB patient register'' and TB treatment register respectively. We performed a multivariate analysis to assess if getting tested is independently associated with unfavourable outcomes (death, loss-to-follow-up, failure, transfer out).

Results

Of 5,829 PT patients, 5306(91%) were tested for drug susceptibility with rapid diagnostics. Overall, 71% (4,113) TB patients were successfully treated - 72% among tested versus 60% among non-tested. Patients who did not get tested at diagnosis had a 34% higher risk of unsuccessful outcomes as compared to those who got tested (aRR - 1.34; 95% CI 1.20-1.50) after adjusting for age, sex, HIV status and type of TB. Unfavourable outcomes (particularly failure and switched to category IV) were higher among INH-resistant patients (39%) as compared to INH-sensitive (29%).

Conclusion

Offering DST at diagnosis improved the treatment outcomes among PT patients. However, even among tested, treatment outcomes remained suboptimal and were related to INH resistance and high loss-to-follow-up. These need to be addressed urgently for further progress.     

Fluorometric procedures for measuring triglyceride concentrations in small amounts of tissue and plasma

It has been previously shown that triglycerides can be specifically hydrolyzed by lipase from Rhizopus arrhizus in the presence of hog liver esterase and sodium dodecyl sulfate. The glycerol produced can then be measured by sequential reactions with glycerokinase, pyruvate kinase, and lactate dehydrogenase: glycerol and ATP are converted to glycerol-3-phosphate and ADP by glycerokinase; the ADP reacts with phosphoenolpyruvate and pyruvate kinase to yield pyruvate; the pyruvate is converted to lactate with lactate dehydrogenase, and the cofactor NAD+ is simultaneously reduced to NADH. This report describes procedures by which either the disappearance of NADH or the appearance of NAD+ was determined fluorometrically, with 10- to 100-fold greater sensitivity than by spectrophotometry. In addition, enzymatic cycling of NAD+ was used to increase the sensitivity of the assay over 1000-fold, and thereby provided accurate measurement of less than 1 ng of triglyceride. Results obtained from the three fluorometric methods were highly correlated with an automated periodate oxidation method using serum samples and lipid extracts of muscle tissue.     

Early generation yield testing versus visual selection in chickpea (Cicer arietinum L.)

Summary Four F₃ populations of chickpea (Cicer arietinum L.) were simultaneously evaluated for yield in an F₃ yield trial and in single plant progeny rows. Ten high yielding, 10 low yielding and 10 randomly sampled lines, along with 10 lines visually selected for yield from the progeny rows, were retained for further evaluation. The lines from each of the four selection groups in each population were bulked and evaluated in a replicated yield trial at three locations and four environments. The bulk of visually selected lines was not superior in yield to the bulk of randomly sampled lines at all locations. The present results indicate that an early generation yield testing selection procedure is more efficient than visual selection for yield improvements in chickpea.