Genetic admixture and population structure analysis of Indian water buffaloes (Bubalus bubalis) using STR markers.

BACKGROUND: India has a vast riverine and swamp buffalo diversity adapted to various agro-ecological conditions. In the present study, genetic diversity data for 10 different buffalo populations of India, using 20 highly polymorphic microsatellite markers has been generated for the genetic diversity analysis. The buffalo populations of Eastern Odisha state, were the primary focus. METHODS AND RESULTS: The minimal spanning network based on Bruvo's distance, PCA (Principal Component Analysis) based on the Fst (Fixation Index) values, and genetic admixture analysis using both the STRUCTURE and 'snapclust' were performed. The analysis could identify the Manda population as distinct from other Odisha buffalo breeds as well as adjoining Chhattisgarhi buffalo breeds. The total observed number of alleles ranged between 143 (Manda) and 301 (Paralakhemundi) with an average of 204 alleles per breed. The Sambhalpuri buffalo population also clustered into two separate subpopulations, half of the unique sub-population located geographically south-wards, displayed no admixture with any of the adjacent buffalo populations. The Manda buffalo population has shown sufficient allelic richness and heterozygosity under random mating being practiced in the field conditions. CONCLUSIONS: The study has led to the identification of the Manda as a distinct buffalo population, and the germplasm has been registered as a new Indian buffalo breed. Whereas, the Sambhalpuri population requires elaborate analysis to confirm the existence of two distinct sub-populations.

Current status and unique attributes of Indian Chilika buffalo for adaptation to brackish water ecology.

Chilika buffalo is native to the Eastern coast of India and well adapted to the largest coastal brackish water lagoon of Asia, Chilika Lake. We present here a report on the Chilika buffalo breed emphasizing the conservational urgency based on unique biochemical and molecular evidence related to liver and kidney functions while comparing it with tropically adapted other water buffalo breeds (Bubalus bubalis) of India. It is found that the Chilika buffalo breed has a better ability to withstand a long dehydration period as evident from its better glomerular filtration and higher expression of the ion transport channel. Mitochondrial D-loop sequencing results have shown these buffaloes being closer to swamp-type buffaloes of Bangladesh and northeast India and represent a unique "hybrid zone" on the eastern coast of India. Conservation of such uniquely adapted germplasm is crucial owing to the current global trend, where the introduction of exotic breeds has negatively impact "sui-generis" germplasm and they require higher managerial resource consumption for maintaining higher productivity. Further, the introduction of unconventional fisheries activities has proved detrimental to the lagoon ecosystem, potentially causing more threat to the buffalo's population.

Mitochondrial sequence-based evolutionary analysis of riverine-swamp hybrid buffaloes of India indicates novel maternal differentiation and domestication patterns.

In this study, mitochondrial D-loop sequence data on riverine, swamp and hybrid buffaloes from India have been generated and compared with other reported Indian riverine, Chinese and Bangladeshi swamp buffalo populations. Sequence analysis revealed the presence of 132 haplotypes, with a haplotype diversity of 0.9611 ± 0.0045 and a nucleotide diversity of 0.04801 ± 0.00126. For the first time, the existence of riverine-swamp hybrids among the Indian Chilika buffalo population has been recorded, having 49 chromosomes, which was also confirmed by mitochondrial haplotype sharing between Chilika and Indian swamp as well as Chinese swamp buffalo populations in the network analysis. Phylogenetic analysis documents the sharing of reported pre-domestication haplogroups 'SA1', 'SA2', 'SA3' and 'SB1' between the Chilika and swamp buffalo populations of India, China and Bangladesh, an indication of the migration of swamp buffaloes towards Bangladesh and adjoining lower parts of India and north towards Chinese domestication sites. The results have also been supplemented by multidimension scaling, grouping Indian and Chinese swamp buffaloes more closely together with Bangladeshi buffaloes, but into a separate quadrant, whereas Chilika grouped away from other riverine as well as swamp buffaloes. These findings thus confirm the previous reports that the northeast region of India, close to the Indo-China border, is the point of evolution of swamp buffaloes with multiple sites of domestication.

Development and evaluation of retort pouch processed chhenapoda (cheese based baked sweet).

A study has been undertaken to optimize ingredient proportions for preparation of chhenapoda and the effect of retort processing on its quality and storability. Chhenapoda was prepared from cottage cheese with standard practices followed by confectioners using different levels of semolina (0, 50, 100, 150, 200 g) and sugar (0, 100, 200, 300, 400 g) per kg cheese and ingredient proportion was optimized based on sensory scores. Prepared chhenapoda sample of 200 g were packed in pre-fabricated 3 side seal multilayer laminated retortable pouches, hermetically sealed and retort processed at different temperatures (100, 110 and 120 °C) and time intervals (15, 30 and 45 min). It was found from Response Surface Methodology (RSM) technique that addition of 18.5% sugar and 7.5% semolina with cottage cheese was optimum for chhenapoda preparation. Microbiological analysis showed that total plate count and yeast and mould count (YMC) decreased from 110 × 107 to 4 × 104 and YMC from 3 × 103 to 0 respectively during retort processing (30 min thermal processing in laminated pouch at 120 °C). From the storage study, it can be concluded that retort processing of chhenapoda in laminated pouch at 120 °C for 30 min resulted in microbiological safe and sensory acceptable product which could be stored up to 30 days under refrigerated condition.

Standardization of process parameters for microwave assisted convective dehydration of ginger.

Ginger (Zingiber Officinale, Cv. Suprava) slices (4 mm thick) were dehydrated at 25°, 40°, 50° and 60 °C with three different microwave power levels, viz. 120, 240, and 360 W in microwave assisted convective dryer up to 0.07 g moisture/g dry solid to observe the feasibility of microwave assisted convective drying for ginger. The samples were also dried without application of microwaves (0 W) at the above air temperatures. The final product quality was compared in terms of rehydration characteristics, oleoresin and volatile oil contents, hardness, color and organoleptic quality. The maximum rehydration ratio of 3.86 ± 0.06 was obtained at 50 °C without application of microwaves and was followed by 120 W-40 °C combination treatment (3.64 ± 0.15). The minimum rehydration ratio was 2.34 ± 0.20 for 360 W with 60 °C. The yield of oleoresin content was higher for 120 W as compared to other power levels, which ranged between 5.12 ± 0.85% and 6.34 ± 0.89%. The maximum retention of oleoresin was observed in case of 120 W-40 °C. The samples dried with microwave power level of 120 W also gave better yields of volatile oil as compared to other power levels. The best color was observed at 120 W-50 °C and 120 W-60 °C conditions with Hunter 'a' (redness) values at 0.50 ± 0.03 and 0.35 ± 0.03, respectively. The sensory analysis also indicated that drying at 120 W-50 °C and 240 W-50 °C combinations gave the most acceptable quality product. Drying ginger with 120 W-50 °C combination helped in a saving of 53% and 44% in drying time as compared to hot air drying at 50° and 60 °C, respectively. Drying at 240 W-50 °C also gave a reasonably acceptable quality product with a net saving of 91% and 89% in drying time as compared to hot air drying at 50° and 60 °C, respectively. However, on the basis of rehydration characteristics, the acceptable process conditions were hot air drying at 50° or 60 °C, or with the 120 W-40 °C combination.

rmpM gene as a genetic marker for human bacterial meningitis.

Meningitis is a bacterial, viral or fungal infection of the protective membrane meninges covering the brain and spinal cord. Viral and other forms of meningitis are mild and get cured within one or two week without any treatment. Whereas, bacterial meningitis can prove lethal if not being diagnosed or treated in time. Meningitis is a contagious infection and can spread from one person to another through coughing, sneezing or close contact. Usually the disease is diagnosed from cerebrospinal fluid (CSF) of the patients using culture, PCR, immunological and biochemical tests. All these methods suffer from one or more limitations. Our lab has developed a quick PCR based detection of Neisseria meningitidis (bacterial meningitis) directly from the patient CSF samples using specific primers of virulent rmpM gene. The overall analysis completes in 80 min for confirmation of the disease. Amplicon of 308 bp of rmpM gene does not show homology with other organisms and can be used as a genetic marker for human bacterial meningitis caused by Neisseria meningitidis.

Detection of rotavirus from hospitalized diarrheic children in uttar pradesh, India.

In the present study 220 stool samples collected from diarrheic children admitted to different hospitals and nursing homes of Uttar Pradesh and Uttarakhand were screened for rotavirus. Of 220 diarrheic samples screened 46 samples were found to be positive for rotavirus by RNA PAGE. All the isolates exhibited 4-2-3-2 migration pattern suggesting group A rotavirus. Both long and short electropherotypes were prevalent in these regions. Six different electropherotypes were detected in this study period. Male diarrheic children were found to be more susceptible to rotavirus infection (22.96 %) than that of the female ones (17.64 %). Viral RNA isolated from stool samples again subjected to VP4 gene amplification by RT-PCR using con2 and con3 primer which resulted 876 bp product suggesting group A rotavirus. Besides virus isolation was successfully done using MA104 cell line.

Adaptability of different mechanisms and kinetic study of methane combustion in steam diluted environments.

The chemical kinetics of methane oxidation in a steam-diluted environment are studied in the present study. Various well-validated mechanisms for methane combustion are adopted and compared with experimental data. Ignition delay, laminar flame speed, and emissions for CH4 combustion with steam dilution are discussed. Cumulative relative error parameter was determined for all mechanisms considered in this study to evaluate the prediction level in quantifiable terms. Reaction pathways under no and steam-diluted environments are analyzed, and key elementary reactions and species are identified in these conditions. The analysis gives a relative idea of the applicability of some of the reduced mechanisms for the diluted steam conditions. This study aims to guide future computational fluid dynamics simulations to accurately predict combustion characteristics in these conditions. Computations of laminar flame speed from GRI-3.0, Aramco3.0, Curran, and San Diego mechanisms were the most precise under diluted steam conditions. Similarly, for the calculation of ignition delay of methane under the steam dilution, the Aramco mechanism and the Curran's mechanism were able to predict the experimentally observed values most closely. Sensitivity study for the OH concentrations shows that the H-abstraction of methane from OH radicals has an opposing trend with dilution for Aramco and GRI-3.0 mechanism. On the other hand, CO and NO emissions were reduced significantly, with the dilution increased from 0 to 20%. The third-body effect of steam is observed to dominate the deviation observed between the detailed and reduced mechanism. For low operating pressure conditions, the GRI-3.0 mechanism gives an excellent prediction, whereas, for applications like gas turbines and furnaces, Aramco-3.0 and Curran mechanisms can be adopted to give good results. The San Diego mechanism can be chosen for low computational facility purposes as it shows very good predictions for ignition delay and laminar flame speed computations.

Precipitation Biases in CMIP5 Models over the South Asian Region.

Using data from 33 models from the CMIP5 historical and AMIP5 simulations, we have carried out a systematic analysis of biases in total precipitation and its convective and large-scale components over the south Asian region. We have used 23 years (1983-2005) of data, and have computed model biases with respect to the PERSIANN-CDR precipitation (with convective/large-scale ratio derived from TRMM 3A12). A clustering algorithm was applied on the total, convective, and large-scale precipitation biases seen in CMIP5 models to group them based on the degree of similarity in the global bias patterns. Subsequently, AMIP5 models were analyzed to conclude if the biases were primarily due to the atmospheric component or due to the oceanic component of individual models. Our analysis shows that the set of individual models falling in a given group is somewhat sensitive to the variable (total/convective/large-scale precipitation) used for clustering. Over the south Asian region, some of the convective and large-scale precipitation biases are common across groups, emphasizing that although on a global scale the bias patterns may be sufficiently different to cluster the models into different groups, regionally, it may not be true. In general, models tend to overestimate the convective component and underestimate the large-scale component over the south Asian region, although with spatially varying magnitudes depending on the model group. We find that the convective precipitation biases are largely governed by the closure and trigger assumptions used in the convection parameterization schemes used in these models, and to a lesser extent on details of the individual cloud models. Using two different methods: (i) clustering, (ii) comparing the bias patterns of models from CMIP5 with their AMIP5 counterparts, we find that, in general, the atmospheric component (and not the oceanic component through biases in SSTs and atmosphere-ocean feedbacks) plays a major role in deciding the convective and large-scale precipitation biases. However, the oceanic component has been found important for one of the convective groups in deciding the convective precipitation biases (over the maritime continent).

Palivizumab Prophylaxis among Infants at Increased Risk of Hospitalization due to Respiratory Syncytial Virus Infection in UAE: A Hospital-Based Study.

Background: Respiratory syncytial virus (RSV) represents a significant public health burden and the leading cause of lower respiratory tract infections globally, and it is the major cause of hospitalization during the winter. We aimed to evaluate the effectiveness of palivizumab prophylaxis to reduce the hospitalization in children at high risk of RSV infection. Methods: We performed a retrospective observational single-arm hospital-based study including five RSV seasons (September to March) from 2012 to 2017. We retrospectively included premature infants born at less than 35 weeks of gestation with chronic lungs disease or hemodynamic significant congenital heart disease for palivizumab prophylaxis against RSV infection according to the criteria presented. Results: A total of 925 children were enrolled in the study over the five RSV seasons. Of them, 410 (44.3%) infants born at <32 weeks of gestation and 515 (55.6%) infants born at 32-35 weeks of gestation with mean (±SD) birth weight of 1104.8 ± 402.85 and 1842.5 ± 377.5, respectively. The compliance with the course of palivizumab was reported in 841 (90.9%) children. Of them, about 75 (8.9%) hospitalized children were reported, and 17 (2.02%) RSV positive children were detected. Hospitalization due to RSV infection was decreased from 9.23% in the 2012-2013 season to 0.67% in the 2016-2017 season. Conclusion: This study demonstrated that palivizumab prophylaxis in children at high risk of developing RSV infection was effective in reducing the risk of hospitalization with a high compliance rate over the five RSV seasons.

Indian Summer Monsoon Simulations: Usefulness of Increasing Horizontal Resolution, Manual Tuning, and Semi-Automatic Tuning in Reducing Present-Day Model Biases.

Coupled Global Climate Models (CGCMs) of the Coupled Model Intercomparison Project Phase 5 (CMIP5) are unable to resolve the spatial and temporal characteristics of the South Asian Monsoon satisfactorily. A CGCM with the capability to reliably project the global as well as the regional climatic features would be a valuable tool for scientists and policymakers. Analysis of 28 CMIP5 models highlights varying degree of biases in precipitation and 2 m surface air temperature (T2m) over south Asia, and the Community Earth System Model (CESM) developed at the National Center for Atmospheric Research is found to be one of the best performing models. However, like all other CMIP5 models, CESM also has some inherent model biases. Using CESM, it is found that the precipitation and T2M biases reduce with increase in the model horizontal resolution from 2° to 0.5°. Further, a few deep convective parameters in the Zhang-McFarlane convection scheme are tuned for 2° and 1° model resolutions using both manual and semi-automatic model tuning methods. Comparing results from the two tuning methods we find that the performance of the manually tuned model is better than that of the semi-automated one.

Preliminary genetic linkage map of Indian major carp, Labeo rohita (Hamilton 1822) based on microsatellite markers.

Linkage map with wide marker coverage is an essential resource for genetic improvement study for any species. Sex-averaged genetic linkage map of Labeo rohita, popularly known as 'rohu', widely cultured in the Indian subcontinent, was developed by placing 68 microsatellite markers generated by a simplified method. The parents and their F1 progeny (92 individuals) were used as segregating populations. The genetic linkage map spans a sex-averaged total length of 1462.2 cM, in 25 linkage groups. The genome length of rohu was estimated to be 3087.9 cM. This genetic linkage map may facilitate systematic searches of the genome to identify genes associated with commercially important characters and marker-assisted selection programmes of this species.

Relationship of conventional and fluorescent microscopic technique to assess in vitro semen quality status of Murrah buffalo males.

In vitro fertility assessment using fluorescent technique is a better predictor of fertility status of bulls as compared to traditional semen quality assessment techniques, therefore, the study was planned to assess in vitro fertility status of bulls based on conventional and fluorescent techniques. Seventy-three ejaculates were collected from 12 Murrah buffalo bulls maintained at Artificial Breeding Research Centre, NDRI, Karnal, India for the experiment and subjected to statistical analysis using SYSTAT. The mean values of ejaculate volume (ml), mass activity, individual motility (%), sperm concentration (millions/ml), live sperm (%), total abnormalities (%), HOST (%) and acrosomal integrity (%) were 2.70 ± 0.28, 2.8 ± 0.14, 63.8 ± 2.16, 1749.7 ± 122.24, 77.3 ± 2.48, 6.2 ± 0.51, 75.1 ± 1.81 and 84.5 ± 2.26, respectively. The repeatability estimates were significant (P<0.05) for ejaculate volume (0.34 ± 0.137), acrosomal integrity (0.29 ± 0.134) and live percentage (0.28 ± 0.133), indicating sufficient bull to bull variation for the parameters. The mean values of seminal attributes of fluorescent based criteria of CMA3 (Chromomycin A3), SYBR-PI and FITC-PNA (fluorescent isothiocynate-conjugated peanut agglutinin) were 5.25 ± 0.41, 67.91 ± 1.24 and 82.00 ± 1.25 percent, respectively. Bulls were ranked on the basis of expected producing ability (EPA) for semen characteristics assessed by conventional and fluorescent criteria. Rank correlations were found to be significant for FITC with most of the parameters evaluated by conventional methods. In conclusion, among the conventional criteria, individual motility (%) revealed ranking of bulls almost similar to that of fluorescent criteria.

Compact panicle architecture is detrimental for growth as well as sucrose synthase activity of developing rice kernels.

The increase of spikelet number in the panicles of modern super rice has made the architecture compact, as the extra spikelets are accommodated mostly on secondary branches than on primary branches. However, the grain yield did not improve because of poor grain filling, which was more visible in the basal spikelets than apical spikelets. The objective of this study was to examine the effect of the compactness and positional difference of spikelets in the panicle on grain filling by comparing the activity and genetic expression of starch synthesising enzymes in the developing kernels of lax-(Upahar and CR3856-45-11-2-7-2-5 (CR-45)) and compact-(Mahalaxmi and CR3856-29-14-2-1-1-1 (CR-29)) panicle cultivars. Upahar and Mahalaxmi are genetically related, whereas CR-45 and CR-29 are recombinant inbred lines. The grain carbohydrate concentration and activity of sucrose synthase (SUS) enzyme were estimated during the active period of grain filling. Further, expression of isoforms of SUS, ADP glucose pyrophosphorylase (APL and APS for large and small units respectively) and starch synthase (SS and GBSS for soluble and granule bound starch synthases respectively) were also assayed through PCR studies. The genotype approach used revealed grain SUS activity and starch concentration high and sugar concentration low in the lax- compared with compact-panicle cultivars and in the apical spikelets compared with basal ones. The margin of variation between apical and basal spikelets was higher in the compact- than the lax-panicle cultivars. Genetic expression of most of the isoforms of the enzymes was higher in the lax- than the compact-panicle cultivars as seen in RT-PCR studies. A quantitative appraisal of transcript levels of isoforms in the qRT-PCR identified greater expression of SUS3 in the basal spikelets of Upahar than that in Mahalaxmi and in CR-45 over CR-29, most prominently during the active period of grain filling. We conclude that proximal location as well as increased density of spikelets on panicles affected SUS3 expression in the basal spikelets. The metabolic dominance of a spikelet in rice panicle is dependent on the expression of the genes for different isoforms of starch synthesising enzymes, but the expression of SUS3 could be more specific than the others. SUS3 expression is most active during grain filling of the lax-panicle cultivars, but its dominance is reduced significantly in the kernels of the compact-panicle cultivars.

Validation of the TRMM Multi Satellite Rainfall Product 3B42 and estimation of scavenging coefficients for (131)I and (137)Cs using TRMM 3B42 rainfall data.

The TRMM rainfall product 3B42 is compared with rain gauge observations for Kaiga, India on monthly and seasonal time scales. This comparison is carried out for the years 2004-2007 spanning four monsoon seasons. A good correlation is obtained between the two data sets however; magnitude wise, the cumulative precipitation of the satellite product on monthly and seasonal time scales is deficient by almost 33-40% as compared to the rain gauge data. The satellite product is also compared with APHRODITE's Monsoon Asia data set on the same time scales. This comparison indicates a much better agreement since both these data sets represent an average precipitation over the same area. The scavenging coefficients for (131)I and (137)Cs are estimated using TRMM 3B42, rain gauge and APHRODITE data. The values obtained using TRMM 3B42 rainfall data compare very well with those obtained using rain gauge and APHRODITE data.

Antibacterial potential assessment of jasmine essential oil against e. Coli.

The antibacterial activity of Jasmine (Jasminum sambac L.) flower hydro steam distilled essential oil, synthetic blends and six major individual components was assessed against Escherichia coli (MTCC-443) strain. The activity was bactericidal. Minimum inhibitory concentration was determined by tube dilution technique, and the Minimum inhibitory concentration ranged between 1.9-31.25 mul/ml. Phenolcoefficient of the oil, synthetic blends and components varied between 0.6-1.7. The activity of the chemicals was possibly due to the inhibition of cell membrane synthesis.

Optimization of Physical and Nutritional Parameters for Hyaluronidase Production by Streptococcus mitis.

The effect of some physical and nutritional parameters were studied for the optimum production of extracellular enzyme hyaluronidase employing Streptococcus mitis MTCC*2695 by submerged fermentation. The effects of initial pH, incubation temperature and time, inoculum level and age of inoculum were studied. The maximum enzymatic activity was obtained with an initial pH 5.8, incubation temperature 37°, incubation time for 48 h and inoculum level 6% with inoculum age 24 h. The effect of different carbon and nitrogen sources and antibiotics were studied. The results indicated that sucrose and ammonium chloride showed the highest enzymatic activity among various carbon and nitrogen sources. Antibiotic clarithromycin showed strong inhibitory effect on hyaluronidase production.

Antibacterial Activity of Barringtonia acutangula against Selected Urinary Tract Pathogens.

Barringtonia acutangula (L.) Gaertn belonging to family Barringtoniaceae was investigated to evaluate In vitro antibacterial activity of aqueous, ethanolic, petroleum ether and chloroform extracts against Staphylococcus aureus, Pseudomonas aeruginosa, Klebsiella pneumoniae, Enterococcus faecalis and Escherichia coli the major urinary tract infection causing pathogens were tested by disc diffusion assay method and the minimum inhibitory concentration was evaluated. Ethanol (95%) extract exhibited broader spectrum of inhibition followed by chloroform, petroleum ether and aqueous extracts against the urinary tract pathogens under test. An attempt has been made to compare the activity of extracts with standard antibiotics against selected urinary tract infection causing pathogens.