De novo assembly, transcriptome characterization and marker discovery in Indian major carp, Labeo rohita through pyrosequencing.

Labeo rohita, one of the Indian major carps, is the most popular culture species in Indian subcontinent due to its consumer preference and delicacy. A selective breeding program for harvest body weight has resulted in an average genetic gain of 17% per generation. Transcriptome resource for this species is scanty. Here, we have characterized the liver and muscle transcriptomes of rohu using Roche 454 GS-FLX next generation sequencing platform. In total, 1.2 million reads were generated, de novo assembly and clustering resulted in 4171 transcripts. Out of these, 4171 had significant blast hit against NCBI nr database, and 2130 transcripts were successfully annotated. In total, 289 SSRs were identified with an identification rate of 5.8%, and dinucleotide repeat motifs were observed to be the most abundant SSRs. Further, 2231 putative SNPs were identified with high confidence. Validation of eight putative SNPs using Sanger sequencing resulted in 100% true SNPs. Significant allelic imbalance of M1, M4 and M5 loci between growth selected and control individual were observed. Furthermore, 13 transcription factors were identified in the present study belonging to six different transcription factor families. The present study demonstrated the utility of RNAseq to develop genomics resources in non-model fish species, and the marker resources developed would support the genetic improvement program of this species.

Genetic gain for rice yield in rainfed environments in India.

The complexity of genotype × environment interactions under drought reduces heritability, which determines the effectiveness of selection for drought tolerance and development of drought tolerant varieties. Genetic progress measured through changes in yield performance over time is important in determining the efficiency of breeding programmes in which test cultivars are replaced each year on the assumption that the new cultivars will surpass the older cultivars. The goal of our study was to determine the annual rate of genetic gain for rice grain yield in a drought-prone rainfed system in a series of multi-environment trials conducted from 2005 to 2014 under the Drought Breeding Network of Indian sites in collaboration with the International Rice Research Institute (IRRI). Our results show a positive trend in grain yield with an annual genetic yield increase of about 0.68 % under irrigated control, 0.87 % under moderate reproductive stage drought stress and 1.9 % under severe reproductive stage drought stress due to breeding efforts. The study also demonstrates the effectiveness of direct selection for grain yield under both irrigated control as well as managed drought stress screening to improve yield in typical rainfed systems. IRRI's drought breeding programme has exhibited a significant positive trend in genetic gain for grain yield over the years under both drought stress as well as favorable irrigated control conditions. Several drought tolerant varieties released from the programme have outperformed the currently grown varieties under varied conditions in the rainfed environments on farmers' fields.

Epistatic interactions of major effect drought QTLs with genetic background loci determine grain yield of rice under drought stress.

Epistatic interactions of QTLs with the genetic background and QTL-QTL interaction plays an important role in the phenotypic performance of introgression lines developed through genomic-assisted breeding (GAB). In this context, NIL pairs developed with various drought QTL (qDTY) combinations in the genetic background of IR64, TDK1-Sub1 and Savitri backgrounds were utilized to study the interactions. Multi-season phenotyping of NIL pairs harboring similar qDTY combinations provided contrasting performance for grain yield under drought (RS) (classified as high and low yielding NILs) but nearly similar performance under non-stress(NS) conditions. Genome wide genotyping data revealed a total of 16, 5 and 6 digenic interactions were detected under RS conditions in low yielding NILs of IR64, TDK1-Sub1 and Savitri respectively while no significant interaction was found in high yielding NILs under RS and NS conditions in any of the genetic backgrounds used in this study. It is evident from this study that existence of epistatic interactions between QTLs with genetic background, QTL-QTL interaction and interactions among background markers loci itself on different chromosomes influences the expression of a complex trait such as grain yield under drought. The generated information will be useful in all the GAB program of across the crops for precise breeding.

HPLC method development and validation of chromafenozide in paddy.

A simple and efficient HPLC-UV method was developed and validated for determination of chromafenozide in paddy as there was no previous report on record in this regard. The residue analysis method of chromafenozide, its dissipation and final residue in paddy along with soil were also studied after field treatment. Residues of chromafenozide were extracted and purified from paddy and soil followed by liquid/liquid partitioning, chromatographic column and determination by HPLC equipped with PDA detector. The separation was performed on a Phenomenex Luna RP C(18) (250 × 4.6 mm i.d, 5 µm particle size) column at room temperature. The mean accuracy of analytical method were 94.92 %, 95.38 %, 94.67 % and 96.90 % in straw, grain, soil and field water respectively. The precision (repeatability) was found in the range of 1.30 %-9.25 % for straw/grain, 1.27 %-11.19 % in soil; 1.0 %-9.25 % in field water. The precision (reproducibility) in straw/grain was ranging from 2.2 % to 12.1 %, in soil it from 2.0 % to 11.7 %. The minimum detectable concentration was 0.01 mg kg(-1). The degradation of chromafenozide formulation in rice, soil and water was determined and results showed that chromafenozide as wettable powder formulation degraded with the half-lives of about 4.4 and 2.9 days in paddy plant and soil respectively for double recommended dose. The results indicated that the developed method is easier and faster then could meet the requirements for determination of chromafenozide in paddy.

Degradation dynamics of chromafenozide in different types of soil.

Chromafenozide is a lepidopteran insecticide. It is highly effective in controlling various lepidopteran pests. Chromafenozide technical and formulation (80WP) was applied at 2.5 and 5.0 µg g(-1) in 4 types of soils (air dried and sieved) separately in laboratory condition. Half-lives of active ingredient were calculated and found at 15.8, 21.6, 25 and 23.9 days for single dose for chromafenozide technical (99.4 %).

Degradation dynamics of chlorfenapyr residue in chili, cabbage and soil.

Chlorfenapyr is a pyrrole group of insecticide, [4-bromo-2-(4-chlorophenyl)-1-ethoxymethyl-5-trifluoromethyl-1H-pyrrole-3-carbonitrile]used as broad spectrum insecticide/acaricide to control whitefly, thrips, caterpillars, mites, leafminers, aphids, etc., chlorfenapyr 10% SC formulation was applied on chili and cabbage twice @ 75 and 100 g a.i./ha along with untreated control. Chlorfenapyr was dissipated in chili, cabbage and soil following the first-order kinetics (logC/C(0) = -kt). The half lives of chlorfenapyr in chili, cabbage and soil were varying from 2.93 to 2.96 days, 2.98 to 3.62 days and 4.06 to 4.36 days respectively, according to the application rate.

The malaria severity score: a method for severity assessment and risk prediction of hospital mortality for falciparum malaria in adults.

BACKGROUND: There is paucity of research to quantify the severity and to predict the mortality risk of severe falciparum malaria even if it affects multiple organ systems during the course of the disease. Therefore, the aim of the present study is to develop a severity score for assessment of disease severity and risk prediction in adult patients of severe falciparum malaria on the first day of hospitalisation. METHODS: A cohort of 2598 patients of falciparum malaria were enrolled in this study of which 2089 patients were included as developmental sample and 509 patients as validation sample. Physiological variables were analyzed for defining and assessment of severity of organ dysfunction (OD). The severity level and corresponding severity score for each organ dysfunction were determined by logistic regression analysis that took both the relative severity among the organ systems and the degree of severity within an organ system into account. Risk of mortality has been calculated for each score. RESULTS: Physiological variables defined dysfunction in 7 organ systems with 3 levels of severity (I to III). Neurologic and renal dysfunction had 3 levels of severity. Hematologic, cardiovascular, and respiratory dysfunction had 2 levels of severity where as hepatic and metabolic dysfunction had 1 level of severity. 1,3, and 5 points were assigned to level I, II, and III severity of organ dysfunction respectively. Malaria without any abnormal physiological variables had been considered as no organ failure and assigned 0 score. The cumulative scores in a patient is known as malaria severity score (MSS) that ranged from 0 to 21. Risk of mortality had been calculated for each score. CONCLUSION: This prospective study provides an objective tool for assessing severity levels for organ dysfunction and prediction of risk of mortality in severe falciparum malaria which can be used for treatment and research. It has been observed that no two patients of falciparum malaria are same in severity. The severity varies over time and malaria can affect single or multiple organs with different levels of severity which can be quantified as level I, II, and III. Neurologic and renal dysfunction were the most severe with level III severity, followed by haematologic, cardiovascular, and respiratory dysfunction with level-II severity, as well as hepatic and metabolic dysfunction the least severe with level-I severity. Patient of malaria can be stratified as low, intermediate, and high risk depending on the MSS. With the help of MSS daily risk estimates and recovery time of OD can be determined.

Structural relaxation and frequency-dependent specific heat in a supercooled liquid.

We have studied the relation between the structural relaxation and the frequency-dependent thermal response or the specific heat, c(p)(omega), in a supercooled liquid. The mode coupling theory (MCT) results are used to obtain c(p)(omega) corresponding to different wave vectors. Due to the two-step relaxation process present in the MCT, an extra peak, in addition to the low-frequency peak, is predicted in specific heat at high frequency.

Heterogeneities in supercooled liquids: a density-functional study.

A metastable state, characterized by a low degree of mass localization, is identified using density-functional theory (DFT). This free energy minimum, located through the proper evaluation of competing terms in the free energy functional, is independent of the specific form of the DFT used. Computer simulation results on particle motion indicate that this heterogeneous state corresponds to the deeply supercooled state.

Metastable state dynamics and power law relaxation in a supercooled liquid.

We consider glassy relaxation by using a model for supercooled liquid where the usual set of hydrodynamic variables is extended to include the presence of very slowly decaying defect densities. The long time limit of the density correlation function, the nonergodicity parameter, is studied in the vicinity of the dynamic transition point, and scaling exponents with respect to the distance from the critical point are obtained. In addition to the usual square root cusp, we also see a linear dependence on distance from transition with respect to the metastability parameters. We analyze the power law relaxation of the density correlation function at the initial stage of the dynamics, and obtain an exponent dependent on temperature. Results are compared with data obtained from light scattering experiments.

Juvenile T waves (a study of 100 normal subjects).

"Juvenile pattern" of T wave inversion in the precordial leads of electrocardiogram was studied in 100 normal healthy Indians of 0 to 70 years of age in both sexes. Incidence of such pattern was observed in 25 subjects upto 19 years of age. Persons of weight/height ratio less than 30% had higher incidence of juvenile T waves. Maximum incidence (48%) of juvenile T waves was observed in the annual income group of Rs. 15000/-. Exercise ECC showed slight flattening of the inverted T waves in V1 to V3 leads in eight subjects only.