Showing papers by "Indian Agricultural Statistics Research Institute published in 2015"

Genome-wide association mapping of salinity tolerance in rice (Oryza sativa)

Abstract: Salinity tolerance in rice is highly desirable to sustain production in areas rendered saline due tovarious reasons. It is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (GWAS). Here, we implemented GWAS to identify loci controlling salinity tolerance in rice. A custom-designed array based on 6,000 single nucleotide polymorphisms (SNPs) in as many stress-responsive genes, distributed at an average physical interval of <100 kb on 12 rice chromosomes, was used to genotype 220 rice accessions using Infinium highthroughput assay. Genetic association was analysed with 12 different traits recorded on these accessions under field conditions at reproductive stage. We identified 20 SNPs (loci) significantly associated with Na + /K + ratio, and 44 SNPs with other traits observed under stress condition. The loci identified for various salinity indices through GWAS explained 5–18% of the phenotypic variance. The region harbouring Saltol, a major quantitative trait loci (QTLs) on chromosome 1 in rice, which is known to control salinity tolerance at seedling stage, was detected as a major association with Na + / K + ratio measured at reproductive stage in our study. In addition to Saltol, we also found GWAS peaks representing new QTLs on chromosomes 4, 6 and 7. The current association mapping panel contained mostly indica accessions that can serve as source of novel salt tolerance genes and alleles. The gene-based SNP array used in this study was found cost-effective and efficient in unveiling genomic regions/candidate genes regulating salinity stress tolerance in rice.

Identification of novel drought-responsive microRNAs and trans-acting siRNAs from Sorghum bicolor (L.) Moench by high-throughput sequencing analysis

Abstract: Small non-coding RNAs (sRNAs) namely microRNAs (miRNAs) and trans-acting small interfering RNAs (tasi-RNAs) play a crucial role in post-transcriptional regulation of gene expression and thus the control plant development and stress responses. In order to identify drought-responsive miRNAs and tasi-RNAs in sorghum, we constructed small RNA libraries from a drought tolerant (M35-1) and susceptible (C43) sorghum genotypes grown under control and drought stress conditions, and sequenced by Illumina Genome Analyzer IIx. Ninety seven conserved and 526 novel miRNAs representing 472 unique miRNA families were identified from sorghum. Ninety-six unique miRNAs were found to be regulated by drought stress, of which 32 were up- and 49 were down-regulated (fold change ≥ 2 or ≤ -2) at least in one genotype, while the remaining 15 miRNAs showed contrasting drought-regulated expression pattern between genotypes. A maximum of 17 and 18 miRNAs was differentially regulated under drought stress condition in the sensitive and tolerant genotypes, respectively. These results suggest that genotype dependent stress responsive regulation of miRNAs may contribute, at least in part, to the differential drought tolerance of sorghum genotypes. We also identified two miR390-directed TAS3 gene homologs and the auxin response factors as tasi-RNA targets. We predicted more than 1300 unique target genes for the novel and conserved miRNAs. These target genes were predicted to be involved in different cellular, metabolic, response to stimulus, biological regulation, and developmental processes. Genome-wide identification of stress-responsive miRNAs, tasi-RNAs and their targets identified in this study will be useful in unraveling the molecular mechanisms underlying drought stress responses and genetic improvement of biomass production and stress tolerance in sorghum.

Identification of Novel SNP in Promoter Sequence of TaGW2-6A Associated with Grain Weight and Other Agronomic Traits in Wheat (Triticum aestivum L.).

Abstract: TaGW2 is an orthologue of rice gene OsGW2, which encodes E3 RING ubiquitin ligase and controls the grain size in rice. In wheat, three copies of TaGW2 have been identified and mapped on wheat homoeologous group 6 viz. TaGW2-6A, TaGW2-6B and TaGW2-6D. In the present study, using as many as 207 Indian wheat genotypes, we identified four SNPs including two novel SNPs (SNP-988 and SNP-494) in the promoter sequence of TaGW2-6A. All the four SNPs were G/A or A/G substitutions (transitions). Out of the four SNPs, SNP-494 was causal, since it was found associated with grain weight. The mean TGW (41.1 g) of genotypes with the allele SNP-494_A was significantly higher than mean TGW (38.6 g) of genotypes with the allele SNP-494_G. SNP-494 also regulates the expression of TaGW2-6A so that the wheat genotypes with SNP-494_G have higher expression and lower TGW and the genotypes with SNP-494_A have lower expression but higher TGW. Besides, SNP-494 was also found associated with grain length-width ratio, awn length, spike length, grain protein content, peduncle length and plant height. This suggested that gene TaGW2-6A not only controls grain size, but also controls other agronomic traits. In the promoter region, SNP-494 was present in ‘CGCG’ motif that plays an important role in Ca2+/calmodulin mediated regulation of genes. A user-friendly CAPS marker was also developed to identify the desirable allele of causal SNP (SNP-494) for use in marker-assisted selection for improvement of grain weight in wheat. Using four SNPs, five haplotypes were identified; of these, Hap_5 (G_A_G_A) was found to be a desirable haplotype having significantly higher grain weight (41.13g) relative to other four haplotypes (36.33-39.16 g).

Harnessing Next Generation Sequencing in Climate Change: RNA-Seq Analysis of Heat Stress-Responsive Genes in Wheat (Triticum aestivum L.)

Abstract: Wheat is a staple food worldwide and provides 40% of the calories in the diet. Climate change and global warming pose a threat to wheat production, however, and demand a deeper understanding of how heat stress might impact wheat production and wheat biology. However, it is difficult to identify novel heat stress associated genes when the genomic information is not available. Wheat has a very large and complex genome that is about 37 times the size of the rice genome. The present study sequenced the whole transcriptome of the wheat cv. HD2329 at the flowering stage, under control (22°±3°C) and heat stress (42°C, 2 h) conditions using Illumina HiSeq and Roche GS-FLX 454 platforms. We assembled more than 26.3 and 25.6 million high-quality reads from the control and HS-treated tissues transcriptome sequences respectively. About 76,556 (control) and 54,033 (HS-treated) contigs were assembled and annotated de novo using different assemblers and a total of 21,529 unigenes were obtained. Gene expression profile showed significant differential expression of 1525 transcripts under heat stress, of which 27 transcripts showed very high (>10) fold upregulation. Cellular processes such as metabolic processes, protein phosphorylation, oxidations-reductions, among others were highly influenced by heat stress. In summary, these observations significantly enrich the transcript dataset of wheat available on public domain and show a de novo approach to discover the heat-responsive transcripts of wheat, which can accelerate the progress of wheat stress-genomics as well as the course of wheat breeding programs in the era of climate change.

Exploration of new drug-like inhibitors for serine/threonine protein phosphatase 5 of Plasmodium falciparum: a docking and simulation study.

Abstract: Protein phosphorylation is an important mechanism that implicates in physiology of any organism including parasitic protozoa. Metallic protein Ser/Thr protein phosphatase 5 (PP5) controls various cellular signaling pathways of Plasmodium falciparum. The structure and inhibitory mechanism of PP5 in P. falciparum is not known. In fact, no experimental structural data are available for P. falciparum Ser/Thr protein phosphatase 5 (PfPP5) till date. Hence, we have proposed computer-generated model of catalytic subunit of PfPP5 and its inhibitory mechanism was analyzed. A set of 42 known natural inhibitors of protein phosphate family were docked against metal-binding catalytic site of PfPP5 and we found that cantharidin and its derivatives shows better binding energy among them. Similarity search was performed by taking these compounds as lead compounds against PubChem and ChemBank. The search result provides 3703 similar compounds; out of which 2245 qualified the Lipinski rule of five. Further, virtual screening of these compounds was performed and selected top 25 were selected on the basis of binding energy. In continuation, rigid and flexible docking of these screened compounds was performed to get the insight of interactions. Finally, top 5 compounds were verified for ADMET properties, and then, all are subjected to MD simulations for 25 ns in order to validate their stability. Compounds CBI: 3554182, CID: 23561913, and CID: 21168680 showed most stable binding, although some of hydrogen bonds pairing varied throughout simulation. These finding would be helpful to the medicinal chemists for the development of antimalarial drugs to combat this deadly disease.

Identification of a diverse mini‐core panel of Indian rice germplasm based on genotyping using microsatellite markers

Abstract: Identification of a small core germplasm set representing the available genetic diversity is essential for its proper evaluation and subsequent utilization in rice improvement programmes. For constituting a small diverse mini-core panel of Indian rice germplasm, a representative set of 6912 accessions drawn based on their geographic origin from the whole rice germplasm collection available in the National Gene Bank was genotyped using 36 microsatellite markers. Automated fragment analysis of amplicons yielded a total of 435 alleles, with an average 12.4 and range of 3–29 alleles per locus. Polymorphism information content (PIC) ranged from 0.08 (RGNMS190) to 0.86 (RM552) with an average of 0.528. Based on genotyping data, a mini-core consisting of 98 genotypes was identified. Ninety-four per cent of the alleles present in the core set were present in the mini-core. The identified small but diverse panel will be useful for further intensive trait-specific evaluation and utilization in allele mining.

Crop diversification for sustainable insect pest management in eggplant (Solanales: Solanaceae)

Abstract: An experiment was conducted to manage the eggplant (brinjal) shoot and fruit borer Leucinodes orbonalis Guenee (Lepidoptera: Crambidae), the leafhopper Amrasca biguttula biguttula (Ishida) (Hemiptera: Cicadellidae), and the whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) during kharif, the southwest monsoon season (Jul-Oct), in 2010 and 2011 at an experimental farm at the Division of Entomology, Indian Agricultural Research Institute, New Delhi. The experiment consisted of 7 different treatments with brinjal or eggplant ‘Pusa Kranti’, Solanum melongena L. (Solanales: Solanaceae), as the main crop and coriander, marigold or mint as intercrops, along with a border crop (maize or cowpea) acting as refuge crops. Treatment T1 (maize as border crop and coriander as intercrop) harbored the smallest cumulative mean leafhopper population (6.90 insects per 3 leaves per plant) and the next to smallest mean whitefly population (9.64 insects per 3 leaves per plant) during monsoon season of 2010 and 2011. Treatment T3 (maize as border crop and marigold as intercrop) was second best in reducing the leafhopper population (7.27 insects per 3 leaves per plant), while it was the best treatment in reducing the whitefly population (8.36 insects per 3 leaves per plant). The sole crop (T7) harbored the largest whitefly (20.17 insects per 3 leaves per plant) and leafhopper (12.61 insects per 3 leaves per plant) populations among the 7 treatments. The lowest mean percentage fruit infestation was recorded from treatment T1 (by number: 27.72; by weight: 27.81). All the treatments involving intercrops showed significantly lower percentage fruit infestation by L. orbonalis than eggplant alone (T7, control), which showed 37.73% infestation by number of fruits and 38.13% by weight of the fruits. The greatest mean number of coccinellids (1.25 per plant) and largest Shannon-Wiener indices were recorded from treatment T1 (maize and coriander). The smallest mean number of coccinellids (0.37 per plant) and smallest Shannon-Wiener indices were recorded from the sole crop control, T7. Various plant volatiles present in the intercrop were identified by the thermal desorption technique. Twenty one volatile compounds were present in coriander, 7 in marigold, and 18 in mint. The current state of knowledge of the behavioral effects (repellency, attractancy, no effect) of each chemical with respect the various herbivorous insects and natural enemies is summarized and this information will facilitate quantitative studies on how different pest and beneficial insects respond to plant volatiles in polycultures.

Exploitation of Nano-Bentonite, Nano-Halloysite and Organically Modified Nano-Montmorillonite as an Adsorbent and Coagulation Aid for the Removal of Multi-Pesticides from Water: A Sorption Modelling Approach

Abstract: The objective of this study was to investigate the removal of multi-pesticides through a combined treatment process with coagulation–adsorption on nano-clay. Nano-clays like nano-bentonite, nano-halloysite and organically modified nano-montmorillonite were used as the adsorbent, and alum and polyaluminium chloride (PAC) were used as the coagulants. The coagulation method alone was not sufficient to purify water, whereas coagulation plus adsorption methods provided superior purification. Amongst the nano-clays used, organically modified nano-montmorillonite gave the best result in terms of pesticide removal from water. In order to evaluate the effect of coagulant addition on the removal efficiency of nano-clay, the respective adsorption isotherms were also calculated in the presence and absence of coagulants. Freundlich isotherm constants have shown that adsorption of pesticides on different nano-clay depends on the type of clay, presence and absence of coagulants as well as the properties of pesticides. The treatment combination having the maximum removal capacity was used efficiently for the removal of pesticides from natural and fortified natural water. The results indicated that alum–PAC coagulation aided by nano-clay as an adsorbent was the superior process for the simultaneous removal of multi-pesticides from water.

Bug prediction modeling using complexity of code changes

Abstract: Researchers have proposed and implemented a plethora of bug prediction approaches in terms of different mathematical models for measuring the reliability growth of the software and to predict the latent bugs lying dormant in the software. During the last four decades, software reliability growth models (SRGM) have been successfully used to measure the reliability growth of closed source software. The SRGM developed were based on either calendar time or on testing effort. In late 90s, due to the advancement in communication and internet technologies, the development of open source software gets an edge and is proven to be very successful in different fields. Recently, researchers have measured the latent bugs in the open source software using an SRGM which has been developed for closed source software and concluded that the existing SRGM can well predict the latent bugs, but, still, it needs more investigation. In open source software, the source codes are frequently changes (the complexity of code changes) to meet the new feature introduction, feature enhancement and bug repair. In this paper, we have developed two complexity of code changes/entropy based bug prediction models namely (i) time vs entropy and (ii) entropy vs bugs. We have compared the proposed models with the existing time vs bugs SRGM. The empirical work has been carried out using three subsystems of Mozilla project. The statistical significance of different approaches has been tested using a non-parametric Kolmogorov–Smirnov (K–S) test. The bug prediction approaches have been compared on the basis of various performance measures namely R-Square (R2), Adjusted R-Square (adj. R2), Bias, variation and root mean square prediction errors. We found that the potential complexity of code changes based bug prediction approach i.e. time vs entropy is better over the time vs bugs and entropy vs bugs on the basis of different comparison criteria and statistical test.

Extrapolation of Inter Domain Communications and Substrate Binding Cavity of Camel HSP70 1A: A Molecular Modeling and Dynamics Simulation Study

Abstract: Heat shock protein 70 (HSP70) is an important chaperone, involved in protein folding, refolding, translocation and complex remodeling reactions under normal as well as stress conditions. However, expression of HSPA1A gene in heat and cold stress conditions associates with other chaperons and perform its function. Experimental structure for Camel HSP70 protein (cHSP70) has not been reported so far. Hence, we constructed 3D models of cHSP70 through multi- template comparative modeling with HSP110 protein of S. cerevisiae (open state) and with HSP70 protein of E. coli 70kDa DnaK (close state) and relaxed them for 100 nanoseconds (ns) using all-atom Molecular Dynamics (MD) Simulation. Two stable conformations of cHSP70 with Substrate Binding Domain (SBD) in open and close states were obtained. The collective mode analysis of different transitions of open state to close state and vice versa was examined via Principal Component Analysis (PCA) and Minimum Distance Matrix (MDM). The results provide mechanistic representation of the communication between Nucleotide Binding Domain (NBD) and SBD to identify the role of sub domains in conformational change mechanism, which leads the chaperone cycle of cHSP70. Further, residues present in the chaperon functioning site were also identified through protein-peptide docking. This study provides an overall insight into the inter domain communication mechanism and identification of the chaperon binding cavity, which explains the underlying mechanism involved during heat and cold stress conditions in camel.

Recycling of Organic Waste through Four Different Composts for Disease Suppression and Growth Enhancement in Mung Beans

Abstract: Compost is beneficial for agriculture fields in many ways such as soil conditioner, fertilizer, and natural pesticide and above all it helps to manage organic wastes and adds vital humic acids to soil. Four indigenous composts prepared from readily availableorganic wastes viz.vermicompost,banana, NADEP, andCalotropiswere used in the present investigation for growth and disease suppression in mung beans. The composts were amended with Trichoderma viride in the concentration of 0.1 and 0.2% to determine their influence on length and weight of roots and shoots, disease incidence, soil moisture, and soil microflora in plants. The best results were observed in the treatment with T. viride (0.2%), followed by T. viride (0.1%) in vermicompost, while the treatment T. viride (0.1%) with Calotropis compost showed little growth and suppression of disease. All composts enhanced the soil moisture content and microbial populations in amended soil resulting in the reduction of disease incidence. Among T. viride enriched composts, the counts of fungi, bacteria, and actinomycetes were higher in the vermicompost and banana compost-amended soils. Thus, preparing these composts from readily available organic wastes and amending soil with T. viride enriched composts hold a great promise for improving soil fertility and suppressing the soilborne plant pathogens for sustainable agriculture.

Adsorption–desorption of tricyclazole: effect of soil types and organic matter

Abstract: Adsorption–desorption of tricyclazole was studied by batch equilibrium method in two soil types, varying in their physical and chemical properties. The adsorption of tricyclazole on the soil matrix exhibited low rate of accumulation with 18.24 ± 0.14 % in Ultisol and moderately high rate with 43.62 ± 0.14 % in Vertisol after 6 h of equilibrium time. For soils amended with farmyard manure (FYM), the adsorption percentage increased to 32.52 ± 0.14 % in Ultisol and 55.14 ± 0.14 % in Vertisol. The Freundlich model was used to describe the adsorption–desorption of the tricyclazole in two soils. The adsorption isotherm suggested a relatively higher affinity of tricyclazole to the adsorption sites at low equilibrium concentrations. Variation in sorption affinities of the soils as indicated by the distribution coefficient (K d) for sorption in the range of 0.78 ± 0.01–1.38 ± 0.03, 1.71 ± 0.03–2.99 ± 0.09, 2.75 ± 0.05–4.69 ± 0.01, and 4.65 ± 0.08–7.64 ± 0.01 mL/g for Ultisol, FYM-amended Ultisol, Vertisol, and FYM-amended Vertisol, respectively. Desorption was slower than adsorption, indicating a hysteresis effect. The hysteresis coefficient varied from 0.023 ± 0.15 to 0.160 ± 0.12 in two test soils. A good fit to the linear and Freundlich isotherms was observed with correlation coefficients >0.96. The results revealed that adsorption–desorption was influenced by soil properties and showed that the maximum sorption and minimum desorption of pesticide were observed in soils with higher organic carbon and clay content. Thus, groundwater contamination may be minimized, on application of tricyclazole in high-sorption soils of rice-growing regions.

Fitting EXPAR Models Through the Extended Kalman Filter

Abstract: Exponential autoregressive (EXPAR) family of parametric nonlinear time-series models, which is a discrete-time approximation of continuous-time nonlinear stochastic dynamical system, is considered. A heartening feature of this model is that it is capable of describing those data sets that depict cyclical variations. The estimation procedure for EXPAR models is developed using extended Kalman filter (EKF). Through simulation studies, it is shown that EKF is very efficient for fitting EXPAR models. Formulae for optimal one-step and two-step ahead out-of-sample forecasts are derived analytically by recursive use of conditional expectation. Conditions for the existence of limit cycle behaviour for EXPAR models are also established. Superiority of EKF method vis-a-vis Genetic algorithms (GA) method for fitting EXPAR models is shown through simulation studies. As an illustration, EXPAR models are employed for modelling and forecasting Oil sardine, Mackerel and Bombay duck time-series landings data in India. It is shown that all the three fitted models exhibit the desirable feature of existence of limit cycle behaviour. It is concluded that the EXPAR model performs better than ARIMA methodology for both modelling and forecasting purposes for the data sets under consideration.

Evaluation of random forest regression for prediction of breeding value from genomewide SNPs

Abstract: Genomic prediction is meant for estimating the breeding value using molecular marker data which has turned out to be a powerful tool for efficient utilization of germplasm resources and rapid improvement of cultivars. Model-based techniques have been widely used for prediction of breeding values of genotypes from genomewide association studies. However, application of the random forest (RF), a model-free ensemble learning method, is not widely used for prediction. In this study, the optimum values of tuning parameters of RF have been identified and applied to predict the breeding value of genotypes based on genomewide single-nucleotide polymorphisms (SNPs), where the number of SNPs (P variables) is much higher than the number of genotypes (n observations) (P > > n). Further, a comparison was made with the model-based genomic prediction methods, namely, least absolute shrinkage and selection operator (LASSO), ridge regression (RR) and elastic net (EN) under P > > n. It was found that the correlations between the predicted and observed trait response were 0.591, 0.539, 0.431 and 0.587 for RF, LASSO, RR and EN, respectively, which implies superiority of the RF over the model-based techniques in genomic prediction. Hence, we suggest that the RF methodology can be used as an alternative to the model-based techniques for the prediction of breeding value at genome level with higher accuracy.

District-wise trend analysis of rainfall pattern in last century (1901-2000) over Gangetic region in West Bengal, India

Abstract: The aim of the present study was to estimate long-term trend in the amount of rainfall for Gangetic West Bengal (GWB) meteorological sub-division of India and each of the 13 districts under GWB separately. Monthly rainfall time series data of 100 years (1901-2000) were analyzed to measure monotonous trend of rainfall employing Sen’s slope estimator. Statistical significance of the trend was determined using non-parametric Mann-Kendall test. An important result derived from the analysis was that the GWB sub-division and South 24 Parganas (S24P) district showed significant increasing trend (mm/year) of annual rainfall measuring 2.025 and 4.99 respectively. An inclining trend of monsoon precipitation, which was significant, found in four districts viz. Bankura, North 24 Parganas (N24P), S24P and West Midnapore along with GWB itself. A major finding of the study revealed that six districts and GWB had significant increasing trend in September rainfall with a maximum value of 1.324 mm/year in S24P district. Contribution of rainfall in October and post-monsoon season as well increased considerably in Kolkata and S24P districts while in December, similar trend was observed for Birbhum and Howrah districts. Murshidabad, S24P and East Midnapore districts experienced significant rising trend of precipitation in July, August and November respectively. On the contrary, Burdwan and Nadia districts, in the month of May and pre-monsoon season, had considerable declining trend of rainfall. Significant decreasing trend (mm/year) of precipitation, a concern for Nadia district, with magnitude of 0.127 and 0.293, was observed in the months of March and April respectively.

Transcriptional profiling of PRKG2-null growth plate identifies putative down-stream targets of PRKG2

Abstract: Kinase activity of cGMP-dependent, type II, protein kinase (PRKG2) is required for the proliferative to hypertrophic transition of growth plate chondrocytes during endochondral ossification. Loss of PRKG2 function in rodent and bovine models results in dwarfism. The objective of this study was to identify pathways regulated or impacted by PRKG2 loss of function that may be responsible for disproportionate dwarfism at the molecular level. Microarray technology was used to compare growth plate cartilage gene expression in dwarf versus unaffected Angus cattle to identify putative downstream targets of PRGK2. Pathway enrichment of 1284 transcripts (nominal p < 0.05) was used to identify candidate pathways consistent with the molecular phenotype of disproportionate dwarfism. Analysis with the DAVID pathway suite identified differentially expressed genes that clustered in the MHC, cytochrome B, WNT, and Muc1 pathways. A second analysis with pathway studio software identified differentially expressed genes in a host of pathways (e.g. CREB1, P21, CTNNB1, EGFR, EP300, JUN, P53, RHOA, and SRC). As a proof of concept, we validated the differential expression of five genes regulated by P53, including CEBPA, BRCA1, BUB1, CD58, and VDR by real-time PCR (p < 0.05). Known and novel targets of PRKG2 were identified as enriched pathways in this study. This study indicates that loss of PRKG2 function results in differential expression of P53 regulated genes as well as additional pathways consistent with increased proliferation and apoptosis in the growth plate due to achondroplastic dwarfism.

Evidence of salicylic acid pathway with EDS1 and PAD4 proteins by molecular dynamics simulation for grape improvement.

Abstract: Biotic stress is a major cause of heavy loss in grape productivity. In order to develop biotic stress-resistant grape varieties, the key defense genes along with its pathway have to be deciphered. ...

Linear Integer Programming Approach to Construction of Balanced Incomplete Block Designs

Abstract: This article proposes a linear integer programming-based algorithm to construct balanced incomplete block designs. Working of the algorithm is illustrated with the help of an example. The algorithm is able to generate balanced incomplete block designs very fast in most of the cases. The performance of the proposed algorithm is compared with other algorithms proposed in the literature. It is demonstrated that the proposed algorithm is competitive with the existing algorithms.

Fate of cadmium at the soil-solution interface: a thermodynamic study as influenced by varying pH at South 24 Parganas, West Bengal, India

Abstract: A study on the sorption kinetics of Cd from soil solution to soils was conducted to assess the persistence of Cd in soil solution as it is related to the leaching, bioavailability, and potential toxicity of Cd. The kinetics of Cd sorption on two non-contaminated alkaline soils from Canning (22° 18' 48.02″ N and 88° 39' 29.0″ E) and Lakshmikantapur (22° 06' 16.61″ N and 88° 19' 08.66″ E) of South 24 Parganas, West Bengal, India, were studied using conventional batch experiment. The variable soil suspension parameters were pH (4.00, 6.00, 8.18, and 9.00), temperatures (308, 318, and 328 K) and Cd concentrations (5-100 mg L(-1)). The average rate coefficient (kavg) and half-life (t1/2) values indicate that the persistence of Cd in soil solution is influenced by both temperature and soil suspension pH. The concentration of Cd in soil solution decreases with increase of temperature; therefore, Cd sorption on the soil-solution interface is an endothermic one. Higher pH decreases the t 1/2 of Cd in soil solution, indicating that higher pH (alkaline) is not a serious concern in Cd toxicity than lower pH (acidic). Based on the energy of activation (Ea) values, Cd sorption in acidic pH (14.76±0.29 to 64.45±4.50 kJ mol(-1)) is a surface control phenomenon and in alkaline pH (9.33±0.09 to 44.60±2.01 kJ mol(-1)) is a diffusion control phenomenon The enthalpy of activation (ΔH∓) values were found to be between 7.28 and 61.73 kJ mol(-1). Additionally, higher positive energy of activation (ΔG∓) values (46.82±2.01 to 94.47±2.36 kJ mol(-1)) suggested that there is an energy barrier for product formation.

Kalman filter-based modelling and forecasting of stochastic volatility with threshold

Abstract: We propose a parametric nonlinear time-series model, namely the Autoregressive-Stochastic volatility with threshold (AR-SVT) model with mean equation for forecasting level and volatility. Methodology for estimation of parameters of this model is developed by first obtaining recursive Kalman filter time-update equation and then employing the unrestricted quasi-maximum likelihood method. Furthermore, optimal one-step and two-step-ahead out-of-sample forecasts formulae along with forecast error variances are derived analytically by recursive use of conditional expectation and variance. As an illustration, volatile all-India monthly spices export during the period January 2006 to January 2012 is considered. Entire data analysis is carried out using EViews and matrix laboratory (MATLAB) software packages. The AR-SVT model is fitted and interval forecasts for 10 hold-out data points are obtained. Superiority of this model for describing and forecasting over other competing models for volatility, namely AR-Gener...

Computational analysis of miRNA-target community network reveals cross talk among different metabolisms.

Abstract: To date, only a few conserved miRNAs have been predicted in hexaploid (AABBDD) bread wheat and till now community behavior among miRNA is still in dark. Analysis of publically available 1287279 ESTs from NCBI resulted 262 putative pre-miRNAs and 39 novel mature miRNAs. A total 22,468 targets were identified on 21 chromosomes. MiRNA target community was identified for genomes with different levels of cross talks. Gene ontology of these community targets suggests their differential involvement in different metabolisms along with common and stringent involvement in nitrogen metabolism.

Quantitative determination of guggulsterone in existing natural populations of Commiphora wightii (Arn.) Bhandari for identification of germplasm having higher guggulsterone content

Abstract: Guggulsterone is an aromatic steroidal ketonic compound obtained from vertical rein ducts and canals of bark of Commiphora wightii (Arn.) Bhandari (Family - Burseraceae). Owing to its multifarious medicinal and therapeutic values as well as its various other significant bioactivities, guggulsterone has high demand in pharmaceutical, perfumery and incense industries. More and more pharmaceutical and perfumery industries are showing interest in guggulsterone, therefore, there is a need for its quantitative determination in existing natural populations of C. wightii. Identification of elite germplasm having higher guggulsterone content can be multiplied through conventional or biotechnological means. In the present study an effort was made to estimate two isoforms of guggulsterone i.e. E and Z guggulsterone in raw exudates of 75 accessions of C. wightii collected from three states of North-western India viz. Rajasthan (19 districts), Haryana (4 districts) and Gujarat (3 districts). Extracted steroid rich fraction from stem samples was fractionated using reverse-phase preparative High Performance Liquid Chromatography (HPLC) coupled with UV/VIS detector operating at wavelength of 250 nm. HPLC analysis of stem samples of wild as well as cultivated plants showed that the concentration of E and Z isomers as well as total guggulsterone was highest in Rajasthan, as compared to Haryana and Gujarat states. Highest concentration of E guggulsterone (487.45 μg/g) and Z guggulsterone (487.68 μg/g) was found in samples collected from Devikot (Jaisalmer) and Palana (Bikaner) respectively, the two hyper-arid regions of Rajasthan, India. Quantitative assay was presented on the basis of calibration curve obtained from a mixture of standard E and Z guggulsterones with different validatory parameters including linearity, selectivity and specificity, accuracy, auto-injector, flow-rate, recoveries, limit of detection and limit of quantification (as per norms of International conference of Hormonization). Present findings revealed the role of environmental factors on biosynthesis of guggulsterone isomers under natural conditions.