Showing papers by "Indian Agricultural Statistics Research Institute published in 2013"

Investigation of heavy metals in frequently utilized medicinal plants collected from environmentally diverse locations of north western India.

Abstract: The increasing prevalence of environmental pollution, especially soil contamination with heavy metals has led to their uptake in the human food chains through plant parts. Accumulation and magnification of heavy metals in human tissues through consumption of herbal remedies can cause hazardous impacts on health. Therefore, chemical profiling of nine heavy metals (Mn, Cr, Pb, Fe, Cd, Co, Zn, Ni and Hg) was undertaken in stem and leaf samples of ten medicinal plants (Acacia nilotica, Bacopa monnieri, Commiphora wightii, Ficus religiosa, Glycyrrhiza glabra, Hemidesmus indicus, Salvadora oleoides, Terminalia bellirica, Terminalia chebula and Withania somnifera) collected from environmentally diverse regions of Haryana and Rajasthan states in North-Western India. Concentration of all heavy metals, except Cr, was within permissible limits in the tested stem and leaf samples. Leaf samples had consistently more Cr compared to respective stem samples with highest concentration in leaf samples of Bacopa monnieri (13.19 ± 0.0480 ppm) and stem samples of Withania somnifera (4.93 ± 0.0185 ppm) both collected from Bahadurgarh (heavy industrial area), Haryana. This amount was beyond the permissible limit of 2.0 ppm defined by WHO for raw herbal material. Other two most perilous metals Pb (2.64 ± 0.0260) and Cd (0.04 ± 0.0274) were also recorded in Bahadurgarh region, although below permissible limits. Concentration of Hg remained below detectable levels in all the leaf and stem samples tested. These results suggested that cultivation of medicinal plants and other dietary herbs should be curtailed near environmentally polluted especially industrial areas for avoidance of health hazards.

Functional quality and antioxidant composition of selected tomato (Solanum lycopersicon L) cultivars grown in Northern India

Abstract: Ten commercial and three exotic/wild cultivars (cvs) grown under Indian conditions were analyzed for variations in lycopene, β-carotene, total phenolics, quercetin, ascorbic acid and antioxidant activity (AOX). AOX was measured using three in vitro assays namely ferric reducing antioxidant power (FRAP), 2,2-diphenyl-1-picrylhydrazyl (DPPH) and Trolox equivalent antioxidant capacity (TEAC) assays. The lycopene content in tomato cvs ranged from 4.31 to 5.97 mg/100 g fw. The wild/exotic cvs had exceptionally high total phenolic content (141.98 mg/100 g fw), quercetin (56 μg/g fw) and total AOX (5.39 μmol TE/g fw). Solanum pimpinellifolium , with nearly six times lycopene content than commercial cvs, may serve as the most desirable gene pool in breeding programmes to develop functional tomatoes. Results suggest that TEAC may be more useful than DPPH assay for detecting total AOX in tomatoes.

Evaluation of Composts from Agricultural Wastes with Fish Pond Sediment as Bulking Agent to Improve Compost Quality

Abstract: Composts with five different ratios of agricultural wastes, viz. rice straw (RS), wheat straw (WS), potato plant (PP), and mustard stover (MS) were prepared with or without fish pond bottom sediment to investigate the compost maturity and their suitability for field application. The composting process was monitored through the changes in physico-chemical parameters and germination index (GI) at every 7 days interval of the composting process. All the composts were dark brown and smelled like forest soil within 56 days of composting, which reflected its matured status. On the basis of the physico-chemical parameters (bulk density: 0.84 g/cm3; pH 7.05; electrical conductivity: 3.52 mS/cm; cation exchange capacity:82.4 cmol/kg; total carbon:321.4 g/kg; total nitrogen: 16.9 g/kg; As: 6.8 mg/kg; Cd: 2.96 mg/kg; Cr: 29.6 mg/kg, Cu: 243.6 mg/kg; Hg: 0.019 mg/kg; Ni: 24.3 mg/kg; Pb: 62.1 mg/kg and Zn: 812 mg/kg) and GI (89–96%), it could be concluded that RS/WS/PP/MS, 1:1:2:1 v/v/v/v with fish pond sediment produced better compost in accordance with the Indian compost standard. Application of a combined randomized block design analysis revealed that there is a significant difference in the responses of the five composts, in relation to the time of composting. Hierarchical clustering algorithm was applied with a view to form homogeneous groups of five different composts on the basis of different physico-chemical parameters. Therefore, the ratio of waste incorporation is an important decision for composting and addition of pond sediment can improve the quality of compost.

A Random Effect Block Bootstrap for Clustered Data

Abstract: Random effects models for hierarchically dependent data, for example, clustered data, are widely used. A popular bootstrap method for such data is the parametric bootstrap based on the same random effects model as that used in inference. However, it is hard to justify this type of bootstrap when this model is known to be an approximation. In this article, we describe a random effect block bootstrap approach for clustered data that is simple to implement, free of both the distribution and the dependence assumptions of the parametric bootstrap, and is consistent when the mixed model assumptions are valid. Results based on Monte Carlo simulation show that the proposed method seems robust to failure of the dependence assumptions of the assumed mixed model. An application to a realistic environmental dataset indicates that the method produces sensible results. Supplementary materials for the article, including the data used for the application, are available online.

Non-segregated municipal solid waste in an open dumping ground: a potential contaminant in relation to environmental health

Abstract: The present article discusses an overview on the contamination of non-segregated open municipal solid waste (MSW) in and around a dumping site at Garchuk in Guwahati city, Assam, India. Analysis showed depth-wise variations in the concentrations of selected heavy metals in MSW and their subsequent accumulations with increasing depths. Zinc was the most abundant heavy metal in MSW. Six-step selective sequential extractions revealed that most of the heavy metals in MSW were in the residual phase except zinc. Analysis of the leachate from MSW showed high concentrations of fluoride, chloride, ammonium–nitrogen and the ratio of biological oxygen demand/chemical oxygen demand. Concentrations of all the heavy metals in the leachates were higher than the Indian national effluent standards. High amounts of biological oxygen demand, heavy metals, total and fecal coliforms in water samples from the adjoining water body (Deepor Beel, a Ramsar site) of the MSW dumping site indicated its unsuitability for domestic use. Principle component analysis showed that influence of MSW leachate was the major source of water contamination in Deepor Beel. Though accumulation of heavy metals in different vegetables growing in MSW dumping site did not exceed the recommended maximum intake, it was a significant additional source of heavy metals in cooked human diet.

First whole genome based microsatellite DNA marker database of tomato for mapping and variety identification

Abstract: Background The cultivated tomato is second most consumed vegetable of the world and is an important part of a diverse and balanced diet as a rich source of vitamins, minerals, phenolic antioxidants and antioxidant lycopene having anti-cancer properties. To reap benefit of genomics of the domestic tomato (Solanum lycopersicum L.) unravelled by Tomato Genome Consortium (The Tomato Genome Consortium, 2012), the bulk mining of its markers in totality is imperative and critically required. The solgenomics has limited number of microsatellite DNA markers (2867) pertaining to solanaceae family. As these markers are of linkage map having relative distance, the choice of selected markers based on absolute distance as of physical map is missing. Only limited microsatellite markers with limitations are reported for variety identification thus there is a need for more markers supplementing DUS test and also for traceability of product in global market.

PIPEMicroDB: microsatellite database and primer generation tool for pigeonpea genome.

Abstract: Molecular markers play a significant role for crop improvement in desirable characteristics, such as high yield, resistance to disease and others that will benefit the crop in long term. Pigeonpea (Cajanus cajan L.) is the recently sequenced legume by global consortium led by ICRISAT (Hyderabad, India) and been analysed for gene prediction, synteny maps, markers, etc. We present PIgeonPEa Microsatellite DataBase (PIPEMicroDB) with an automated primer designing tool for pigeonpea genome, based on chromosome wise as well as location wise search of primers. Total of 123 387 Short Tandem Repeats (STRs) were extracted from pigeonpea genome, available in public domain using MIcroSAtellite tool (MISA). The database is an online relational database based on ‘three-tier architecture’ that catalogues information of microsatellites in MySQL and user-friendly interface is developed using PHP. Search for STRs may be customized by limiting their location on chromosome as well as number of markers in that range. This is a novel approach and is not been implemented in any of the existing marker database. This database has been further appended with Primer3 for primer designing of selected markers with left and right flankings of size up to 500 bp. This will enable researchers to select markers of choice at desired interval over the chromosome. Furthermore, one can use individual STRs of a targeted region over chromosome to narrow down location of gene of interest or linked Quantitative Trait Loci (QTLs). Although it is an in silico approach, markers’ search based on characteristics and location of STRs is expected to be beneficial for researchers. Database URL: http://cabindb.iasri.res.in/pigeonpea/

How far in-silico computing meets real experiments. A study on the structure and dynamics of spin labeled vinculin tail protein by molecular dynamics simulations and EPR spectroscopy

Abstract: Investigation of conformational changes in a protein is a prerequisite to understand its biological function. To explore these conformational changes in proteins we developed a strategy with the combination of molecular dynamics (MD) simulations and electron paramagnetic resonance (EPR) spectroscopy. The major goal of this work is to investigate how far computer simulations can meet the experiments. Vinculin tail protein is chosen as a model system as conformational changes within the vinculin protein are believed to be important for its biological function at the sites of cell adhesion. MD simulations were performed on vinculin tail protein both in water and in vacuo environments. EPR experimental data is compared with those of the simulated data for corresponding spin label positions. The calculated EPR spectra from MD simulations trajectories of selected spin labelled positions are comparable to experimental EPR spectra. The results show that the information contained in the spin label mobility provides a powerful means of mapping protein folds and their conformational changes. The results suggest the localization of dynamic and flexible regions of the vinculin tail protein. This study shows MD simulations can be used as a complementary tool to interpret experimental EPR data.

In silico mining of putative microsatellite markers from whole genome sequence of water buffalo (Bubalus bubalis) and development of first BuffSatDB

Abstract: Though India has sequenced water buffalo genome but its draft assembly is based on cattle genome BTau 4.0, thus de novo chromosome wise assembly is a major pending issue for global community. The existing radiation hybrid of buffalo and these reported STR can be used further in final gap plugging and “finishing” expected in de novo genome assembly. QTL and gene mapping needs mining of putative STR from buffalo genome at equal interval on each and every chromosome. Such markers have potential role in improvement of desirable characteristics, such as high milk yields, resistance to diseases, high growth rate. The STR mining from whole genome and development of user friendly database is yet to be done to reap the benefit of whole genome sequence. By in silico microsatellite mining of whole genome, we have developed first STR database of water buffalo, BuffSatDb (Buffalo MicroSatellite Database ( http://cabindb.iasri.res.in/buffsatdb/ ) which is a web based relational database of 910529 microsatellite markers, developed using PHP and MySQL database. Microsatellite markers have been generated using MIcroSAtellite tool. It is simple and systematic web based search for customised retrieval of chromosome wise and genome-wide microsatellites. Search has been enabled based on chromosomes, motif type (mono-hexa), repeat motif and repeat kind (simple and composite). The search may be customised by limiting location of STR on chromosome as well as number of markers in that range. This is a novel approach and not been implemented in any of the existing marker database. This database has been further appended with Primer3 for primer designing of the selected markers enabling researcher to select markers of choice at desired interval over the chromosome. The unique add-on of degenerate bases further helps in resolving presence of degenerate bases in current buffalo assembly. Being first buffalo STR database in the world , this would not only pave the way in resolving current assembly problem but shall be of immense use for global community in QTL/gene mapping critically required to increase knowledge in the endeavour to increase buffalo productivity, especially for third world country where rural economy is significantly dependent on buffalo productivity.

Improving the Quality of Software by Quantifying the Code Change Metric and Predicting the Bugs

Abstract: “When you can measure what you are speaking about and express it in numbers, you know something about it; but when you cannot measure, when you cannot express it in numbers, your knowledge is of a meagre and unsatisfactory kind; it may be the beginning of knowledge, but you have scarcely, in your thoughts, advanced to the stage of science” LORD WILLIAM KELVIN (1824 – 1907) During the last decade, the quantification of software engineering process has got a pace due to availability of a huge amount of software repositories These repositories include source code, bug, communication among developers/users, changes in code, etc Researchers are trying to find out useful information from these repositories for improving the quality of software

Exploring spatial dependence in area-level random effect model for disaggregate-level crop yield estimation

Abstract: This paper describes an application of small area estimation (SAE) techniques under area-level spatial random effect models when only area (or district or aggregated) level data are available. In particular, the SAE approach is applied to produce district-level model-based estimates of crop yield for paddy in the state of Uttar Pradesh in India using the data on crop-cutting experiments supervised under the Improvement of Crop Statistics scheme and the secondary data from the Population Census. The diagnostic measures are illustrated to examine the model assumptions as well as reliability and validity of the generated model-based small area estimates. The results show a considerable gain in precision in model-based estimates produced applying SAE. Furthermore, the model-based estimates obtained by exploiting spatial information are more efficient than the one obtained by ignoring this information. However, both of these model-based estimates are more efficient than the direct survey estimate. In many dist...

An Empirical Validation of the Complexity of Code Changes and Bugs in Predicting the Release Time of Open Source Software

Abstract: With the increasing popularity of open source software, the changes in source code are inevitable. These changes in code are due to feature enhancement, new feature introduction and bug repair or fixed. It is important to note that these changes can be quantified by using entropy based measures. The pattern of bug fixing scenario with complexity of code change is responsible for the next release as these changes will cover the number of requirements and fixes. In this paper, we are proposing a method to predict the next release problem based on the complexity of code change and bugs fixed. We applied multiple linear regression to predict the time of the next release of the product and measured the performance using different residual statistics, goodness of fit curve and R2. We observed from the results of multiple linear regression that the predicted value of release time is fitting well with the observed value of number of months for the next release.

Computational identification and characterization of putative miRNAs in Heliothis virescens.

Abstract: Heliothis virescens, a polyphagous pest, is one of the most destructive pests of many crops and vegetables. Various insecticides and pesticides are used by agriculturalists to stop the growth and development of this pest. RNA interference is a new area for the management of pests/insects by inhibiting the growth related RNAs. This involves the miRNAs identification and its characterization. In the present study, computational approach is applied to predict putative miRNA candidates along with their possible target(s) in the Heliothis virescens. A total of 63,662 ESTs were downloaded from dbEST database and processed, trimmed and masked through EGassembler. The H. virescens contigs database obtained after assembly was now used to find the putative miRNA candidates by performing a local BLAST with the miRNAs of insects retrieved from miRBase. We have predicted putative miRNA candidates by homology search against all the reported insect miRNAs. These putative miRNAs candidates were further validated and filtered by different features. In addition, we have also attempted to predict the putative targets of these filtered miRNAs, by making use of 3' untranslated regions of mRNAs from B. mori. These miRNAs and their targets in H. virescens will help in improved understanding of molecular mechanisms of miRNA and development of novel and more precise techniques for better understanding some post transcriptional gene silencing.

Design and development of portal for biological database in agriculture.

Abstract: The application of novel and modern techniques in genetic engineering and genomics has resulted in information explosion in genomics. Three major genome databases under International Nucleotide Sequence Database collaboration NCBI, DDBJ and EMBL have been providing a convenient platform for submission of sequences which they share among themselves. Many institutes in India under Indian Council of Agricultural Research have scientists working on biotechnology and bioinformatics research. The various studies conducted by them, generate massive data related to biological information of plants, animals, insects, microbes and fisheries. These scientists are dependent on NCBI, EMBL, DDBJ and other portals for their sequence submissions, analysis and other data mining tasks. Due to various limitations imposed on these sites and the poor connectivity problem prevents them to conduct their studies on these open domain databases. The valued information generated by them needs to be shared by the scientific communities to eliminate the duplication of efforts and expedite their knowledge extended towards new findings. A secured common submission portal system with user-friendly interfaces, integrated help and error checking facilities has been developed in such a way that the database at the backend consists of a union of the items available on the above mentioned databases. Standard database management concepts have been employed for their systematic storage management. Extensive hardware resources in the form of high performance computing facility are being installed for deployment of this portal. Availability http://cabindb.iasri.res.in:8080/sequence_portal/

Development of a model webserver for breed identification using microsatellite DNA marker

Abstract: Identification of true to breed type animal for conservation purpose is imperative. Breed dilution is one of the major problems in sustainability except cases of commercial crossbreeding under controlled condition. Breed descriptor has been developed to identify breed but such descriptors cover only “pure breed” or true to the breed type animals excluding undefined or admixture population. Moreover, in case of semen, ova, embryo and breed product, the breed cannot be identified due to lack of visible phenotypic descriptors. Advent of molecular markers like microsatellite and SNP have revolutionized breed identification from even small biological tissue or germplasm. Microsatellite DNA marker based breed assignments has been reported in various domestic animals. Such methods have limitations viz. non availability of allele data in public domain, thus each time all reference breed has to be genotyped which is neither logical nor economical. Even if such data is available but computational methods needs expertise of data analysis and interpretation. We found Bayesian Networks as best classifier with highest accuracy of 98.7% using 51850 reference allele data generated by 25 microsatellite loci on 22 goat breed population of India. The FST values in the study were seen to be low ranging from 0.051 to 0.297 and overall genetic differentiation of 13.8%, suggesting more number of loci needed for higher accuracy. We report here world’s first model webserver for breed identification using microsatellite DNA markers freely accessible at http://cabin.iasri.res.in/gomi/ . Higher number of loci is required due to less differentiable population and large number of breeds taken in this study. This server will reduce the cost with computational ease. This methodology can be a model for various other domestic animal species as a valuable tool for conservation and breed improvement programmes.

Row-Column Designs for 2(n) factorial 2-Colour Microarray Experiments for Estimation of Main Effects and Two-Factor Interactions with Orthogonal Parameterization

Abstract: A method of construction of row–column designs for estimation of main effects and two factor interaction effects in 2 n factorial microarray experiments based on orthogonal parameterization has been developed in minimum number of replications. A catalogue of designs for 2 ≤ n ≤ 9 has been prepared. The catalogue also gives the main effects and two-factor interactions confounded in different replications and the factorial effects that are not confounded in a replication. The efficiency factor of estimable main effects and two-factor interactions has been given. For each 2 n factorial, two designs have been given, one in which main effects are estimated with more efficiency and another in which two-factor interactions are estimated with more efficiency. A procedure of construction of row–column designs for estimation of all factorial effects with odd number of factors has been given. Row–column designs with unequal replication of different treatment combinations have also been obtained for estimation of all main effects and two-factor interactions.

Weather based forecast models for diseases in mustard crop

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Expression analysis of genes responsible for amino acid biosynthesis in halophilic bacterium Salinibacter ruber.

Abstract: The degeneracy of the genetic code allows for multiple codons to encode the same amino acid. However, alternative codons and amino acids are used unevenly among genes, a phenomenon termed codon-usage bias. Genes regulating amino acid biosynthesis of Salinibacter ruber, an extremely halophilic bacterium were studied in order to determine the synonymous codon usage patterns. Factors responsible for codon usage variation among the genes were investigated using codon usage indices and multi-variate statistical approach. Overall codon usage data analysis indicated that codons ending in G and/or C were predominant among the genes. Multi-variate statistical analysis showed that there was a single major trend in the codon usage variation among the genes, which had a strong positive correlation (r = 0.93, P < 0.01) with (G + C) content of the genes. Further, correlation analysis indicated that genes with higher expression level and showing a greater degree of codon usage bias were GC-rich and preferred codons with C or G nucleotides at the third position. A set of thirteen codons were identified through Chi-square test as optimal codons, which were preferred in highly expressed genes. It could be concluded that mutational bias had a profound effect on codon usage pattern. In addition, translational selections also operated with a proper balance, making the genes translationally more efficient. The frequency of these codons appeared to be correlated with the level of gene expression and might be a useful indicator in the case of genes (or open-reading-frames) whose expression levels are unknown.

A multiple-frame approach to crop yield estimation from satellite-remotely sensed data

Abstract: Many studies have recently explored information from satellite-remotely sensed data SRSD for estimating crop production statistics The value of this information depends on the aerial and spatial resolutions of SRSD SRSD with fine spatial resolution is costly and aerial coverage is less Use of multiple frames of SRSD in the estimation process of crop production can increase the precision We propose an estimator for the average yield of wheat for the state of Haryana, India This estimator uses information from Wide Field Sensor WiFS and Linear Imaging Self Scanner LISS-III data from the Indian Remote Sensing IRS-1D satellite and crop-cutting experiment data collected by probability sampling design from a list frame of villages We find that relative efficiencies of multiple-frame estimators are high in comparison to single-frame estimators

Universally optimal second order neighbour designs

Abstract: This paper deals with optimality aspects of complete block designs with interference effects arising from the neighbouring units up to distance 2 (first and second order) from one side. Conditions have been obtained for the block design to be universally optimal for estimating direct and interference effects. Some classes of balanced and strongly balanced complete block designs have been identified to be universally optimal for the estimation of direct effects, first order neighbour effects and second order neighbour effects.

Workflow management systems for gene sequence analysis and evolutionary studies - A Review.

Abstract: Post 'omic' era has resulted in the development of many primary, secondary and derived databases. Many analytical and visualization bioinformatics tools have been developed to manage and analyze the data available through large sequencing projects. Availability of heterogeneous databases and tools make it difficult for researchers to access information from varied sources and run different bioinformatics tools to get desired analysis done. Building integrated bioinformatics platforms is one of the most challenging tasks that bioinformatics community is facing. Integration of various databases, tools and algorithm is a challenging problem to deal with. This article describes the bioinformatics analysis workflow management systems that are developed in the area of gene sequence analysis and phylogeny. This article will be useful for biotechnologists, molecular biologists, computer scientists and statisticians engaged in computational biology and bioinformatics research.

Analysis and functional annotation of expressed sequence tags of water buffalo.

Abstract: An elucidated genome of domestic livestock river buffalo will contribute enormously to economy and better understanding of genome evolution as well. An attempt is made to obtain genomic information on buffalo, based on total Expressed Sequence Tags (ESTs) of Bubalus bubalis available in public domain. These ESTs were annotated and classified into 15 different functional categories based on their homology to the known proteins. Interestingly, 41.79% of the contigs were found to be buffalo specific novel ESTs with respect to other species used in analysis which needs further studies. Also, 224 pSNPs (putative Single Nucleotide Polymorphism) were detected. This study will provide a home base for further genomic studies of buffalo and comparative studies enabling a starting point for the genome annotation of the organism. Supplementary materials are available for this article online.

Universally optimal balanced changeover designs with first residuals

Abstract: Considering the presence of first order residual effects of treatments, a family of variance balanced changeover designs has been presented and universal optimality of the designs is established. The designs use only v experimental units and (v − 1)/2 periods for v = 4t + 3 prime or prime power number of treatments; t being a positive integer. A special feature of the proposed designs is that ‘in the order of presentation of treatments to experimental units over periods, each treatment is once immediately preceded by only half of the other treatments and is immediately followed once by the remaining half of the treatments’. This characteristic results in reducing the size of the variance balanced designs considerably.

Bug prediction using entropy-based measures

Abstract: In the available literature, researchers have proposed and implemented a plethora of bug prediction approaches, which vary in terms of accuracy, complexity and the input data they require, but very few of them has predicted the number of bugs in the software based on the entropy or the complexity of code changes. To use the entropy of code change as a bug predictor, firstly, the history of complexity metric HCM defined with different decay weight and decay models were assigned to it Hassan, 2009. But, they did not propose any method to find out the value of decay rate/factor. In this paper, we proposed a new weight to HCM, a method to find out the value of decay rate/factor and proposed some novel decay-based methods. We have applied simple linear regression SLR and support vector regression SVR to predict the bugs based on existing and proposed methods of HCM. We have also studied the performance of different complexity of code changes entropy-based bug prediction approaches on the basis of various performance measures using four subsystems of Mozilla project. We found that decay models for SVR show better results in comparison with SLR.