Annual Report 2011-2012 - Nabi.res.in

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NATIONAL AGRI-FOOD BIOTECHNOLOGY INSTITUTE5.1.2 Wheat genechip microarray data mining out of the 61127 probe sets of wheat.for identification of SFPs in Indian cultivars and Optimization of script is under progress.annotation of hypothetical proteinsIntroduction:5.1.3 Development of small RNA analysispipelineSNPs and insertion or deletions of one or morenucleotides (indels) are DNA polymorphisms thatcan affect hybridization of DNA or cRNA to aprobe on an array. The Affymetrix Gene Chiparrays are suitable to detect such variationsbecause each gene is represented by a set of eleven25-bp probes that are sensitive to target mismatchowing to their short sequence. A target sequencethat matches the sequence of a probe binds withmuch greater affinity than one with a mismatchsequence. The resulting difference inhybridization intensity between two genotypes foran individual probe is called a SFP, where a featurerefers to a probe in the array. A SFP may be causedby a SNP, a multiple nucleotide polymorphism, oran indel.Research Objective:To predict SFPs in the genomes of the followingwheat varieties: C-306, LOK1, Sonalika andWH291, using microarray data.Research in Progress:1. An algorithm was written for predictingSFPs using the normalized expression signalvalues of the four wheat varieties.2. Standard deviation values were computedusing the normalized signal intensity valuesof perfect match probes of a probeset for allthe four wheat varieties 7 DAA,14 DAA and 28 DAA.Introduction:miRNAs are small and endogenous RNAs thatregulate endogenous genes or gene expression.miRNAs are important for implementingdevelopmental programs in animals and plants.Our research focus is on plant miRNA predictionand its target prediction (miRNA). In plants, these~18-24 nt RNAs are processed from stem-loopregions of long primary transcripts by a dicer-likeenzyme and are loaded into silencing complexes,where they generally direct cleavage ofcomplementary mRNAs. NABI has initiatedexperiments to generate small RNA sequencesusing Illumina platform for RNA isolated fromcontrasting samples of wheat, custard apple, litchiand mango to understand small RNA regulationand identify novel regulatory small RNA. Longterm goal under this component is to reconstructgene regulatory networks using multi-dimensiondata. Small RNA prediction and its targetprediction will be done using in-house developedpipeline of open source prediction tools andcustomized scripts. Bench marking of differentsoftwares (in the pipeline) is in progress usingdatasets available in public domain.Research Objectives:lBench-marking of miRNA prediction andmiRNA-target prediction tools.3.l Development of small RNA analysisFour average standard deviation values werePipeline.used as reference values to predict SFP. SFPis predicted if the standard deviation valuesl Development of in-house small RNAof a probe of a probeset are less than or equal database.to the minimum of the four average standarddeviation values.l Comparative analysis of small RNA4. Python script was written based on the aboveregulation.written statistical logic for predicting SFPs l Reconstruction of gene regulatory networks.39
NATIONAL AGRI-FOOD BIOTECHNOLOGY INSTITUTEEMERGING AREAS1. Probing B-ZIP transcription factors role in 2. Developing carbohydrate and lipidroot and seed development in plants: Use of a derivative based nano molecular vehicles fordesigned dominant negative proteinbioavailability of micronutrientsInvestigator: Vikas RishiInvestigator:Nitin K. SinghalThere are approximately 72 B-ZIP transcriptionfactors in Arabidopsis and a number of these areinvolved in root and seed development. The B-ZIPmotif is a long bipartite α-helix. The C-terminalhalf is an amphipathic α-helix that dimerizes toform a parallel dimeric coiled-coil termed asMicronutrient deficiency such as iron deficiencymay arise from inadequate intake and impairedabsorption leading to anaemia, reduce cognitivedevelopment and lower work capacity. Althoughiron deficiency therapy with oral ferrous salts iswidespread, the bioavailability of iron from suchsalts is poor. Anti-nutrient components, such asphytate in whole grain and bran, oxalic acid inspinach, phosphates in practically all foods, andtannins from black tea and coffee may decrease+2the bioavailability of ferrous iron Fe by forminginsoluble complexes .FeSO 4 is water soluble compound, but is easily+ 3oxidized to low soluble Fe form after contactFigure 1: Design of dominant negative to B-ZIP:A-ZIP. with oxygen. This may often cause unacceptablechange in the color and taste of foods. Moreover,leucine zipper. The N-terminal half is a basic +2Fe frequently causes gastrointestinal side effects.region that binds sequence specific DNA. AIt is highly desirable to find a better alternativedominant negative (DN) protein called A-ZIP inwhich the basic DNA binding region of a B-ZIPiron source that can overcome the gastrointestinaltranscription factor (TF) is replaced by a rationally side effects of iron. Iron oxide/hydroxidedesigned acidic extension has been used nanoparticles with neutral and hydrophilicsuccessfully in mammalian systems to study the carbohydrate nanosize shell can be used asrole of these TFs in growth, development and alternatives to ferrous salts. In these formulationsdifferentiation (Figure 1). These DN proteins gastrointestinal side effects are rare becauseheterodimerize with the wild type proteins and3+hundreds of Fe atoms are safely packed ininhibit their function by not allowing them to bind nanoscaled cores surrounded by the solubilizingto promoter of a gene. DN is biologically active shell. There are some evidences that particles inreagent because a heterodimer is more stable thanthe range of nanometre show different propertiesa B-ZIP homodimer bound to DNA. This strategyas compared to larger particles. This and the factwill be used to study root and seed development inthat very large surface area of nanoparticles allowsArabidopsis. Use of dominant negative forsilencing genes has advantage over other RNAiron to be much more bioavailable, suggesting thebased technologies like siRNA and miRNA. potential of designing and producing particles ofThese designed dominant negatives can inhibit the nano dimension. Nanoparticle based deliveryfunctions of all the TFs belonging to the same systems can boost iron bioavailability and mayfamily, thus overcoming the problem of play a vital role in food applications in the nearredundancy, a phenomenon common in biological future for treating micronutrient deficiencies.systems.40
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