@article { ISI:000228094400009, title = {Gene expression patterns of helicoverpa armigera gut proteases}, journal = {Insect Biochemistry and Molecular Biology}, volume = {35}, number = {4}, year = {2005}, month = {APR}, pages = {355-367}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, type = {Article}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {

Relative quantification of reported gut proteinase cDNAs from Helicoverpa armigera larvae fed on various host plants (cotton, chickpea, pigeonpea, tomato and okra), non-host plant Pis (winged bean, bitter gourd, ground nut, and capsicum) and during larval development has been carried out using semi-quantitative RT-PCR. Five trypsin-like and three chymotrypsin-like proteinases were categorized as insensitive or sensitive to most of the proteinase inhibitors (Pis) and insensitive/sensitive to specific Pis based on their expression analysis. These results were supported by amino acid sequence analysis, where diverged amino acids were observed in the regions, which are reported to be involved in typical trypsin trypsin inhibitor interactions and critical for proteinase inhibitor resistance. Among exopeptidases (five aminopeptidase and three carboxypeptidase), HaAmi4 and HaAmi5 of aminopeptidase and HaCar1 of carboxypeptidase exhibited considerable differential expression. Elastase and cathepsin B-like proteinases were expressed at negligible levels. The proteases identified in the study would be ideal candidates for further interactions studies with protease inhibitors to understand the structural reasons of protease inhibitor insensitivity (c) 2005 Elsevier Ltd. All rights reserved.

}, keywords = {expression, gut proteinases, Helicoverpa armigera, Proteinase inhibitors, RT-PCR}, issn = {0965-1748}, doi = {10.1016/j.ibmb.2005.01.006}, author = {Chougule, Nanasaheb P. and Giri, Ashok P. and Sainani, Mohini N. and Gupta, Vidya S.} } @article { ISI:000250820000027, title = {Genetic diversity analysis of mango cultivars using inter simple sequence repeat markers}, journal = {Current Science}, volume = {93}, number = {8}, year = {2007}, month = {OCT}, pages = {1135-1141}, publisher = {CURRENT SCIENCE ASSOC}, type = {Article}, address = {C V RAMAN AVENUE, PO BOX 8005, BANGALORE 560 080, INDIA}, abstract = {

With 33 polymorphic Inter Simple Sequence Repeat (ISSR) markers, genetic diversity among 70 mango cultivars and a distant outgroup was analysed. Clustering was done using Dice and Jaccard coefficients with bootstrapping. Multivariate analysis was conducted using the Euclidean distances. Among the total 420 bands, 408 were polymorphic. Probability that any ISSR fragment is shared by two different cultivars was calculated to be 2.54 x 10(-1). Non-Indian mango cultivars were found genetically diverged from Indian mango germ pool. No separation was observed between North Indian and South Indian cultivars. Twelve different cultivar-specific bands were detected for six cultivars, which approved the effectiveness of ISSR markers in mango genetic diversity analysis.

}, keywords = {DNA finger printing, inter simple sequence repeat, Mangifera indica, principle coordinate analysis}, issn = {0011-3891}, author = {Pandit, Sagar S. and Mitra, Sirsha Sribas and Giri, Ashok P. and Pujari, Keshav H. and Patil, Bhimarao P. and Jambhale, Narayan D. and Gupta, Vidya S.} } @article { ISI:000295666100008, title = {Geographic variation in the flavour volatiles of alphonso mango}, journal = {Food Chemistry}, volume = {130}, number = {1}, year = {2012}, month = {JAN}, pages = {58-66}, publisher = {ELSEVIER SCI LTD}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND}, abstract = {

Alphonso, one of the most popular cultivars of mango in India is known to exhibit geographic variation in the flavour of ripe fruits. To get chemical insight into this difference, volatiles were studied in the ripening fruits of Alphonso mangoes from three cultivation locations in India. Ripe fruits from Deogad had lower content of mono- and sesquiterpenes and higher content of lactones and furanones as compared to the fruits from Dapoli: whereas fruits from Vengurle had average quantities of these chemicals in comparison with Deogad and Dapoli fruits. This variation was clearly reflected as separate clustering of the localities in the Principal Component Analysis. The localities were indistinguishable from each other in terms of raw fruit volatiles. This study exemplifies a case of phenotypic plasticity; since the plants chosen were clonally propagated, such geographic variation in the volatiles can be attributed to varied abiotic conditions at these three localities. (C) 2011 Elsevier Ltd. All rights reserved.

}, keywords = {Mango, Phenotypic plasticity, Ripening, Volatiles}, issn = {0308-8146}, doi = {10.1016/j.foodchem.2011.06.053}, author = {Kulkarni, Ram S. and Chidley, Hemangi G. and Pujari, Keshav H. and Giri, Ashok P. and Gupta, Vidya S.} } @article { ISI:000316759800020, title = {Genome-wide identification and characterization of microRNA genes and their targets in flax (Linum usitatissimum)}, journal = {Planta}, volume = {237}, number = {4}, year = {2013}, month = {APR}, pages = {1149-1161}, publisher = {SPRINGER}, address = {233 SPRING ST, NEW YORK, NY 10013 USA}, abstract = {

MicroRNAs (miRNAs) are small (20-24 nucleotide long) endogenous regulatory RNAs that play important roles in plant growth and development. They regulate gene expression at the post-transcriptional level by translational repression or target degradation and gene silencing. In this study, we identified 116 conserved miRNAs belonging to 23 families from the flax (Linum usitatissimum L.) genome using a computational approach. The precursor miRNAs varied in length; while most of the mature miRNAs were 21 nucleotide long, intergenic and showed conserved signatures of RNA polymerase II transcripts in their upstream regions. Promoter region analysis of the flax miRNA genes indicated prevalence of MYB transcription factor binding sites. Four miRNA gene clusters containing members of three phylogenetic groups were identified. Further, 142 target genes were predicted for these miRNAs and most of these represent transcriptional regulators. The miRNA encoding genes were expressed in diverse tissues as determined by digital expression analysis as well as real-time PCR. The expression of fourteen miRNAs and nine target genes was independently validated using the quantitative reverse transcription PCR (qRT-PCR). This study suggests that a large number of conserved plant miRNAs are also found in flax and these may play important roles in growth and development of flax.

}, keywords = {Digital expression analysis, Gene cluster, Linseed, miRNA, MiRNA target transcript, Promoter analysis}, issn = {0032-0935}, doi = {10.1007/s00425-012-1833-5}, author = {Barvkar, Vitthal T. and Pardeshi, Varsha C. and Kale, Sandip M. and Qiu, Shuqing and Rollins, Meaghen and Datla, Raju and Gupta, Vidya S. and Kadoo, Narendra Y.} } @article { ISI:000316557400002, title = {Genome-wide identification and characterization of nucleotide binding site leucine-rich repeat genes in linseed reveal distinct patterns of gene structure}, journal = {Genome}, volume = {56}, number = {2}, year = {2013}, month = {FEB}, pages = {91-99}, publisher = {CANADIAN SCIENCE PUBLISHING, NRC RESEARCH PRESS}, address = {1200 MONTREAL ROAD, BUILDING M-55, OTTAWA, ON K1A 0R6, CANADA}, abstract = {

Plants employ different disease-resistance genes to detect pathogens and to induce defense responses. The largest class of these genes encodes proteins with nucleotide binding site (NBS) and leucine-rich repeat (LRR) domains. To identify the putative NBS-LRR encoding genes from linseed, we analyzed the recently published linseed genome sequence and identified 147 NBS-LRR genes. The NBS domain was used for phylogeny construction and these genes were classified into two well-known families, non-TIR (CNL) and TIR related (TNL), and formed eight clades in the neighbor-joining bootstrap tree. Eight different gene structures were observed among these genes. An unusual domain arrangement was observed in the TNL family members, predominantly in the TNL-5 clade members belonging to class D. About 12\% of the genes observed were linseed specific. The study indicated that the linseed genes probably have an ancient origin with few progenitor genes. Quantitative expression analysis of five genes showed inducible expression. The in silico expression evidence was obtained for a few of these genes, and the expression was not correlated with the presence of any particular regulatory element or with unusual domain arrangement in those genes. This study will help in understanding the evolution of these genes, the development of disease resistant varieties, and the mechanism of disease resistance in linseed.

}, keywords = {Flax, in silico gene expression, motif analysis, NBS-LRR, Phylogenetic analysis, Promoter analysis}, issn = {0831-2796}, doi = {10.1139/gen-2012-0135}, author = {Kale, Sandip M. and Pardeshi, Varsha C. and Barvkar, Vitthal T. and Gupta, Vidya S. and Kadoo, Narendra Y.} } @article {45682, title = {Genomic and functional characterization of coleopteran insect-specific alpha-amylase inhibitor gene from amaranthus species}, journal = {Plant Molecular Biology}, volume = { 94 }, year = {2017}, month = {JUN}, pages = {319-332}, type = {Article}, abstract = {The smallest 32 amino acid alpha-amylase inhibitor from Amaranthus hypochondriacus (AAI) is reported. The complete gene of pre-protein (AhAI) encoding a 26 amino acid (aa) signal peptide followed by the 43 aa region and the previously identified 32 aa peptide was cloned successfully. Three cysteine residues and one disulfide bond conserved within known alpha-amylase inhibitors were present in AhAI. Identical genomic and open reading frame was found to be present in close relatives of A. hypochondriacus namely Amaranthus paniculatus, Achyranthes aspera and Celosia argentea. Interestingly, the 3{\textquoteright}UTR of AhAI varied in these species. The highest expression of AhAI was observed in A. hypochondriacus inflorescence; however, it was not detected in the seed. We hypothesized that the inhibitor expressed in leaves and inflorescence might be transported to the seeds. Sub-cellular localization studies clearly indicated the involvement of AhAI signal peptide in extracellular secretion. Full length rAhAI showed differential inhibition against alpha-amylases from human, insects, fungi and bacteria. Particularly, alpha-amylases from Helicoverpa armigera (Lepidoptera) were not inhibited by AhAI while Tribolium castaneum and Callosobruchus chinensis (Coleoptera) alpha-amylases were completely inhibited. Molecular docking of AhAI revealed tighter interactions with active site residues of T. castaneum alpha-amylase compared to C. chinensis alpha-amylase, which could be the rationale behind the disparity in their IC50. Normal growth, development and adult emergence of C. chinensis were hampered after feeding on rAhAI. Altogether, the ability of AhAI to affect the growth of C. chinensis demonstrated its potential as an efficient bio-control agent, especially against stored grain pests.}, doi = {10.1007/s11103-017-0609-5}, author = {Bhide, Amey J. and Channale, Sonal M. and Yadav, Yashpal and Bhattacharjee, Kabita and Pawar, Pankaj K. and Maheshwari, V. L. and Gupta, Vidya S. and Ramasamy, Sureshkumar and Giri, Ashok P.} } @article {44479, title = {GA3 application in grapes (Vitis vinifera L.) modulates different sets of genes at cluster emergence, full bloom, and berry stage as revealed by RNA sequence-based transcriptome analysis}, journal = {Functional \& Integrative Genomics}, volume = {18}, year = {2018}, month = {JUL}, pages = {439{\textendash}455}, abstract = {In grapes (Vitis vinifera L.), exogenous gibberellic acid (GA3) is applied at different stages of bunch development to achieve desirable bunch shape and berry size in seedless grapes used for table purpose. RNA sequence-based transcriptome analysis was used to understand the mechanism of GA3 action at cluster emergence, full bloom, and berry stage in table grape variety Thompson Seedless. At cluster emergence, rachis samples were collected at 6 and 24 h after application of GA3, whereas flower clusters and berry samples were collected at 6, 24, and 48 h after application at full bloom and 3{\textendash}4 mm berry stages. Seven hundred thirty-three genes were differentially expressed in GA3-treated samples. At rachis and flower cluster stage respectively, 126 and 264 genes were found to be significantly differentially expressed within 6 h of GA3 application. The number of DEG reduced considerably at 24 h. However, at berry stage, major changes occurred even at 24 h and a number of DEGs at 6 and 24 h were 174 and 191, respectively. As compared to upregulated genes, larger numbers of genes were downregulated. Stage-specific response to the GA3 application was observed as evident from the unique set of DEGs at each stage and only a few common genes among three stages. Among the DEGs, 67 were transcription factors. Functional categorization and enrichment analysis revealed that several transcripts involved in sucrose and hexose metabolism, hormone and secondary metabolism, and abiotic and biotic stimuli were enriched in response to application of GA3. A high correlation was recorded for real-time PCR and transcriptome data for selected DEGs, thus indicating the robustness of transcriptome data obtained in this study for understanding the GA3 response at different stages of berry development in grape. Chromosomal localization of DEGs and identification of polymorphic microsatellite markers in selected genes have potential for their use in breeding for varieties with improved bunch architecture.}, keywords = {Bunch architecture, GA3 response, Microsatellite markers, RNA seq, Transcription factors, Vitis vinifera}, issn = {1438-793X}, doi = {10.1007/s10142-018-0605-0}, author = {Upadhyay, Anuradha and Maske, Smita and Jogaiah, Satisha and Kadoo, Narendra Y. and Gupta, Vidya S.} } @article {45422, title = {Genetic and phytochemical investigations for understanding population variability of the medicinally important tree Saraca asoca to help develop conservation strategies}, journal = {Phytochemistry}, volume = {156}, year = {2018}, month = {DEC}, pages = {43-54}, type = {Article}, abstract = {Saraca asoca (Roxb.) De Wilde (Caesalpiniaceae) is a highly traded IUCN red listed tree species used in Ayurvedic medicines for the treatment of various disorders, especially gynaecological problems. However, information about the genetic variations between populations and corresponding variation in specialized metabolites of S. asoca remains unclear. To address this issue, we analysed 11 populations of S. asoca with 106 accessions collected from Western Ghats of India using ISSR markers along with selected phytocompounds using RP-HPLC. Twenty primers were screened, out of which seven were selected for further analysis based on generation of clear polymorphic banding patterns. These seven ISSR primers produced 74 polymorphic loci. AMOVA showed 43\% genetic variation within populations and 57\% among the populations of S. asoca. To estimate the genetic relationships among S. asoca populations, UPGMA and Bayesian Models were constructed, which revealed two clusters of similar grouping patterns. However, excluding minor deviations, UPGMA and dissimilarity analysis showed close association of genotypes according to their geographical locations. Catechin (CAT), epicatechin (EPI) and gallic acid (GA) were quantified from bark and leaf samples of corresponding genotypes collected from 106 accessions. ROC plots depicted the sensitivity and specificity of the concentrations of tested phytocompounds at various cut-off points. Although, multiple logistic regression analysis predicted some association between few loci with GA, EPI and CAT, but PCA for phytochemical data failed to distinguish the populations. Overall, there were no significant trends observed to distinguish the populations based on these phytocompounds. Furthermore, the study advocates the delineate provenance regions of S. asoca genotypes/chemotype snapshots for in-situ conservation and ex-situ cultivation.}, issn = {0031-9422}, doi = {10.1016/j.phytochem.2018.08.016}, author = {Hegde, Satisha and Pai, Sandeep Ramchandra and Bhagwat, Rasika M. and Saini, Archana and Rathore, Poonam Kanwar and Jalalpure, Sunil Satyappa and Hegde, Harsha Vasudev and Sugunan, Attayoor Purushottaman and Gupta, Vidya S. and Kholkute, Sanjiva D. and Roy, Subarna} } @article {47484, title = {Global study of MFS superfamily transporters in arabidopsis and grapes reveals their functional diversity in plants}, journal = {Plant Gene}, volume = {18}, year = {2019}, month = {JUN }, type = {Article}, abstract = {The Major Facilitator Superfamily (MFS) is the largest superfamily of secondary transporters present in all organisms, from prokaryotes to higher eukaryotes, that facilitates transport of diverse molecules like sugars, vitamins, amino-acids, hormones, etc. across cell membranes. The superfamily was further expanded to MFS Superfamily (MFSS) to integrate MFS with nine more families. The present study revealed their land plant specific diversity through identification across six species from unicellular alga to higher flowering plants. We identified 71, 131, 254, 260, 213 and 203 MFSS transporters in Chlamydomonas reinhardtii, Physcomitrella patens, Selaginella moellendorffii, Oryza sativa (var. Japonica), Arabidopsis thaliana and Vitis vinifera, respectively and classified them into MFSS families and subfamilies based on their transporter classification identifiers (TCIDs). Detailed analysis of 20 land plant specific subfamilies was conducted in A. thaliana and V. vinifera. Phylogenetic and gene duplication studies revealed the expansion of sugar porter and proton dependent oligopeptide transporter families in Arabidopsis and grape. The subcellular localization of the majority of the transporters was predicted to be in the plasma membrane. Furthermore, the microarray expression analysis of MFSS transporters from Arabidopsis and grapes revealed their multi-tissue-specificity and differential regulation under biotic and abiotic stress conditions. Studies of the transmembrane topology highlighted the presence of central cytoplasmic loop along with family specific topological variations that were evident from phylogenetic analysis. Overall, this study adds to the knowledge of functional and structural diversity and evolution of MFSS transporters in plants and opens the scope for detailed physiological and functional studies on these proteins.}, doi = {10.1016/j.plgene.2019.100179}, author = {Patil, Sucheta S. and Prashant, Ramya and Kadoo, Narendra Y. and Upadhyay, Anuradha and Gupta, Vidya S.} } @article {47802, title = {Gibberellic acid induces unique molecular responses in {\textquoteleft}thompson seedless{\textquoteright} grapes as revealed by non-targeted metabolomics}, journal = {Journal of Plant Growth Regulation}, volume = {40}, year = {2021}, month = {FEB}, pages = {293 - 304}, type = {Article}, abstract = {Compact clusters and small berry size are the major problems associated with the commercialization of table grapes. The application of gibberellic acid 3 (GA3) has been a long-followed practice to overcome these issues. To analyze the molecular response of {\textquoteleft}Thompson Seedless{\textquoteright} grapes to GA3 treatment, we investigated the metabolomes of its rachises, clusters, and berries, 6~h and 24~h after the treatment. Metabolite profiling using non-targeted metabolomics approach revealed several metabolites, including arginine, proline, tyrosine, kaempferol, resveratrol, catechin, and so on as possible biomarkers of GA3 treatment in grapes. GA3 treatment greatly impacted the alanine, aspartate, and glutamate metabolism pathways, and the GA3-mediated alterations in the levels of certain plant growth regulators and primary metabolites were in accordance with important growth and developmental processes in grapes. This study highlights the effect of GA3 on the profiles of certain polyphenols impacting the flavone and flavonol biosynthesis pathways and hence the nutritional aspect of grapes. The results of this study would be useful to develop self-elongating varieties simplifying the grape cultivation.}, isbn = {1435-8107}, doi = {10.1007/s00344-020-10102-7}, author = {Jadhav, Uma and Mundhe, Swapnil and Kumar, Yashwant and Jogaiah, Satisha and Upadhyay, Anuradha and Gupta, Vidya S. and Kadoo, Narendra Y.} } @article {46917, title = {Gibberellic acid induces unique molecular responses in {\textquoteleft}thompson seedless{\textquoteright} grapes as revealed by non-targeted metabolomics}, journal = {Journal of Plant Growth Regulation}, volume = {40}, year = {2021}, month = {FEB}, pages = {293-304}, type = {Article}, abstract = {

Compact clusters and small berry size are the major problems associated with the commercialization of table grapes. The application of gibberellic acid 3 (GA(3)) has been a long-followed practice to overcome these issues. To analyze the molecular response of {\textquoteleft}Thompson Seedless{\textquoteright} grapes to GA(3) treatment, we investigated the metabolomes of its rachises, clusters, and berries, 6 h and 24 h after the treatment. Metabolite profiling using non-targeted metabolomics approach revealed several metabolites, including arginine, proline, tyrosine, kaempferol, resveratrol, catechin, and so on as possible biomarkers of GA(3) treatment in grapes. GA(3) treatment greatly impacted the alanine, aspartate, and glutamate metabolism pathways, and the GA(3)-mediated alterations in the levels of certain plant growth regulators and primary metabolites were in accordance with important growth and developmental processes in grapes. This study highlights the effect of GA(3) on the profiles of certain polyphenols impacting the flavone and flavonol biosynthesis pathways and hence the nutritional aspect of grapes. The results of this study would be useful to develop self-elongating varieties simplifying the grape cultivation.

}, keywords = {Biosynthetic pathways, GA(3) response, GA(3) signaling, Sultana grapes, Untargeted metabolomics}, issn = {0721-7595}, doi = {10.1007/s00344-020-10102-7, Early Access Date = MAR 2020}, author = {Jadhav, Uma and Mundhe, Swapnil and Kumar, Yashwant and Jogaiah, Satisha and Upadhyay, Anuradha and Gupta, Vidya S. and Kadoo, Narendra Y.} }