ORCID Profile
0000-0003-0753-792X
Current Organisations
University of Western Australia
,
University of Horticultural Sciences
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: SAGE Publications
Date: 2014
DOI: 10.4137/BBI.S19057
Abstract: Biological enrichment analysis using gene ontology (GO) provides a global overview of the functional role of genes or proteins identified from large-scale genomic or proteomic experiments. Phenomic enrichment analysis of gene lists can provide an important layer of information as well as cellular components, molecular functions, and biological processes associated with gene lists. Plant phenomic enrichment analysis will be useful for performing new experiments to better understand plant systems and for the interpretation of gene or proteins identified from high-throughput experiments. Plant ontology (PO) is a compendium of terms to define the erse phenotypic characteristics of plant species, including plant anatomy, morphology, and development stages. Adoption of this highly useful ontology is limited, when compared to GO, because of the lack of user-friendly tools that enable the use of PO for statistical enrichment analysis. To address this challenge, we introduce Plant Ontology Enrichment Analysis Server (POEAS) in the public domain. POEAS uses a simple list of genes as input data and performs enrichment analysis using Ontologizer 2.0 to provide results in two levels, enrichment results and visualization utilities, to generate ontological graphs that are of publication quality. POEAS also offers interactive options to identify user-defined background population sets, various multiple-testing correction methods, different enrichment calculation methods, and res ling tests to improve statistical significance. The availability of such a tool to perform phenomic enrichment analyses using plant genes as a complementary resource will permit the adoption of PO-based phenomic analysis as part of analytical workflows. POEAS can be accessed using the URL caps.ncbs.res.in oeas .
Publisher: Springer Science and Business Media LLC
Date: 22-05-2021
DOI: 10.1007/S11033-021-06396-9
Abstract: Coriander (Coriandrum sativum L.) is well known vegetable and spice crop grown globally for its leaves and seeds. Stem gall (Protomyces macrosporus L.) is a fungal disease affecting its quality and yield. However, no information is available on SSR markers linked to disease resistance in coriander. Hence, development of co-dominant genetic markers is prerequisite for disease investigations in coriander. In-house stem gall resistance and susceptible cultivars transcriptome data were utilized. Totally, 59,933 and 56,861 transcripts were examined, 9141 and 8346 Simple Sequence Repeats (SSR) were identified and the most abundant type was the tri, followed by di, tetra, penta and hexa nucleotide repeats. A total of ten selected SSR-Functional Domain Markers (FDM) were developed based on functional annotation terms associated with pathogen response and validated among ten coriander cultivars and their transferability was examined in five fennel (Foeniculum vulgare L.) cultivars. Nine primer pairs resulted from lified bands. Marker ACorSGD-1 shown monomorphic bands among coriander genotypes except Acr-1 showed heterologouse and multiple bands in fennel cultivars. Markers ACorSGD-4, 5, 7 and 9 shown presence in resistant cultivars and absence of bands among susceptible cultivars of coriander and thus, considered to be the candidate markers for disease screening. Marker ACorSGD-6 shown monomorphic bands among coriander. Markers ACorSGD-1, 2, 3, and 5 shown transferability among fennel cultivars. A total of 136 alleles in coriander and fennel were produced. Using UPGMA clustering method a dendrogram was generated and cultivars were grouped into two separate clusters with coriander and fennel. Identified and developed SSR-FDM markers are useful for linkage mapping for disease resistant in coriander.
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3MB70072K
Abstract: Biotic and abiotic stresses adversely affect agriculture by reducing crop growth and productivity worldwide. To investigate the abiotic stress-responsive genes in Arabidopsis thaliana, we compiled a dataset of stress signals and differentially upregulated genes (>= 2.5 fold change) from Stress-responsive transcription Factors DataBase (STIFDB) with additional set of stress signals and genes curated from PubMed and Gene Expression Omnibus. A dataset of 3091 genes differentially upregulated due to 14 different stress signals (abscisic acid, aluminum, cold, cold-drought-salt, dehydration, drought, heat, iron, light, NaCl, osmotic stress, oxidative stress, UV-B and wounding) were curated and used for the analysis. Details about stress-responsive enriched genes and their association with stress signals can be obtained from STIFDB2 database . The gene-stress-signal data were analyzed using an enrichment-based meta-analysis framework consisting of two different ontologies (Gene Ontology and Plant Ontology), biological pathway and functional domain annotations. We found several shared and distinct biological processes, cellular components and molecular functions associated with stress-responsive genes. Pathway analysis revealed that stress-responsive genes perturbed the pathways under the "Metabolic pathways" category. We also found several shared and stress-signal specific protein domains, suggesting functional mechanisms regulating stress-response. Phenomic characteristics of abiotic stress-responsive genes were ascertained for several stresses and found to be shared by multiple stresses in both anatomy and temporal categories of Plant Ontology. We found several constitutive stress-responsive genes that are differentially upregulated due to perturbation of different stress signals, for ex le a gene (AT1G68440) involved in phenylpropanoid metabolism and polyamine catabolism as responsive to seven different stress signals. We also performed structure-function prediction of five genes associated responsive to multiple abiotic stress signals. We envisage that results from our analysis that provide insight into functional repertoire, metabolic pathways and phenomic characteristics common and specifically associated with stress signals would help to understand abiotic stress regulome in Arabidopsis thaliana and may also help to develop an improved plant variety using molecular breeding and genetic engineering techniques that are rapidly stress-responsive and tolerant.
Publisher: Springer Science and Business Media LLC
Date: 16-09-2022
DOI: 10.1007/S10142-022-00899-9
Abstract: Knowledgebase for rice sheath blight information (KRiShI) is a manually curated user-friendly knowledgebase for rice sheath blight (SB) disease that allows users to efficiently mine, visualize, search, benchmark, download, and update meaningful data and information related to SB using its easy and interactive interface. KRiShI collects and integrates widely scattered and unstructured information from various scientific literatures, stores it under a single window, and makes it available to the community in a user-friendly manner. From basic information, best management practices, host resistance, differentially expressed genes, proteins, metabolites, resistance genes, pathways, and OMICS scale experiments, KRiShI presents these in the form of easy and comprehensive tables, diagrams, and pictures. The "Search" tab allows users to verify if their input rice gene id(s) are Rhizoctonia solani (R. solani) responsive and/or resistant. KRiShI will serve as a valuable resource for easy and quick access to data and information related to rice SB disease for both the researchers and the farmers. To encourage community curation a submission facility is made available. KRiShI can be found at www.tezu.ernet.in/krishi .
Publisher: Elsevier BV
Date: 08-2019
DOI: 10.1016/J.PBIOMOLBIO.2018.12.002
Abstract: Plants are essential facilitators of human life on planet earth. Plants play a critical functional role in mediating the quality of air, availability of food and the sustainability of agricultural resources. However, plants are in constant interaction with its environment and often h ered by various types of stresses like biotic and abiotic ones. Biotic stress is a significant reason for crop-loss and causes yield loss in the range of 31-42%, post-harvest loss due to biotic stress is in the range of 6-20%, and abiotic stress causes 6-20% of the crop damage. Recognizing the molecular factors driving plant stress-related events, and developing molecular strategies to aid plants to tolerate, resist or adapt to biotic and abiotic stress are critical for sustainable agriculture practice. In this review, we discuss how recent advances in bioinformatics, plant genomics, and data science could help to improve our understanding of plant stress biology and improve the scale of global food production. We present various areas of scientific and technological advances, such as increased availability of genomics data through whole genome sequencing that require attention. We also discuss emerging techniques including CRISPR-Cas9 based genome engineering systems to develop plant varieties that can handle combinatorial stress signals. Growing trend of converging multiple omics technologies and availability of accurate, multi-scale models of plant stress through the study of orthologs and synteny studies, would improve our knowledge of how plants perceive, respond, and manage stress to thrive as resilient crop species and thus help to reduce global food crisis.
Publisher: Apple Academic Press
Date: 17-04-2023
Publisher: Springer Science and Business Media LLC
Date: 28-08-2015
Publisher: Public Library of Science (PLoS)
Date: 16-03-2016
Publisher: Springer Science and Business Media LLC
Date: 06-03-2020
Publisher: Springer Nature Singapore
Date: 2023
Publisher: Bentham Science Publishers Ltd.
Date: 17-05-2018
DOI: 10.2174/0929866525666180115121853
Abstract: The midgut of silkworm (Bombyx mori L.) plays an important role as a natural barrier and source of innate immunity. We had purified the novel red fluorescent protein (RFP) from the midgut of the silkworm Bombyx mori L. and bioassay studies confirmed RFPs possess antiviral, antifungal and antibacterial properties. N-terminal sequence of RFP analysis predicted chbp gene and it belongs to lipocalin gene family and is known to involve in anti-pathogenic activities. The main objective of this study was to purify RFP from the midgut of Kolar Gold silkworm and confirm its antimicrobial activity. For isolation of RFP, midgut juice was collected by brief exposure to chloroform vapours to fifth instar Kolar Gold silkworm larvae. Juice was purified by 40 % ammonium sulfate precipitation and purified by gel filtration chromatography (GFC) and fractions with fluorescence red under Ultra violet (UV) were collected. Molecular weight and purity of RFP was identified using PAGE, MALDI-TOF and HPLC. Antimicrobial property of purified RFP against BmNPV, Escherichia coli, Klebsiella pneumonia, Bacillus subtilis and Phytophthora meadii was performed. N-terminal sequencing of RFP was performed using Edman degradation method. Using ten amino acid sequence, using default parameter BLAST search was performerd. From the fifth day old fifth instar silkworm midgut mRNA was isolated and cDNA was synthesized using oligo-dt primer and lification of ChBP gene was carried out by using cDNA as the template and ChBP gene specific primers. chbp protein sequence as a input built the homology model by using SWISS-MODEL. RFP was purified by 40 % ammonium sulfate precipitation and gel filtration chromatography (GFC) and fractions with fluorescence red under Ultra violet (UV) were collected and SDS - PAGE revealed a size of 40 kDa. RFP purified by GFC was further reconfirmed by HPLC with a single peak with a retention time of 8.755 min. MALDI-TOF produced a peak at a molecular mass of 40 kDa. RFP from the midgut juice showed antiviral activity against the silkworm virus BmNPV, antibacterial activity against Escherichia coli, Klebsiella pneumonia, Bacillus subtilis and Phytophthora meadii. N-terminal sequencing of RFP by Edman degradation method sequenced TQTIETDYWV amino acids and BLAST analysis predicted the Chlorophyllide-a Binding Protein (chbp) with B. mori. PCR product was sequenced and obtained 911bp nucleotides encoding 302 amino acid residues and deposited with the accession number KX186723 in NCBI. Sequence analysis revealed Chbp belongs to lipocalin gene family and known to involve in antiviral, antifungal and anti-bacterial properties. Chbp gene homology model was predicted using crystal structure of insecticyanin A from the tobacco hornworm as a template. Our results indicated RFP present in midgut juice of 5th instar larvae of kolar gold silkworm. We have purified novel RFP with molecular mass of 40 kDa and showed its antipathogenic activities. Chbp gene synthesises RFP and further it could be utilized for agriculture and pharmaceutical industry.
Publisher: Oxford University Press (OUP)
Date: 10-01-2013
DOI: 10.1093/PCP/PCS185
Publisher: Springer Science and Business Media LLC
Date: 07-2020
Publisher: Elsevier BV
Date: 06-2020
Publisher: Springer Science and Business Media LLC
Date: 23-10-2022
DOI: 10.1186/S41938-022-00617-4
Abstract: Microbial biological control agents are gaining worldwide attention to manage insect pests as an alternative to synthetic insecticides. Entomopathogenic fungi (EPF) meet eco-friendly pest management’s demand since mere contact of infective propagules is sufficient to cause disease in insect pests, unlike other entomopathogens. However, epiphytic fungal isolates encounter multiple challenges including direct exposure of conidia to sunlight and UV light, high temperature, and low moisture content that reduce their efficacy at the field level. Therefore, utilization of endophytic EPF is becoming more popular because they get protection from adverse conditions compared to the epiphytic EPF as they reside inside the host tissue. In addition, the endophytic EPF also give protection against crop diseases and promote plant growth, degradation of heavy metals, and tolerance to abiotic stress. The increased mortality of Spodoptera litura (Fab.) (Noctuidae: Lepidoptera) was achieved through endophytic colonization of indigenous Beauveria bassiana UHSB-END-1 (OM131742). The bioassay proved the highest mortality 2nd instar larvae of S. litura at 40 dpi, both in vivo and in planta experiment. Further, larvae fed with fungal colonized leaves of tomato plant ended with abnormal growth and developmental process. The recovery of B. bassiana from different plant parts (stem, leaves, and roots) was the highest (100%) in all the methods of colonization at 14, 40, 60, 80 dpi, and it was decreased at 120 dpi (80%). The colonization rate was again increased in the next-generation seeds and seedlings (25 days old). This isolate gets vertically transmitted to their progenies via seeds, and it is the first report in tomato crop. After ensuring the safeness of this isolate against non-target organisms, it can be one of the constitutes in sustainable cost-effective strategy for management of pests affecting tomato as one of the components in integrated pests management. Inoculation of endophytic EPF into seed/seedling reduces environmental impacts and also easy, economical, and sustainable approach for pest management in horticulture crops which are often consumed as raw. Although field studies are required to support the present finding, this appears to be an interesting tool that should be considered for pest biocontrol.
Publisher: Elsevier BV
Date: 2020
DOI: 10.1016/J.YGENO.2019.04.014
Abstract: Moringa oleifera is a plant well-known for its nutrition value, drought resistance and medicinal properties. cDNA libraries from five different tissues (leaf, root, stem, seed and flower) of M. oleifera cultivar Bhagya were generated and sequenced. We developed a bioinformatics pipeline to assemble transcriptome, along with the previously published M. oleifera genome, to predict 17,148 gene models. Few candidate genes related to biosynthesis of secondary metabolites, vitamins and ion transporters were identified. Expressions were further confirmed by real-time quantitative PCR experiments for few promising leads. Quantitative estimation of metabolites, as well as elemental analysis, was also carried out to support our observations. Enzymes in the biosynthesis of vitamins and metabolites like quercetin and kaempferol are highly expressed in leaves, flowers and seeds. The expression of iron transporters and calcium storage proteins were observed in root and leaves. In general, leaves retain the highest amount of small molecules of interest.
Publisher: Elsevier BV
Date: 2020
Publisher: Springer Science and Business Media LLC
Date: 08-08-2022
DOI: 10.1038/S41598-022-17779-8
Abstract: Fenugreek ( Trigonella foenum-graecum L.) is a self-pollinated leguminous crop belonging to the Fabaceae family. It is a multipurpose crop used as herb, spice, vegetable and forage. It is a traditional medicinal plant in India attributed with several nutritional and medicinal properties including antidiabetic and anticancer. We have performed a combined transcriptome assembly from RNA sequencing data derived from leaf, stem and root tissues. Around 209,831 transcripts were deciphered from the assembly of 92% completeness and an N50 of 1382 bases. Whilst secondary metabolites of medicinal value, such as trigonelline, diosgenin, 4-hydroxyisoleucine and quercetin, are distributed in several tissues, we report transcripts that bear sequence signatures of enzymes involved in the biosynthesis of such metabolites and are highly expressed in leaves, stem and roots. One of the antidiabetic alkaloid, trigonelline and its biosynthesising enzyme, is highly abundant in leaves. These findings are of value to nutritional and the pharmaceutical industry.
Publisher: Elsevier
Date: 2021
Publisher: Springer Science and Business Media LLC
Date: 09-05-2019
Publisher: Springer Science and Business Media LLC
Date: 26-02-2019
Publisher: Oxford University Press (OUP)
Date: 17-12-2015
DOI: 10.1093/NAR/GKV1463
No related grants have been discovered for Mahantesha B N Naika.