Browsing by Author "Thakur, Sapna"
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Item Adaptability of Rhododendrons in high altitude habitats(Northeast Forestry University, 2020-01-03T00:00:00) Choudhary, Shruti; Thakur, Sapna; Majeed, Aasim; Bhardwaj, PankajTree species dominate many ecosystems throughout the world and their response to climate, in light of global warming, is a matter of primary concern. This review describes past and ongoing research in Rhododendron, an ecologically important and well-adapted genus of more than 1000 species, occupying diverse habitats. Research to date indicates survival ability and mechanisms, with an emphasis on cold tolerance. The capability of long-distance gene flow in these species increases their genetic variability which in turn enhances their adaptability to newer niches as well as to environmental gradients (mainly temperature). Attempts to explain the molecular basis of morphological and behavioural changes in Rhododendron against cold-induced damage has been made. Gradual advances in �omics� have led to an enriched genomic resource dissecting the role and interaction of multiple molecular factors participating in cold adaptability. However, fewer genetic studies are available on species with an inherent or a default cold-tolerance ability. Considering this fact, understanding specific features of an adapted species can provide insights on overriding the effects of desiccation and determining phase transitions in other plants as well. We propose to integrate ecological and evolutionary studies with functional genomics to improve predictions of tree responses to their environment. � 2020, Northeast Forestry University.Item Adaptability of Rhododendrons in high altitude habitats(Northeast Forestry University, 2020-01-03T00:00:00) Choudhary, Shruti; Thakur, Sapna; Majeed, Aasim; Bhardwaj, PankajTree species dominate many ecosystems throughout the world and their response to climate, in light of global warming, is a matter of primary concern. This review describes past and ongoing research in Rhododendron, an ecologically important and well-adapted genus of more than 1000 species, occupying diverse habitats. Research to date indicates survival ability and mechanisms, with an emphasis on cold tolerance. The capability of long-distance gene flow in these species increases their genetic variability which in turn enhances their adaptability to newer niches as well as to environmental gradients (mainly temperature). Attempts to explain the molecular basis of morphological and behavioural changes in Rhododendron against cold-induced damage has been made. Gradual advances in �omics� have led to an enriched genomic resource dissecting the role and interaction of multiple molecular factors participating in cold adaptability. However, fewer genetic studies are available on species with an inherent or a default cold-tolerance ability. Considering this fact, understanding specific features of an adapted species can provide insights on overriding the effects of desiccation and determining phase transitions in other plants as well. We propose to integrate ecological and evolutionary studies with functional genomics to improve predictions of tree responses to their environment. � 2020, Northeast Forestry University.Item Aldose Reductase: a cause and a potential target for the treatment of diabetic complications(Pharmaceutical Society of Korea, 2021-07-19T00:00:00) Thakur, Sapna; Gupta, Sonu Kumar; Ali, Villayat; Singh, Priyanka; Verma, MalkheyDiabetes mellitus, a disorder of metabolism, results in the elevation of glucose level in the blood. In this hyperglycaemic condition, aldose reductase overexpresses and leads to further complications of diabetes through the polyol pathway. Glucose metabolism-related disorders are the accumulation of sorbitol, overproduction of NADH and fructose, reduction in NAD+, and excessive NADPH usage, leading to diabetic pathogenesis and its complications such as�retinopathy, neuropathy, and nephropathy. Accumulation of sorbitol results in the alteration of osmotic pressure and leads to osmotic stress. The overproduction of NADH causes an increase in reactive oxygen species production which leads to oxidative stress. The overproduction of fructose causes cell death and non-alcoholic fatty liver disease. Apart from these disorders, many other complications have also been discussed in the literature. Therefore, the article overviews the aldose reductase as the causative agent and a potential target for the treatment of diabetic complications. So, aldose reductase inhibitors have gained much importance worldwide right now. Several inhibitors, like derivatives of carboxylic acid, spirohydantoin, phenolic derivatives, etc. could prevent diabetic complications are discussed in this article. � 2021, The Pharmaceutical Society of Korea.Item Comparative transcriptome profiling reveals the reprogramming of gene networks under arsenic stress in Indian mustard.(Canadian Science Publishing, 2019) Thakur, Sapna; Choudhary, Shruti; Dubey, Preeti; Bhardwaj, PankajArsenic is a widespread toxic metalloid that is classified as a class I carcinogen known to cause adverse health effects in humans. In the present study, we investigated arsenic accumulation potential and comparative gene expression in Indian mustard. The amount of arsenic accumulated in shoots varied in the range of 15.99-1138.70 mg/kg on a dry weight basis among five cultivars. Comparative expression analysis revealed 10?870 significantly differentially expressed genes mostly belonging to response to stress, metabolic processes, signal transduction, transporter activity, and transcription regulator activity to be up-regulated, while most of the genes involved in photosynthesis, developmental processes, and cell growth were found to be down-regulated in arsenic-treated tissues. Further, pathway analysis using the KEGG Automated Annotation server (KAAS) revealed a large-scale reprogramming of genes involved in genetic and environmental information processing pathways. Top pathways with maximum KEGG orthology hits included carbon metabolism (2.5%), biosynthesis of amino acids (2.1%), plant hormone signal transduction (1.4%), and glutathione metabolism (0.6%). A transcriptomic investigation to understand the arsenic accumulation and detoxification in Indian mustard will not only help to improve its phytoremediation efficiency but also add to the control measures required to check bioaccumulation of arsenic in the food chain.Item Comparative Transcriptome Profiling Under Cadmium Stress Reveals the Uptake and Tolerance Mechanism in Brassica juncea(Springer, 2019) Thakur, Sapna; Choudhary, Shurti; Bhardwaj, PankajCadmium (Cd) is a biologically non-essential and phytotoxic heavy metal pollutant. In this study, we estimated the Cd accumulation potential of Indian mustard and identified factors responsible for Cd uptake, tolerance, and detoxification. Eight transcriptomic libraries were sequenced and ??230 million good quality reads were generated. The alignment rate against B. juncea reference genome V1.5 varied in the range of 85.03-90.06%. Comparative expression analysis using DESeq2 revealed 11,294 genes to be significantly differentially expressed under Cd treatment. The agriGO singular enrichment analysis revealed genes related to response to chemical, oxidative stress, transport, and secondary metabolic process were upregulated, whereas multicellular organismal development, developmental process, and photosynthesis were downregulated by Cd treatment. Furthermore, 616 membrane transport proteins were found to be significantly differentially expressed. Cd-related transporters such as metal transporter (Nramp1), metal tolerance protein (MTPC2, MTP11), cadmium-transporting ATPase, and plant cadmium resistance protein (PCR2, PCR6) were upregulated whereas cadmium/zinc-transporting ATPase (HMA2, HMA3, HMA4), high-affinity calcium antiporter (CAX1), and iron transport protein (IRT1) were downregulated by Cd treatment. A total of 332 different gene-networks affected by Cd stress were identified using KAAS analysis. Various plant hormones signaling cascades were modulated suggesting their role in Cd stress tolerance. The regulation overview using MapMan analysis also revealed gene expression related to plant hormones, calcium regulation, and MAP kinases were altered under Cd stress.Item Development and characterization of genomic microsatellite markers in Melia azedarach(Central University of Punjab, 2014) Thakur, Sapna; Bhardwaj, PankajMelia azedarach is ecologically imperative species known for its innumerable biological benefits such as antiviral, anthelminthic, antibacterial, etc. In this study, we developed 43 genomic microsatellite markers from (AG)n enriched library and subsequently employed 23 of them for genetic diversity and population structure analysis of Melia azedarach growing in Indian Thar desert. Fourteen populations encompassing 95 genotypes were selected for analysis and we found a moderate level of diversity (Na = 3.211, Ho = 0.558, He = 0.549, P = 94.41%) in them. Gene diversity (h) among population pairs varied from 0.566 to 0.714 with very low overall genetic differentiation (F = 0.021). The highest value of ΔK estimated using STRUCTURE indicated 2 subpopulations (K=2) and admixed cluster occupied maximum area (75.79%) under Bar plot. Genetic distance based UPGMA dendrogram also identified 2 major clusters among 14 Melia azedarach populations. UNJ tree based on genetic dissimilarity clustered genotypes from different population together. No significant correlation between geographical and genetic distance was found in present study (Rxy = 0.261, P = 0.18). Allele frequency distribution under “mode-shift” indicator was normal L-shaped, suggesting populations under study are not experiencing any recent bottleneck. This study laid the foundation for more precise inference about the biogeography and management of M. azedarach in the Indian Thar DesertItem Development and characterization of genomic microsatellite markers in Prosopis cineraria(Elsevier B.V., 2017) Anand, Shashi Shekhar; Thakur, Sapna; Gargi, Madhuranjana; Choudhary, Shruti; Bhardwaj, Pankaj; Anand, S.S.; Thakur, S.; Gargi, M.; Choudhary, S.; Bhardwaj, P.Characterization of genetic diversity is a must for exploring the genetic resources for plant development and improvement. Prosopis cineraria is ecologically imperative species known for its innumerable biological benefits. Since there is a lack of genetic resources for the species, so it is crucial to unravel the population dynamics which will be very effective in plant improvement and conservation strategies. Of the 41 genomic microsatellite markers designed from (AG)n enriched library, 24 were subsequently employed for characterization on 30 genotypes of Indian arid region. A total of 93 alleles with an average 3.875 could be amplified by tested primer pairs. The average observed and expected heterozygosity was 0.5139 and 0.5786, respectively with 23 primer pairs showing significant deviations from Hardy-Weinberg equilibrium. Polymorphic information content average to 0.5102 and the overall polymorphism level was found to be 93.27%. STRUCTURE analysis and DARwin exhibited the presence of 4 clusters among 30 genotypes. ? 2017 The AuthorsItem Development and characterization of genomic microsatellite markers in Rhododendron arboreum(Kluwer Academic Publishers, 2014) Choudhary, Shruti; Thakur, Sapna; Saini, Ram Gopal; Bhardwaj, Pankaj; Choudhary, S.; Thakur, S.; Saini, R.G.; Bhardwaj, P.Population genetics characteristics are the fundamentals of conservation and management practices. Rhododendronarboreum, a key biodiversity component inhabiting Indian Himalayas, suffers from overexploitation and global warming. Using biotin?streptavidin hybridization technique, 41 microsatellite markers were designed from an enriched DNA library to provide a genetic background and an insight into the population structure of the species. With a range of 2?14 alleles amplified from 38 loci, the populations were reported with observed and expected heterozygosity of 0.167?0.933 and 0.422?0.917 respectively. Some of the loci showed significant deviations from Hardy?Weinberg equilibrium and overall no linkage disequilibrium was detected. These markers will support genetic diversity and further genotyping studies in R. arboreum. ? 2014, Springer Science+Business Media Dordrecht.Item Development and characterization of genomic microsatellite markers in Tinospora cordifolia(Springer India, 2017) Gargi, Madhuranjana; Thakur, Sapna; Anand, Shashi Shekhar; Choudhary, Shruti; Bhardwaj, Pankaj; Gargi, M.; Thakur, S.; Anand, S.S.; Choudhary, S.; Bhardwaj, P.Item Exploring microRNA profiles for circadian clock and flowering development regulation in Himalayan Rhododendron(Elsevier, 2018) Choudhary, Shruti; Thakur, Sapna; Majeed, Aasim; Bhardwaj, PankajmiRNA is a non-coding, yet crucial entity in remodeling the genetic architecture. Rhododendron arboreum of Himalayas grows and even flower under fluctuating climate. sRNA from leaves of vegetative and reproductive periods was sequenced to elucidate its seasonal associations. Conserved (256) and novel (210) miRNAs and their precursors were located based on homology with plant databases and transcriptome of the species. 27,139 predicted targets were involved with metabolism, reproduction, and response to abiotic stimuli. A comparative analysis showed differential expression of 198 miRNAs with season-specific abundance of 103 miRNAs. Specific isoforms of 11 miRNA families exhibited a temporal expression and targeted different genes implying a complex regulation. The variable miRNA expression among the tissues of different conditions can be associated with the adaptability of the species, which will prove essential for further study on miRNAs mediating seasonal response. Moreover, exogenous cues also mediate phase transition via networking of flowering pathways and their components. In this context, 18 known families and 77 novel miRNAs modulating 117 genes crucial in circadian entrainment were filtered. A negative correlation was obtained between the expression of 18 of these miRNAs and their targets when tested through quantitative-PCR. It highlighted the role of miRNA-target pairs in perceiving environmental variabilities and monitoring flowering growth. Furthermore, a phylogenetic clustering was performed, which supported the lineage-specific evolution and function of putative miR156 sequence in the species. This documentation of genome-wide profiling of miRNA, their targets, and expression will enhance the understanding of developmental and climate-tolerance strategies in high-altitude trees.Item Gene and metabolite profiling reveals flowering and survival strategies in Himalayan Rhododendron arboreum(Elsevier, 2019) Choudhary, Shurti; Thakur, Sapna; Jaitak, Vikas; Bhardwaj, PankajRhododendron arboreum inhabits the Himalayan climate otherwise detrimental to many species, though the underlying survival mechanism remains unclear. Such temperate species have an inherent endurance towards freezing temperature which is prerequisite for an initiation and transition to flowering phase. Orchestrating the molecular architecture is vital towards managing distinct abiotic signals. To determine the molecular factors directing growth, development, and tolerance under environmental extremes in the species, the high-throughput transcriptome and metabolome data from vegetative as well as cold-acclimatized flowering season tissues were generated. Firstly, the de novo assembly pertaining to the foliar and floral tissues comprising of 157,427 unigenes was examined for a comparative analysis. 4149 of 12,577 transcripts observed with a significant fluctuating expression corresponded to seasonal retorts. Following the interactive network, 525 genes were distinguished as the epicenters of sense, response, and tolerance. Secondly, liquid chromatography coupled to mass spectrometry was adopted to profile the extent of metabolite richness across the tissues of two seasons. Taking into account the formula-based mappings offered by MetaboSearch tool, 421 unique ions obtained were annotated to 173 KEGG compounds, especially secondary metabolites. Moreover, by integrating the transcript and metabolite annotations, it was found that right from active metabolism, signaling, development, and their regulations, supplementary response to abiotic/biotic stimuli was induced. A multifaceted response displayed during flowering not only sponsored the climatic encounters but brought the shift from vegetative to reproductive growth. Overall, this comprehensive approach following transcriptome and non-targeted metabolome elucidated the contribution of genetic and metabolic factors in environmental responsesItem Genetic diversity and population structure of Melia azedarach in North-Western Plains of India(Springer Verlag, 2016) Thakur, Sapna; Choudhary, Shruti; Singh, Amandeep; Ahmad, Kamal; Sharma, Gagan; Majeed, Aasim; Bhardwaj, PankajKey message: Genetic structure amongM. azedarachpopulations was detected and two subpopulations were present among them. A significant ?isolation by distance? was found inM. azedarachpopulation in North-Western Plains of India. Abstract: Melia azedarach is an important forest tree with pharmaceutical, insecticidal, pesticidal, and commercial significance. It is a good reforestation tree because of its fast growth and drought hardy nature. Genetic variation in a species allows itself to adapt, evolve and respond to environmental stress. It provides the basis for survival of a species and critically influences its evolutionary potential. Assessment of genetic diversity is necessary for improvement and conservation of a species. For this, microsatellite markers are of particular interest given the attributes like co-dominance, reproducibility, hyper variability and abundance throughout the genome. In the present study, we analyzed the genetic diversity and population structure of M. azedarach, an ecologically imperative species growing in the North-Western Plains of India. We developed 43 microsatellite markers, of which 20 were subsequently employed for analysis of diversity and population structure among 33 populations encompassing 318 genotypes representing North-Western Plains of India. A moderate level of diversity (Na?=?5.1, Ho?=?0.506, He?=?0.712, I?=?1.386) was assessed. The highest value of ?K estimated using STRUCTURE indicated 2 subpopulations (K?=?2). AMOVA exhibited 73?% variation within populations and 12?% variation was found among regions. Significant positive correlation between geographical and genetic distance was found (Rxy?=?0.365, P?=?0.010). The present study lays a foundation on a better understanding of genetic dynamics of the species and reveals its diversity and population structure in North-Western Plains of India. ? 2016, Springer-Verlag Berlin Heidelberg.Item Transcriptomic investigations of gene networks in response to arsenic accumulation in Brassica juncea (L.) Czern & Coss(Central University of Punjab, 2019) Thakur, Sapna; Bhardwaj, PankajArsenic (As), a widespread toxic metalloid is class I carcinogen known to cause adverse health effects in human. In the present study, As accumulation potential and differential gene expression in B. juncea is investigated. The amount of arsenic accumulated varied in the range of 15.99 to 1138.70 mg/Kg on dry weight basis in five cultivars. A decrease in chlorophyll content and increase in membrane damage and enzymatic activities of antioxidants was observed with increase in As concentration in the B. juncea cultivars. Using maximum As accumulating cultivar (RLM514), a total of 10,870 significantly differentially expressed transcripts in response to As treatment were identified. Further, the pathway analysis revealed a large scale reprogramming of genes involving carbon metabolism (2.5%), plant hormone signaling (1.4%), and glutathione metabolism (0.6%). Moreover, a comparative account of Cd toxicity revealed a total of 11,294 transcripts to be significantly differentially expressed. The genes related to response to chemical, oxidative stress, transport, and secondary metabolism were upregulated whereas multicellular organismal development, developmental process, photosynthesis were downregulated by Cd treatment. Furthermore, 616 membrane transport proteins were found to be significantly differentially expressed. Cd-related transporters such as metal transporter (Nramp1), metal tolerance protein (MTPC2, MTP11), cadmiumtransporting ATPase, and plant cadmium resistance protein (PCR2, PCR6) were upregulated while cadmium/zinc- transporting ATPase (HMA2, HMA3, HMA4), highaffinity calcium antiporter (CAX1), and iron transport protein (IRT1) were downregulated by Cd treatment. Pathway analysis revealed signaling cascades including plant hormones signaling, MAPK signaling and Ca signaling was modulated suggesting their role in Cd-stress tolerance. The regulation overview using MapMan also revealed gene expression related to plant hormones, calcium regulation and MAP kinases were altered under Cd-stress.