Browsing by Author "Thakur S."

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Adaptability of Rhododendrons in high altitude habitats
(Northeast Forestry University, 2020) Choudhary S.; Thakur S.; Majeed A.; Bhardwaj P.
Tree 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.
Bio-analytical applications of nicking endonucleases assisted signal-amplification strategies for detection of cancer biomarkers -DNA methyl transferase and microRNA
(Elsevier Ltd, 2019) Mittal S.; Thakur S.; Mantha A.K.; Kaur H.
The low concentrations of cancer biomarkers in the blood have limited the utility of quantitative bioassays developed for the purpose. The advent of nicking endonucleases (NEases) as signal amplification tools have greatly enhanced the detection efficiency and provided a multi-optional platform to design target specific detection methods. The present review focuses on the prominent features of NEases, modified DNA probes (such as hairpin (HP) probes, molecular beacons, and G- quadruplex) that mediate cyclic cascade and role of helper enzymes. Application of NEase assisted signal amplification (NESA) has been discussed for diagnosis of two prominent cancer biomarkers viz. DNA methyl transferase (Dam MTase) and microRNA (miRNA). NESA mediated techniques such as rolling circle amplification (RCA), strand displacement amplification (SDA) and isothermal exponential amplification (EXPAR), have been compared in light of their future applications in clinical diagnosis. Significance of nanomaterials to achieve further amplification and NESA assays for simultaneous detection of miRNAs has also been conversed. It is anticipated that the information gained from the analyses of the prospects and limitations of NESA-based assays will be useful towards understanding the applications, and improvement of efficient isothermal exponential amplification strategies for highly sensitive and selective detection of cancer biomarkers.
Comparative transcriptome profiling reveals the reprogramming of gene networks under arsenic stress in Indian mustard
(Canadian Science Publishing, 2019) Thakur S.; Choudhary S.; Dubey P.; Bhardwaj P.
Arsenic 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.
Exploring microRNA profiles for circadian clock and flowering development regulation in Himalayan Rhododendron
(Academic Press Inc., 2019) Choudhary S.; Thakur S.; Majeed A.; Bhardwaj P.
miRNA 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.
Insights into the Molecular Mechanism of Arsenic Phytoremediation
(Springer New York LLC, 2019) Thakur S.; Choudhary S.; Majeed A.; Singh A.; Bhardwaj P.
Arsenic (As) is a widespread carcinogenic pollutant. Phytoremediation is the most suited technology for alleviating the As contamination of soil. In this review, we have discussed the uptake mechanism and the associated transporters for different As species. Glutathione, phytochelatins, metallothionins, and secondary metabolites play important role in As detoxification and enhancing tolerance. The roles of MAPK signaling and calcium signaling are highlighted in the perception of As stress along with phytohormones signaling in stress tolerance. Furthermore, transcription factors involved in regulation of gene expression under As stress are discussed. High-throughput sequencing has reduced the time duration and enhanced the knowledge regarding understanding the molecular mechanism of phytoremediation. The role of CRISPR/Cas9 and synthetic genes in context to phytoremediation is discussed. We have provided a holistic understanding of the present knowledge about phytoremediation in the context of mechanisms of the As uptake and tolerance. A complete understanding of the phytoremediation process is essential for As-risk mitigation and will help in augmenting its efficiency and true potential.