12 research outputs found
The cientificWorldJOURNAL Research Article Evidence for Directed Evolution of Larger Size Motif in Arabidopsis thaliana Genome
No full textTranscription control of gene expression depends on a variety of interactions mediated by the core promoter region, sequence specific DNA-binding proteins, and their cognate promoter elements. The prominent group of cis acting elements in plants contains an ACGT core. The cis element with this core has been shown to be involved in abscisic acid, salicylic acid, and light response. In this study, genome-wide comparison of the frequency of occurrence of two ACGT elements without any spacers as well as those separated by spacers of different length was carried out. In the first step, the frequency of occurrence of the cis element sequences across the whole genome was determined by using BLAST tool. In another approach the spacer sequence was randomized before making the query. As expected, the sequence ACGTACGT had maximum occurrence in Arabidopsis thaliana genome. As we increased the spacer length, one nucleotide at a time, the probability of its occurrence in genome decreased. This trend continued until an unexpectedly sharp rise in frequency of (ACGT)N25(ACGT). The observation of higher probability of bigger size motif suggests its directed evolution in Arabidopsis thaliana genome
Evidence for Directed Evolution of Larger Size Motif in Arabidopsis thaliana Genome
No full textTranscription control of gene expression depends on a variety of interactions mediated by the core promoter region, sequence specific DNA-binding proteins, and their cognate promoter elements. The prominent group of cis acting elements in plants contains an ACGT core. The cis element with this core has been shown to be involved in abscisic acid, salicylic acid, and light response. In this study, genome-wide comparison of the frequency of occurrence of two ACGT elements without any spacers as well as those separated by spacers of different length was carried out. In the first step, the frequency of occurrence of the cis element sequences across the whole genome was determined by using BLAST tool. In another approach the spacer sequence was randomized before making the query. As expected, the sequence ACGTACGT had maximum occurrence in Arabidopsis thaliana genome. As we increased the spacer length, one nucleotide at a time, the probability of its occurrence in genome decreased. This trend continued until an unexpectedly sharp rise in frequency of (ACGT)N25(ACGT). The observation of higher probability of bigger size motif suggests its directed evolution in Arabidopsis thaliana genome
PP2C – like promoter and its deletion variants are induced by ABA but not by MeJA and SA in Arabidopsis thaliana
No full textGene expression is mediated through interaction between cis regulatory elements and its cognate transcription factors. Cis regulatory elements are defined as non-coding DNA sequences that provide the binding sites for transcription factors and are clustered in the upstream region of genes. ACGT cis regulatory element is one of the important cis regulatory elements found to be involved in diverse biological processes like auxin response, salicylic acid response, UV light response, ABA response and jasmonic acid response .We identified through in silico analysis that the upstream region of protein phosphatase 2C (PP2C) gene has a distinct genetic architecture of ACGT elements. In the present study, the activation of the full length promoter and its deletion constructs like 900 base pair, 500 base pair, 400 base pair and NRM were examined by stable transformation in Arabidopsis thaliana using β glucuronidase as the reporter gene. Evaluation of deletion constructs of PP2C- like promoter was carried out in the presence of phytohormones like abscisic acid (ABA), salicylic acid (SA) and jasmonic acid (JA). Our result indicated that the full length and 900 base pair promoter-reporter constructs of PP2C-like promoter was induced in response to ABA but not to methyl jasmonate and salicylic acid
Genome Wide Analysis of Protein Phosphatase 2C (PP2C) Genes in Glycine max and Sorghum bicolor
No full text
Metabolomic and proteomic signature of Gloriosa superba leaves treated with mercuric chloride and phenylalanine, a precursor of colchicine alkaloid
No full textGloriosa superba is a tropical, medicinally important plant used in the treatment of gout, rheumatism, and other ailments. It produces pharmaceutically important alkaloids like colchicine, gloriosine, thiocolchicoside and others. In the present study, gas chromatography (GC)-mass spectrometry (MS) method has been deployed for the identification of low abundance phytochemicals in mercuric chloride (elicitor)-treated leaves. The analysis revealed nearly 500 molecules including 15 key secondary metabolites like estragole, N-methylloline (alkaloid), aphidocolin, 3-hydroxykynurenine, octyl salicylate, butibufen, anonaine (aporhine alkaloid), bolasterone, austricin, bolandione, octahydrocoumarin, jacaranone, bonducellin, quinacridone, and β-carotene that may have medicinal importance. Liquid chromatography-mass spectrometry (LC-MS) analysis of leaf proteome in the control and phenylalanine (a precursor of colchicine)-treated tissues revealed a total of 982 and 937 proteins respectively. In precursor-treated tissues, 364 differentially expressed proteins were noticed besides others. Key proteins involved in shikimate/chorismate pathway such as phenylalanine ammonia-lyase, chalcone-flavone isomerase (associated with flavonoid biosynthesis), chalcone synthase (involved in the synthesis of bioactive compounds in plants), chorismate synthetase, chorismate mutase, tryptophan synthase, and medium chain triglyceride protein were detected. Importantly, detection of nearly 154 proteins with unknown functions may hold key and play a role in colchicine biosynthetic pathway. These studies suggest that while metabolomic studies help to detect new secondary plant products, proteomic studies assist us in identifying key enzymes implicated in the biosynthetic pathway of alkaloids in G. superba
DataSheet_1_The Omic Insights on Unfolding Saga of COVID-19.xls
No full textThe year 2019 has seen an emergence of the novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease of 2019 (COVID-19). Since the onset of the pandemic, biological and interdisciplinary research is being carried out across the world at a rapid pace to beat the pandemic. There is an increased need to comprehensively understand various aspects of the virus from detection to treatment options including drugs and vaccines for effective global management of the disease. In this review, we summarize the salient findings pertaining to SARS-CoV-2 biology, including symptoms, hosts, epidemiology, SARS-CoV-2 genome, and its emerging variants, viral diagnostics, host-pathogen interactions, alternative antiviral strategies and application of machine learning heuristics and artificial intelligence for effective management of COVID-19 and future pandemics.</p
