Elucidating the key players of molecular mechanism that mediate the complex stress-responses in plants system is an important step to develop improved variety of stress tolerant crops. Understanding the effects of different types of biotic and abiotic stress is a rapidly emerging domain in the area of plant research to develop better, stress tolerant plants. Information about the transcription factors, transcription factor binding sites, function annotation of proteins coded by genes expressed during abiotic stress (for example: drought, cold, salinity, excess light, abscisic acid, and oxidative stress) response will provide better understanding of this phenomenon. STIFDB is a database of abiotic stress responsive genes and their predicted abiotic transcription factor binding sites in Arabidopsis thaliana. We integrated 2269 genes upregulated in different stress related microarray experiments and surveyed their 1000 bp and 100 bp upstream regions and 5′UTR regions using the STIF algorithm and identified putative abiotic stress responsive transcription factor binding sites, which are compiled in the STIFDB database. STIFDB provides extensive information about various stress responsive genes and stress inducible transcription factors of Arabidopsis thaliana. STIFDB will be a useful resource for researchers to understand the abiotic stress regulome and transcriptome of this important model plant system.
Abstract:The expressions of proteins in the cell are carefully regulated by transcription factors that interact with their downstream targets in specific signal transduction cascades. Our understanding of the regulation of functional genes responsive to stress signals is still nascent. Plants like Arabidopsis thaliana, are convenient model systems to study fundamental questions related to regulation of the stress transcriptome in response to stress challenges. Microarray results of the Arabidopsis transcriptome indicate that several genes could be upregulated during multiple stresses, such as cold, salinity, drought etc. Experimental biochemical validations have proved the involvement of several transcription factors could be involved in the upregulation of these stress responsive genes. In order to follow the intricate and complicated networks of transcription factors and genes that respond to stress situations in plants, we have developed a computer algorithm that can identify key transcription factor binding sites upstream of a gene of interest. Hidden Markov models of the transcription factor binding sites enable the identification of predicted sites upstream of plant stress genes. The search algorithm, STIF, performs very well, with more than 90% sensitivity, when tested on experimentally validated positions of transcription factor binding sites on a dataset of 60 stress upregulated genes.
Melia dubia Cav. of family Meliaceae is a fast growing, high value tree species native to India. Isolating DNA from matured dried leaves of M. dubia was difficult due to accumulation of secondary metabolites, majorly polyphenolics, which resulted in dark brown to black colour of the pellet. In this study, a modified STE-(Sucrose, Tris-HCl and Ethylene Diamine Tetra Acetic Acid) CTAB (hexadecyltrimethylammonium bromide) method was standardized for removal of polyphenolics. The protocol developed yielded 200 -1000 ng/µl of quality DNA without any impurities as evident by A260/280 ratio ranging from 1.75 -2.0. It was also suitable for extracting quality DNA from other members of Meliaceae like Azadirachta indica and Melia azedarach. In downstream applications, the extracted DNA was used for PCR amplification by using ISSR and SSR markers. ISSR PCR conditions were optimized in a reaction volume of 25 µl, consisting of 30 ng of template DNA, 1.5 mM MgCl2, 200 µM of each of dNTPs and 2 U of Taq polymerase. The best amplification was observed and the same was applicable for SSR markers.
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