Bioclues Organization

Hyderabad, India

Bioclues Organization

Hyderabad, India
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Anil Kumar S.,Osmania University | Hima Kumari P.,Osmania University | Sundararajan V.S.,Bioclues Organization | Suravajhala P.,Bioclues Organization | And 2 more authors.
Plant Molecular Biology Reporter | Year: 2014

Plants produce various proteins to overcome biotic and abiotic stresses. Current plant stress databases report plant genes without protein annotations specific to these stresses. To date, according to our findings, a unique plant stress protein database for both biotic and abiotic stresses is not available explicitly for plant biologists that describe linking out to other related databases. This need initiated us to formulate a distinctive database that includes important resources for stress-based factors. We developed the Plant Stress Protein Database (PSPDB), a web-accessible resource that covers 2,064 manually curated plant stress proteins from a wide array of 134 plant species with 30 different types of biotic and abiotic stresses. Functional and experimental validation of proteins associated with biotic and abiotic stresses has been employed as the sole criterion for inclusion in the database. The database is available at http://www.bioclues.org/pspdb. © 2014 Springer Science+Business Media New York.


Kumar A.,Advance Center for Computational & Applied Biotechnology | Kumar S.,Bioinformatics Center | Kumar U.,Center for Excellence in Mountain Biology | Suravajhala P.,Bioclues. Organization | Gajula M.N.V.P.,Rajendra Agricultural University
Computational Biology and Chemistry | Year: 2016

Triticum aestivum L. known as common wheat is one of the most important cereal crops feeding a large and growing population. Various environmental stress factors including drought, high salinity and heat etc. adversely affect wheat production in a significant manner. Dehydration-responsive element-binding (DREB1A) factors, a class of transcription factors (TF) play an important role in combating drought stress. It is known that DREB1A specifically interacts with the dehydration responsive elements (DRE/CRT) inducing expression of genes involved in environmental stress tolerance in plants. Despite its critical interplay in plants, the structural and functional aspects of DREB1A TF in wheat remain unresolved. Previous studies showed that wheat DREBs (DREB1 and DREB2) were isolated using various methods including yeast two-hybrid screens but no extensive structural models were reported. In this study, we made an extensive in silico study to gain insight into DREB1A TF and reported the location of novel DREB1A in wheat chromosomes. We inferred the three-dimensional structural model of DREB1A using homology modelling and further evaluated them using molecular dynamics(MD) simulations yielding refined modelled structures. Our biochemical function predictions suggested that the wheat DREB1A orthologs have similar biochemical functions and pathways to that of AtDREB1A. In conclusion, the current study presents a structural perspective of wheat DREB1A and helps in understanding the molecular basis for the mechanism of DREB1A in response to environmental stress. © 2016 Elsevier Ltd


Panchangam S.S.,Indian International Crops Research Institute for the Semi Arid Tropics | Mallikarjuna N.,Indian International Crops Research Institute for the Semi Arid Tropics | Gaur P.M.,Indian International Crops Research Institute for the Semi Arid Tropics | Suravajhala P.,Bioclues Organization
Indian Journal of Experimental Biology | Year: 2014

Double haploid technique is not routinely used in legume breeding programs, though recent publications report haploid plants via anther culture in chickpea (Cicer arietinum L.). The focus of this study was to develop an efficient and reproducible protocol for the production of double haploids with the application of multiple stress pre-treatments such as centrifugation and osmotic shock for genotypes of interest in chickpea for their direct use in breeding programs. Four genotypes, ICC 4958, WR315, ICCV 95423 and Arearti were tested for anther culture experiments. The yield was shown to be consistent with 3-5 nucleate microspores and 2-7 celled structures with no further growth. To gain a further insight into the molecular mechanism underlying the switch from microsporogenesis to androgenesis, bioinformatics tools were employed. The challenges on the roles of such genes were reviewed while an attempt was made to find putative candidates for androgenesis using Expressed Sequenced Tags (EST) and interolog based protein interaction analyses.


Kavi K.P.B.,Osmania University | Bandopadhyay R.,Birla Institute of Technology | Suravajhala P.,Bioclues Organization
Agricultural Bioinformatics | Year: 2014

A common approach to understanding the functional repertoire of a genome is through functional genomics. With systems biology burgeoning, bioinformatics has grown to a larger extent for plant genomes where several applications in the form of protein-protein interactions (PPI) are used to predict the function of proteins. With plant genes evolutionarily conserved, the science of bioinformatics in agriculture has caught interest with myriad of applications taken from bench side to in silico studies. A multitude of technologies in the form of gene analysis, biochemical pathways and molecular techniques have been exploited to an extent that they consume less time and have been cost-effective to use. As genomes are being sequenced, there is an increased amount of expression data being generated from time to time matching the need to link the expression profiles and phenotypic variation to the underlying genomic variation. This would allow us to identify candidate genes and understand the molecular basis/phenotypic variation of traits. While many bioinformatics methods like expression and whole genome sequence data of organisms in biological databases have been used in plants, we felt a common reference showcasing the reviews for such analysis is wanting. We envisage that this dearth would be facilitated in the form of this Springer book on Agricultural Bioinformatics. We thank all the authors and the publishers Springer, Germany for providing us an opportunity to review the bioinformatics works that the authors have carried in the recent past and hope the readers would find this book attention grabbing. © Springer India 2014. All rights reserved.


Suravajhala P.,Bioclues Organization | Singh T.R.,Bioclues Organization | Singh T.R.,Jaypee University of Information Technology
International Journal of Bioinformatics Research and Applications | Year: 2015

Protein-Protein Interactions (PPI) play a crucial role in deciphering function besides identifying candidates. While the experimental analysis is often time consuming involving number of experiments like pulldown assays, they are not necessarily limiting the ability to detect novel protein interactors. In this work, we discuss the role and putative interactors of SNAI2, a slug protein which is involved in the development of cancer progression. The protein interactions have been deciphered by domain pair exclusion method which gives confidence to already precluded interaction pairs. Additionally, conservation patterns of the slug protein have also been analysed by estimating site-specific evolutionary rates at structural level. Based upon the computational analysis, we consider HNF4A could be a putative candidate to study zinc finger protein slug. We believe, this candidate study augmented with structural conservation will definitely provide novel insights into the design and discovery of new interactions for zinc finger class of proteins besides providing possible clues for discovery of various cancer types associated with this class of proteins. Copyright © 2015 Inderscience Enterprises Ltd.


Singhania R.R.,Bioclues Organization | Madduru D.,Bioclues Organization | Pappu P.,Bioclues Organization | Panchangam S.,Bioclues Organization | And 2 more authors.
PLoS Computational Biology | Year: 2014

The Women in Biology forum (WiB) of Bioclues (India) began in 2009 to promote and support women pursuing careers in bioinformatics and computational biology. WiB was formed in order to help women scientists deprived of basic research, boost the prominence of women scientists particularly from developing countries, and bridge the gender gap to innovation. WiB has also served as a platform to highlight the work of established female scientists in these fields. Several award-winning women researchers have shared their experiences and provided valuable suggestions to WiB. Headed by Mohanalatha Chandrasekharan and supported by Dr. Reeta Rani Singhania and Renuka Suravajhala, WiB has seen major progress in the last couple of years particularly in the two avenues Mentoring and Research, off the four avenues in Bioclues: Mentoring, Outreach, Research and Entrepreneurship (MORE).In line with the Bioclues vision for bioinformatics in India, the WiB Journal Club (JoC) recognizes women scientists working on functional genomics and bioinformatics, and provides scientific mentorship and support for project design and hypothesis formulation. As a part of Bioclues, WiB members practice the group's open-desk policy and its belief that all members are free to express their own thoughts and opinions. The WiB forum appreciates suggestions and welcomes scientists from around the world to be a part of their mission to encourage women to pursue computational biology and bioinformatics. © 2014 Singhania et al.


Anil Kumar S.,Osmania University | Hima Kumari P.,Osmania University | Shravan Kumar G.,Osmania University | Mohanalatha C.,Bioclues Organization | Kavi Kishor P.B.,Osmania University
Frontiers in Plant Science | Year: 2015

Osmotin is a stress responsive antifungal protein belonging to the pathogenesis-related (PR)-5 family that confers tolerance to both biotic and abiotic stresses in plants. Protective efforts of osmotin in plants range from high temperature to cold and salt to drought. It lyses the plasma membrane of the pathogens. It is widely distributed in fruits and vegetables. It is a differentially expressed and developmentally regulated protein that protects the cells from osmotic stress and invading pathogens as well, by structural or metabolic alterations. During stress conditions, osmotin helps in the accumulation of the osmolyte proline, which quenches reactive oxygen species and free radicals. Osmotin expression results in the accumulation of storage reserves and increases the shelf-life of fruits. It binds to a seven-transmembrane-domain receptorlike protein and induces programmed cell death in Saccharomyces cerevisiae through RAS2/cAMP signaling pathway. Adiponectin, produced in adipose tissues of mammals, is an insulin-sensitizing hormone. Strangely, osmotin acts like the mammalian hormone adiponectin in various in vitro and in vivo models. Adiponectin and osmotin, the two receptor binding proteins do not share sequence similarity at the amino acid level, but interestingly they have a similar structural and functional properties. In experimental mice, adiponectin inhibits endothelial cell proliferation and migration, primary tumor growth, and reduces atherosclerosis. This retrospective work examines the vital role of osmotin in plant defense and as a potential targeted therapeutic drug for humans. © 2015 2015 Anil Kumar, Hima Kumari, Shravan Kumar, Mohanalatha and Kavi Kishor.


Ijaq J.,Bioclues Organization | Chandrasekharan M.,Bioclues Organization | Poddar R.,Bioclues Organization | Bethi N.,Bioclues Organization | Sundararajan V.S.,Bioclues Organization
Frontiers in Genetics | Year: 2015

Hypothetical proteins (HPs) are the proteins predicted to be expressed from an open reading frame, making a substantial fraction of proteomes in both prokaryotes and eukaryotes. Genome projects have led to the identification of many therapeutic targets, the putative function of the protein, and their interactions. In this review we enlist various methods linking annotation to structural and functional prediction of HPs that assist in the discovery of new structures and functions serving as markers and pharmacological targets for drug designing, discovery, and screening. Further we give an overview of how mass spectrometry as an analytical technique is used to validate protein characterisation. We discuss how microarrays and protein expression profiles help understanding the biological systems through a systems-wide study of proteins and their interactions with other proteins and non-proteinaceous molecules to control complex processes in cells. Finally, we articulate challenges on how next generation sequencing methods have accelerated multiple areas of genomics with special focus on uncharacterized proteins. © 2015 Ijaq, Chandrasekharan, Poddar, Bethi and Sundararajan.


PubMed | Bioclues Organization
Type: | Journal: Frontiers in genetics | Year: 2015

Hypothetical proteins (HPs) are the proteins predicted to be expressed from an open reading frame, making a substantial fraction of proteomes in both prokaryotes and eukaryotes. Genome projects have led to the identification of many therapeutic targets, the putative function of the protein, and their interactions. In this review we enlist various methods linking annotation to structural and functional prediction of HPs that assist in the discovery of new structures and functions serving as markers and pharmacological targets for drug designing, discovery, and screening. Further we give an overview of how mass spectrometry as an analytical technique is used to validate protein characterisation. We discuss how microarrays and protein expression profiles help understanding the biological systems through a systems-wide study of proteins and their interactions with other proteins and non-proteinaceous molecules to control complex processes in cells. Finally, we articulate challenges on how next generation sequencing methods have accelerated multiple areas of genomics with special focus on uncharacterized proteins.


PubMed | Bioclues Organization and Osmania University
Type: | Journal: Frontiers in plant science | Year: 2015

Osmotin is a stress responsive antifungal protein belonging to the pathogenesis-related (PR)-5 family that confers tolerance to both biotic and abiotic stresses in plants. Protective efforts of osmotin in plants range from high temperature to cold and salt to drought. It lyses the plasma membrane of the pathogens. It is widely distributed in fruits and vegetables. It is a differentially expressed and developmentally regulated protein that protects the cells from osmotic stress and invading pathogens as well, by structural or metabolic alterations. During stress conditions, osmotin helps in the accumulation of the osmolyte proline, which quenches reactive oxygen species and free radicals. Osmotin expression results in the accumulation of storage reserves and increases the shelf-life of fruits. It binds to a seven-transmembrane-domain receptor-like protein and induces programmed cell death in Saccharomyces cerevisiae through RAS2/cAMP signaling pathway. Adiponectin, produced in adipose tissues of mammals, is an insulin-sensitizing hormone. Strangely, osmotin acts like the mammalian hormone adiponectin in various in vitro and in vivo models. Adiponectin and osmotin, the two receptor binding proteins do not share sequence similarity at the amino acid level, but interestingly they have a similar structural and functional properties. In experimental mice, adiponectin inhibits endothelial cell proliferation and migration, primary tumor growth, and reduces atherosclerosis. This retrospective work examines the vital role of osmotin in plant defense and as a potential targeted therapeutic drug for humans.

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