Life Sciences

<p>Shiv Nadar University is a comprehensive, multidisciplinary, research-focused, and student-centric University offering a full range of academic programs at the undergraduate, postgraduate and doctoral level. With state-of-the-art infrastructure, the University comprises of academic wings, sophisticated labs, international standard sports facilities, amphitheaters, auditorium, conference rooms and smart classrooms. The University&rsquo;s goal is to become internationally recognized for the quality of its research and creative endeavors and their applicability to improving quality of life, generating new insights and expanding the boundaries of human knowledge creativity. Committed to excellence in teaching, research and service, the University aims to serve the higher education needs of India and the world beyond.</p>

Shiv Nadar University

Development of informative polymorphic simple sequence repeat (SSR) markers at a genome-wide scale is essential for efficient large-scale genotyping applications. We identified genome-wide 1835 SSRs showing polymorphism between desi and kabuli chickpea. A total of 1470 polymorphic SSR markers from diverse coding and non-coding regions of the chickpea genome were developed. These physically mapped SSR markers exhibited robust amplification efficiency (73.9%) and high intra- and inter-specific polymorphic potential (63.5%), thereby suggesting their immense use in various genomics-assisted breeding applications. The SSR markers particularly derived from intergenic and intronic sequences revealed high polymorphic potential. Using the mapped SSR markers, a wider functional molecular diversity (16–94%, mean: 68%), and parentage- and cultivar-specific admixed domestication pattern and phylogenetic relationships in a structured population of desi and kabuli chickpea genotypes was evident. The intra-specific polymorphism (47.6%) and functional molecular diversity (65%) potential of polymorphic SSR markers developed in our study is much higher than that of previous documentations. Finally, we have developed a user-friendly web resource, Chickpea Microsatellite Database (CMsDB; http://www.nipgr.res.in/CMsDB.html), which provides public access to the data and results reported in this study. The developed informative SSR markers can serve as a resource for various genotyping applications, including genetic enhancement studies in chickpea. © 2015 Parida, Verma, Yadav, Ambawat, Das, Garg and Jain.

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Frontiers in Plant Science

Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource

The wilt caused by Fusarium oxysporum f.sp. Ciceris is a major problem for chickpea. The large-scale discovery of DNA polymorphisms in different cultivars can provide insights into the genetic basis of phenotypic differences. In the present study, we sequenced the transcriptomes of four chickpea cultivars with contrasting response to Fusarium infection, including susceptible JG62 and resistant/tolerant ICCV2, K850 and WR315. Based on the analysis of their transcriptome sequences, we identified at least 303 polymorphic microsatellites, of which 64 % could be physically mapped on the chickpea genome. Further, we identified a total of 14,462 single nucleotide polymorphisms (SNPs) and 1864 insertions/deletions (InDels) among the chickpea cultivars analysed. More than 50 % of the SNPs and 19 % of the InDels were detected in the predicted coding regions, and about 46 % of these SNPs resulted in nonsynonymous changes. In addition, we identified at least 60 large-effect SNPs and 248 InDels that affected the integrity of the encoded protein. Several defence-related genes involved in different cellular processes were found to harbour nonsynonymous and/or large-effect SNPs and/or InDels. These data will provide functional markers and promising target genes for wilt resistance and present a valuable resource for molecular breeding for this important trait in chickpea. © 2015, Springer Science+Business Media Dordrecht.

Molecular Breeding

Discovery of molecular markers for Fusarium wilt via transcriptome sequencing of chickpea cultivars

DNA methylation is an epigenetic mechanism that play an important role in gene regulation in response to environmental conditions. The understanding of DNA methylation at the whole genome level can provide insights into the regulatory mechanisms underlying abiotic stress response/adaptation. We report DNA methylation patterns and their influence on transcription in three rice (Oryza sativa) cultivars (IR64, stress-sensitive; Nagina 22, drought-tolerant; Pokkali, salinity-tolerant) via an integrated analysis of whole genome bisulphite sequencing and RNA sequencing. We discovered extensive DNA methylation at single-base resolution in rice cultivars, identified the sequence context and extent of methylation at each site. Overall, methylation levels were significantly different in the three rice cultivars. Numerous differentially methylated regions (DMRs) among different cultivars were identified and many of which were associated with differential expression of genes important for abiotic stress response. Transposon-associated DMRs were found coupled to the transcript abundance of nearby protein-coding gene(s). Small RNA (smRNA) abundance was found to be positively correlated with hypermethylated regions. These results provide insights into interplay among DNA methylation, gene expression and smRNA abundance, and suggest a role in abiotic stress adaptation in rice.

Scientific Reports

Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response

Growth hormone auxin regulates various cellular processes by altering the expression of diverse genes in plants. Among various auxin-responsive genes, GH3 genes maintain endogenous auxin homeostasis by conjugating excess of auxin with amino acids. GH3 genes have been characterized in many plant species, but not in legumes. In the present work, we identified members of GH3 gene family and analyzed their chromosomal distribution, gene structure, gene duplication and phylogenetic analysis in different legumes, including chickpea, soybean, Medicago, and Lotus. A comprehensive expression analysis in different vegetative and reproductive tissues/stages revealed that many of GH3 genes were expressed in a tissue-specific manner. Notably, chickpea CaGH3-3, soybean GmGH3-8 and-25, and Lotus LjGH3-4,-5,-9 and-18 genes were up-regulated in root, indicating their putative role in root development. In addition, chickpea CaGH3-1 and-7, and Medicago MtGH3-7,-8, and-9 were found to be highly induced under drought and/or salt stresses, suggesting their role in abiotic stress responses.We also observed the examples of differential expression pattern of duplicated GH3 genes in soybean, indicating their functional diversification. Furthermore, analyses of three-dimensional structures, active site residues and ligand preferences provided molecular insights into function of GH3 genes in legumes. The analysis presented here would help in investigation of precise function of GH3 genes in legumes during development and stress conditions. © 2015 Singh, Jain and Garg. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).

Genome-wide analysis and expression profiling suggest diverse roles of GH3 genes during development and abiotic stress responses in legumes

Expression of synthetic proteins from intergenic regions of E. coli and their functional association was recently demonstrated (Dhar et al. in J Biol Eng 3:2, 2009. doi:10.1186/1754-1611-3-2). This gave birth to the question: if one can make ‘user-defined’ genes from non-coding genome—how big is the artificially translatable genome? (Dinger et al. in PLoS Comput Biol 4, 2008; Frith et al. in RNA Biol 3(1):40–48, 2006a; Frith et al. in PLoS Genet 2(4):e52, 2006b). To answer this question, we performed a bioinformatics study of all reported E. coli intergenic sequences, in search of novel peptides and proteins, unexpressed by nature. Overall, 2500 E. coli intergenic sequences were computationally translated into ‘protein sequence equivalents’ and matched against all known proteins. Sequences that did not show any resemblance were used for building a comprehensive profile in terms of their structure, function, localization, interactions, stability so on. A total of 362 protein sequences showed evidence of stable tertiary conformations encoded by the intergenic sequences of E. coli genome. Experimental studies are underway to confirm some of the key predictions. This study points to a vast untapped repository of functional molecules lying undiscovered in the non-expressed genome of various organisms. © 2015, Springer Science+Business Media Dordrecht.

Systems and Synthetic Biology

Predicting stable functional peptides from the intergenic space of E. coli

Metastasis is a major cause of mortality and remains a hurdle in the search for a cure for cancer. Not much is known about metastatic cancer cells and endothelial cross-talk, which occurs at multiple stages during metastasis. Here we report a dynamic regulation of the endothelium by cancer cells through the formation of nanoscale intercellular membrane bridges, which act as physical conduits for transfer of microRNAs. The communication between the tumour cell and the endothelium upregulates markers associated with pathological endothelium, which is reversed by pharmacological inhibition of these nanoscale conduits. These results lead us to define the notion of 'metastatic hijack': cancer cell-induced transformation of healthy endothelium into pathological endothelium via horizontal communication through the nanoscale conduits. Pharmacological perturbation of these nanoscale membrane bridges decreases metastatic foci in vivo. Targeting these nanoscale membrane bridges may potentially emerge as a new therapeutic opportunity in the management of metastatic cancer. © 2015 Macmillan Publishers Limited. All rights reserved.

Nature Communications

Physical nanoscale conduit-mediated communication between tumour cells and the endothelium modulates endothelial phenotype

The present climatic deterioration including the much debated anthropogenic acceleration to the global warming phenomenon has drawn the attention of scientific community, policy makers as well as the general public to the problem of climate change. Chemostratigraphic techniques have proven to be very useful to understand the past climate of the earth that has been changing naturally on timescales ranging from decades to millions of years. Therefore, it is important to filter out the natural signal to correctly gauge the effects induced by humans. This is where the science of paleoclimatology becomes very important. It helps us to understand the pattern of evolution of the earth's climate system, its rhythm, and pulse using various natural archives such as marine and lacustrine sediments, speleothems, ice cores, corals, trees, etc., that hold the clue to the past climate variability. Several proxies are studied from such natural archives to reconstruct the past climatic changes. Out of these, the stable isotopes are one of the most useful and widely employed. In this present study, we explain the methodology behind the application of the stable isotopes as a proxy to reconstruct past climatic changes. We present here a few examples of the stable isotopes of the most widely used elements viz oxygen, carbon, and nitrogen from the marine realm and their systematics. The use of chemostratigraphic techniques like application of oxygen isotopes in stratigraphy, temperature, salinity, and ice-volume reconstruction; Cenozoic oxygen and carbon isotope curves; the limitations in the form of vital effect and diagenesis in the case of foraminifera; use of nitrogen and carbon isotopes as productivity and provenance indicator, respectively, are presented in this paper. © 2015 Elsevier Inc. All rights reserved.

Chemostratigraphy: Concepts, Techniques, and Applications

Stable Isotopes: Tools for Understanding Past Climatic Conditions and Their Applications in Chemostratigraphy

1-Nitropyrene (1-NP), an environmental pollutant, induces DNA damage in vivo and is considered to be carcinogenic. The DNA adducts formed by the 1-NP metabolites stall replicative DNA polymerases but are presumably bypassed by error-prone Y-family DNA polymerases at the expense of replication fidelity and efficiency in vivo. Our running start assays confirmed that a site-specifically placed 8-(deoxyguanosin-N2-yl)-1-aminopyrene (dG1,8), one of the DNA adducts derived from 1-NP, can be bypassed by Sulfolobus solfataricus DNA polymerase IV (Dpo4), although this representative Y-family enzyme was paused strongly by the lesion. Pre-steady-state kinetic assays were employed to determine the low nucleotide incorporation fidelity and establish a minimal kinetic mechanism for the dG1,8 bypass by Dpo4. To reveal a structural basis for dCTP incorporation opposite dG1,8, we solved the crystal structures of the complexes of Dpo4 and DNA containing a templating dG1,8 lesion in the absence or presence of dCTP. The Dpo4{\textperiodcentered}DNA-dG1,8 binary structure shows that the aminopyrene moiety of the lesion stacks against the primer/template junction pair, while its dG moiety projected into the cleft between the Finger and Little Finger domains of Dpo4. In the Dpo4{\textperiodcentered}DNA-dG1,8{\textperiodcentered}dCTP ternary structure, the aminopyrene moiety of the dG1,8 lesion, is sandwiched between the nascent and junction base pairs, while its base is present in the major groove. Moreover, dCTP forms a Watson-Crick base pair with dG, two nucleotides upstream from the dG1,8 site, creating a complex for "-2" frameshift mutation. Mechanistically, these crystal structures provide additional insight into the aforementioned minimal kinetic mechanism.

Journal of the American Chemical Society

Mechanistic Basis for the Bypass of a Bulky DNA Adduct Catalyzed by a Y-Family DNA Polymerase

The majority of mitochondrial proteins are targeted to mitochondria by N-terminal presequences and use the TIM23 complex for their translocation across the mitochondrial inner membrane. During import, translocation through the channel in the inner membrane is coupled to the ATP-dependent action of an Hsp70-based import motor at the matrix face. How these two processes are coordinated remained unclear. We show here that the two domain structure of Tim44 plays a central role in this process. The N-terminal domain of Tim44 interacts with the components of the import motor, whereas its C-terminal domain interacts with the translocation channel and is in contact with translocating proteins. Our data suggest that the translocation channel and the import motor of the TIM23 complex communicate through rearrangements of the two domains of Tim44 that are stimulated by translocating proteins. © Banerjee et al.

eLife

Protein translocation channel of mitochondrial inner membrane and matrix-exposed import motor communicate via two-domain coupling protein

Determination of maintainer and restorer status of germplasm collections is a prerequisite for their use in development of hybrid employing CMS system. In the present study, restorer and maintainer status of 372 Indian genotypes was determined using fertility restoration (Rf) linked microsatellite marker RM6100. A total of seven alleles for the marker locus, including four novel and three known, were identified in the study material. Maximum frequency was observed for the 144bp allele (44.89%) while minimum frequency was for 138bp allele (0.27%).Though most of the novel alleles were minor, occurring in less than 5% frequency, cumulatively they accounted for 9.2% frequency in the study material. Of the known alleles, which were found in 90.8% (338 genotypes) of the tested rice genotypes, 36% had maintainer type allele (132bp allele similar to Pusa 6B) while the rest had restorer type (144 or 150 bp) alleles. The spikelet fertility data generated on a subset of the study material agreed well with the established associations for the already reported alleles. Of the novel alleles, two (141 and 147 bp) were represented in the spikelet fertility dataset, both of which restored fertility, though their representation was low. This allelic information would be useful in selection of parental lines for development of hybrids in rice. © 2014, Indian Society of Genetics and Plant Breeding. All rights reserved.