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

The land degradation due to salinity and waterlogging is a global phenomenon, afflicting about one billion hectares within the sovereign borders of at least 75 countries. Besides staring at the food security, it has far reaching and unacceptable socio-economic consequences since a large proportion of this land is inhabited by smallholder farmers. The anthropogenic-environmental changes and the climate change are further adding to the problem of salinity and waterlogging. The phenomenon of sea-level rise will bring more areas under waterlogged salinity due to inundation by sea water. Thus, dealing with the salinity in reality is becoming a highly onerous task owing to its complex nature, uncertainty and differential temporal and spatial impacts. Nevertheless, with the need to provide more food, feed, fuel, fodder and fiber to the expanding population, and non-availability of new productive land, there is a need for productivity enhancement of these lands. In fact, the salt-affected and waterlogged lands cannot be neglected since huge investments have been made throughout the world in the development of irrigation and drainage infrastructure. The social, economic and environmental costs being high for theon-and/off-farm reclamation techniques, saline agriculture including agroforestry inculcated with modern innovative techniques, is now emerging as a potential tool not only for arresting salinity and waterlogging but for other environmental services like mitigate climate change, sequester carbon and biodiversity restoration. This publication attempts to address a wide range of issues, principles and practices related to the salinity involved in rehabilitation of waterlogged saline soils and judicious use of saline waters including sea water. Many of the site specific case studies typical to the saline environment including coastal ecologies sustaining productivity, rendering environmental services, conserving biodiversity and mitigating climate change have been described in detail. Written by leading researchers and experts of their own fields, the book is a must, not only for salinity experts but also for policy makers, environmentalists, students and educationists alike. More importantly, it contributes to reversing the salinity trends and teaches to sustain with salinity ensuring the livelihood of resource-poor farming families leaving in harsh ecologies including coastal areas which are more vulnerable to climate change. © Springer India 2016.

World University root node

(SoNS) School of Natural Sciences

Innovative Saline Agriculture

Innovative saline agriculture

DnaK or Hsp70 of Escherichia coli is a master regulator of the bacterial proteostasis network. Allosteric communication between the two functional domains of DnaK, the N-terminal nucleotide-binding domain (NBD) and the C-terminal substrate- or peptide-binding domain (SBD) regulate its activity. X-ray crystallography and NMR studies have provided snapshots of distinct conformations of Hsp70 proteins in various physiological states; however, the conformational heterogeneity and dynamics of allostery-driven Hsp70 activity remains underexplored. In this work, we employed single-molecule Förster resonance energy transfer (sm-FRET) measurements to capture distinct intradomain conformational states of a region within the DnaK-SBD known as the lid. Our data conclusively demonstrate prominent conformational heterogeneity of the DnaK lid in ADP-bound states; in contrast, the ATP-bound open conformations are homogeneous. Interestingly, a nonhydrolysable ATP analogue, AMP-PNP, imparts heterogeneity to the lid conformations mimicking the ADP-bound state. The cochaperone DnaJ confers ADP-like heterogeneous lid conformations to DnaK, although the presence of the cochaperone accelerates the substrate-binding rate by a hitherto unknown mechanism. Irrespective of the presence of DnaJ, binding of a peptide substrate to the DnaK-SBD leads to prominent lid closure. Lid closure is only partial upon binding to molten globule-like authentic cellular substrates, probably to accommodate non-native substrate proteins of varied structures. © 2016 Federation of European Biochemical Societies

FEBS Journal

Monitoring conformational heterogeneity of the lid of DnaK substrate-binding domain during its chaperone cycle

Cancer of large intestine is commonly referred as colorectal cancer, which is also the third most frequently prevailing neoplasm across the globe. Though, much of work is being carried out to understand the mechanism of carcinogenesis and advancement of this disease but, fewer studies has been performed to collate the scattered information of alterations in tumorigenic cells like genes, mutations, expression changes, epigenetic alteration or post translation modification, genetic heterogeneity. Earlier findings were mostly focused on understanding etiology of colorectal carcinogenesis but less emphasis were given for the comprehensive review of the existing findings of individual studies which can provide better diagnostics based on the suggested markers in discrete studies. Colon Rectal Cancer Gene Database (CoReCG), contains 2056 colon-rectal cancer genes information involved in distinct colorectal cancer stages sourced from published literature with an effective knowledge based information retrieval system. Additionally, interactive web interface enriched with various browsing sections, augmented with advance search facility for querying the database is provided for user friendly browsing, online tools for sequence similarity searches and knowledge based schema ensures a researcher friendly information retrieval mechanism. Colorectal cancer gene database (CoReCG) is expected to be a single point source for identification of colorectal cancer-related genes, thereby helping with the improvement of classification, diagnosis and treatment of human cancers. © The Author(s) 2016.

Fulltext

Database

CoReCG: A comprehensive Database of genes associated with colon-rectal cancer

Rice hybrids are known to withstand moisture deficit stress better than their parental purelines. To study the effect of water deficit stress in rice hybrids, in terms of productivity related traits and physiological parameters pertaining to drought stress, 22 rice hybrids and their parental lines were evaluated under well irrigated and water deficit conditions. Sixteen F1 hybrids showed positive heterosis over their respective mid-parental means for yield and spikelet fertility. Pusa 6A and Vandana was the best cross combination for developing high yielding hybrid rice varieties under drought since they had the highest positive standard heterosis and heterobeltiosis for grain yield, spikelet fertility and membrane stability index (MSI). Among the physiological parameters, MSI was found to reflect the drought tolerance ability of a genotype (pureline/hybrid) better. A set of 60 genome-wide SSR markers were used for prediction of heterotic potential of genotypes under well irrigated and water deficit conditions which revealed that genetic distances and spikelet fertility had a positive and significant correlation. © 2016, Indian Society of Genetics and Plant Breeding. All rights reserved.

Indian Journal of Genetics and Plant Breeding

Physiological and molecular basis of water-deficit stress tolerance in F1 hybrids and their parental lines in rice

Multifunctional reduced graphene oxide (RGO) coated cloths were prepared through the thermal treatment of GO coated cloths without using any harmful reducing agent. The effect of heating temperature on the wetting properties of the cloths was also monitored through contact angle measurement. The highest contact angle 141° was observed for the RGO coated dense cloth while the highest contact angle exhibited by the RGO coated sparse cloth was 130°. The as prepared RGO coated cloths were utilized as a filter and an absorbent for oil/water separation. The RGO coated sparse cloth was utilized as a filter for the separation of an oil/water mixture while the dense cloth was utilized as an absorbent for the selective absorption of oil from water. RGO coated cloths were also explored as an antibacterial agent and the effect of the microstructure of coated cloths on their antibacterial properties was also investigated. The cloth with the dense structure exhibited higher antibacterial activity compared to the sparse cloth. A significant loss of percentage viability up to 98\% was achieved using the RGO coated cloth, proving it highly efficient as an antibacterial agent, which makes it a suitable bandage material for the dressing of open wounds. Apart from being antibacterial, the RGO coated cloths are also hydrophobic in nature so they can protect wound from water and atmospheric moisture which is not possible with ordinary bandages. © 2016 The Royal Society of Chemistry.

RSC Advances

Multifunctional reduced graphene oxide coated cloths for oil/water separation and antibacterial application

Microsomal prostaglandin E synthase-1 (mPGES-1) is a membrane protein which plays crucial role in arachidonic acid metabolism, in the catalysis of PGH2 to PGE2. It is a potential drug target involved in variety of human cancers and inflammatory disorders. In the present study we made an attempt to identify crucial amino acid residues involved in the effective binding of its inhibitors at the active site. Molecular docking and Structure Activity Relationship (SAR) studies were performed. In the present study 127 inhibitors having significant variability in parent scaffold were considered. The results clearly indicated that in the GSH and PGH2 binding site Arg70, Arg73, Asn74, Glu77, His113, Tyr117, Arg126, Ser127, Tyr130, Thr131 and Ala138 consistently form crucial interactions with inhibitors of different classes/scaffolds. These findings are consistent with that of existing reports on the active site residues pivotal at mPGES-1 active site. Further analysis suggested that out of all important amino acid residues identified; Arg73, Asn74, His113, Tyr117, Arg126, Ser127, Tyr130, Thr131 and Ala138 play a crucial role in hydrogen and π-π interactions. The identified amino acid residues can act as target sites for the design and development of drug candidates against mPGES-1. © 2016 Elsevier B.V.

International Journal of Biological Macromolecules

Insights into the structure activity relationship of mPGES-1 inhibitors: Hints for better inhibitor design

Drought and salinity are the major factors that limit chickpea production worldwide. We performed whole transcriptome analyses of chickpea genotypes to investigate the molecular basis of drought and salinity stress response/adaptation. Phenotypic analyses confirmed the contrasting responses of the chickpea genotypes to drought or salinity stress. RNA-seq of the roots of drought and salinity related genotypes was carried out under control and stress conditions at vegetative and/or reproductive stages. Comparative analysis of the transcriptomes revealed divergent gene expression in the chickpea genotypes at different developmental stages. We identified a total of 4954 and 5545 genes exclusively regulated in drought-tolerant and salinity-tolerant genotypes, respectively. A significant fraction (∼47%) of the transcription factor encoding genes showed differential expression under stress. The key enzymes involved in metabolic pathways, such as carbohydrate metabolism, photosynthesis, lipid metabolism, generation of precursor metabolites/energy, protein modification, redox homeostasis and cell wall component biogenesis, were affected by drought and/or salinity stresses. Interestingly, transcript isoforms showed expression specificity across the chickpea genotypes and/or developmental stages as illustrated by the AP2-EREBP family members. Our findings provide insights into the transcriptome dynamics and components of regulatory network associated with drought and salinity stress responses in chickpea.

Scientific Reports

Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea

DNA, in addition to the canonical B-form, can acquire a variety of alternate structures, such as G-quadruplexes. These structures have been implicated in several cellular processes in animals. In this study, we identified different types of G-quadruplex forming sequences (GQSes) in 15 sequenced plants and analyzed their distribution in various genomic features, including gene body, coding, intergenic and promoter regions. G2-type GQSes were most abundant in all the plant species analyzed. A strong association of G3-type GQSes with intergenic, promoter and intronic regions was found. However, G2-type GQSes were enriched in genic, CDS, exonic and untranslated regions. Further, we identified GQSes present in the conserved genes among monocots and dicots. The genes involved in development, cell growth and size, transmembrane transporter, and regulation of gene expression were found to be significantly enriched. In the promoter region, we detected strong co-occurrence of Telobox, ERF, MYB, RAV1B and E2F motifs with GQSes. Further, we validated the structure formation of several plant GQSes, demonstrated their effect on stalling in-vitro replication and revealed their interaction with plant nuclear proteins. Our data provide insights into the prevalence of GQSes in plants, establish their association with different genomic features and functional relevance.

Genome-wide discovery of G-quadruplex forming sequences and their functional relevance in plants

Iron deficiency is associated with neuropsychological changes such as restless leg syndrome (RLS), pica, hair loss, etc. Our objective was to assess usefulness of history of RLS and pica in relation with iron stores in blood donors. During medical examination, apart from routine questionnaires specific history of RLS and pica was elicited. Along with hemoglobin markers of iron deficiency such as s. iron, s. ferritin and mean corpuscular volume were analyzed. Out of 400 blood donors 41 had h/o pica/RLS/pagophagia. Positive and negative predictive value of above history is 73.17% and 80.5% respectively. We recommend the use of a screening question for pica and/or RLS in blood donor questionnaire. © 2015 Elsevier Ltd.

Transfusion and Apheresis Science

Importance of donor history of restless leg syndrome and pica to asses iron deficiency

In this work, we aim to synthesize water soluble and surface functionalized superparamagnetic iron oxide nanoparticles (SPIONs) using novel surfactants such as terephthalic acid (TA), 2-aminoterephthalic acid (ATA), trimesic acid (TMA) and pyromellitic acid (PMA) through one-step facile chemical co-precipitation and thermal decomposition methods. The as-synthesized SPIONs are characterized using X-ray diffraction (XRD), transmission electron microscopy (TEM), dynamic light scattering (DLS) measurements, Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA) and vibrating sample magnetometer (VSM). The as-synthesized SPIONs showed very good water solubility and a high magnetization value (Ms = 55-73 emu g-1). Furthermore, the as-synthesized ATA-coated SPIONs are conjugated with a fluorophore (Alexa Fluor 488) to demonstrate their ability for further chemical/biological conjugation without any additional surface modifications. Moreover, above 90\% cell viability in MCF-7 cancer cells has been observed, thus confirming good cytocompatibility of the SPIONs. Therefore, these hydrophilic and carboxyl-amine functionalized SPIONs are very promising candidates to be used for biomedical applications. © 2016 Royal Society of Chemistry.