<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

(SoNS) School of Natural Sciences

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.

World University root node

Life Sciences

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.

Fulltext

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).

Frontiers in Plant Science

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

Malaria a global pandemic has engulfed nearly 0.63 million people globally. It is high time that a cure for malaria is required to stop its ever increasing menace. Our commentary discusses the advent and contribution of genetic algorithm (GA) in the drug discovery efforts towards developing cure for malaria. GAs are computational models of Darwinian evolution, ideally capture and mimic the principles of genetic variation and natural selection to evolve good solutions through multiple iterations on the space of all possible candidate solutions, called the search space, to a given optimization problem. Herein we will discuss the applications, advantages, disadvantages and future directions of GA with respect to malaria. © 2015, Springer Science+Business Media Dordrecht.

Mathematics

Chemistry

Systems and Synthetic Biology

Innovative techniques to discover novel antimalarials

Ta and Nb substituted TiO2 are important transparent conducting oxides that have potential for applications in photovoltaics, photocatalysis, and water splitting/CO2 sequestration. In addition to donating electrons, what are the effects of Nb and Ta substitution? Here we observe strong experimental evidence that Ta and Nb substitution induces large and small polarons in anatase TiO2 epitaxial thin films. The degenerate donor electrons (from both Nb and Ta) show a high temperature T3 dependence on electrical resistivity, which confirms the presence of large polarons, along with room temperature metallic transport. This is further confirmed by the enhancement in the electron effective mass, which was estimated from thermopower measurements. Femtosecond transient absorption (fs-TA) reveals the life time of the Ti-t2g and eg levels and the separation of these levels are consistent with the X-ray absorption spectroscopy (XAS) measurement. In addition, fs-TA reveals the presence of small polarons with a life time substantially &gt;1 ns, which arises from defect levels and is a consequence of Ta and Nb substitution. X-ray photoelectron spectroscopy (XPS) provides evidence of Ti3+, which may be identified as the defects responsible for the small polarons. These long-lived small polarons may provide a way to minimize recombination dynamics in TiO2-based electrodes for photo-excited devices. © The Royal Society of Chemistry 2015.

Physics

Journal of Materials Chemistry C

Effect of Nb and Ta substitution on donor electron transport and ultrafast carrier dynamics in anatase TiO2 thin films

Al-doped ZnO (AZO) thin films of thicknesses 5,10, 15, 20, and 30nm were deposited on 500eV argon ion-beam fabricated nanoscale self-organized rippled-Si substrates at room temperature and are compared with similar films deposited on pristine-Si substrates (without ripples). It is observed that morphology of self-organized AZO films is driven by the underlying substrate morphology. For instance, for pristine-Si substrates, a granular morphology evolves for all AZO films. On the other hand, for rippled-Si substrates, morphologies having chain-like arrangement (anisotropic in nature) are observed up to a thickness of 20nm, while a granular morphology evolves (isotropic in nature) for 30nm-thick film. Photoluminescence studies reveal that excitonic peaks corresponding to 5-15nm-thick AZO films, grown on rippled-Si templates, show a blue shift of 8nm and 3nm, respectively, whereas the peak shift is negligible for 20-nm thick film (with respect to their pristine counter parts). The observed blue shifts are substantiated by diffuse reflectance study and attributed to quantum confinement effect, associated with the size of the AZO grains and their spatial arrangements driven by the anisotropic morphology of underlying rippled-Si templates. The present findings will be useful for making tunable AZO-based light-emitting devices. © 2015 AIP Publishing LLC.

Journal of Applied Physics

Thickness-dependent blue shift in the excitonic peak of conformally grown ZnO:Al on ion-beam fabricated self-organized Si ripples

The problem associated with metal nanoparticle (NP) agglomeration when trying to achieve a high loading amount has been solved by a new method of functionalization of MOFs' pores with terminal alkyne moieties. The alkynophilicity of the Au3+ ions has been utilized successfully for an exceptionally high loading (∼50 wt%) of Au-NPs on supported functionalized MOFs.

Chemical Communications

A smart approach to achieve an exceptionally high loading of metal nanoparticles supported by functionalized extended frameworks for efficient catalysis

Abstract: We study the viability of having two relatively light top squarks (‘stops') in the framework of the Next-to-Minimal Supersymmetric Standard Model (NMSSM). Such light stops render the NMSSM rather ‘natural'. These are shown to be allowed by the relevant direct searches at the Large Hadron Collider (LHC) and to be compatible with the latest LHC results on the Higgs sector, other low energy electroweak constraints and recent constraints from the dark matter (DM) sector. We propose dedicated searches for such light stops at the LHC within a ‘simplified' scenario that may have a bino-like or a singlino-like neutralino LSP as the DM candidate and point out various final states carrying the imprint of their collective presence. Under certain circumstances, in such a scenario, presence of two light stops may give rise to final states which are not so typical in their search. Thorough studies at the detector level reveal the status of such a scenario after the 8 TeV run of the LHC and shed light on the prospects of its 13 and 14 TeV runs. In favorable regions of the NMSSM parameter space, with low-lying spectra, signals with significance ≳ 5$\sigma$ are possible with a few tens to a few hundreds of fb<sup>−1</sup> of integrated luminosity in diverse final states.

Journal of High Energy Physics

Two light stops in the NMSSM and the LHC

Aim: Development of highly sensitive diagnostic nanoprobe for cancer imaging based on surface-enhanced Raman scattering (SERS) platform. Materials & methods: Synthesis of novel squaraine dyes as a Raman signature molecule denoted as lipoic-squaraine-lipoic (LSL), propyl-squaraine-lipoic (PSL) and propyl-squaraine-propyl (PSP). The SERS-nanotag constructed with a Raman signature molecule which is attached on gold nanoparticle and further encapsulated with heterofunctionalized PEG. Antibody conjugation with best SERS-nanotag for target specific recognition. Results: SERS nanotag Au-LSL-PEG showed significant signal intensity and remarkable stability. Anti-EGF receptor and Her2-conjugated Au-LSL-PEG-nanotag were successfully applied for selective recognition of cancer cells like A549, OSCC and MCF7. Conclusion: The newly developed SERS-nanotag Au-LSL-PEG serves as a valuable tool for diagnostic detection of cancer cells, and may find potential applications for cancer screening in real patient samples. © 2015 Future Medicine Ltd.

Nanomedicine

New insight of squaraine-based biocompatible surface-enhanced Raman scattering nanotag for cancer-cell imaging

Long-term real-time visualization of lysosomal dynamics has been challenging at the onset of mitosis due to the lack of fluorescent probes enabling convenient imaging of dividing cells. We developed a long-term real-time photostable mitotic or proliferating marker, CDy6, a BODIPY-derived compound of designation yellow 6, which labels lysosome. In long-term real-time, CDy6 displayed a sharp increase in intensity and change in localization in mitosis, improved photostability, and decreased toxicity compared with other widely used lysosomal and DNA markers, and the ability to label cells in mouse xenograft models. Therefore, CDy6 may open new possibilities to target and trace lysosomal contents during mitosis and to monitor cell proliferation, which can further our knowledge of the basic underlying biological mechanisms in the management of cancer. © 2015 Elsevier Ltd.