<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

miRNAs are some of the key epigenetic regulators of gene expression. They act through hybridization with their target mRNA and modulate the level of respective proteins via different mechanisms. Various cancer conditions are known to be associated with up- and downregulation of the oncogenic and tumor suppressor miRNAs, respectively. The levels of aberrantly expressed oncogenic miRNAs can be downregulated in different ways. Similarly, restoration of tumor suppressor miRNAs to their normal levels can be achieved using miRNA mimics. However, the use of miRNA mimics is limited by their reduced biostability and function. We have studied the hybridization thermodynamics of the miRNA 26a (11-mer, including the seed sequence) guide strand with the mRNA (11-mer) target strand in the absence and presence of AfPiwi protein. We have also inserted locked nucleic acids (LNAs) and 2-O-methyl-modified nucleotides into the guide strand, in a walk-through manner, to assess their effect on the binding efficiency between guide and target RNA. Insertion of LNA and 2-O-methyl-modified nucleotides into the guide strand helped to strengthen the binding affinity irrespective of the position of insertion. However, in the presence of AfPiwi protein, these modifications reduced the binding affinity to different extents depending on the position of insertion. Insertion of a modification leads to an increase in the enthalpic contribution with an increased unfavorable entropic contribution, which negatively compensates for the higher favorable enthalpy. © 2014 American Chemical Society.

World University root node

Life Sciences

Biochemistry

Understanding the effect of locked nucleic acid and 2- O-methyl modification on the hybridization thermodynamics of a miRNA-mRNA pair in the presence and absence of AfPiwi protein

GaSb(1 0 0) samples were irradiated with 60 keV Ar + -ions at normal incidence for fluences in the range of 7 × 10 16 to 3 × 10 18 ions cm -2 at room temperature, showing gradual evolution of a porous surface layer containing interconnected nanofibers. In particular, fluence dependent formation of patches on the nanoporous layer is observed by scanning electron microscopy. Combined results of grazing incidence x-ray diffraction and transmission electron microscopy reveal the presence of nanocrystallites in the porous structures. Compositional analysis by x-ray photoelectron spectroscopy indicates the development of oxide phases, mainly Ga 2 O 3 and Sb 2 O 3 where the former increases with fluence. We have proposed a model addressing a competition between ion-induced-defect driven growth of the nanoporous layer and redeposition of sputtered target atoms on the growing layer. © 2014 Elsevier B.V.

Physics

Applied Surface Science

Evolution of porous network in GaSb under normally incident 60 keV Ar + -ion irradiation

Purpose. Large copy number variations (CNV) can contribute to increased burden for neurodegenerative diseases. In this study, we analyzed the genome-wide burden of large CNVs &gt; 100 kb in primary open angle glaucoma (POAG), a neurodegenerative disease of the eye that is the largest cause of irreversible blindness. Methods. Genome-wide analysis of CNVs &gt; 100 kb were analyzed in a total of 1720 individuals, including an Indian cohort (347 POAG cases and 345 controls) and a Caucasian cohort (624 cases and 404 controls). All the CNV data were obtained from experiments performed on Illumina 660W-Quad (infinium) arrays. Results. We observed that for both the populations CNVs &gt; 1 Mb was significantly enriched for gene-rich regions unique to the POAG cases (P &lt; 10-11). In the Indian cohort CNVs &gt; 1 Mb (39 calls) in patients influenced 125 genes while in controls 31 such CNVs influenced only 5 genes with no overlap. In both cohorts we observed 1.9-fold gene enrichment in patients for deletions compared to duplications, while such a bias was not observed in controls (0.3-fold). Overall duplications &gt; 1 Mb were more than deletions (Del/Dup = 0.82) confirming that the enrichment of gene-rich deletions in patients was associated with the disease. Of the 39 CNVs &gt; 1 Mb from Indian patients, 28 (72\%) also were implicated in other neurodegenerative disorders, like autism, schizophrenia, sensorineural hearing loss, and so forth. We found one large duplication encompassing CNTN4 gene in Indian and Caucasian POAG patients that was absent in the controls. Conclusions. To our knowledge, our study is the first report on large CNV bias for gene-rich regions in glaucomatous neurodegeneration, implicating its impact across populations of contrasting ethnicities. We identified CNTN4 as a novel candidate gene for POAG. © 2014 The Association for Research in Vision and Ophthalmology, Inc.

Mathematics

Fulltext

Investigative Ophthalmology and Visual Science

Gene-rich large deletions are overrepresented in POAG patients of Indian and Caucasian origins

The advancement of surface-enhanced Raman scattering (SERS) is significantly increasing as an ultra-sensitive sensing technology in biomedical research. In this review, we focus on the most recent developments of biocompatible nanoprobes for cancer research. First, we discuss coating approaches to enhance the biocompatibility of SERS substrate and Raman reporters. Furthermore, interesting ligands such as antibodies, aptamers and polypeptides are attached to the surface of nanotags for targeting the cancerous cells in vitro. The unique multiplexing capabilities of the SERS technique have been applied for simultaneous multiple target recognition. Finally, these noninvasive, ultrasensitive tools are mostly highlighted for in vivo tumor detection. Potential application of SERS nanotags in therapeutic study and the possibility of SERS nanotags in biomedical applications are outlined briefly in this review. © 2014 Future Medicine Ltd.

Chemistry

Nanomedicine

Biocompatible surface-enhanced Raman scattering nanotags for in vivo cancer detection

We study the physics of Kaluza-Klein (KK) top quarks in the framework of a non-minimal Universal Extra Dimension (nmUED) with an orbifolded (S 1 /Z 2) flat extra spatial dimension in the presence of brane-localized terms (BLTs). In general, BLTs affect the masses and the couplings of the KK excitations in a non-trivial way including those for the KK top quarks. On top of that, BLTs also influence the mixing of the top quark chiral states at each KK level and trigger mixings among excitations from different levels with identical KK parity (even or odd). The latter phenomenon of mixing of KK levels is not present in the popular UED scenario known as the minimal UED (mUED) at the tree level. Of particular interest are the mixings among the KK top quarks from level '0' and level '2' (driven by the mass of the Standard Model (SM) top quark). These open up new production modes in the form of single production of a KK top quark and the possibility of its direct decays to SM particles leading to rather characteristic signals at the colliders. Experimental constraints and the restrictions they impose on the nmUED parameter space are discussed. The scenario is implemented in MadGraph 5 by including the quark, lepton, the gauge-boson and the Higgs sectors up to the second KK level. A few benchmark scenarios are chosen for preliminary studies of the decay patterns of the KK top quarks and their production rates at the LHC in various different modes. Recast of existing experimental analyzes in scenarios having similar states is found to be not so straightforward for the KK top quarks of the nmUED scenario under consideration. © 2014 The Author(s).

Journal of High Energy Physics

Non-minimal Universal Extra Dimensions with Brane Local Terms: The top quark sector

Four neutral polynuclear magnetic clusters, [MnIII6MnII2NaI2(N 3)8($\mu$4-O)2(L1) 6(CH3OH)2] (1), [MnIII6NaI2(N3) 4($\mu$4-O)2(L2)4(CH 3COO)4] (2), [NiII5(N 3)4(HL1)4(HCOO)2(CH 3OH)2(H2O)2]{\textperiodcentered}2CH 3OH (3) and [NiII4NaI2(N3)4(HL2)6] {\textperiodcentered}2CH3OH (4) have been synthesized using tetradentate ligands H2L1-2 along with azide as a co-ligand. H 2L1-2 are the products formed in situ upon condensation of 2-hydroxy-3-methoxybenzaldehyde with 1-aminopropan-2-ol and 1-aminopropan-3-ol, respectively. Single crystal X-ray diffraction and bond valence sum calculation showed that complex 1 is composed of both MnIII and MnII. Complex 3 contains coordinated formate, which was formed upon in situ oxidation of methanol. The magnetic study over a wide range of temperatures of all the complexes (1-4) showed that 1 and 2 are antiferromagnetic whereas other two (3-4) are predominantly ferromagnetic. The estimated ground states of the complexes are S ≈ 3(1), S = 4(2), S = 5(3) and S ≈ 4(4), respectively. {\textcopyright} 2013 Elsevier B.V. All rights reserved.

Inorganica Chimica Acta

Tuning nuclearity of clusters by positional change of functional group: Synthesis of polynuclear clusters, crystal structures and magnetic properties

Room temperature implantation of 60 keV Ar+-ions in GaSb to the fluences of 7 × 1016 to 3 × 1018 ions cm -2 is carried out at two incidence angles, viz 0° and 60°, leading to formation of a nanoporous layer. As the ion fluence increases, patches grow on the porous layer under normal ion implantation, whereas the porous layer gradually becomes embedded under a rough top surface for oblique incidence of ions. Grazing incidence x-ray diffraction and cross-sectional transmission electron microscopy studies reveal the existence of nanocrystallites embedded in the ion-beam amorphized GaSb matrix up to the highest fluence used in our experiment. Oxidation of the nanoporous layers becomes obvious from x-ray photoelectron spectroscopy and Raman mapping. The correlation of ion-beam induced structural modification with photoluminescence signals in the infrared region has further been studied, showing defect induced emission of additional peaks near the band edge of GaSb. © 2014 AIP Publishing LLC.

Journal of Applied Physics

Argon-ion-induced formation of nanoporous GaSb layer: Microstructure, infrared luminescence, and vibrational properties

Genetic algorithms (GA) have been widely used in quantitative structure-activity/property relationship (QSAR/QSPR) modeling in recent years and have been shown to generate accurate and robust predictions. In a GA, a population of chromosomes is evolved through the processes of random mutation and crossover and evaluated using a fitness function. Here, we will review the basic principles underlying GA and provide a survey of recent applications in QSAR/QSPR, bioinformatics, and in silico drug design, with particular emphasis on the use of GAs in feature selection and dimensionality reduction, model optimization, conformational search, docking, and diversity analysis. © 2014 Springer International Publishing Switzerland. All rights reserved.

Applications of Metaheuristics in Process Engineering

Applications of genetic algorithms in QSAR/QSPR modeling

Chemically textured Si with improved absorption in the complete range of solar spectrum is investigated by ultraviolet/visible/near-infrared (UV/Vis/NIR) spectroscopy, showing an average specular reflectance of ∼0.4\% in the wavelength of 500-3000nm. The pyramidal structures on such solar-blind Si can reduce the reflectance further below 0.1\% in the UV region by conformal growth of granular Al-doped ZnO (AZO) films. X-ray diffraction analyses suggest the growth of polycrystalline AZO on faceted-Si. Moreover, marginal increase in electrical conductivity of AZO is found on textured surfaces, whereas rise in leakage current in Schottky-like Ag/AZO/Si/Ag heterostructure devices is noticed with increasing Si surface area. © 2014 AIP Publishing LLC.

Applied Physics Letters

Improved broadband antireflection in Schottky-like junction of conformal Al-doped ZnO layer on chemically textured Si surfaces

The application of small molecules to modulate proteins by direct interactions has evolved as a powerful tool for the study of complex biological systems. Conventional genetic approaches have examined biological systems by generating random mutations which were then screened in search of a precise cellular phenotype. Analogous to the genetic approach, large random collections of small molecules can be used to elucidate the roles of specific proteins in many biological pathways. The crux of this 'chemical genetic' approach is the design and synthesis of libraries of compounds which span large tracts of biologically relevant chemical space. Diversity-oriented asymmetric synthesis (DOAS) is an exceptional methodology for preparing structurally and stereochemically diverse small molecule libraries which show a greater variety not only in their physiochemical properties but also in their biological activities. Herein, we describe some of the most effective strategies that have been used in asymmetric diversity-oriented synthesis library design and preparation. 1 Introduction 2 Philosophy of DOAS 3 Stoichiometric Reactions 3.1 DOAS with Chiral Auxiliaries 3.2 DOAS with Chiral Templates 3.3 DOAS with Chiral 'Linchpins' 3.4 DOAS from Natural Products via a Ring-Distortion Strategy 3.5 DOAS via Chiral Reactions 4 DOAS towards Peptidomimetics 5 Catalytic Reactions 6 Conclusion. © Georg Thieme Verlag Stuttgart. New York.