<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

Tropical calcific pancreatitis (TCP) is a juvenile, non-alcoholic form of chronic pancreatitis with its exclusive presence in tropical regions associated with the low economic status. TCP initiates in the childhood itself and then proliferates silently. mutTCPdb is a manually curated and comprehensive disease specific single nucleotide variant (SNV) database. Extensive search strategies were employed to create a repository while SNV information was collected from published articles. Several existing databases such as the dbSNP, Uniprot, miRTarBase2.0, HGNC, PFAM, KEGG, PROSITE, MINT, BIOGRID 3.4 and Ensemble Genome Browser 87 were queried to collect information specific to the gene. mutTCPdb is running on the XAMPP web server with MYSQL database in the backend for data storage and management. Currently, the mutTCPdb enlists 100 variants of all 11 genes identified in TCP, out of which 45 are non-synonymous (missense, nonsense, deletions and insertions), 46 are present in non-coding regions (UTRs, promoter region and introns) and 9 are synonymous variants. The database is highly curated for disease-specific gene variants and provides complete information on function, transcript information, pathways, interactions, miRNAs and PubMed references along with remarks. It is an informative portal for clinicians and researchers for a better understanding of the disease, as it may help in identifying novel targets and diagnostic markers, hence, can be a source to improve the strategies for TCP management. © The Author(s) 2018. Published by Oxford University Press.

Life Sciences

Fulltext

Database

MutTCPdb: A comprehensive database for genomic variants of a tropical country neglected disease - Tropical calcific pancreatitis

Polystyrene is a chemically inert synthetic aromatic polymer. This widely used form of plastic is recalcitrant to biodegradation. The exponential production and consumption of polystyrene in various sectors has presented a great environment risk and raised the problem of waste management. Biodegradation by bacteria has previously shown great potential against various xenobiotics but there are only a few reports concerning polyolefins. By screening wetland microbes, we found two bacterial species-Exiguobacterium sibiricum strain DR11 and Exiguobacterium undae strain DR14 which showed promising biodegradation potential against polystyrene. In this study, we report the degradation of non-irradiated solid polystyrene material after incubation with these isolates. Growth studies suggested that the Exiguobacterium strains utilize polystyrene as a carbon source. Moreover, our data suggest that polymer degradation was initiated by biofilm formation over the PS surface leading to alteration in the physical properties of the material. Surface property analysis by AFM revealed significantly enhanced roughness resulting in reduced surface hydrophobicity of polystyrene. Fourier-transfer infrared (FT-IR) spectroscopic analysis showed breakdown of polystyrene backbone by oxidation. The extent of deterioration was further determined by percent weight reduction of polystyrene after incubation with bacteria. Our data support the fact that strains of extremophile bacterium Exiguobacterium are capable of degrading polystyrene and can be further used to mitigate the environmental pollution caused by plastics. © The Royal Society of Chemistry.

RSC Advances

Biofilm formation by Exiguobacterium sp. DR11 and DR14 alter polystyrene surface properties and initiate biodegradation

Quantitative Structure Activity Relationship (QSAR) is one of the widely used ligand based drug design strategies. Although a number of QSAR studies have been reported, debates over the limitations and accuracy of QSAR models are at large. In this review the applicability of various classes of molecular descriptors in QSAR has been explained. Protocol for QSAR model development and validation is presented. Here we discuss a case study on 7-Phenyl-imidazoquinolin-4(5H)-one derivatives as potent mPGES-1 inhibitors to identify crucial physicochemical properties responsible for mPGES-1 inhibition. The case study explains the methodology for QSAR analysis, validation of the developed models and role of diverse classes of molecular descriptors in defining the inhibitory activity of considered inhibitors. Various molecular descriptors derived from 2D/3D structure and quantum mechanics were considered in the study. Initially, QSAR models for the training set compounds were developed individually for each class of molecular descriptors. Further, a combined QSAR model was developed using the best descriptor from all the classes. The models obtained were further validated using an external test set. Combined QSAR model exhibited the best correlation (r = 0.80) between the predicted and experimental biological activities of test set compounds. The results of the QSAR analysis were further backed by docking studies. From the results of the case study it is evident that rather than a single class of molecular descriptors, a combination of molecular descriptors belonging to different classes significantly improves the QSAR predictions. The techniques and protocol discussed in the present work might be of significant importance while developing QSAR models of various drug targets. © 2018 Bentham Science Publishers.

World University root node

Current Topics in Medicinal Chemistry

Role of topological, electronic, geometrical, constitutional and quantum chemical based descriptors in QSAR: mPGES-1 as a case study

Ionospheric perturbations in possible association with a major earthquake (EQ) (M = 8.5) which occurred in India-Oceania region are investigated by monitoring subionospheric propagation of VLF signals transmitted from the NWC transmitter (F = 19.8 kHz), Australia to a receiving station at Varanasi (geographic lat. 25.3°N, long 82.99°E), India. The EQ occurred on 11 April 2012 at 08:38:35 h UT (magnitude ≈ 8.5, depth = 10 km, and lat. = 2.3°N, long. = 93.0°E). A significant increase of few days before the EQ has been observed by using the VLF nighttime amplitude fluctuation method (fixed frequency transmitter signal). The analysis of total electron contents (TEC) derived from the global positioning system (GPS) at three different stations namely, Hyderabad (latitude 17.38°N, longitude 78.48°E), Singapore (latitude 1.37°N, longitude 103.84°E) and Port Blair (latitude 11.62°N, longitude 92.72°E) due to this EQ has also been presented. Significant perturbation in TEC data (enhancements and depletion) is noted before and after the main shock of the EQ. The possible mechanisms behind these perturbations due to EQ have also been discussed. © 2017 COSPAR

Advances in Space Research

Seismogenic ionospheric anomalies associated with the strong Indonesian earthquake occurred on 11 April 2012 (M = 8.5)

Biophysical Journal

Structural Dynamics of Slow-Inactivation in a Voltage-Gated Sodium Channel

Sepantronium bromide (YM155) is a small molecule antitumor agent currently in phase II clinical trials. Although developed as survivin suppressor, YM155's primary mode of action has recently been found to be DNA damage. However, the mechanism of DNA damage by YM155 is still unknown. Knowing the mechanism of action of an anticancer drug is necessary to formulate a rational drug combination and select a cancer type for achieving maximum clinical efficacy. Using cell-based assays, we showed that YM155 causes extensive DNA cleavage and reactive oxygen species generation. DNA cleavage by YM155 was found to be inhibited by radical scavengers and desferal. The reducing agent DTT and the cellular reducing system xanthine/xanthine oxidase were found to reductively activate YM155 and cause DNA cleavage. Unlike quinones, DNA cleavage by YM155 occurs in the presence of catalase and under hypoxic conditions, indicating that hydrogen peroxide and oxygen are not necessary. Although YM155 is a quinone, it does not follow a typical quinone mechanism. Consistent with these observations, a mechanism has been proposed that suggests that YM155 can cause oxidative DNA cleavage upon 2-electron reductive activation. © 2018 American Chemical Society.

Chemical Research in Toxicology

Quinone-Based Antitumor Agent Sepantronium Bromide (YM155) Causes Oxygen-Independent Redox-Activated Oxidative DNA Damage

Achieving red phosphorescence from purely organic system is a challenging feat due to the predominant thermal nonradiative decay pathways of the excited electrons. Here, we design single-component charge-transfer (CT) complexes based on phenoxazine-quinoline conjugates (PQ1-PQ3), in which the phenoxazine ring is covalently attached to the quinolinyl fragment via a C-N bond. These conjugates in concentration-dependent absorption studies show a new low-energy CT absorption band along with the parent Ï€-Ï€∗ band with binding constants of up to 102 M-1 due to self-association via intermolecular CT (I2CT). Steady-state emission and phosphorescence decay transient measurements of all of the conjugates in solutions, thin films, and crystals reveal the signature of I2CT that leads to orange-red phosphorescence (ORP) at ambient conditions. Theoretical calculations show the existence of dimer with stronger I2CT characteristics and reduced energy gap between the lowest singlet (S1) and triplet (T1) states (Î"EST = 0.05-0.14 eV), which is in line with emission measurements. These conjugates are used for solid-state dichloromethane vapor sensors, and PQ3 can be transformed into oxygen sensor. These studies give an insight into the ORP properties and provide a rational strategy for the design of single-component self-CT complexes with ORP feature at ambient conditions. © 2018 American Chemical Society.

Chemistry

Journal of Physical Chemistry C

Roomerature Orange-Red Phosphorescence by Way of Intermolecular Charge Transfer in Single-Component Phenoxazine-Quinoline Conjugates and Chemical Sensing

We comment on the paper 'Cutset Bounds on the Capacity of MIMO Relay Channels' by Jeong et al. and point out that, unlike what appears from a remark and some other contents by these authors, the matrix distribution for the sum of two complex random Wishart matrices has already been derived by Kumar for the general case of arbitrary covariance matrices and not only for the special case when one of them is assumed proportional to the identity matrix. The latter assumption has been made only for deriving the corresponding eigenvalue distribution. Furthermore, we draw attention to the result that when all covariance matrices are chosen proportional to the identity matrix, then it is possible to obtain exact and closed form expressions for the sum of an arbitrary number of Wishart matrices and not only for two as considered by Jeong et al. © 2013 IEEE.

Physics

IEEE Access

Comments on "cutset Bounds on the Capacity of MIMO Relay Channels"

Incidence of whooping cough exhibits variable dynamics across time and space. The periodicity of this disease varies from annual to five years in different geographic regions in both developing and developed countries. Many hypotheses have been put forward to explain this variability such as nonlinearity and seasonality, stochasticity, variable recruitment of susceptible individuals via birth, immunization, and immune boosting. We propose an alternative hypothesis to describe the variability in periodicity – the intricate dynamical variability of whooping cough may arise from interactions between its dominant etiological agents of Bordetella pertussis and Bordetella parapertussis. We develop a two-species age-structured model, where two pathogens are allowed to interact by age-dependent convalescence of individuals with severe illness from infections. With moderate strength of interactions, the model exhibits multi-annual coexisting attractors that depend on the R0 of the two pathogens. We also examine how perturbation from case importation and noise in transmission may push the system from one dynamical regime to another. The coexistence of multi-annual cycles and the behavior of switching between attractors suggest that variable dynamics of whopping cough could be an emergent property of its multi-agent etiology. © 2018 The Authors

Mathematics

Epidemics

Species interactions may help explain the erratic periodicity of whooping cough dynamics

Vertically aligned nitrogen-doped nanocrystalline diamond nanorods are fabricated from nitrogen-doped nanocrystalline diamond films using reactive ion etching in oxygen plasma. These nanorods show enhanced thermionic electron emission (TEE) characteristics, viz., a high current density of 12.0 mA/cm2 and a work function value of 4.5 eV with an applied voltage of 3 V at 923 K. The enhanced TEE characteristics of these nanorods are ascribed to the induction of nanographitic phases at the grain boundaries and the field penetration effect through the local field enhancement from nanorods owing to a high aspect ratio and an excellent field enhancement factor. Copyright © Materials Research Society 2018.

MRS Communications

Fabrication, microstructure, and enhanced thermionic electron emission properties of vertically aligned nitrogen-doped nanocrystalline diamond nanorods