Department of Bioscience & Bioengineering

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IIT Jodhpur

In this study, novel organogel based lyotropic liquid crystals (LLC) were prepared and investigated as controlled release matrices. The LLC gels were prepared using mixtures of Span 80-Tween 80 (1:2 w/w), aqueous solution of polyvinyl alcohol (10% w/w) and sesame oil. The prepared gels were characterized by microscopy, mechanical testing and thermal studies. The biocompatibility of the gels was tested against human keratinocytes. Metronidazole loaded gels were used for in vitro drug release and antimicrobial tests. The formation of water-in-oil emulsion gels was confirmed by fluorescent microscopy. Polarized micrographs showed the formation of lamellar structures within the aqueous phase of the matrices. Mechanical studies confirmed the viscoelastic nature of the gels with solid like consistency. The melting points of the gels were in the range of 44-51°C. The gels did not elicit any cytotoxic effect on the human keratinocytes. The release of metronidazole from the gels was diffusion mediated. The drug loaded gels showed good antimicrobial efficacy against Escherichia coli. ©2015 Published by Elsevier Ltd.

World University root node

European Polymer Journal

Novel organogel based lyotropic liquid crystal physical gels for controlled delivery applications

Several studies have demonstrated the role of climatic factors in shaping skin phenotypes, particularly pigmentation. Keratinization is another well-designed feature of human skin, which is involved in modulating transepidermal water loss (TEWL). Although this physiological process is closely linked to climate, presently it is not clear whether genetic diversity is observed in keratinization and whether this process also responds to the environmental pressure. To address this, we adopted a multipronged approach, which involved analysis of 1) copy number variations in diverse Indian and HapMap populations from varied geographical regions; 2) genetic association with geoclimatic parameters in 61 populations of dbCLINE database in a set of 549 genes from four processes namely keratinization, pigmentation, epidermal differentiation, and housekeeping functions; 3) sequence divergence in 4,316 orthologous promoters and corresponding exonic regions of human and chimpanzee with macaque as outgroup, and 4) protein sequence divergence (Ka/Ks) across nine vertebrate classes, which differ in their extent of TEWL. Our analyses demonstrate that keratinization and epidermal differentiation genes are under accelerated evolution in the human lineage, relative to pigmentation and housekeeping genes. We show that this entire pathway may have been driven by environmental selection pressure through concordant functional polymorphisms across several genes involved in skin keratinization. Remarkably, this underappreciated function of skin may be a crucial determinant of adaptation to diverse environmental pressures across world populations. © Crown copyright 2014.

Fulltext

Molecular Biology and Evolution

Population diversity and adaptive evolution in Keratinization genes: Impact of environment in shaping skin phenotypes

Brains of adult monkeys with chronic lesions of dorsal columns of spinal cord at cervical levels undergo large-scale reorganization. Reorganization results in expansion of intact chin inputs, which reactivate neurons in the deafferented hand representation in the primary somatosensory cortex (area 3b), ventroposterior nucleus of the thalamus and cuneate nucleus of the brainstem. A likely contributing mechanism for this large-scale plasticity is sprouting of axons across the hand–face border. Here we determined whether such sprouting takes place in area 3b. We first determined the extent of intrinsic corticocortical connectivity between the hand and the face representations in normal area 3b. Small amounts of neuroanatomical tracers were injected in these representations close to the electrophysiologically determined hand–face border. Locations of the labeled neurons were mapped with respect to the detailed electrophysiological somatotopicmapsand histologically determined hand–face border revealed in sections of the flattened cortex stained for myelin. Results show that intracortical projections across the hand–face border are few. In monkeys with chronic unilateral lesions of the dorsal columns and expanded chin representation, connections across the hand–face border were not different compared with normal monkeys. Thalamocortical connections from the hand and face representations in the ventroposterior nucleus to area 3b also remained unaltered after injury. The results show that sprouting of intrinsic connections in area 3b or the thalamocortical inputs does not contribute to large-scale cortical plasticity. © 2015 the authors.

Journal of Neuroscience

Intracortical and thalamocortical connections of the hand and face representations in somatosensory area 3b of macaque monkeys and effects of chronic spinal cord injuries

A subset L subset of V of a graph G = (V, E) is called a liar's dominating set of G if (i) vertical bar N-G{[}u] boolean AND L vertical bar >= 2 for every vertex u is an element of V, and (ii) vertical bar N-G {[}u] boolean OR N-G{[}v]) boolean AND L vertical bar >= 3 for every pair of distinct vertices u, v is an element of V. The MIN LIAR Dom SET problem is to find a liar's dominating set of minimum cardinality of a given graph G and the DECIDE LIAR Dom SET problem is the decision version of the MIN LIAR Dom SET problem. The DECIDE LIAR DOM SET problem is known to be NP-complete for general graphs. In this paper, we first present approximation algorithms and hardness of approximation results of the MIN LIAR Dom SET problem in general graphs, bounded degree graphs, and p-claw free graphs. We then show that the DECIDE LIAR Dom SET problem is NP-complete for doubly chordal graphs and propose a linear time algorithm for computing a minimum liar's dominating set in block graphs. (C) 2015 Elsevier B.V. All rights reserved.

THEORETICAL COMPUTER SCIENCE

Hardness results, approximation and exact algorithms for liar's domination problem in graphs

The microRNAs are small, endogenous non-coding RNAs found in plants, animals, and some viruses, which function in RNA silencing and post-transcriptional regulation of gene expression. It is suggested by various genome-wide studies that a substantial fraction of miRNA genes is likely to form clusters. The coherent expression of the miRNA clusters can then be used to classify samples according to the clinical outcome. In this regard, a new clustering algorithm, termed as rough hypercuboid based supervised attribute clustering (RH-SAC), is proposed to find such groups of miRNAs. The proposed algorithm is based on the theory of rough set, which directly incorporates the information of sample categories into the miRNA clustering process, generating a supervised clustering algorithm for miRNAs. The effectiveness of the new approach is demonstrated on several publicly available miRNA expression data sets using support vector machine. The so-called B.632+ bootstrap error estimate is used to minimize the variability and biasedness of the derived results. The association of the miRNA clusters to various biological pathways is also shown by doing pathway enrichment analysis. © The Royal Society of Chemistry.

Molecular BioSystems

Rough hypercuboid based supervised clustering of miRNAs

Gene–environment (G × E) interactions have been invoked to account, at least in part, for the gap between the known heritability of common human diseases and the phenotypic variation hitherto explained by genetic variants. Noteworthy in this context, a case-only (CO) design has been proposed in the past as a means to detect G × E interactions possibly more efficiently than by using classical case–control and cohort designs. So far, however, most CO studies have followed a candidate (or single) gene approach, and the genome-wide utility of the CO design is still more or less unknown. In particular, the way in which linkage disequilibrium (LD) impacts upon the chance to detect G × E interaction through the analysis of proxy markers has not been studied in much detail before. Therefore, we systematically assessed the power to indirectly detect a given G × E interaction through exploiting LD in a CO design. Our simulations revealed a strong relationship between LD and detection power that was subsequently validated in a real colorectal cancer data set. © 2014, Springer-Verlag Berlin Heidelberg.

Human Genetics

The role of linkage disequilibrium in case-only studies of gene–environment interactions

Nature genetics

Genomic landscapes of breast fibroepithelial tumors

Single molecule Förster resonance energy transfer (FRET) has been applied, for the first time, to monitor the growth (polymerization) and the shrinkage (depolymerization) of the dynamic microtubules, employing EGFP (attached to Mal3) as a donor and alexa-568 bound to tubulin as an acceptor. This journal © the Owner Societies 2015

Physical Chemistry Chemical Physics

Direct observation of the growth and shrinkage of microtubules by single molecule Förster resonance energy transfer

A molecular dynamics study on the collisional dynamics of soft and sticky single face-centered cubic crystal nanoparticles is presented. The softness and stickiness of the nanoparticles are controlled by varying parameters in the Lennard-Jones potential that is used to describe the interatomic interactions. Softening of nanoparticles due to extensive plastic deformations is observed as was previously found in hard nanoparticles. Further, two primary plastic deformation modes, slip and twinning, of the nanoparticles are found to play important roles in the temperature dependence of the coefficient of restitution. Additionally, we observe the effects of surface roughness, facets, and edges in the collisional behaviors of the sticky nanoparticles in low-velocity collisions. Nevertheless, the Johnson-Kendall-Roberts theory for macroscopic adhesive bodies still remains valid in nearly spherical nanoparticles. © 2015 American Physical Society.

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Rich collision dynamics of soft and sticky crystalline nanoparticles: Numerical experiments

Designing various inorganic nanomaterials that are cost effective, water soluble, optically photostable, highly fluorescent and biocompatible for bioimaging applications is a challenging task. Similar to semiconducting quantum dots (QDs), silicon QDs are another alternative and are highly fluorescent, but non-water soluble. Several surface modification strategies were adopted to make them water soluble. However, the photoluminescence of Si QDs was seriously quenched in the aqueous environment. In this report, highly luminescent, water-dispersible, blue- and green-emitting Si QDs were prepared with good photostability. In vitro studies in monocytes reveal that Si QDs exhibit good biocompatibility and excellent distribution throughout the cytoplasm region, along with the significant fraction translocated into the nucleus. The in vivo zebrafish studies also reveal that Si QDs can be evenly distributed in the yolk-sac region. Overall, our results demonstrate the applicability of water-soluble and highly fluorescent Si QDs as excellent in vitro and in vivo bioimaging probes. © 2015 IOP Publishing Ltd.