Department of Bioscience & Bioengineering

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Flexibility in curriculum, in all its academic programs, encompassing elements of teaching, research, creativity, innovation and entrepreneurship is the most unique feature of IIT Jodhpur. The Department of Science and Technology (DST), under the National Mission on Cyber Physical Systems, has identified IIT Jodhpur as a Technology &amp; Innovation Hub in the area of Augmented Reality and Virtual Reality. The institute has also been nominated as the coordinator for the Jodhpur City and Knowledge Cluster by the Office of Principal Scientific Adviser, Government of India.

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IIT Jodhpur

Among the large number of gene selection algorithms available in literature, the rough set based maximum relevance-maximum significance (RSMRMS) algorithm has been shown to be successful for selecting a set of relevant and significant genes from microarray data. However, the analysis of functional diversity of a gene set is essential to understand the role of genes in a particular disease as well as to evaluate the effectiveness of a gene selection algorithm. In this regard, a gene ontology based quantitative index, termed as degree of functional diversity (DoFD), is proposed to quantify the functional diversity of a set of genes selected by any gene selection algorithm. Moreover, a new gene selection algorithm is presented, integrating judiciously the merits of both DoFD and RSMRMS, to select relevant and significant genes those are also functionally diverse. The performance of the proposed gene selection algorithm, along with a comparison with other gene selection methods, is studied using the proposed DoFD and predictive accuracy of K-nearest neighbor rule and support vector machine on six cancer and one arthritis microarray data sets. An important finding is that the proposed gene ontology based quantitative index can accurately evaluate functional diversity of a set of genes. Also, the proposed gene selection algorithm is shown to be effective for selecting relevant, significant, and functionally diverse genes from microarray data. © 2012 Springer-Verlag.

World University root node

International Journal of Machine Learning and Cybernetics

Gene ontology based quantitative index to select functionally diverse genes

Indolicidin (IR13), a 13-residue antimicrobial peptide from the cathelicidin family, is known to exhibit a broad spectrum of antimicrobial activity against various microorganisms. This peptide inhibits bacterial DNA synthesis resulting in cell filamentation. However, the precise mechanism remains unclear and requires further investigation. The central PWWP motif of IR13 provides a unique structural element that can wrap around, and thus stabilize, duplex B-type DNA structures. Replacements of the central Trp-Trp pair with Ala-Ala, His-His, or Phe-Phe residues in the PxxP motif significantly affects the ability of the peptide to stabilize duplex DNA. Results of microscopy studies in conjunction with spectroscopic data confirm that the DNA duplex is stabilized by IR13, thereby inhibiting DNA replication and transcription. In this study we provide high-resolution structural information on the interaction between indolicidin and DNA, which will be beneficial for the design of novel therapeutic antibiotics based on peptide scaffolds. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fulltext

ChemMedChem

Indolicidin targets duplex DNA: Structural and mechanistic insight through a combination of spectroscopy and microscopy

In this Letter we report on controllable transition of aggregated γ-Cyclodextrins (γ-CDs) nanostructures by tuning the concentration of a long chain ionic liquid, 1-dodecyl-3-methyl imidazolium chloride (C 12mimCl) added to the aqueous solution of γ-CDs. The gradual increase in concentration of C12mimCl first results in the breaking of γ-CDs aggregates by the formation of inclusion complexes with C 12mimCl and then self-organizes into a new supramolecular aggregate. This spontaneous transition from one nanostructure to another has been established by spectroscopic and microscopic studies. It is worth to mention that addition of 1-octyl-3-methyl imidazolium chloride (C8mimCl) does not lead to any such transition. © 2014 Published by Elsevier B.V.

Chemical Physics Letters

Effect of room temperature surface active ionic liquids on aggregated nanostructures of γ-Cyclodextrins: A picosecond fluorescence spectroscopic study

An amyloid inhibitor octapeptide simultaneously forms amyloid type fibrous aggregates on its own and interacts with the microtubule lattice three times stronger than a Xenopus Microtubule Associated Protein (XMAP215). © 2014 Royal Society of Chemistry.

Chemical Communications

An amyloid inhibitor octapeptide forms amyloid type fibrous aggregates and affects microtubule motility

Some 30 years have passed since we learned that any velocity perturbation develops into a propagating solitary wave in a granular chain, and over a decade has passed since we learned that these solitary waves break and reform upon collision, leaving behind small secondary solitary waves. The production of the latter eventually precipitates the quasiequilibrium state characterized by large energy fluctuations in dissipation-free granular systems. Here we present dynamical simulations on the effects of soft boundaries on solitary wave interaction in granular chains held between fixed walls. We show that at short time scales, a gradient in the distribution of kinetic energy between the boundaries is indeed sustained. At long times, however, such a gradient gets obliterated and there is no measurable difference between the average kinetic energies of the particles adjacent to walls. Our findings suggest that (i) the quasiequilibrium state can effectively erase small gradients of the average kinetic energies of the particles adjacent to walls in a system, (ii) Boltzmann distribution of grain speeds is realized in the system of interest, and (iii) time and space averages yield the same result, thus suggesting that the system is ergodic. © 2014 American Physical Society.

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

Granular chain between asymmetric boundaries and the quasiequilibrium state

We study the penetration dynamics of a projectile incident normally on a substrate comprising of smaller granular particles in three-dimensions using the discrete element method. Scaling of the penetration depth is consistent with experimental observations for small velocity impacts. Our studies are consistent with the observation that the normal or drag force experienced by the penetrating grain obeys the generalized Poncelet law, which has been extensively invoked in understanding the drag force in the recent experimental data. We find that the normal force experienced by the projectile consists of position and kinetic-energy-dependent pieces. Three different penetration regimes are identified in our studies for low-impact velocities. The first two regimes are observed immediately after the impact and in the early penetration stage, respectively, during which the drag force is seen to depend on the kinetic energy. The depth dependence of the drag force becomes significant in the third regime when the projectile is moving slowly and is partially immersed in the substrate. These regimes relate to the different configurations of the bed: the initial loose surface packed state, fluidized bed below the region of impact, and the state after the crater formation commences. © 2014 American Physical Society.

Drag-force regimes in granular impact

The task scheduling problem for multi-core processors is an important algorithm design issue. Dynamic voltage scaling (DVS) is used to reduce the energy consumption of cores. We ponder the problem of task scheduling on a multi-core processor with software controlled DVS where the objective is to reduce the energy consumption. We consider a system with a single multi-core processor with software controlled DVS having a finite set of core speeds and discuss a task scheduling problem associated with it. The problem that we address is to find a minimum energy task schedule for a given set of independent tasks that have to be completed within a given common deadline. We propose a Monte Carlo algorithm of complexity O(t(mp + q + log(t)) + p(t + q)(D-pq + n)) for solving the task scheduling problem and compare it with the optimal algorithm. Here t is the number of tasks, p is the number of cores, q is the number of core speeds, m is an integer parameter that is the number of iterations we should try to get a feasible solution before declaring that no solution is possible, n is an integer parameter that is the number of iterations we should try to reduce the energy consumption when we get a feasible solution, and D is the common deadline of the tasks. (C) 2013 Elsevier Inc. All rights reserved.

APPLIED MATHEMATICAL MODELLING

A Monte Carlo algorithm for real time task scheduling on multi-core processors with software controlled dynamic voltage scaling

This research is mainly focusing on one-step biosynthesis of graphene from graphene oxide and its stabilization using naturally occurring milk protein, casein. The synthesis of casein reduced graphene oxide (CRGO) was completed within 7 h under reflux at 90 C with the formation of few layered fine graphene nanosheets. UV-Vis, XRD, XPS analysis data revealed the reduction process of the graphene oxide. Results of FT-IR, HPLC and TEM analysis have shown that the ensuing material consists of graphene decorated with casein molecules. Aspartic acid and glutamic acid residue present in casein molecules are responsible for the reduction of graphene oxide. © 2014 Elsevier B.V. All rights reserved.

Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy

Casein mediated green synthesis and decoration of reduced graphene oxide

Previously, gold nanoshells were shown to be able to effectively convert photon energy to heat, leading to hyperthermia and suppression of tumor growths in mice. Herein, we show that in addition to the nanomaterial-mediated photothermal effects (NmPTT), gold nanoshells (including, nanocages, nanorod-in-shell and nanoparticle-in-shell) not only are able to absorb NIR light, but can also emit fluorescence, sensitize formation of singlet oxygen and exert nanomaterial-mediated photodynamic therapeutic (NmPDT) complete destruction of solid tumors in mice. The modes of NmPDT and NmPTT can be controlled and switched from one to the other by changing the excitation wavelength. In the invitro experiments, gold nanocages and nanorod-in-shell show larger percentage of cellular deaths originating from NmPDT along with the minor fraction of NmPTT effects. In contrast, nanoparticle-in-shell exhibits larger fraction of NmPTT-induced cellular deaths together with minor fraction of NmPDT-induced apoptosis. Fluorescence emission spectra and DPBF quenching studies confirm the generation of singlet O2 upon NIR photoirradiation. Both NmPDT and NmPTT effects were confirmed by measurements of reactive oxygen species (ROS) and subsequent sodium azide quenching, heat shock protein expression (HSP 70), singlet oxygen sensor green (SOSG) sensing, changes in mitochondria membrane potential and apoptosis in the cellular experiments. In vivo experiments further demonstrate that upon irradiation at 980nm under ultra-low doses (~150mW/cm2), gold nanocages mostly exert NmPDT effect to effectively suppress the B16F0 melanoma tumor growth. The combination of NmPDT and NmPTT effects on destruction of solid tumors is far better than pure NmPTT effect by 808nm irradiation and also doxorubicin. Overall, our study demonstrates that gold nanoshells can serve as excellent multi-functional theranostic agents (fluorescence imaging+NmPDT+NmPTT) upon single photon NIR light excitation under ultra-low laser doses. © 2014 Elsevier Ltd.

Biomaterials

Gold nanoshells-mediated bimodal photodynamic and photothermal cancer treatment using ultra-low doses of near infra-red light

Cowpea (Vigna unguiculata L. Walp) is an important grain legume cultivated in drought-prone parts of the world, having higher tolerance to heat and drought than many other crops. The transcription factor, Dehydration-Responsive Element-Binding protein 2A (DREB2A), controls expression of many genes involved in osmotic and heat stress responses of plants. In Arabidopsis, DREB2A-interacting proteins (DRIPs), which function as E3 ubiquitin ligases (EC 6.3.2.19), regulate the stability of DREB2A by targeting it for proteasome-mediated degradation. In this study, we cloned the cowpea ortholog of DRIP (VuDRIP) using PCR based methods. The 1614bp long VuDRIP mRNA encoded a protein of 433 amino acids having a C3HC4-type Really Interesting New Gene (RING) domain in the N-terminus and a C-terminal conserved region, similar to Arabidopsis DRIP1 and DRIP2. We found VuDRIP up-regulation in response to various abiotic stresses and phytohormones. Using yeast (Saccharomyces cerevisae) two-hybrid analysis, VuDRIP was identified as a VuDREB2A-interacting protein. The results indicate negative regulation of VuDREB2A by ubiquitin ligases in cowpea similar to Arabidopsis along with their other unknown roles in stress and hormone signaling pathways. © 2014 Elsevier Masson SAS.