Department of Bioscience & Bioengineering

&ldquo;IIT Jodhpur is committed to impart quality education to facilitate the creation of qualified, competent and responsible human resources to meet the emerging technological challenges of the world. It is working towards creating an equitable learning platform that is positive, accessible and effective in the face of the modern societal and scientific advancements.

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.

The sprawling 852-acre IIT Jodhpur campus is a majestic tribute to the deep-rooted diverse cultural heritage of the region. The campus is an architectural masterpiece, which is slated to become an international exemplar of sustainability with net-zero energy, and advanced water and waste management strategies.&rdquo;

IIT Jodhpur

Multiple sclerosis (MS) is a chronic disabling disease of the central nervous system (CNS) that is characterized by lesions with inflammatory cells, axons with the insulating myelin sheath damaged, and axonal loss. The causes of MS are not known and there is as yet no cure. The purpose of this research was to evaluate a physically motivated network model for lesion formation in the brain. The parsimonious network model contained two elements: (i) a spatially spreading pathological process causing cell damage and death leading to neuro-degeneration and, (ii) generation of alarm signals by the damaged cells that lead to activation of programmed death of cells surrounding the lesions in an attempt to contain the spatial spread of the pathologic process. Simulation results with a range of network geometries indicated that the model was capable of describing lesion progression and arrest. The modeling results also demonstrated dynamical complexity with sensitivity to initial conditions. © 2008 World Scientific Publishing Company.

World University root node

International Journal of Modern Physics E

A computational model for lesion dynamics in multiple sclerosis of the brain

E6-AP is a founding member of HECT (homologous to E6-AP C terminus) domain subfamily of E3 ubiquitin ligases. It degrades tumor suppressor p53 in association with the E6 oncoprotein of the human papilloma virus. However, there are conflicting reports on its role in the degradation of p53 in the absence of E6 oncoprotein. Here, we studied the role of E6-AP in regulation of p53 in mouse neuro 2a cells. Overexpression of E6-AP in neuro 2a cells increased the ubiquitylation and degradation of p53, which could be prevented upon deletion of HECT domain. E6-AP also directly ubiquitylated p53 in an in vitro ubiquitylation assay. Partial knockdown of E6-AP increased the levels of p53 and p53-dependent transcription. Partial knockdown also increased neuronal cell death, which may be mediated partly via p53. Our result suggests that E6-AP not only enhances the degradation of p53 but also regulates the neuronal cell growth. © 2008 Birkhaueser.

Cellular and Molecular Life Sciences

Regulation of turnover of tumor suppressor p53 and cell growth by E6-AP, a ubiquitin protein ligase mutated in Angelman mental retardation syndrome

Laccase from basidiomycete fungus Cyathus bulleri was evaluated for its ability to decolorize a number of reactive and acidic dyes in the presence of natural and synthetic mediators. The extent of decolorization was monitored at different mediator/dye concentrations and incubation time. Among the synthetic mediators, 2,2-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) was effective at low mediator/dye ratios and resulted in 80-95% decolorization at rates that varied from 226∈±∈4 nmol min-1 mg -1 for Reactive Orange 1 to 1,333∈±∈15 nmol min -1 mg-1 for Reactive Red 198. Other synthetic mediators like 1-hydroxybenzotriazole and violuric acid showed both concentration- and time-dependent increases in percent decolorization. Natural mediators like vanillin, on the other hand, were found to be less effective on all the dyes except Reactive Orange 1. Computed rates of decolorization were about twofold lower than that with ABTS. The laccase-ABTS system also led to nearly 80% decolorization for the simulated dye mixture. No clear correlation between laccase activity on the mediator and its ability to decolorize dyes was found, but pH had a significant effect: Optimum pH for decolorization coincided with the optimum pH for mediator oxidation. The treated samples were also evaluated for toxicity in model microbial systems. The laccase-mediator system appears promising for treatment of textile wastewaters. © 2008 Humana Press.

Applied Biochemistry and Biotechnology

Mediator-assisted decolorization and detoxification of textile dyes/dye mixture by cyathus bulleri laccase

Cyathus bulleri, a ligninolytic fungus, produces a single laccase the internal peptides (3) of which bear similarity to laccases of several white rot fungi. Comparison of the total amino acid composition of this laccase with several fungal laccases indicated dissimilarity in the proportion of some basic and hydrophobic amino acids. Analysis of the circular dichroism spectrum of the protein indicated 37% α-helical, 26% β-sheet and 38% random coil content which differed significantly from that in the solved structures of other laccases, which contain higher β-sheet structures. The critical role of the carboxylic group containing amino acids was demonstrated by determining the kinetic parameters at different pH and this was confirmed by the observation that a critical Asp is strongly conserved in both Ascomycete and Basidiomycete laccases. The enzyme was denatured in the presence of a number of denaturing agents and refolded back to functional state with copper. In the folding experiments under alkaline conditions, zinc could replace copper in restoring 100% of laccase activity indicating the non-essential role of copper in this laccase. The laccase was expressed in Escherichia coli by a modification of the ligation-anchored PCR approach making it the first fungal laccase to be expressed in a bacterial host. The laccase sequence was confirmed by way of analysis of a 435 bp sequence of the insert. © 2007 Elsevier B.V. All rights reserved.

Biochimica et Biophysica Acta - Proteins and Proteomics

Laccase of Cyathus bulleri: structural, catalytic characterization and expression in Escherichia coli

Variations in the production and activity of cytokines have been reported by several investigators which influence the susceptibility and/ or resistance to various infectious agents and cancer. Differences in the cytokine production between individuals are often caused by single nucleotide polymorphism (SNP) in the promoter or coding regions of cytokine genes. Although the SNP cytokine gene variations are basically mutations, they are designated as polymorphisms, because these changes do not modify the alleles to rare or abnormal variants. The two important cytokine genes IL-4 and IL-6 of 343 unrelated healthy individuals from North India were compared with the published polymorphism of other populations. It was seen that our population differs from South Indian population as well as from other Caucasian populations except, Taiwanese population at IL-4 locus and Spanish and Polish population at the IL-6 gene locus. This study may be helpful for predicting clinical outcome of various infectious and immunoregulated disorders as well as explore for risk alleles for various cancers.

Asian Pac J Cancer Prev

Do IL-4 intron 3 VNTR and IL-6 (-174) G/C variants reflect ethnic variation? A comparative study between the global and North Indian populations

The triskelion peptide conjugate 1, having a Trp-Trp dipeptide unit on the three arms, was synthesized and studied for the interaction of peptide-based soft structures with metal ions, by fluorescence and microscopic analyses. We observed that fluorescence was significantly quenched upon addition of Cu(II) metal ions, whereas the addition of other metal ions also caused moderate to insignificant changes in the fluorescence emission, suggesting specificity of this triskelion peptide 1 for Cu(II) ions. The addition of Cu(II) and other metal ions also altered the morphology of preformed vesicles obtained from triskelion peptide 1 in a concentration-dependent fashion, as observed from microscopic analysis. Such metal-responsive soft structures may find potential use as novel materials for delivery and sensing applications. © 2007 Elsevier Ltd. All rights reserved.

Tetrahedron

Morphological consequences of metal ion-peptide vesicle interaction

Solitary waves are lumps of energy. We consider the study of dynamical solitary waves, meaning cases where the energy lumps are moving, as opposed to topological solitary waves where the lumps may be static. Solitary waves have been studied in some form or the other for nearly 450 years. Subsequently, there have been many authoritative works on solitary waves. Nevertheless, some of the most recent studies reveal that these peculiar objects are far more complex than what we might have given them credit for. In this review, we introduce the physics of solitary waves in alignments of elastic beads, such as glass beads or stainless steel beads. We show that any impulse propagates as a new kind of highly interactive solitary wave through such an alignment and that the existence of these waves seems to present a need to re-examine the very definition of the concept of equilibrium. We further discuss the possibility of exploiting nonlinear properties of granular alignments to develop exciting technological applications. © 2008 Elsevier B.V. All rights reserved.

Physics Reports

Solitary waves in the granular chain

We propose that a battle between two conflicting entities can be modeled as a kinematic problem on a lattice. We examine the parameters relevant to such simulations, and describe global patterns emerging from a lattice model of a conflict with a few simple rules. We conclude that models of this type display interesting and relevant properties and warrant more in-depth analysis. The focus in this work is on the role of knowledge of the "neighborhood" in winning a battle. © 2008 World Scientific Publishing Company.

Winning a battle: The importance of knowing the "neighborhood"

The accumulation of intracellular protein deposits as inclusion bodies is the common pathological hallmark of most age-related neurodegenerative disorders including polyglutamine diseases. Appearance of aggregates of the misfolded mutant disease proteins suggest that cells are unable to efficiently degrade them, and failure of clearance leads to the severe disturbances of the cellular quality control system. Recently, the quality control ubiquitin ligase CHIP has been shown to suppress the polyglutamine protein aggregation and toxicity. Here we have identified another ubiquitin ligase, called E6-AP, which is able to promote the proteasomal degradation of misfolded polyglutamine proteins and suppress the polyglutamine protein aggregation and polyglutamine protein-induced cell death. E6-AP interacts with the soluble misfolded polyglutamine protein and associates with their aggregates in both cellular and transgenic mouse models. Partial knockdown of E6-AP enhances the rate of aggregate formation and cell death mediated by the polyglutamine protein. Finally, we have demonstrated the up-regulation of E6-AP in the expanded polyglutamine protein-expressing cells as well as cells exposed to proteasomal stress. These findings suggest that E6-AP is a critical mediator of the neuronal response to misfolded polyglutamine proteins and represents a potential therapeutic target in the polyglutamine diseases. © 2008 by The American Society for Biochemistry and Molecular Biology, Inc.

Fulltext

Journal of Biological Chemistry

E6-AP promotes misfolded polyglutamine proteins for proteasomal degradation and suppresses polyglutamine protein aggregation and toxicity

India currently has the world’s second-largest population along with a fast-growing economy and significant economic disparity. It also continues to experience a high rate of infectious disease and increasingly higher rates of chronic diseases. However, India cannot afford to import expensive technologies and therapeutics nor can it, as an emerging economy, emulate the health-delivery systems of the developed world. Instead, to address these challenges it is looking to biotechnology-based innovation in the field of genomics. The Indian Genome variation (IGv) consortium, a government-funded collaborative network among seven local institutions, is a reflection of these efforts. The IGv has recently developed the first large-scale database of genomic diversity in the Indian population that will facilitate research on disease predisposition, adverse drug reactions and population migration. © 2008 Macmillan Publishers Limited.