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.

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

A compressive applied force at the zero frequency limit applied on confined granular alignments is shown to result in tunable and higher frequency nonlinear granular breathing. We use extensive dynamical simulations and simple arguments to probe the origins of these breathing processes. In the presence of dissipation, the breathing has a lifetime that is inversely proportional to the dissipation constant. The possible use of the concept of nonlinear granular breathing in recovering the energy released at the beaches by surface gravity waves using a system made largely of nonmoving parts is mentioned as a possible application. © 2009 American Institute of Physics.

World University root node

Applied Physics Letters

Nonlinear breathing processes in granular alignments

Objective: To investigate the association of tumour necrosis factor-α gene (TNF-α) polymorphisms T-1031C, C-863A, and C-857T with bladder cancer risk and recurrence after bacille Calmette-Guérin (BCG) immunotherapy, as TNF-α regulates inflammatory process influencing bladder cancer susceptibility and outcome of BCG immunotherapy. PATIENTS AND METHODS In all, 220 patients with bladder cancer and 206 controls were recruited. Genotyping was done using allele specific-polymerase chain reaction. RESULTS A T-1031C, CC genotype and haplotype -1031C/-863C/-857T showed enhanced susceptibility to bladder cancer, with an odds ratio (OR) of 2.23 and 95% confidence interval (CI) of 1.17-4.26; and an OR of 6.05 and 95%CI of 2.46-14.90, respectively. A T-1031C, CC genotype had a reduced risk of recurrence after BCG treatment (hazard ratio 0.38, 95%CI 0.14-0.98). CONCLUSION The present data suggests that T-1031C (CC) genotype and C/C/T haplotype may confer risk for bladder cancer, moreover T-1031C (CC) decreased the risk of recurrence after BCG immunotherapy. © 2009 BJU International.

BJU International

Association of tumour necrosis factor-α gene (T-1031C, C-863A, and C-857T) polymorphisms with bladder cancer susceptibility and outcome after bacille Calmette-Guérin immunotherapy

The programmed cell death gene 4 (Pdcd4) gene has been implicated as a new tumor suppressor gene in the development of several types of human cancer. Pdcd4 interacts with the translation initiation factor, eIF4A, and is thought to act as a translation inhibitor. Here, we have used the chicken B-cell line DT40 to disrupt the Pdcd4 gene by homologous recombination. Our study shows that cells lacking a functional Pdcd4 gene are viable and have no obvious defects when cultivated under normal growth conditions. However, Pdcd4 knockout cells show an increased sensitivity to agents that cause DNA damage, such as UV light, etoposide or ethyl-methanesulfonate. In summary, our findings show that Pdcd4 has an important function in the cellular response to DNA damage. Low Pdcd4 expression, which is frequently observed in tumor cells, might therefore contribute to tumorigenesis by disturbing the cellular DNA-damage response. © 2009 Macmillan Publishers Limited All rights reserved.

Fulltext

Oncogene

Disruption of the Pdcd4 tumor suppressor gene in chicken DT40 cells reveals its role in the DNA-damage response

Stratification in heterogeneous populations poses an enormous challenge in linkage disequilibrium (LD) based identification of causal loci using surrogate markers. In this study, we demonstrate the enormous potential of endogamous Indian populations for mapping mutations in candidate genes using minimal SNPs, mainly due to larger regions of LD. We show this by a case study of the PPP2R2B gene (∼400 kb) that harbours a CAG repeat, expansion of which has been implicated in spinocerebellar ataxia type 12 (SCA12). Using LD information derived from Indian Genome Variation database (IGVdb) on populations which share similar ethnic and linguistic backgrounds as the SCA12 study population, we could map the causal loci using a minimal set of three SNPs, without the generation of additional basal data from the ethnically matched population. We could also demonstrate transferability of tagSNPs from a related HapMap population for mapping the mutation. © Indian Academy of Sciences.

Journal of Genetics

Utilizing linkage disequilibrium information from Indian Genome variation database for mapping mutations: SCA12 case study

Transection of dorsal columns of the spinal cord in adult monkeys results in large-scale expansion of the face inputs into the deafferented hand region in the primary somatosensory cortex (area 3b) and the ventroposterior nucleus of thalamus. Here, we determined whether the upstream cortical areas, secondary somatosensory (S2) and parietal ventral (PV) areas, also undergo reorganization after lesions of the dorsal columns. Areas S2, PV, and 3b were mapped after long-term unilateral lesions of the dorsal columns at cervical levels in adult macaque monkeys. In areas S2 and PV, we found neurons responding to touch on the face in regions in which responses to touch on the hand and other body parts are normally seen. In the reorganized parts of S2 and PV, inputs from the chin as well as other parts of the face were observed, whereas in area 3b only the chin inputs expand into the deafferented regions. The results show that deafferentations lead to a more widespread brain reorganization than previously known. The data also show that reorganization in areas S2 and PV shares a common substrate with area 3b, but there are specific features that emerge in S2 and PV. Copyright © 2009 Society for Neuroscience.

Journal of Neuroscience

Large-scale expansion of the face representation in somatosensory areas of the lateral sulcus after spinal cord injuries in monkeys

Laccase/mediator systems are important bioremediation agents as the rates of reactions can be enhanced in the presence of the mediators. The decolorization mechanism of two triarylmethane dyes, namely, Basic Green 4 and Acid Violet 17 is reported using Cyathus bulleri laccase. Basic Green 4 was decolorized through N-demethylation by laccase alone, while in mediator assisted reactions, dye breakdown was initiated from oxidation of carbinol form of the dye. Benzaldehyde and N,N-dimethyl aniline were the major end products. With Acid Violet 17, laccase carried out N-deethylation and in mediator assisted reactions, oxidation of the carbinol form of the dye occurred resulting in formation of formyl benzene sulfonic acid, carboxy benzene sulfonic acid and benzene sulfonic acid. Toxicity analysis revealed that Basic Green 4 was toxic and treatment with laccase/mediators resulted in 80-100% detoxification. The treatment of the textile dye solution using laccase and 2,2′-azino-di-(-ethylbenzothiazoline-6-sulfonic acid) (ABTS) was demonstrated in an enzyme membrane reactor. At a hydraulic retention time of 6 h, the process was operated for a period of 15 days with nearly 95% decolorization, 10% reduction in flux and 70% recovery of active ABTS. © 2009 Elsevier B.V. All rights reserved.

Journal of Biotechnology

Laccase/mediator assisted degradation of triarylmethane dyes in a continuous membrane reactor

We consider a simple problem that of a horizontal alignment of identical grains, and insure that the grains are in gentle mutual contact and held between two rigid fixed end walls. Grain-grain interactions are intrinsically nonlinear according to the Hertz law and hence no sound waves can propagate through this alignment. The discussions here concern the solitary wave nature of propagation of any perturbation and its subsequent dispersion in the same vein as we probe the dispersion of a perturbation in linear response theory in statistical physics. We show that a perturbed granular alignment exhibits both decaying and growing solitary waves and can indeed reach an equilibrium-like state. We suggest that this equilibrium-like state may not be the equilibrium state commonly reached in thermodynamics and statistical physics. Moving beyond the effort to develop a deeper understanding of the energy transport problem in granular systems, we discuss a new application of a granular alignment system, that of driven granular alignments that show rich nonlinear dynamics and can turn out to be technologically meaningful entities. © 2009 American Institute of Physics.

AIP Conference Proceedings

Nonlinear, statistical and applied physics of solitary wavelike objects in granular systems

The association of interleukin-1β (IL-1B) -511C>T and IL-1 receptor antagonist (IL-1RN) VNTR, transforming growth factor-β (TGF-B1) 28C>T and interferon-γ (IFN-G)874T>A polymorphisms with bladder cancer (CaB) susceptibility and risk of recurrence in Bacillus CalmetteGurin (BCG)-treated patients was analyzed in 287 controls and 213 CaB patients (73 BCG treated). Increased risk was observed with the IL-1RN*2 allele (odds ratio (OR) 5.01) and the IFN-G 874 A allele (OR 1.78). TGF-B TT and IFN-G 874 A carriers were associated with reduced (hazard ratio (HR) 0.37) and enhanced (HR 2.24) risk of recurrence after BCG immunotherapy, respectively. The study suggests that cytokine gene variants may modulate CaB susceptibility and risk of recurrence after BCG immunotherapy. © 2009 Informa UK Ltd.

Biomarkers

Cytokine gene polymorphisms are associated with risk of urinary bladder cancer and recurrence after BCG immunotherapy

Analyses of frequency profiles of markers on disease or drug-response related genes in diverse populations are important for the dissection of common diseases. We report the results of analyses of data on 405 SNPs from 75 such genes and a 5.2 Mb chromosome, 22 genomic region in 1871 individuals from diverse 55 endogamous Indian populations. These include 32 large (> 10 million individuals) and 23 isolated populations, representing a large fraction of the people of India. We observe high levels of genetic divergence between groups of populations that cluster largely on the basis of ethnicity and language. Indian populations not only overlap with the diversity of HapMap populations, but also contain population groups that are genetically distinct. These data and results are useful for addressing stratification and study design issues in complex traits especially for heterogeneous populations. © Indian Academy of Sciences.

Genetic landscape of the people of India: A canvas for disease gene exploration

Background: Ayurveda is an ancient system of personalized medicine documented and practiced in India since 1500 B.C. According to this system an individual's basic constitution to a large extent determines predisposition and prognosis to diseases as well as therapy and life-style regime. Ayurveda describes seven broad constitution types (Prakritis) each with a varying degree of predisposition to different diseases. Amongst these, three most contrasting types, Vata, Pitta, Kapha, are the most vulnerable to diseases. In the realm of modern predictive medicine, efforts are being directed towards capturing disease phenotypes with greater precision for successful identification of markers for prospective disease conditions. In this study, we explore whether the different constitution types as described in Ayurveda has molecular correlates. Methods: Normal individuals of the three most contrasting constitutional types were identified following phenotyping criteria described in Ayurveda in Indian population of Indo-European origin. The peripheral blood samples of these individuals were analysed for genome wide expression levels, biochemical and hematological parameters. Gene Ontology (GO) and pathway based analysis was carried out on differentially expressed genes to explore if there were significant enrichments of functional categories among Prakriti types. Results: Individuals from the three most contrasting constitutional types exhibit striking differences with respect to biochemical and hematological parameters and at genome wide expression levels. Biochemical profiles like liver function tests, lipid profiles, and hematological parameters like haemoglobin exhibited differences between Prakriti types. Functional categories of genes showing differential expression among Prakriti types were significantly enriched in core biological processes like transport, regulation of cyclin dependent protein kinase activity, immune response and regulation of blood coagulation. A significant enrichment of housekeeping, disease related and hub genes were observed in these extreme constitution types. Conclusion: Ayurveda based method of phenotypic classification of extreme constitutional types allows us to uncover genes that may contribute to system level differences in normal individuals which could lead to differential disease predisposition. This is a first attempt towards unraveling the clinical phenotyping principle of a traditional system of medicine in terms of modern biology. An integration of Ayurveda with genomics holds potential and promise for future predictive medicine. © 2008 Prasher et al; licensee BioMed Central Ltd.