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

Indian population, comprising of more than a billion people, consists of 4693 communities with several thousands of endogamous groups, 325 functioning languages and 25 scripts. To address the questions related to ethnic diversity, migrations, founder populations, predisposition to complex disorders or pharmacogenomics, one needs to understand the diversity and relatedness at the genetic level in such a diverse population. In this backdrop, six constituent laboratories of the Council of Scientific and Industrial Research (CSIR), with funding from the Government of India, initiated a network program on predictive medicine using repeats and single nucleotide polymorphisms. The Indian Genome Variation (IGV) consortium aims to provide data on validated SNPs and repeats, both novel and reported, along with gene duplications, in over a thousand genes, in 15,000 individuals drawn from Indian subpopulations. These genes have been selected on the basis of their relevance as functional and positional candidates in many common diseases including genes relevant to pharmacogenomics. This is the first large-scale comprehensive study of the structure of the Indian population with wide-reaching implications. A comprehensive platform for Indian Genome Variation (IGV) data management, analysis and creation of IGVdb portal has also been developed. The samples are being collected following ethical guidelines of Indian Council of Medical Research (ICMR) and Department of Biotechnology (DBT), India. This paper reveals the structure of the IGV project highlighting its various aspects like genesis, objectives, strategies for selection of genes, identification of the Indian subpopulations, collection of samples and discovery and validation of genetic markers, data analysis and monitoring as well as the project's data release policy. © Springer-Verlag 2005.

World University root node

Human Genetics

The Indian Genome Variation database (IGVdb): A project overview

Mechanical energy, such as sound waves and impulses, have been used to detect shallow buried objects for more than half a century. Yet, very little is understood about how mechanical energy propagates into one of the simplest kinds of soil, namely, a granular bed. Here we present an overview of the state of the art in our understanding of mechanical energy propagation in granular beds. © World Scientific Publishing Company.

International Journal of Modern Physics B

Using mechanical energy as a probe for the detection and imaging of shallow buried inclusions in dry granular beds

We perform measurements, numerical simulations, and quantitative comparisons with available theory on solitary wave propagation in a linear chain of beads without static preconstraint. By designing a nonintrusive force sensor to measure the impulse as it propagates along the chain, we study the solitary wave reflection at a wall. We show that the main features of solitary wave reflection depend on wall mechanical properties. Since previous studies on solitary waves have been performed at walls without these considerations, our experiment provides a more reliable tool to characterize solitary wave propagation. We find, for the first time, precise quantitative agreements. © 2005 The American Physical Society.

Fulltext

Physical Review Letters

How hertzian solitary waves interact with boundaries in a 1D granular medium

There is a wide variation in prevalence of spinocerebellar ataxia type 1 (SCA1) in different populations. In the present study, we observed SCA1 in approximately 22% (37/167 families) of the autosomal dominant cerebellar ataxias (ADCAs) in the Indian population. We investigated the role of various genetic factors like repeat length, interruption pattern and chromosomal background in predisposing the repeats to instability in these families. We analyzed 12 markers (9 SNPs and 3 microsatellite markers) and found 3 of them, spanning a region of approximately 65 kbp to be linked with the disease locus in the Indian population. The haplotype C-4-C defined by rs1476464 (SNP9)-D6S288-rs2075974 (SNP1), which was extremely rare in nonaffected chromosomes (approximately 3%), was observed to be significantly (P<0.0000) associated with the expanded chromosomes in approximately 44% of SCA1 families. This haplotype was found in all nonhuman primates. SNP1 (C/T), which showed a skewed allelic distribution between large (LN > 30 repeats) and small normal (SN <or= 30 repeats) alleles (P<0.0000) had similar allelic distribution (P=0.3477) in LN and expanded alleles. Our study suggested that LN and expanded chromosomes linked with the ancestral C allele of SNP1 might have originated simultaneously during evolution by the lengthening of repeats. The LN alleles might have accumulated repeat stabilizing non-CAG interruptions during this process. Similar proportions of T allele in SN with single interruptions, LN and expanded chromosomes lend credence to the origin of expanded alleles from singly-interrupted chromosomes. Our analyses using markers linked (anchoring) to SCA1 suggest that prevalence of SCA1 is correlated to both repeat length and number of interruptions in the Indian population. The spectrum of these alleles also points toward the antiquity of SCA1 mutation in the Indian population.

Human genetics

Insights into the mutational history and prevalence of SCA1 in the Indian population through anchored polymorphisms.

Spinocerebellar ataxia type 7 (SCA7) is an autosomal dominant cerebellar ataxia caused by CAG repeat expansion. We found expansion at SCA7 locus in only two out of 235 Indian families clinically diagnosed for ataxia. In one of the families, a de novo mutation was observed wherein a paternal allele in intermediate range of 31 CAG repeats expanded to 59 in the offspring leading to the disease. No expanded alleles were observed in the sperm of the transmitting parent by small pool PCR. This suggests that de novo expansion by a pre-zygotic event is unlikely and could be post-zygotic. SCA7 expanded alleles from the two families were present on different genetic backgrounds, indicating multiple origins of the mutation. © The Japan Society of Human Genetics and Springer-Verlag 2005.

Journal of Human Genetics

Post-zygotic de novo trinucleotide repeat expansion at spinocerebellar ataxia type 7 locus: Evidence from an Indian family

Making shock proof layers is an outstanding challenge. Elastic spheres are known to repel softer than springs when gently squeezed but develop strong repulsion upon compression and the forces between adjacent spheres lead to ballistic-like energy transfer between them. Here we demonstrate that a small alignment of progressively shrinking spheres of a strong, light-mass material, placed horizontally in an appropriate casing, can absorb ∼80% (∼90%) of the incident force (energy) pulse. The system can be scaled down in size. Effects of varying the size, radius shrinkage and restitutive losses are shown via computed "dynamical phase diagrams." © 2005 American Institute of Physics.

Applied Physics Letters

Absorption of short duration pulses by small, scalable, tapered granular chains

We provide a brief update to our current efforts in studying shock mitigation using one-dimensional arrays of adjacent metal spheres that may progressively shrink in size. These tapered chains are characterized by the number of spheres, N, the amount of tapering, q, and restitutive losses, ω. Spheres are assumed to interact via the nonlinear Hertz potential, V∞δ5/2, where δ is the amount of overlap of adjacent grains used to emulate compression. To gauge the effectiveness of such chains at absorbing transient pulses, we look at the normalized kinetic energy, KEN, as a function of N,q,ω. Finally the concept for a tapered chain armor panel is reviewed and evaluated.

Proceedings - 22nd International Symposium on Ballistics

Shock mitigation for blast protection using hertzian tapered chains

We consider a 1D system with purely non-linear interactions such that no acoustic propagation is possible, We show that our system can attain an equilibrium-like state, which we call the "quasi-equilibrium" state. The quasi-equilibrium state is found to be independent of the initial conditions with the particle velocities satisfying a Gaussian velocity distribution, However, in the absence of sound propagation in the system, no energy equi-partitioning is achieved, Our system shows huge temperature fluctuations, Linear response theory seems inapplicable in describing the propagation of a perturbation in the quasi-equilibrium state.

Journal of the Korean Physical Society

The quasi-equilibrium state: A tale of certain soundless systems

Background: The primate-specific Alu elements, which originated 65 million years ago, exist in over a million copies in the human genome. These elements have been involved in genome shuffling and various diseases not only through retrotransposition but also through large scale Alu-Alu mediated recombination. Only a few subfamilies of Alus are currently retropositionally active and show insertion/deletion polymorphisms with associated phenotypes. Retroposition occurs by means of RNA intermediates synthesised by a RNA polymerase III promoter residing in the A-Box and B-Box in these elements. Alus have also been shown to harbour a number of transcription factor binding sites, as well as hormone responsive elements. The distribution of Alus has been shown to be non-random in the human genome and these elements are increasingly being implicated in diverse functions such as transcription, translation, response to stress, nucleosome positioning and imprinting. Results: We conducted a retrospective analysis of putative functional sites, such as the RNA pol III promoter elements, pol II regulatory elements like hormone responsive elements and ligand-activated receptor binding sites, in Alus of various evolutionary ages. We observe a progressive loss of the RNA pol III transcriptional potential with concomitant accumulation of RNA pol II regulatory sites. We also observe a significant over-representation of Alus harboring these sites in promoter regions of signaling and metabolism genes of chromosome 22, when compared to genes of information pathway components, structural and transport proteins. This difference is not so significant between functional categories in the intronic regions of the same genes. Conclusions: Our study clearly suggests that Alu elements, through retrotransposition, could distribute functional and regulatable promoter elements, which in the course of subsequent selection might be stabilized in the genome. Exaptation of regulatory elements in the preexisting genes through Alus could thus have contributed to evolution of novel regulatory networks in the primate genomes. With such a wide spectrum of regulatory sites present in Alus, it also becomes imperative to screen for variations in these sites in candidate genes, which are otherwise repeat-masked in studies pertaining to identification of predisposition markers. © 2004 Shankar et al; licensee BioMed Central Ltd.

BMC Evolutionary Biology

Evolution and distribution of RNA polymerase II regulatory sites from RNA polymerase III dependant mobile Alu elements

We report a particle dynamics based simulational study of the propagation of [Formula presented] function mechanical impulses in idealized three-dimensional hexagonal close packed lattices of monosized Hertz spheres. This paper presents five key results on the kinetic energy of grains at the surface of a granular bed after the generation of a normal impulse into the bed. (i) We find that the time integrated or cumulative average kinetic energy per surface grain, [Formula presented], drops as an impulse penetrates into the bed. The minimum value of [Formula presented], say [Formula presented], is reached at some time [Formula presented] after the impulse has been generated. (ii) This value, [Formula presented], depends upon the restitutional losses at the grain contacts and [Formula presented] increases as restitutional losses at granular contacts increase in magnitude. (iii) The asymptotic value of [Formula presented] is denoted by [Formula presented]. Our data show that increasing the area across which an impulse is generated, [Formula presented], leads to [Formula presented]. (iv) If we assign random masses to our monosized grains, [Formula presented] grows quadratically as a function of the range of mass variation about a mean mass. We find that at large times, i.e., [Formula presented], [Formula presented], where the constant [Formula presented] is roughly independent of restitution for the typical values of restitution encountered. (v) Our data suggest that at early times, the backscattering process carries signatures of ballistic propagation of the mechanical energy while at late times, the backscattering process is reminiscent of vibrations of an essentially ergodic system. Given the ballisticlike propagation of mechanical energy into granular beds, we conclude that a wave equation based description of mechanical energy propagation into granular beds may not always be appropriate. © 2004 The American Physical Society.