Department of Bioscience & Bioengineering

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Motivation: Transposon-derived Alu repeats are exclusively associated with primate genomes. They have gained considerable importance in the recent times with evidence of their involvement in various aspects of gene regulation, e.g. alternative splicing, nucleosome positioning, CpG methylation, binding sites for transcription factors and hormone receptors, etc. The objective of this study is to investigate the factors that influence the distribution of Alu repeat elements in the human genome. Such analysis is expected to yield insights into various aspects of gene regulation in primates. Results: Analysis of Alu repeat distribution for the human genome build 32 (released in January 2003) reveals that they occupy nearly one-tenth portion of the sequenced regions. Huge variations in Alu frequencies were seen across the genome with chromosome 19 being the most and chromosome Y being the least Alu dense chromosomes. The highlights of the analysis are as follows: (1) three-fourth of the total genes in the genome are associated with Alus. (2) Alu density is higher in genes as compared with intergenic regions in all the chromosomes except 19 and 22. (3) Alu density in human genome is highly correlated with GC content, gene density and intron density with GC content being major deterministic factor compared with other two. (4) Alu densities were correlated more with gene density than intron density indicating the insertion of Alus in untranslated regions of exons. © Oxford University Press 2004; all rights reserved.

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Bioinformatics

Alu repeat analysis in the complete human genome: Trends and variations with respect to genomic composition

Connections of the forepaw regions of somatosensory cortex (S1) were determined in rats reared to maturity after spinal cord overhemisections at cervical level C3 on postnatal day 3. Overhemisections cut all ascending and descending pathways and intervening gray on one side of the spinal cord and the pathways of the dorsal funiculus contralaterally. Bilateral lesions of the dorsal columns reduced the size of the brainstem nuclei by 41%, and the ventroposterior lateral subnucleus (VPL) of the thalamus by 20%. Bilateral lesions also prevented the emergence of the normal cytochrome oxidase barrel pattern in forepaw and hindpaw regions of S1. Injections of wheat germ agglutinin conjugated to horseradish peroxidase were placed in the forepaw region of granular S1 and surrounding dysgranular S1 contralateral to the hemisection. The VPL nucleus was densely labeled, whereas the adjoining ventroposterior medial subnucleus, VPM, representing the head, was unlabeled. Thus, there was no evidence of abnormal connections of VPM to forepaw cortex. Foci of transported label in the ipsilateral hemisphere appeared to be in normal locations and of normal extents, but connections in the opposite hemisphere were broadly and nearly uniformly distributed in sensorimotor cortex in a pattern similar to that in postnatal rats. Rats with incomplete lesions that spared the dorsal column pathway on the left side but not the right demonstrated surprisingly normal distributions of callosal connections in the nondeprived right hemisphere, even though the injected left hemisphere was deprived. Thus, the development of the normal pattern of callosal connections depends on dorsal column input and not on normal interhemsipheric interactions. © 2004 Wiley-Liss, Inc.

Journal of Comparative Neurology

Bilateral effects of spinal overhemisections on the development of the somatosensory system in rats

We consider 1D systems of masses, which can transfer energy via harmonic and/or anharmonic interactions of the form V(xi,i+1) ∼ x i,i+1β, where β &gt; 2, and where the potential energy is physically meaningful. The systems are placed within boundaries or satisfy periodic boundary conditions. Any velocity perturbation in these (non-integrable) systems is found to travel as discrete solitary waves. These solitary waves very nearly preserve themselves and make tiny secondary solitary waves when they collide or reach a boundary. As time t → ∞, these systems cascade to an equilibrium-like state, with Boltzmann-like velocity distributions, yet with no equipartitioning of energy, which we refer to and briefly describe as the "quasi-equilibrium" state. © 2004 Elsevier B.V. All rights reserved.

Physica A: Statistical Mechanics and its Applications

The quasi-equilibrium phase in nonlinear 1D systems

Most environments inhabited by living beings have dust. Much of that dust comes from the continuous flaking of our own skin and atmosphere borne particles of submicron size. Dust mites seem to play an important role in integrating fine scale dust, which they consume to grow, resulting in larger length scale dust. Dust continues to agglomerate and grow. Air filters are designed to remove dust and control dust agglomeration. We report a simple scaling law, based on kinematic simulations of dust filtration through a one dimensional idealized filter. The results reveal insights regarding how filters may clog in time. Our results may be of use to someone interested in designing customized air filters for optimum dust removal in an environment with a known dust distribution. Copyright © 2004 SAE International.

SAE Technical Papers

Removing dust from confined air volumes - A toy model

We describe a consanguineous Indian family having spinocerebellar ataxia type 2 (SCA2) expansions with complex phenotypes (early-onset, dopa-responsive parkinsonism, ataxia and retinitis pigmentosa). The two probands having homozygous SCA2 mutations presenting with early-onset dopa-responsive parkinsonism without ataxia develop dyskinesias within a year of starting levodopa. Their siblings, heterozygous for SCA2 mutations, had retinitis pigmentosa with or without ataxia. Approximately 38% of family members with SCA2 mutations were asymptomatic.

Annals of Neurology

Complex Phenotypes in an Indian Family with Homozygous SCA2 Mutations

The propagation of δ function mechanical impulses in idealized three-dimensional hexagonal close packed lattices of monosized Hertz sphere was investigated using particle dynamics based simulation. The kinetic energy behavior of grains at cumulative surface of a granular bed after the generation of a normal impulse into the bed was also analyzed. It was found that the cumulative average kinetic energy per surface grain, κ, decreased with the penetration of the impulse into the bed. The results show that the minimum value of κ depends upon restitutional losses at the grain contacts.

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

Impulse penetration into idealized granular beds: Behavior of cumulative surface kinetic energy

Water-soluble ferrofluids typically have ferrolluid grains ≤20 nm or so in diameter. We argue that one maybe able to use a single liquid coated ferrofluid grain as an "ink drop" of a hypothetical inkjet printer. Such line scale drops may not be best suited for the desktop inkjet printer but may find a niche in other applications such as in tagging commodities to be protected from easy counterfeiting. © 2004 by Marcel Dekker, Inc.

Journal of Dispersion Science and Technology

Nanoprinting with nanoparticles: Concept of a novel inkjet printer with possible applications in invisible tagging of objects

We consider the dynamical behavior of horizontal alignments of elastic grains placed within confining walls and placed under a constant acceleration that is applied at one end of the system. We show that these systems vibrate under such a compressive force. Certain universal properties of this vibration are mentioned. These systems may be useful in designing devices for filtering out mechanical noise. Copyright © 2004 SAE International.

Periodic dynamics in driven granular chain systems

CAG repeat expansion is the cause of an ever-increasing list of neurodegenerative disorders, especially hereditary ataxias. However, genes responsible for 10-50% of the clinically diagnosed ataxias are still unidentified in different populations. Traditional linkage and repeat expansion-detection based methods complemented with human genome sequence and expression information can now accelerate the pace of identification of putative disease candidates. We have analyzed two CAG repeat containing loci, human SMARCA2 and THAP11, which are expressed in the brain as putative candidates for SCAs, using computational as well as polymorphism scanning approaches. Both loci exhibited features characteristic of genes associated with repeat disorders. These loci are polymorphic with respect to size and interruption pattern in the Indian population. Furthermore, computational analysis of glutamine-stretch embedded domains in the respective proteins predicted these regions to be "natively unfolded" beyond a threshold of 40 glutamines. Comparative genome analysis suggested a stabilizing influence of CAA interspersions in repeat tract in THAP11 but not in SMARCA2. Although repeat expansion could not be detected within these genes in unidentified ataxia patients reported in India, we suggest that these loci be screened in other populations, as there is a wide heterogeneity in the prevalence of these disorders in different populations. © The Japan Society of Human Genetics and Springer-Verlag 2004.

Journal of Human Genetics

SMARCA2 and THAP11: Potential candidates for polyglutamine disorders as evidenced from polymorphism and protein-folding simulation studies

The normal development of the somatosensory system requires intact sensory inputs from the periphery during a critical window of time early in development. Here we determined how the removal of only part of the ascending spinal inputs early in development affects the anatomical and neurophysiological development of the somatosensory system. We performed spinal overhemisections in rat pups at C3/C4 levels on the third day after birth. This procedure hemisects the spinal cord on one side and transects the dorsal funiculus on the other side. When the rats were 6 - 8 months old, the responsiveness and somatotopy of the primary somatosensory cortex (S1) contralateral to the hemisection were determined using standard multiunit mapping techniques. Sections of the flattened cortex were processed for cytochrome oxidase activity, Nissl substance, or myelin. We found that histologically apparent modules that are normally present in the regions of the forepaw and the hindpaw representations were absent, whereas the lateral barrel field representing the face was completely normal. The neurons in the forepaw regions of S1 either did not respond to the stimulation of the skin of any region of the body or responded to the stimulation of the upper arm afferents that enter the spinal cord rostral to the site of the lesion. The results show that a lack of normal sensory inputs via ascending pathways in the dorsal spinal cord during early development results in massive anatomical and neurophysiological abnormalities in the cortex. Intact crossed spinothalamic pathways are unable to support the normal development of the forepaw barrels.