RISCI - Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes

<p>Abstract</p> <p>Background -</p> <p>The availability of multiple whole genome sequences has facilitated <it>in silico </it>identification of fixed and polymorphic transposable elements (TE). Whereas polymorphic loci serve as makers for phylogenetic and forensic analysis, fixed species-specific transposon insertions, when compared to orthologous loci in other closely related species, may give insights into their evolutionary significance. Besides, TE insertions are not isolated events and are frequently associated with subtle sequence changes concurrent with insertion or post insertion. These include duplication of target site, 3' and 5' flank transduction, deletion of the target locus, 5' truncation or partial deletion and inversion of the transposon, and post insertion changes like inter or intra element recombination, disruption etc. Although such changes have been studied independently, no automated platform to identify differential transposon insertions and the associated array of sequence changes in genomes of the same or closely related species is available till date. To this end, we have designed RISCI - 'Repeat Induced Sequence Changes Identifier' - a comprehensive, comparative genomics-based, <it>in silico </it>subtractive hybridization pipeline to identify differential transposon insertions and associated sequence changes using specific alignment signatures, which may then be examined for their downstream effects.</p> <p>Results -</p> <p>We showcase the utility of RISCI by comparing full length and truncated L1HS and AluYa5 retrotransposons in the reference human genome with the chimpanzee genome and the alternate human assemblies (Celera and HuRef). Comparison of the reference human genome with alternate human assemblies using RISCI predicts 14 novel polymorphisms in full length L1HS, 24 in truncated L1HS and 140 novel polymorphisms in AluYa5 insertions, besides several insertion and post insertion changes. We present comparison with two previous studies to show that RISCI predictions are broadly in agreement with earlier reports. We also demonstrate its versatility by comparing various strains of <it>Mycobacterium tuberculosis </it>for IS 6100 insertion polymorphism.</p> <p>Conclusions -</p> <p>RISCI combines comparative genomics with subtractive hybridization, inferring changes only when exclusive to one of the two genomes being compared. The pipeline is generic and may be applied to most transposons and to any two or more genomes sharing high sequence similarity. Such comparisons, when performed on a larger scale, may pull out a few critical events, which may have seeded the divergence between the two species under comparison.</p

The formation of human populations in South and Central Asia

By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization’s decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages

Optical properties (VUV region) of ABO(3) ferroelectrics: Application of syncrotron radiation

10th European Meeting on Ferroelectricity -- AUG 03-08, 2003 -- Univ Cambridge, Cambridge, ENGLANDWOS: 000222471200026The method of vacuum ultraviolet (VUV) spectroscopy were used to study the optical properties of ABO(3) ferroelectrics (LiNbO3, LiTaO3, BaxSr1-xNb2O6, Ba2NaNb5O15, SrTiO3, BaTiO3, PbMg1/3Nb2/3O3, KTaO3, KNbO3) in the photon range from 1.0 eV to 35.0 eV at temperatures T=10-600 K. The results were used to calculate the optical junctions, density of states and energy spectra of these compounds. A comparison of the experimental results with theoretical calculations shows the fundamental significance of the BO6 octahedron in the formation of the energy spectra of ABO(3) ferroelectrics.Taylor & Francis, Aixacct, Radiant Technologies & Epichem Inorgtec

Trapping parameters of repulsive centers in SbSI single crystals

Charge trapping centers in antimony sulphide iodide (SbSI) single crystals have been investigated by the use of thermally stimulated current (TSC) technique. The TSC spectrum consists of only one apparent peak which is found to be associated with a single trapping level. Those traps are experimentally found to obey the monomolecular kinetics. The trapping parameters as the energy depth, temperature dependent frequency factor and capture cross section together with the concentrations of the corresponding discrete trapping level are determined. The TSC signal is found to be strongly dependent on illumination temperature of the sample and this is explained by the model in which the traps are considered to be surrounded by repulsive potential barriers

Electronic structure and phase transition effects in some ABO(3) materials

10th International Meeting on Ferroelectricity -- SEP 03-07, 2001 -- MADRID, SPAINWOS: 000176862200052In this work a new theoretical study is undertaken of the electronic structure of ABO(3) materials and role of the BO6 octahedron containing Ti, Nb, and Ta in paraelectric and ferroelectric phases. The results of this work show that, cluster calculations by the X-alpha method (in ferroelectric and paraelectric phases) even for a minimum cluster can describe the nonlocal electronic properties of ABO(3) and can be used in discussions of the physical properties of these compounds