oalib

Publish in OALib Journal

ISSN: 2333-9721

APC: Only $99

Submit

Any time

2020 ( 69 )

2019 ( 320 )

2018 ( 408 )

2017 ( 390 )

Custom range...

Search Results: 1 - 10 of 340018 matches for " David J Witherspoon "
All listed articles are free for downloading (OA Articles)
Page 1 /340018
Display every page Item
Modeling the amplification dynamics of human alu retrotransposons.
Hedges Dale J,Cordaux Richard,Xing Jinchuan,Witherspoon David J
PLOS Computational Biology , 2005,
Abstract: Retrotransposons have had a considerable impact on the overall architecture of the human genome. Currently, there are three lineages of retrotransposons (Alu, L1, and SVA) that are believed to be actively replicating in humans. While estimates of their copy number, sequence diversity, and levels of insertion polymorphism can readily be obtained from existing genomic sequence data and population sampling, a detailed understanding of the temporal pattern of retrotransposon amplification remains elusive. Here we pose the question of whether, using genomic sequence and population frequency data from extant taxa, one can adequately reconstruct historical amplification patterns. To this end, we developed a computer simulation that incorporates several known aspects of primate Alu retrotransposon biology and accommodates sampling effects resulting from the methods by which mobile elements are typically discovered and characterized. By modeling a number of amplification scenarios and comparing simulation-generated expectations to empirical data gathered from existing Alu subfamilies, we were able to statistically reject a number of amplification scenarios for individual subfamilies, including that of a rapid expansion or explosion of Alu amplification at the time of human-chimpanzee divergence.
Mobile element scanning (ME-Scan) by targeted high-throughput sequencing
David J Witherspoon, Jinchuan Xing, Yuhua Zhang, W Scott Watkins, Mark A Batzer, Lynn B Jorde
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-410
Abstract: Here we present a novel method for identifying nearly all insertions of a ME subfamily in the whole genomes of multiple individuals and simultaneously genotyping (for presence or absence) those insertions that are variable in the population. We use ME-specific primers to construct DNA libraries that contain the junctions of all ME insertions of the subfamily, with their flanking genomic sequences, from many individuals. Individual-specific "index" sequences are designed into the oligonucleotide adapters used to construct the individual libraries. These libraries are then pooled and sequenced using a ME-specific sequencing primer. Mobile element insertion loci of the target subfamily are uniquely identified by their junction sequence, and all insertion junctions are linked to their individual libraries by the corresponding index sequence. To test this method's feasibility, we apply it to the human AluYb8 and AluYb9 subfamilies. In four individuals, we identified a total of 2,758 AluYb8 and AluYb9 insertions, including nearly all those that are present in the reference genome, as well as 487 that are not. Index counts show the sequenced products from each sample reflect the intended proportions to within 1%. At a sequencing depth of 355,000 paired reads per sample, the sensitivity and specificity of ME-Scan are both approximately 95%.Mobile Element Scanning (ME-Scan) is an efficient method for quickly genotyping mobile element insertions with very high sensitivity and specificity. In light of recent improvements to high-throughput sequencing technology, it should be possible to employ ME-Scan to genotype insertions of almost any mobile element family in many individuals from any species.Mobile elements (MEs) are DNA sequences that can replicate and insert themselves into new loci within larger host genomes. This strategy has proved very successful: MEs are evolutionarily ancient, highly diversified in form, ubiquitous in distribution, and often extremely numerous with
Modeling the Amplification Dynamics of Human Alu Retrotransposons
Dale J Hedges ,Richard Cordaux ,Jinchuan Xing,David J Witherspoon,Alan R Rogers,Lynn B Jorde,Mark A Batzer
PLOS Computational Biology , 2005, DOI: 10.1371/journal.pcbi.0010044
Abstract: Retrotransposons have had a considerable impact on the overall architecture of the human genome. Currently, there are three lineages of retrotransposons (Alu, L1, and SVA) that are believed to be actively replicating in humans. While estimates of their copy number, sequence diversity, and levels of insertion polymorphism can readily be obtained from existing genomic sequence data and population sampling, a detailed understanding of the temporal pattern of retrotransposon amplification remains elusive. Here we pose the question of whether, using genomic sequence and population frequency data from extant taxa, one can adequately reconstruct historical amplification patterns. To this end, we developed a computer simulation that incorporates several known aspects of primate Alu retrotransposon biology and accommodates sampling effects resulting from the methods by which mobile elements are typically discovered and characterized. By modeling a number of amplification scenarios and comparing simulation-generated expectations to empirical data gathered from existing Alu subfamilies, we were able to statistically reject a number of amplification scenarios for individual subfamilies, including that of a rapid expansion or explosion of Alu amplification at the time of human–chimpanzee divergence.
Products in Hochschild cohomology and Grothendieck rings of group crossed products
Sarah J. Witherspoon
Mathematics , 2002,
Abstract: We give a general construction of rings graded by the conjugacy classes of a finite group. Some examples of our construction are the Hochschild cohomology ring of a finite group algebra, the Grothendieck ring of the Drinfel'd double of a group, and the orbifold cohomology ring for a global quotient. We generalize the first two examples by deriving product formulas for the Hochschild cohomology ring of a group crossed product and for the Grothendieck ring of an abelian extension of Hopf algebras. Our results account for similarities in the product structures among these examples.
Clifford correspondence for algebras
Sarah J. Witherspoon
Mathematics , 2001,
Abstract: We give a Clifford correspondence for an algebra A over an algebraically closed field, that is an algorithm for constructing some finite-dimensional simple A-modules from simple modules for a subalgebra and endomorphism algebras. This applies to all finite-dimensional simple A-modules in the case that A is finite-dimensional and semisimple with a given semisimple subalgebra. We discuss connections between our work and earlier results, with a view towards applications particularly to finite-dimensional semisimple Hopf algebras.
Twisted Graded Hecke Algebras
Sarah J. Witherspoon
Mathematics , 2005,
Abstract: We generalize graded Hecke algebras to include a twisting two-cocycle for the associated finite group. We give examples where the parameter spaces of the resulting twisted graded Hecke algebras are larger than that of the graded Hecke algebras. We prove that twisted graded Hecke algebras are particular types of deformations of a crossed product.
Skew Derivations and Deformations of a Family of Group Crossed Products
Sarah J. Witherspoon
Mathematics , 2005,
Abstract: We obtain deformations of a crossed product of a polynomial algebra with a group, under some conditions, from universal deformation formulas. We show that the resulting deformations are nontrivial by a comparison with Hochschild cohomology. The universal deformation formulas arise from actions of Hopf algebras generated by automorphisms and skew derivations, and are universal in the sense that they apply to deform all algebras with such Hopf algebra actions.
Alu repeats increase local recombination rates
David J Witherspoon, W Scott Watkins, Yuhua Zhang, Jinchuan Xing, Whitney L Tolpinrud, Dale J Hedges, Mark A Batzer, Lynn B Jorde
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-530
Abstract: We carried out sequencing, SNP identification, and SNP genotyping around 19 AluY insertion loci in 347 individuals sampled from diverse populations, then used the SNP genotypes to estimate local recombination rates around the AluY loci. The loci and SNPs were chosen so as to minimize other factors (such as SNP ascertainment bias and SNP density) that could influence recombination rate estimates. We detected a significant increase in recombination rate within ~2 kb of the AluY insertions in our African population sample. To test this observation against a larger set of AluY insertions, we applied our locus- and SNP-selection design and analyses to the HapMap Phase II data. In that data set, we observed a significantly increased recombination rate near AluY insertions in both the CEU and YRI populations.We show that the presence of a fixed AluY insertion is significantly predictive of an elevated local recombination rate within 2 kb of the insertion, independent of other known predictors. The magnitude of this effect, approximately a 6% increase, is comparable to the effects of some recombinogenic DNA sequence motifs identified via their association with recombination hot spots.Approximately one-half of the human genome consists of the remnants of past transpositional bursts [1]. LINE-1 non-LTR retrotransposons and the Alu elements they mobilize continue to replicate in the human gene pool to this day [2]. As a result of Alu retroposition, our genomes are littered with more than one million small (~300 bp), non-allelic regions whose DNA sequences are nearly identical to each other. Their recombinogenic impact is evident: these scattered homologies trigger non-allelic homologous recombination (NAHR) events that lead to translocations, deletions, duplications, and other chromosomal abnormalities and copy number variations [2-6]. These events have affected the long-term evolution of the human genome and of the Alu insertions themselves [7-11]. Alu repeats have been impli
Genetic analysis of ancestry, admixture and selection in Bolivian and Totonac populations of the New World
W Scott Watkins, Jinchuan Xing, Chad Huff, David J Witherspoon, Yuhua Zhang, Ugo A Perego, Scott R Woodward, Lynn B Jorde
BMC Genetics , 2012, DOI: 10.1186/1471-2156-13-39
Abstract: We analyzed common genomic regions from native Bolivian and Totonac populations to identify 324 highly predictive Native American ancestry informative markers (AIMs). As few as 40–50 of these AIMs perform nearly as well as large panels of random genome-wide SNPs for predicting and estimating Native American ancestry and admixture levels. These AIMs have greater New World vs. Old World specificity than previous AIMs sets. We identify highly-divergent New World SNPs that coincide with high-frequency haplotypes found at similar frequencies in all populations examined, including the HGDP Pima, Maya, Colombian, Karitiana, and Surui American populations. Some of these regions are potential candidates for positive selection. European admixture in the Bolivian sample is approximately 12%, though individual estimates range from 0–48%. We estimate that the admixture occurred ~360–384?years ago. Little evidence of European or African admixture was found in Totonac individuals. Bolivians with pre-Columbian mtDNA and Y-chromosome haplogroups had 5–30% autosomal European ancestry, demonstrating the limitations of Y-chromosome and mtDNA haplogroups and the need for autosomal ancestry informative markers for assessing ancestry in admixed populations.
Shared and Unique Signals of High-Altitude Adaptation in Geographically Distinct Tibetan Populations
Tana Wuren, Tatum S. Simonson, Ga Qin, Jinchuan Xing, Chad D. Huff, David J. Witherspoon, Lynn B. Jorde, Ri-Li Ge
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0088252
Abstract: Recent studies have used a variety of analytical methods to identify genes targeted by selection in high-altitude populations located throughout the Tibetan Plateau. Despite differences in analytic strategies and sample location, hypoxia-related genes, including EPAS1 and EGLN1, were identified in multiple studies. By applying the same analytic methods to genome-wide SNP information used in our previous study of a Tibetan population (n = 31) from the township of Maduo, located in the northeastern corner of the Qinghai-Tibetan Plateau (4200 m), we have identified common targets of natural selection in a second geographically and linguistically distinct Tibetan population (n = 46) in the Tuo Tuo River township (4500 m). Our analyses provide evidence for natural selection based on iHS and XP-EHH signals in both populations at the p<0.02 significance level for EPAS1, EGLN1, HMOX2, and CYP17A1 and for PKLR, HFE, and HBB and HBG2, which have also been reported in other studies. We highlight differences (i.e., stratification and admixture) in the two distinct Tibetan groups examined here and report selection candidate genes common to both groups. These findings should be considered in the prioritization of selection candidate genes in future genetic studies in Tibet.
Page 1 /340018
Display every page Item


Home
Copyright © 2008-2017 Open Access Library. All rights reserved.