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Search Results: 1 - 10 of 171884 matches for " Catherine E Ingle "
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Modifier Effects between Regulatory and Protein-Coding Variation
Antigone S. Dimas,Barbara E. Stranger,Claude Beazley,Robert D. Finn,Catherine E. Ingle,Matthew S. Forrest,Matthew E. Ritchie,Panos Deloukas,Simon Tavaré,Emmanouil T. Dermitzakis
PLOS Genetics , 2008, DOI: 10.1371/journal.pgen.1000244
Abstract: Genome-wide associations have shown a lot of promise in dissecting the genetics of complex traits in humans with single variants, yet a large fraction of the genetic effects is still unaccounted for. Analyzing genetic interactions between variants (epistasis) is one of the potential ways forward. We investigated the abundance and functional impact of a specific type of epistasis, namely the interaction between regulatory and protein-coding variants. Using genotype and gene expression data from the 210 unrelated individuals of the original four HapMap populations, we have explored the combined effects of regulatory and protein-coding single nucleotide polymorphisms (SNPs). We predict that about 18% (1,502 out of 8,233 nsSNPs) of protein-coding variants are differentially expressed among individuals and demonstrate that regulatory variants can modify the functional effect of a coding variant in cis. Furthermore, we show that such interactions in cis can affect the expression of downstream targets of the gene containing the protein-coding SNP. In this way, a cis interaction between regulatory and protein-coding variants has a trans impact on gene expression. Given the abundance of both types of variants in human populations, we propose that joint consideration of regulatory and protein-coding variants may reveal additional genetic effects underlying complex traits and disease and may shed light on causes of differential penetrance of known disease variants.
Fast-evolving noncoding sequences in the human genome
Christine P Bird, Barbara E Stranger, Maureen Liu, Daryl J Thomas, Catherine E Ingle, Claude Beazley, Webb Miller, Matthew E Hurles, Emmanouil T Dermitzakis
Genome Biology , 2007, DOI: 10.1186/gb-2007-8-6-r118
Abstract: Here we identify 1,356 CNC sequences that appear to have undergone dramatic human-specific changes in selective pressures, at least 15% of which have substitution rates significantly above that expected under neutrality. The 1,356 'accelerated CNC' (ANC) sequences are enriched in recent segmental duplications, suggesting a recent change in selective constraint following duplication. In addition, single nucleotide polymorphisms within ANC sequences have a significant excess of high frequency derived alleles and high FSTvalues relative to controls, indicating that acceleration and positive selection are recent in human populations. Finally, a significant number of single nucleotide polymorphisms within ANC sequences are associated with changes in gene expression. The probability of variation in an ANC sequence being associated with a gene expression phenotype is fivefold higher than variation in a control CNC sequence.Our analysis suggests that ANC sequences have until very recently played a role in human evolution, potentially through lineage-specific changes in gene regulation.The manner in which the expression of genes is regulated defines and determines many of the cellular and developmental processes in an organism. It has been hypothesized that variation in gene regulation is responsible for much of the phenotypic diversity within and between species [1]. In particular, it was proposed a few decades ago that the phenotypic divergence between human and chimpanzees is largely due to changes in gene regulation rather than changes in the protein-coding sequences of genes [2]. Although it has been long recognized that regulatory sequences play an important role in genome function, the fine structure and evolutionary patterns of such sequences are not well understood [3], mainly because such sequences have a much more complex functional code and appear not to be restricted to particular sequence motifs. One of the most powerful approaches with which to identify regula
Patterns of Cis Regulatory Variation in Diverse Human Populations
Barbara E. Stranger equal contributor,Stephen B. Montgomery equal contributor,Antigone S. Dimas equal contributor,Leopold Parts,Oliver Stegle,Catherine E. Ingle,Magda Sekowska,George Davey Smith,David Evans,Maria Gutierrez-Arcelus,Alkes Price,Towfique Raj,James Nisbett,Alexandra C. Nica,Claude Beazley,Richard Durbin,Panos Deloukas,Emmanouil T. Dermitzakis
PLOS Genetics , 2012, DOI: 10.1371/journal.pgen.1002639
Abstract: The genetic basis of gene expression variation has long been studied with the aim to understand the landscape of regulatory variants, but also more recently to assist in the interpretation and elucidation of disease signals. To date, many studies have looked in specific tissues and population-based samples, but there has been limited assessment of the degree of inter-population variability in regulatory variation. We analyzed genome-wide gene expression in lymphoblastoid cell lines from a total of 726 individuals from 8 global populations from the HapMap3 project and correlated gene expression levels with HapMap3 SNPs located in cis to the genes. We describe the influence of ancestry on gene expression levels within and between these diverse human populations and uncover a non-negligible impact on global patterns of gene expression. We further dissect the specific functional pathways differentiated between populations. We also identify 5,691 expression quantitative trait loci (eQTLs) after controlling for both non-genetic factors and population admixture and observe that half of the cis-eQTLs are replicated in one or more of the populations. We highlight patterns of eQTL-sharing between populations, which are partially determined by population genetic relatedness, and discover significant sharing of eQTL effects between Asians, European-admixed, and African subpopulations. Specifically, we observe that both the effect size and the direction of effect for eQTLs are highly conserved across populations. We observe an increasing proximity of eQTLs toward the transcription start site as sharing of eQTLs among populations increases, highlighting that variants close to TSS have stronger effects and therefore are more likely to be detected across a wider panel of populations. Together these results offer a unique picture and resource of the degree of differentiation among human populations in functional regulatory variation and provide an estimate for the transferability of complex trait variants across populations.
Genetic diversity among Indian phytopathogenic isolates of Fusarium semitectum Berkeley and Ravenel  [PDF]
Avinash Ingle, Mahendra Rai
Advances in Bioscience and Biotechnology (ABB) , 2011, DOI: 10.4236/abb.2011.23023
Abstract: We report total ten isolates of F. semitectum recovered from different hosts. Identity of these isolates was determined by morphological and cultural characteristics and confirmed by RAPD-PCR analysis using forty random primers. Morphologically all the ten isolates showed similarity, but based on RAPD-PCR analysis, these isolates can be categorized in three groups depending upon similarity co-efficient. Genetic similarity coefficients between pair wise isolates varied from 0.00 to 1.95 based on an unweighted paired group method of arithmetic average (UPGMA) cluster analysis. RAPD-PCR technique can be used as an important tool for the genetic differentiation among isolates of F. semitectum.
Preparing for rural surgery: Procedure or skills?
RF Ingle
South African Family Practice , 2003,
Generational Difference in Feminist Identities? Exploring Gender Conscious Identities Among African American Men and Women
Catherine E. Harnois
Sociation Today , 2009,
Abstract: Studies of the general population have found strong generational differences in how women and men relate to feminism. But how well do these findings reflect feminism among African American men and women? The results of this study show that generational differences are very important for understanding feminism within the Black community. Also important are gender and involvement in the paid labor force. For African Americans of the baby bust generation, working in the paid labor force seems an especially important even in the development of gender-conscious identities.
Prespectives de l'adquisició d'una segona llengua: implicacions per a l'educació bilingüe
Catherine E. Snow
Temps d'Educació , 1999,
Ageing Populations in Post-Industrial Democracies: Comparative Studies of Policies and Politics
Catherine E Gordon
The Canadian Journal of Sociology , 2012,
Abstract: Book Review
Voltage-Gated Channel Mechanosensitivity: Fact or Friction?
Catherine E. Morris
Frontiers in Physiology , 2011, DOI: 10.3389/fphys.2011.00025
Abstract: The heart is a continually active pulsatile fluid pump. It generates appropriate forces by precisely timed and spaced engagement of its contractile machinery. Largely, it makes its own control signals, the most crucial of which are precisely timed and spaced fluxes of ions across the sarcolemma, achieved by the timely opening and closing of diverse voltage-gated channels (VGC). VGCs have four voltage sensors around a central ion-selective pore that opens and closes under the influence of membrane voltage. Operation of any VGC is secondarily tuned by the mechanical state (i.e., structure) of the bilayer in which it is embedded. Rates of opening and closing, in other words, vary with bilayer structure. Thus, in the intensely mechanical environment of the myocardium and its vasculature, VGCs kinetics might be routinely modulated by reversible and irreversible nano-scale changes in bilayer structure. If subtle bilayer deformations are routine in the pumping heart, VGCs could be subtly transducing bilayer mechanical signals, thereby tuning cardiac rhythmicity, collectively contributing to mechano-electric feedback. Reversible bilayer deformations would be expected with changing shear flows and tissue distension, while irreversible bilayer restructuring occurs with ischemia, inflammation, membrane remodeling, etc. I suggest that tools now available could be deployed to help probe whether/how the inherent mechanosensitivity of VGCs – an attribute substantially reflecting the dependence of voltage sensor stability on bilayer structure – contributes to cardiac rhythmicity. Chief among these tools are voltage sensor toxins (whose inhibitory efficacy varies with the mechanical state of bilayer) and arrhythmia-inducing VGC mutants with distinctive mechano-phenotypes.
Importance of structural distortions in enhancement of transition temperature in FeSe$_{1-x}$Te$_{x}$ superconductors
Kapil E. Ingle,K. R. Priolkar,Rayees A. Zargar,V. P. S. Awana,S. Emura
Physics , 2014, DOI: 10.1088/0953-2048/28/1/015015
Abstract: Temperature (12K $\le$ T $\le$ 300K) dependent extended X-ray absorption fine structure (EXAFS) studies at the Fe K edge in FeSe$_{1-x}$Te$_x$ (x = 0, 0.5 and 1.0) compounds have been carried out to understand the reasons for increase in T$_C$ upon Te doping in FeSe. While local distortions are present near superconducting onset in FeSe and FeSe$_{0.5}$Te$_{0.5}$, they seem to be absent in non superconducting FeTe. Of crucial importance is the variation of anion height. In FeSe$_{0.5}$Te$_{0.5}$, near superconducting onset, the two heights, $h_{Fe-Se}$ and $h_{Fe-Te}$ show a nearly opposite behaviour. These changes indicate a possible correlation between Fe-chalcogen hybridization and the superconducting transition temperature in these Fe-chalcogenides.
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