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Search Results: 1 - 10 of 298158 matches for " Sheldon J. McKay "
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Comparative RNAi Screens in C. elegans and C. briggsae Reveal the Impact of Developmental System Drift on Gene Function
Adrian J. Verster,Arun K. Ramani,Sheldon J. McKay,Andrew G. Fraser
PLOS Genetics , 2014, DOI: doi/10.1371/journal.pgen.1004077
Abstract: Although two related species may have extremely similar phenotypes, the genetic networks underpinning this conserved biology may have diverged substantially since they last shared a common ancestor. This is termed Developmental System Drift (DSD) and reflects the plasticity of genetic networks. One consequence of DSD is that some orthologous genes will have evolved different in vivo functions in two such phenotypically similar, related species and will therefore have different loss of function phenotypes. Here we report an RNAi screen in C. elegans and C. briggsae to identify such cases. We screened 1333 genes in both species and identified 91 orthologues that have different RNAi phenotypes. Intriguingly, we find that recently evolved genes of unknown function have the fastest evolving in vivo functions and, in several cases, we identify the molecular events driving these changes. We thus find that DSD has a major impact on the evolution of gene function and we anticipate that the C. briggsae RNAi library reported here will drive future studies on comparative functional genomics screens in these nematodes.
Studying Inter-Cluster Galaxy Filaments Through Stacking GMBCG Galaxy Cluster Pairs
Yuanyuan Zhang,J?rg P. Dietrich,Timothy A. McKay,Erin S. Sheldon,Alex T. Q. Nguyen
Physics , 2013, DOI: 10.1088/0004-637X/773/2/115
Abstract: We present a method to study the photometric properties of galaxies in filaments by stacking the galaxy populations between pairs of galaxy clusters. Using Sloan Digital Sky Survey data, this method can detect the inter-cluster filament galaxy overdensity with a significance of $\sim 5 \sigma$ out to $z=0.40$. Using this approach, we study the $g-r$ color and luminosity distribution of filament galaxies as a function of redshift. Consistent with expectation, filament galaxies are bimodal in their color distribution and contain a larger blue galaxy population than clusters. Filament galaxies are also generally fainter than cluster galaxies. More interestingly, the observed filament population seems to show redshift evolution at $0.12
nGASP – the nematode genome annotation assessment project
Avril Coghlan, Tristan J Fiedler, Sheldon J McKay, Paul Flicek, Todd W Harris, Darin Blasiar, the nGASP Consortium, Lincoln D Stein
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-549
Abstract: The most accurate gene-finders were 'combiner' algorithms, which made use of transcript- and protein-alignments and multi-genome alignments, as well as gene predictions from other gene-finders. Gene-finders that used alignments of ESTs, mRNAs and proteins came in second. There was a tie for third place between gene-finders that used multi-genome alignments and ab initio gene-finders. The median gene level sensitivity of combiners was 78% and their specificity was 42%, which is nearly the same accuracy reported for combiners in the human genome. C. elegans genes with exons of unusual hexamer content, as well as those with unusually many exons, short exons, long introns, a weak translation start signal, weak splice sites, or poorly conserved orthologs posed the greatest difficulty for gene-finders.This experiment establishes a baseline of gene prediction accuracy in Caenorhabditis genomes, and has guided the choice of gene-finders for the annotation of newly sequenced genomes of Caenorhabditis and other nematode species. We have created new gene sets for C. briggsae, C. remanei, C. brenneri, C. japonica, and Brugia malayi using some of the best-performing gene-finders.The promise of comparative genomics among the nematodes has motivated sequencing in Caenorhabditis elegans, C. briggsae, C. brenneri, C. remanei, and C. japonica [1-3]. While the C. elegans genome has been extensively annotated, relatively little information is available for the other Caenorhabditis genomes [4]. In addition, the genome of the distantly related nematode Brugia malayi was recently published [5], and those of many other nematodes are currently being sequenced such as Pristionchus, Haemonchus, Meloidogyne, and Trichinella. An essential step in the analysis of these genomes will be to identify and annotate their protein-coding genes, but it is not known which gene prediction systems perform best on nematode genomes. To address this issue, the nematode genome annotation assessment project (nGA
Weak Gravitational Lensing by the Nearby Cluster Abell 3667
M. Joffre,P. Fischer,J. Frieman,T. McKay,J. Mohr,R. Nichol,D. Johnston,E. Sheldon,G. Berstein
Physics , 1999, DOI: 10.1086/312681
Abstract: We present two weak lensing reconstructions of the nearby ($z_{cl}=0.055$) merging cluster Abell 3667, based on observations taken $\sim 1$ year apart under different seeing conditions. This is the lowest redshift cluster with a weak lensing mass reconstruction to date. The reproducibility of features in the two mass maps demonstrate that weak lensing studies of low-redshift clusters are feasible. These data constitute the first results from an X-ray luminosity-selected weak lensing survey of 19 low-redshift ($z< 0.1$) southern clusters.
Weak Lensing Mass of Nearby Clusters of Galaxies
M. Joffre,P. Fischer,J. Frieman,D. Johnston,T. McKay,J. Mohr,B. Nichol,E. Sheldon,C. Cantaloupo,G. Griffin,J. Peterson,A. K. Romer
Physics , 1999,
Abstract: We describe first results of a project to create weak lensing mass maps for a complete, X-ray luminosity-limited sample of 19 nearby (z < 0.1) southern galaxy clusters scheduled for Sunyaev-Zel'dovich observations by the Viper Telescope at the South Pole. We have collected data on 1/3 of the sample and present motivation for the project as well as projected mass maps of two clusters.
SDSS-RASS: Next Generation of Cluster-Finding Algorithms
R. Nichol,C. Miller,A. Connolly,S. Chong,C. Genovese,A. Moore,D. Reichart,J. Schneider,L. Wasserman,J. Annis,J. Brinkman,H. Bohringer,F. Castander,R. Kim,T. McKay,M. Postman,E. Sheldon,I. Szapudi,K. Romer,W. Voges
Physics , 2000, DOI: 10.1007/10849171_81
Abstract: We outline here the next generation of cluster-finding algorithms. We show how advances in Computer Science and Statistics have helped develop robust, fast algorithms for finding clusters of galaxies in large multi-dimensional astronomical databases like the Sloan Digital Sky Survey (SDSS). Specifically, this paper presents four new advances: (1) A new semi-parametric algorithm - nicknamed ``C4'' - for jointly finding clusters of galaxies in the SDSS and ROSAT All-Sky Survey databases; (2) The introduction of the False Discovery Rate into Astronomy; (3) The role of kernel shape in optimizing cluster detection; (4) A new determination of the X-ray Cluster Luminosity Function which has bearing on the existence of a ``deficit'' of high redshift, high luminosity clusters. This research is part of our ``Computational AstroStatistics'' collaboration (see Nichol et al. 2000) and the algorithms and techniques discussed herein will form part of the ``Virtual Observatory'' analysis toolkit.
An archived activation tagged population of Arabidopsis thaliana to facilitate forward genetics approaches
Stephen J Robinson, Lily H Tang, Brent AG Mooney, Sheldon J McKay, Wayne E Clarke, Matthew G Links, Steven Karcz, Sharon Regan, Yun-Yun Wu, Margaret Y Gruber, Dejun Cui, Min Yu, Isobel AP Parkin
BMC Plant Biology , 2009, DOI: 10.1186/1471-2229-9-101
Abstract: We have developed a population of almost 50,000 activation tagged A. thaliana lines that have been archived as individual lines to the T3 generation. The population is an excellent tool for both reverse and forward genetic screens and has been used successfully to identify a number of novel mutants. Insertion site sequences have been generated and mapped for 15,507 lines to enable further application of the population, while providing a clear distribution of T-DNA insertions across the genome. The population is being screened for a number of biochemical and developmental phenotypes, provisional data identifying novel alleles and genes controlling steps in proanthocyanidin biosynthesis and trichome development is presented.This publicly available population provides an additional tool for plant researcher's to assist with determining gene function for the many as yet uncharacterised genes annotated within the Arabidopsis genome sequence http://aafc-aac.usask.ca/FST webcite. The presence of enhancer elements on the inserted T-DNA molecule allows both knock-out and dominant activation phenotypes to be identified for traits of interest.The adoption of Arabidopsis thaliana as a model plant was suggested as early as 1943, yet its prominence in the study of plant genetics and physiology did not emerge until the 1980's with the recognition that its small genome and ease of manipulation offered the opportunity to mutate and study every gene within the genome [1]. The ability to fully realise this objective has been facilitated through the development of an elegantly simple transformation system [2] and the completion of the genome sequence [3]. The most recent annotation of the genome sequence has identified a total of 33,282 genes comprising 27,235 protein coding genes, 4,759 pseudogenes or transposable elements and 1,288 non coding RNAs (TAIR8 release; http://www.arabidopsis.org webcite). Computational biology tools allow the potential function of almost half of these prot
Dynamical Confirmation of SDSS Weak Lensing Scaling Laws
Timothy A. McKay,Erin Scott Sheldon,David Johnston,Eva K. Grebel,Francisco Prada,Hans-Walter Rix,Neta A. Bahcall,J. Brinkmann,István Csabai,Masataka Fukugita,D. Q. Lamb,Donald G. York
Physics , 2002, DOI: 10.1086/341364
Abstract: Galaxy masses can be estimated by a variety of methods; each applicable in different circumstances, and each suffering from different systematic uncertainties. Confirmation of results obtained by one technique with analysis by another is particularly important. Recent SDSS weak lensing measurements of the projected-mass correlation function reveal a linear relation between galaxy luminosities and the depth of their dark matter halos (measured on 260 \hinv kpc scales). In this work we use an entirely independent dynamical method to confirm these results. We begin by assembling a sample of 618 relatively isolated host galaxies, surrounded by a total of 1225 substantially fainter satellites. We observe the mean dynamical effect of these hosts on the motions of their satellites by assembling velocity difference histograms. Dividing the sample by host properties, we find significant variations in satellite velocity dispersion with host luminosity. We quantify these variations using a simple dynamical model, measuring \mtsd a dynamical mass within 260 \hinv kpc. The appropriateness of this mass reconstruction is checked by conducting a similar analysis within an N-body simulation. Comparison between the dynamical and lensing mass-to-light scalings shows reasonable agreement, providing some quantitative confirmation for the lensing results.
Modular Solutions to Equations of Generalized Halphen Type
J. Harnad,J. McKay
Physics , 1998, DOI: 10.1098/rspa.2000.0517
Abstract: Solutions to a class of differential systems that generalize the Halphen system are determined in terms of automorphic functions whose groups are commensurable with the modular group. These functions all uniformize Riemann surfaces of genus zero and have $q$--series with integral coefficients. Rational maps relating these functions are derived, implying subgroup relations between their automorphism groups, as well as symmetrization maps relating the associated differential systems.
Modular Invariants and Generalized Halphen Systems
J. Harnad,J. McKay
Physics , 1999,
Abstract: Generalized Halphen systems are solved in terms of functions that uniformize genus zero Riemann surfaces, with automorphism groups that are commensurable with the modular group. Rational maps relating these functions imply subgroup relations between their automorphism groups and symmetrization relations between the associated differential systems.
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