3,562 Results

• Detecting Amino Acid Sites Under Positive Selection and Purifying Selection

  Tim Massingham, Nick Goldman

  Genetics March 2005 169: 1753-1762; https://doi.org/10.1534/genetics.104.032144

  ...ABSTRACT An excess of nonsynonymous over synonymous substitution at individual amino acid sites is an important indicator that positive selection has affected the evolution of a protein between the extant sequences under study and their most recent common ancestor. Several methods exist to detect ~~~
• Statistical Tests of the Coalescent Model Based on the Haplotype Frequency Distribution and the Number of Segregating Sites

  Hideki Innan, Kangyu Zhang, Paul Marjoram, Simon Tavaré, Noah A. Rosenberg

  Genetics March 2005 169: 1763-1777; https://doi.org/10.1534/genetics.104.032219

  ...CB2 2XZ, United Kingdom Manuscript received June 18, 2004 Accepted for publication December 8, 2004 ABSTRACT Several tests of neutral evolution employ the observed number of segregating sites and properties of the haplotype frequency distribution as summary statistics and use simulations to obtain ~~~
• Genome-Wide Characterization of Tetrahymena thermophila Chromosome Breakage Sites. I. Cloning and Identification of Functional Sites

  Eileen Hamilton, Peter Bruns, Cindy Lin, Virginia Merriam, Eduardo Orias, Linh Vong, Donna Cassidy-Hanley

  Genetics August 2005 170: 1611-1621; https://doi.org/10.1534/genetics.104.031401

  ...for publication May 10, 2005 ABSTRACT The chromosomes of the macronuclear (expressed) genome of Tetrahymena thermophila are generated by developmental fragmentation of the five micronuclear (germline) chromosomes. This fragmentation is site specific and directed by a conserved 15-bp chromosome breakage sequence ~~~
• Effect of Misoriented Sites on Neutrality Tests With Outgroup

  Emmanuelle Baudry, Frantz Depaulis

  Genetics November 2003 165: 1619-1622;

  ...population of constant size. which is based on the total number of polymorphicDepartures from this model are typically attributed to sites, and Tajimas (1983) diversity (respectively) toselective or demographic effects. A rarely considered e, the number of derived unique mutations (mutationsalternative ~~~
• Genome-Wide Characterization of Tetrahymena thermophila Chromosome Breakage Sites. II. Physical and Genetic Mapping

  Donna Cassidy-Hanley, Yelena Bisharyan, Vladimir Fridman, Joseph Gerber, Cindy Lin, Eduardo Orias, Judith D. Orias, Hilary Ryder, Linh Vong, Eileen P. Hamilton

  Genetics August 2005 170: 1623-1631; https://doi.org/10.1534/genetics.104.031435

  ...) genome of Tetrahymena thermophila are generated by developmental fragmentation of the five micronuclear (germline) chromosomes. This fragmentation is site specific, directed by a conserved chromosome breakage sequence (Cbs element). An accompanying article in this issue reports the development ~~~
• Alternative Transcription Initiation Sites and Polyadenylation Sites Are Recruited During Mu Suppression at the rf2a Locus of Maize

  Xiangqin Cui, An-Ping Hsia, Feng Liu, Daniel A. Ashlock, Roger P. Wise, Patrick S. Schnable

  Genetics February 2003 163: 685-698;

  ...a novel Mu transposon insertion (Mu10) in its 5 untranslated region (UTR). The suppressible rf2a-m9390 allele has a Mu1 insertion in its 5 UTR. During suppression, alternative transcription initiation sites flanking the Mu1 transposon yield functional transcripts. The suppressible rf2a-m8110 allele has ~~~
• Loss-of-Function Alleles of the JIL-1 Histone H3S10 Kinase Enhance Position-Effect Variegation at Pericentric Sites in Drosophila Heterochromatin

  Xiaomin Bao, Huai Deng, Jørgen Johansen, Jack Girton, Kristen M. Johansen

  Genetics June 2007 176: 1355-1358; https://doi.org/10.1534/genetics.107.073676

  ...Accepted for publication April 12, 2007 ABSTRACT In this study we show that loss-of-function alleles of the JIL-1 histone H3S10 kinase act as enhancers of position-effect variegation at pericentric sites whereas the gain-of-function JIL-1Su(var)3-13 allele acts as a suppressor strongly supporting ~~~
• The Distribution of Transgene Insertion Sites in Barley Determined by Physical and Genetic Mapping

  Haroldo Salvo-Garrido, Silvia Travella, Lorelei J. Bilham, Wendy A. Harwood, John W. Snape

  Genetics July 2004 167: 1371-1379; https://doi.org/10.1534/genetics.103.023747

  ...received November 6, 2003 Accepted for publication April 2, 2004 ABSTRACT The exact site of transgene insertion into a plant host genome is one feature of the genetic transformation process that cannot, at present, be controlled and is often poorly understood. The site of transgene insertion may have ~~~
• Mapping Sites of Positive Selection and Amino Acid Diversification in the HIV Genome

  Tulio de Oliveira, Marco Salemi, Michelle Gordon, Anne-Mieke Vandamme, Estrelita Janse van Rensburg, Susan Engelbrecht, Hoosen M. Coovadia, Sharon Cassol

  Genetics July 2004 167: 1047-1058; https://doi.org/10.1534/genetics.103.018135

  ...to identify positively selected sites that are likely to be involved in the immune control of HIV-1. Analysis of subtypes B and C revealed widespread adaptive evolution. Positively selected amino acids were detected in all nine HIV-1 proteins, including Env. Of particular interest was the high level ~~~
• Properties of Natural Double-Strand-Break Sites at a Recombination Hotspot in Saccharomyces cerevisiae

  Stuart J. Haring, George R. Halley, Alex J. Jones, Robert E. Malone

  Genetics September 2003 165: 101-114;

  ..., 2003 ABSTRACT This study addresses three questions about the properties of recombination hotspots in Saccharomyces cerevisiae : How much DNA is required for double-strand-break (DSB) site recognition? Do naturally occurring DSB sites compete with each other in meiotic recombination? What role does ~~~

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