Genetics back issues from December 2007:
The Historical Discovery of the Nine Species in the Drosophila melanogaster Species Subgroup
Dec 01, 2007; ... DROSOPHILA melanogaster has played a central role in genetics research since the Morgan lab in the early years of the previous century. Yet, it has played a lesser role in the study of speciation. This is due to the fact that, until recently, there was only one closely related species, D ....
Large-Scale Survey of Cytosine Methylation of Retrotransposons and the Impact of Readout Transcription From Long Terminal Repeats on Expression of Adjacent Rice Genes
Dec 01, 2007; ... ABSTRACT Transposable elements (TEs) represent ~45% of the human genome and 50-90% of some grass genomes. While most elements contain inactivating mutations, others are reversibly inactivated (silenced) by epigenetic mechanisms, including cytosine methylation. Previous studies have shown ...
Extensive Allelic Variation in Gene Expression in Populus F^sub 1^ Hybrids
Dec 01, 2007; ... ABSTRACT Hybridization between plant species can induce speciation as well as phenotypic novelty and heterosis. Hybrids also can show genome rearrangements and gene expression changes compared with their parents. Here we determined the allelic variation in gene expression in Populus ...
Two Zinc-Cluster Transcription Factors Control Induction of Alternative Oxidase in Neurospora crassa
Dec 01, 2007; ... ABSTRACT The alternative oxidase transfers electrons from ubiquinol to molecular oxygen, providing a mechanism for bypassing the later steps of the standard cytochrome-mediated electron transport chain. The enzyme is found in an array of organisms and in many cases is known to be ...
Characterization of New Spt3 and TATA-Binding Protein Mutants of Saccharomyces cerevisiae: Spt3-TBP Allele-Specific Interactions and Bypass of Spt8
Dec 01, 2007; ... ABSTRACT The Spt-Ada-Gcn5-acetyltransferase (SAGA) complex of Saccharomyces cerevisiae is a multifunctional coactivator complex that has been shown to regulate transcription by distinct mechanisms. Previous results have shown that the Spt3 and Spt8 components of SAGA regulate initiation ...
Deletion-Mutant mtDNA Increases in Somatic Tissues but Decreases in Female Germ Cells With Age
Dec 01, 2007; ... ABSTRACT The proportions of mutant and wild-type mtDNA are crucial in determining the severity of mitochondrial diseases. It has been generally considered that deletion-mutant mtDNA has replication advantages and accumulates with time. Here, we examine the tissue-by-tissue proportions of ...
Differential Nuclear Localization Does Not Determine the Silencing Status of Saccharomyces cerevisiae Telomeres
Dec 01, 2007; ... In Saccharomyces cerevisiae, genes near telomeres are transcriptionally repressed, a phenomenon termed telomere position effect (TPE). Yeast telomeres cluster near the nuclear periphery, as do foci of proteins essential for TPE: Rap1p, Sir2-4p, and yKu70p/yKu80p. However, it is not clear if ...
Multiple Functions and Dynamic Activation of MPK-1 Extracellular Signal-Regulated Kinase Signaling in Caenorhabditis elegans Germline Development
Dec 01, 2007; ... ABSTRACT The raison d'etre of the germline is to produce oocytes and sperm that pass genetic material and cytoplasmic constituents to the next generation. To achieve this goal, many developmental processes must be executed and coordinated. ERK, the terminal MAP kinase of a number of ...
A Measurable Increase in Oxidative Damage Due to Reduction in Superoxide Detoxification Fails to Shorten the Life Span of Long-Lived Mitochondrial Mutants of Caenorhabditis elegans
Dec 01, 2007; ... ABSTRACT SOD-1 and SOD-2 detoxify superoxide in the cytoplasm and mitochondria. We find that, although several long-lived mutants of Caenorhabditis elegans have increased SOD levels, this phenomenon does not correlate with life span or growth rate. Furthermore, although disruption of ...
Evidence for Different Origins of Sex Chromosomes in Closely Related Oryzias Fishes: Substitution of the Master Sex-Determining Gene
Dec 01, 2007; ... ABSTRACT The medaka Oryzias latipes and its two sister species, O. curvinotus and O. luzonensis, possess an XX-XY sex-determination system. The medaka sex-determining gene DMY has been identified on the orthologous Y chromosome [O. latipes linkage group 1 (LG1)] of O. curvinotus ....
Genomewide Spatial Correspondence Between Nonsynonymous Divergence and Neutral Polymorphism Reveals Extensive Adaptation in Drosophila
Dec 01, 2007; ... ABSTRACT The effect of recurrent selective sweeps is a spatially heterogeneous reduction in neutral polymorphism throughout the genome. The pattern of reduction depends on the selective advantage and recurrence rate of the sweeps. Because many adaptive substitutions responsible for these ...
Differential Effect of Allorecognition Loci on Phenotype in Hydractinia symbiolongicarpus (Cnidaria: Hydrozoa)
Dec 01, 2007; ... ABSTRACT The allorecognition complex of Hydractinia symbiolongicarpus is a chromosomal interval containing two loci, alr1 and alr2, that controls fusion between genetically distinct colonies. Recombination between these two loci has been associated with a heterogeneous class of ...
On the Genealogy of a Duplicated Microsatellite
Dec 01, 2007; ... ABSTRACT When a microsatellite locus is duplicated in a diploid organism, a single pair of PCR primers may amplify as many as four distinct alleles. To study the evolution of a duplicated microsatellite, we consider a coalescent model with symmetric stepwise mutation. Conditional on the ...
Investigation of the Demographic and Selective Forces Shaping the Nucleotide Diversity of Genes Involved in Nod Factor Signaling in Medicago truncatula
Dec 01, 2007; ... ABSTRACT Symbiotic nitrogen-fixing rhizobia are able to trigger root deformation in their Fabaceae host plants, allowing their intracellular accommodation. They do so by delivering molecules called Nod factors. We analyzed the patterns of nucleotide polymorphism of five genes controlling ...
Analytical Description of Mutational Effects in Competing Asexual Populations
Dec 01, 2007; ... ABSTRACT The adaptation of a population to a new environment is a result of selection operating on a suite of stochastically occurring mutations. This article presents an analytical approach to understanding the population dynamics during adaptation, specifically addressing a system in ...
On Recombination-Induced Multiple and Simultaneous Coalescent Events
Dec 01, 2007; ... ABSTRACT Coalescent theory deals with the dynamics of how sampled genetic material has spread through a population from a single ancestor over many generations and is ubiquitous in contemporary molecular population genetics. Inherent in most applications is a continuous-time ...
Linkage Disequilibrium in Related Breeding Lines of Chickens
Dec 01, 2007; ... ABSTRACT High-density genotyping of single-nucleotide polymorphisms (SNPs) enables detection of quantitative trait loci (QTL) by linkage disequilibrium (LD) mapping using LD between markers and QTL and the subsequent use of this information for marker-assisted selection (MAS). The ...
Expression of 10 S-Class SLF-like Genes in Nicotiana alata Pollen and Its Implications for Understanding the Pollen Factor of the S Locus
Dec 01, 2007; ... ABSTRACT The S locus of Nicotiana alata encodes a polymorphic series of ribonucleases (S-RNases) that determine the self-incompatibility (SI) phenotype of the style. The pollen product of the S locus (pollen S) in N. alata is unknown, but in species from the related genus Petunia and in ...
Selection Against Demographic Stochasticity in Age-Structured Populations
Dec 01, 2007; ... ABSTRACT It has been shown that differences in fecundity variance can influence the probability of invasion of a genotype in a population; i.e., a genotype with lower variance in offspring number can be favored in finite populations even if it has a somewhat lower mean fitness than a ...
Inferring Human Population Sizes, Divergence Times and Rates of Gene Flow From Mitochondrial, X and Y Chromosome Resequencing Data
Dec 01, 2007; ... ABSTRACT We estimate parameters of a general isolation-with-migration model using resequence data from mitochondrial DNA (mtDNA), the Y chromosome, and two loci on the X chromosome in samples of 25-50 individuals from each of 10 human populations. Application of a coalescent-based Markov ...
The Evolution of Two Mutations During Clonal Expansion
Dec 01, 2007; ... ABSTRACT Knudson's two-hit hypothesis proposes that two genetic changes in the RB1 gene are the rate-limiting steps of retinoblastoma. In the inherited form of this childhood eye cancer, only one mutation emerges during somatic cell divisions while in sporadic cases, both alleles of RB1 ...
The Extent of Linkage Disequilibrium in Rice (Oryza sativa L.)
Dec 01, 2007; ... ABSTRACT Despite its status as one of the world's major crops, linkage disequilibrium (LD) patterns have not been systematically characterized across the genome of Asian rice (Oryza sativa). Such information is critical to fully exploit the genome sequence for mapping complex traits ...
Developmental and Cell Cycle Progression Defects in Drosophila Hybrid Males
Dec 01, 2007; ... ABSTRACT Matings between D. melanogaster females and males of sibling species in the D. melanogaster complex yield hybrid males that die prior to pupal differentiation. We have reexamined a previous report suggesting that the developmental defects in these lethal hybrid males reflect a ...
Diversification Rates Increase With Population Size and Resource Concentration in an Unstructured Habitat
Dec 01, 2007; ... ABSTRACT Understanding the mechanisms controlling the generation and maintenance of biodiversity provides some of the planet's greatest and most pressing challenges. Variation in resource concentration, which varies widely at multiple scales, may cause biodiversity to increase, decrease, ...
Joint Inference of the Distribution of Fitness Effects of Deleterious Mutations and Population Demography Based on Nucleotide Polymorphism Frequencies
Dec 01, 2007; ... ABSTRACT The distribution of fitness effects of new mutations (DFE) is important for addressing several questions in genetics, including the nature of quantitative variation and the evolutionary fate of small populations. Properties of the DFE can be inferred by comparing the ...
Gene-Based Sequence Diversity Analysis of Field Pea (Pisum)
Dec 01, 2007; ... ABSTRACT Sequence diversity of 39 dispersed gene loci was analyzed in 48 diverse individuals representative of the genus Pisum. The different genes show large variation in diversity parameters, suggesting widely differing levels of selection and a high overall diversity level for the ...
Nucleotide Variation in Wild and Inbred Mice
Dec 01, 2007; ... ABSTRACT The house mouse is a well-established model organism, particularly for studying the genetics of complex traits. However, most studies of mice use classical inbred strains, whose genomes derive from multiple species. Relatively little is known about the distribution of genetic ...
The Reacquisition of Biotin Prototrophy in Saccharomyces cerevisiae Involved Horizontal Gene Transfer, Gene Duplication and Gene Clustering
Dec 01, 2007; ... ABSTRACT The synthesis of biotin, a vitamin required for many carboxylation reactions, is a variable trait in Saccharomyces cerevisiae. Many S. cerevisiae strains, including common laboratory strains, contain only a partial biotin synthesis pathway. We here report the identification of ...
Detection of Quantitative Trait Loci Influencing Recombination Using Recombinant Inbred Lines
Dec 01, 2007; ... ABSTRACT The genetic basis of variation in recombination in higher plants is polygenic and poorly understood, despite its theoretical and practical importance. Here a method of detecting quantitative trait loci (QTL) influencing recombination in recombinant inbred lines (RILs) is ...
Interspecific Recombinant Congenic Strains Between C57BL/6 and Mice of the Mus spretus Species: A Powerful Tool to Dissect Genetic Control of Complex Traits
Dec 01, 2007; ... ABSTRACT Complex traits are under the genetic control of multiple genes, often with weak effects and strong epistatic interactions. We developed two new collections of mouse strains to improve genetic dissection of complex traits. They are derived from several backcrosses of the Mus ...
Quantitative Trait Loci for the Circadian Clock in Neurospora crassa
Dec 01, 2007; ... ABSTRACT Neurospora crassa has been a model organism for the study of circadian clocks for the past four decades. Among natural accessions of Neurospora crassa, there is significant variation in clock phenotypes. In an attempt to investigate natural allelic variants contributing to ...
Major Regulatory Genes in Maize Contribute to Standing Variation in Teosinte (Zea mays ssp. parviglumis)
Dec 01, 2007; ... ABSTRACT In plants, many major regulatory genes that control plant growth and development have been identified and characterized. Despite a detailed knowledge of the function of these genes little is known about how they contribute to the natural variation for complex traits. To ...
Mapping Quantitative Trait Loci From a Single-Tail Sample of the Phenotype Distribution Including Survival Data
Dec 01, 2007; ... ABSTRACT A new effective Bayesian quantitative trait locus (QTL) mapping approach for the analysis of single-tail selected samples of the phenotype distribution is presented. The approach extends the affected-only tests to single-tail sampling with quantitative traits such as the ...
Genetic Analysis of Craniofacial Traits in the Medaka
Dec 01, 2007; ... ABSTRACT Family and twin studies suggest that a substantial genetic component underlies individual differences in craniofacial morphology. In the current study, we quantified 444 craniofacial traits in 100 individuals from two inbred medaka (Oryzias latipes) strains, HNI and Hd-rR ....
The Impact of Genetic Relationship Information on Genome-Assisted Breeding Values
Dec 01, 2007; ... ABSTRACT The success of genomic selection depends on the potential to predict genome-assisted breeding values (GEBVs) with high accuracy over several generations without additional phenotyping after estimating marker effects. Results from both simulations and practical applications have ...
Quantifying Evidence for Candidate Gene Polymorphisms: Bayesian Analysis Combining Sequence-Specific and Quantitative Trait Loci Colocation Information
Dec 01, 2007; ... ABSTRACT We calculate posterior probabilities for candidate genes as a function of genomic location. Posterior probabilities for quantitative trait loci (QTL) presence in a small interval are calculated using a Bayesian model-selection approach based on the Bayesian information criterion ...
Mapping Quantitative Trait Loci Affecting Susceptibility to Marek's Disease Virus in a Backcross Population of Layer Chickens
Dec 01, 2007; ... ABSTRACT Marek's disease (MD), caused by the oncogenic MD avian herpes virus (MDV), is a major source of economic losses to the poultry industry. A reciprocal backcross (BC) population (total 2052 individuals) was generated by crossing two partially inbred commercial Leghorn layer lines ...
Flowering Time Quantitative Trait Loci Analysis of Oilseed Brassica in Multiple Environments and Genomewide Alignment with Arabidopsis
Dec 01, 2007; ... ABSTRACT Most agronomical traits exhibit quantitative variation, which is controlled by multiple genes and are environmentally dependent. To study the genetic variation of flowering time in Brassica napus, a DH population and its derived reconstructed F^sub 2^ population were planted in ...
The Formation of the Central Element of the Synaptonemal Complex May Occur by Multiple Mechanisms: The Roles of the N- and C-Terminal Domains of the Drosophila C(3)G Protein in Mediating Synapsis and Recombination
Dec 01, 2007; ... ABSTRACT In Drosophila melanogaster oocytes, the C(3)G protein comprises the transverse filaments (TFs) of the synaptonemal complex (SC). Like other TF proteins, such as Zip1p in yeast and SCP1 in mammals, C(3)G is composed of a central coiled-coil-rich domain flanked by N- and ...
A Microsatellite Genetic Map of the Turbot (Scophthalmus maximus)
Dec 01, 2007; ... ABSTRACT A consensus microsatellite-based linkage map of the turbot (Scophthalmus maximus) was constructed from two unrelated families. The mapping panel was derived from a gynogenetic family of 96 haploid embryos and a biparental diploid family of 85 full-sib progeny with known linkage ...
Zinc Regulates the Stability of Repetitive Minisatellite DNA Tracts During Stationary Phase
Dec 01, 2007; ... ABSTRACT Repetitive minisatellite DNA tracts are stable in mitotic cells but unstable in meiosis, altering in repeat number and repeat composition. As relatively little is known about the factors that influence minisatellite stability, we isolated mutations that destabilize a ...
Investigating the Genetic Circuitry of Mastermind in Drosophila, a Notch Signal Effector
Dec 01, 2007; ... ABSTRACT Notch signaling regulates multiple developmental processes and is implicated in various human diseases. Through use of the Notch transcriptional co-activator mastermind, we conducted a screen for Notch signal modifiers using the Exelixis collection of insertional mutations, ...
Construction of a Sequence-Tagged High-Density Genetic Map of Papaya for Comparative Structural and Evolutionary Genomics in Brassicales
Dec 01, 2007; ... ABSTRACT A high-density genetic map of papaya (Carica papaya L.) was constructed using microsatellite markers derived from BAC end sequences and whole-genome shot gun sequences. Fifty-four F^sub 2^ plants derived from varieties AU9 and SunUp were used for linkage mapping. A total of 707 ...
Genomic Instability Within Centromeres of Interspecific Marsupial Hybrids
Dec 01, 2007; ... ABSTRACT Several lines of evidence suggest that, within a lineage, particular genomic regions are subject to instability that can lead to specific types of chromosome rearrangements important in species incompatibility. Within family Macropodidae (kangaroos, wallabies, bettongs, and ...
The Hermes Transposon of Musca domestica Is an Efficient Tool for the Mutagenesis of Schizosaccharomyces pombe
Dec 01, 2007; ... ABSTRACT Currently, no transposon-based method for the mutagenesis of Schizosaccharomyces pombe exists. We have developed such a system based on the introduction of the hermes transposon from the housefly into S. pombe. This system efficiently disrupts open reading frames and allows the ...
Synthetic Lethal Interactions Identify Phenotypic "Interologs" of the Spindle Assembly Checkpoint Components
Dec 01, 2007; ... ABSTRACT Here, we report genetic interactions with mdf-1(gk2)/MAD1 in Caenorhabditis elegans. Nine are evolutionarily conserved or phenotypic "interologs" and two are novel enhancers, hcp-1 and bub-3. We show that HCP-1 and HCP-2, the two CENP-F-related proteins, recently implicated in ...
The Tetrad-Pollen Model Fails to Explain the Bias in Mendel's Pea (Pisum sativum) Experiments
Dec 01, 2007; ... ABSTRACT For >40 years, geneticists and science historians have appealed to the tetrad-pollen model as an explanation of the bias toward expectation in Mendel's data, albeit without experimental support. Our experiments demonstrate that pollen sampling during self-pollination in pea ...
The Role of Double-Stranded Break Repair in the Creation of Phenotypic Diversity at Cereal VRN1 Loci
Dec 01, 2007; ... ABSTRACT Nonhomologous repair of double-stranded breaks, although fundamental to the maintenance of genomic integrity in all eukaryotes, has received little attention as to its evolutionary consequences in the generation and selection of phenotypic diversity. Here we document the role of ...
Subtelomeric Elements Influence But Do Not Determine Silencing Levels at Saccharomyces cerevisiae Telomeres
Dec 01, 2007; ... ABSTRACT In Saccharomyces cerevisiae, genes placed near telomeres are transcriptionally repressed (telomere position effect, TPE). Although telomeric DNA sequence is the same at all chromosome ends, the subtelomeric elements (STEs) and level of TPE vary from telomere to telomere. We ...
Cell Cycle Arrest of Stamen Initials in Maize Sex Determination
Dec 01, 2007; ... ABSTRACT The maize sex determination pathway results in the arrest of stamen in ear spikelets and the abortion of pistils in both the tassel spikelets and in the secondary florets of ear spikelets. Arrested stamen cells showed no signs of DNA fragmentation, an absence of CYCLIN B ...
Evolution and Horizontal Transfer of a DD37E DNA Transposon in Mosquitoes
Dec 01, 2007; ... ABSTRACT ITmD37E, a unique class II transposable element (TE) with an ancient origin, appears to have been involved in multiple horizontal transfers in mosquitoes as ITmD37E sequences from 10 mosquito species of five genera share high nucleotide (nt) identities. For example, ITmD37E ...