Genetics back issues from May 2007:
Molecular Clock: An Anti-neo-Darwinian Legacy
May 01, 2007; ... AS early as the time of the rediscovery of Mendel's laws, George H. F. Nuttal measured the amount of precipitate of normal sera from great apes,monkeys, and some other mammals. His crude method, using rabbit antiserum directed against whole human serum, indicated that except for flying lemurs, ...
Why Are There Still Over 1000 Uncharacterized Yeast Genes?
May 01, 2007; ... ABSTRACT The yeast genetics community has embraced genomic biology, and there is a general understanding that obtaining a full encyclopedia of functions of the ~6000 genes is a worthwhile goal. The yeast literature comprises over 40,000 research papers, and the number of yeast ...
Proofreading and Secondary Structure Processing Determine the Orientation Dependence of CAG*CTG Trinucleotide Repeat Instability in Escherichia coli
May 01, 2007; ... ABSTRACT Expanded CAG*CTG trinucleotide repeat tracts are associated with several human inherited diseases, including Huntington's disease, myotonic dystrophy, and spinocerebellar ataxias. Here we describe a new model system to investigate repeat instability in the Escherichia coli ...
Diverse Roles for Histone H2A Modifications in DNA Damage Response Pathways in Yeast
May 01, 2007; ... ABSTRACT There are many types of DNA damage that are repaired by a multiplicity of different repair pathways. All damage and repair occur in the context of chromatin, and histone modifications are involved in many repair processes. We have analyzed the roles of H2A and its modifications ...
Neurospora Spore Killers Sk-2 and Sk-3 Suppress Meiotic Silencing by Unpaired DNA
May 01, 2007; ... ABSTRACT In Neurospora crassa, pairing of homologous DNA segments is monitored during meiotic prophase I. Any genes not paired with a homolog, as well as any paired homologs of that gene, are silenced during the sexual phase by a mechanism known as meiotic silencing by unpaired DNA ...
Meiotic Recombination in Drosophila Msh6 Mutants Yields Discontinuous Gene Conversion Tracts
May 01, 2007; ... ABSTRACT Crossovers (COs) generated through meiotic recombination are important for the correct segregation of homologous chromosomes during meiosis. Several models describing the molecular mechanism of meiotic recombination have been proposed. These models differ in the arrangement of ...
Heteroduplex DNA in Meiotic Recombination in Drosophila mei-9 Mutants
May 01, 2007; ... ABSTRACT Meiotic recombination gives rise to crossovers, which are required in most organisms for the faithful segregation of homologous chromosomes during meiotic cell division. Characterization of crossover-defective mutants has contributed much to our understanding of the molecular ...
Genetic Positioning of Centromeres Using Half-Tetrad Analysis in a 4x-2x Cross Population of Potato
May 01, 2007; ... ABSTRACT From biological and genetic standpoints, centromeres play an important role in the delivery of the chromosome complement to the daughter cells at cell division. The positions of the centromeres of potato were determined by half-tetrad analysis in a 4x-2x population where the ...
Suppression of the Schizosaccharomyces pombe cut12.1 Cell-Cycle Defect by Mutations in cdc25 and Genes Involved in Transcriptional and Translational Control
May 01, 2007; ... ABSTRACT Cdc25 phosphatase primes entry to mitosis by removing the inhibitory phosphate that is transferred to mitosis promoting factor (MPF) by Wee1 related kinases. A positive feedback loop then boosts Cdc25 and repressesWee1 activities to drive full-scale MPF activation and commitment ...
Suppressors of zyg-1 Define Regulators of Centrosome Duplication and Nuclear Association in Caenorhabditis elegans
May 01, 2007; ... ABSTRACT In Caenorhabditis elegans, the kinase ZYG-1 is required for centrosome duplication. To identify factors that interact with ZYG-1, we used a classical genetic approach and identified 21 szy (suppressor of zyg-1) genes that when mutated restore partial viability to a zyg-1 mutant ....
Integrative Mapping of Gossypium hirsutum L. by Meiotic Fluorescent in Situ Hybridization of a Tandemly Repetitive Sequence (B77)
May 01, 2007; ... ABSTRACT We determined the relative positions of the tandem-repeat molecular cytogenetic marker B77, translocation breakpoints, and telosome arms in Gossypium hirsutum cytogenetic stocks by fluorescence in situ hybridization (FISH) analysis of meiotic quadrivalents in 16 single and 2 ...
Transcriptional Control of Gluconeogenesis in Aspergillus nidulans
May 01, 2007; ... ABSTRACT Aspergillus nidulans can utilize carbon sources that result in the production of TCA cycle intermediates, thereby requiring gluconeogenesis. We have cloned the acuG gene encoding fructose-1,6 bisphosphatase and found that expression of this gene is regulated by carbon catabolite ...
Specific Defects in Different Transcription Complexes Compensate for the Requirement of the Negative Cofactor 2 Repressor in Saccharomyces cerevisiae
May 01, 2007; ... ABSTRACT Negative cofactor 2 (NC2) has been described as an essential and evolutionarily conserved transcriptional repressor, although in vitro and in vivo experiments suggest that it can function as both a positive and a negative effector of transcription. NC2 operates by interacting ...
Role of the mod(mdg4) Common Region in Homolog Segregation in Drosophila Male Meiosis
May 01, 2007; ... ABSTRACT Homologous chromosomes must pair and establish stable connections during prophase I of meiosis to segregate reliably from each other at anaphase I. In most organisms, the stable connections, called chiasmata, arise from crossovers. In Drosophila males, homologs pair and ...
Differential Epigenetic Regulation Within an Arabidopsis Retroposon Family
May 01, 2007; ... ABSTRACT We previously reported a novel family of Arabidopsis thaliana nonautonomous retroposons, Sadhu, showing epigenetic variation in natural populations. Here, we show that transcripts corresponding to Sadhu elements accumulate in a subset of mutants carrying disruptions in genes ...
Modulation of Ubc4p/Ubc5p-Mediated Stress Responses by the RING-Finger-Dependent Ubiquitin-Protein Ligase Not4p in Saccharomyces cerevisiae
May 01, 2007; ... ABSTRACT The Ccr4-Not complex consists of nine subunits and acts as a regulator of mRNA biogenesis in Saccharomyces cerevisiae. The human ortholog of yeast NOT4, CNOT4, displays UbcH5B-dependent ubiquitin-protein ligase (E3 ligase) activity in a reconstituted in vitro system. However, an ...
The Biologically Relevant Targets and Binding Affinity Requirements for the Function of the Yeast Actin-Binding Protein 1 Src-Homology 3 Domain Vary With Genetic Context
May 01, 2007; ... ABSTRACT Many protein-protein interaction domains bind to multiple targets. However, little is known about how the interactions of a single domain with many proteins are controlled and modulated under varying cellular conditions. In this study, we investigated the in vivo effects of ...
Genetic Modifiers of Drosophila Palmitoyl-Protein Thioesterase 1-Induced Degeneration
May 01, 2007; ... ABSTRACT Infantile neuronal ceroid lipofuscinosis (INCL) is a pediatric neurodegenerative disease caused by mutations in the human CLN1 gene. CLN1 encodes palmitoyl-protein thioesterase 1 (PPT1), suggesting an important role for the regulation of palmitoylation in normal neuronal ...
Caenorhabditis elegans Mutants Resistant to Attachment of Yersinia Biofilms
May 01, 2007; ... ABSTRACT The detailed composition and structure of the Caenorhabditis elegans surface are unknown. Previous genetic studies used antibody or lectin binding to identify srf genes that play roles in surface determination. Infection by Microbacterium nematophilum identified bus (bacterially ...
basA Regulates Cell Wall Organization and Asexual/Sexual Sporulation Ratio in Aspergillus nidulans
May 01, 2007; ... ABSTRACT Sphingolipid C4 hydroxylase catalyzes the conversion of dihydrosphingosine to phytosphingosine. In Saccharomyces cerevisiae, Sur2 is essential for sphingolipid C4 hydroxylation activity but not essential for normal growth. Here we demonstrate that the Aspergillus nidulans Sur2 ...
DDB2, DDB1A and DET1 Exhibit Complex Interactions During Arabidopsis Development
May 01, 2007; ... ABSTRACT Damaged DNA-binding proteins 1 and 2 (DDB1 and DDB2) are subunits of the damaged DNA-binding protein complex (DDB). DDB1 is also found in the same complex as DE-ETIOLATED 1 (DET1), a negative regulator of light-mediated responses in plants. Arabidopsis has two DDB1 homologs, ...
LIN-61, One of Two Caenorhabditis elegans Malignant-Brain-Tumor-Repeat-Containing Proteins, Acts With the DRM and NuRD-Like Protein Complexes in Vulval Development but Not in Certain Other Biological Processes
May 01, 2007; ... ABSTRACT Vulval development in Caenorhabiditis elegans is inhibited by the redundant functions of the synthetic multivulva (synMuv) genes. At least 26 synMuv genes have been identified, many of which appear to act via transcriptional repression. Here we report the molecular ...
Divergent Regulatory OsMADS2 Functions Control Size, Shape and Differentiation of the Highly Derived Rice Floret Second-Whorl Organ
May 01, 2007; ... ABSTRACT Functional diversification of duplicated genes can contribute to the emergence of new organ morphologies. Model eudicot plants like Arabidopsis thaliana and Antirrhinum majus have a single PI/GLO gene that together with AP3/DEF regulate petal and stamen formation. Lodicules of ...
Evolutionary Conservation of the FLOWERING LOCUS C-Mediated Vernalization Response: Evidence From the Sugar Beet (Beta vulgaris)
May 01, 2007; ... ABSTRACT In many plant species, exposure to a prolonged period of cold during the winter promotes flowering in the spring, a process termed vernalization. In Arabidopsis thaliana, the vernalization requirement of winter-annual ecotypes is caused by the MADS-box gene FLOWERING LOCUS C ...
Concerted Evolution Within the Drosophila dumpy Gene
May 01, 2007; ... ABSTRACT We have determined by reverse Southern analysis and direct sequence comparisons that most of the dumpy gene has evolved in the dipteran and other insect orders by purifying selection acting on amino acid replacements. One region, however, is evolving rapidly due to unequal ...
Test of Genetical Isochronism for Longitudinal Samples of DNA Sequences
May 01, 2007; ... ABSTRACT Longitudinal samples of DNA sequences, the DNA sequences sampled from the same population at different time points, have increasingly been used to study the evolutionary process of fast-evolving organisms, e.g., RNA virus, in recent years. We propose in this article several ...
The Genetics of Hybrid Male Sterility Between the Allopatric Species Pair Drosophila persimilis and D. pseudoobscura bogotana: Dominant Sterility Alleles in Collinear Autosomal Regions
May 01, 2007; ... ABSTRACT F^sub 1^ hybrid male sterility is thought to result from interactions between loci on the X chromosome and dominant-acting loci on the autosomes. While X-linked loci that contribute to hybrid male sterility have been precisely localized in many animal taxa, their dominant ...
Genetic Similarities Within and Between Human Populations
May 01, 2007; ... ABSTRACT The proportion of human genetic variation due to differences between populations is modest, and individuals from different populations can be genetically more similar than individuals from the same population. Yet sufficient genetic data can permit accurate classification of ...
Natural Selection on Fecundity Variance in Subdivided Populations: Kin Selection Meets Bet Hedging
May 01, 2007; ... ABSTRACT In a series of seminal articles in 1974, 1975, and 1977, J. H. Gillespie challenged the notion that the "fittest" individuals are those that produce on average the highest number of offspring. He showed that in small populations, the variance in fecundity can determine fitness ...
Quantitative Trait Loci Associated with Photoperiodic Response and Stage of Diapause in the Pitcher-Plant Mosquito, Wyeomyia smithii
May 01, 2007; ... ABSTRACT A wide variety of temperate animals rely on length of day (photoperiodism) to anticipate and prepare for changing seasons by regulating the timing of development, reproduction, dormancy, and migration. Although the molecular basis of circadian rhythms regulating daily activities ...
Comparative Physical Mapping Between Oryza sativa (AA Genome Type) and O. punctata (BB Genome Type)
May 01, 2007; ... ABSTRACT A comparative physical map of the AA genome (Oryza sativa) and the BB genome (O. punctata) was constructed by aligning a physical map of O. punctata, deduced from 63,942 BAC end sequences (BESs) and 34,224 fingerprints, onto the O. sativa genome sequence. The level of ...
A Novel Type of Sequence Variation: Multiple-Nucleotide Length Polymorphisms Discovered in the Bovine Genome
May 01, 2007; ... ABSTRACT Three types of sequence variations-single-nucleotide polymorphisms (SNPs), insertions and deletions (indels), and short tandem repeats (STRs)-have been extensively reported in mammalian genomes. In this study, we discovered a novel type of sequence variation, i.e., ...
Control of Sigma Virus Multiplication by the ref(2)P Gene of Drosophila melanogaster: An in Vivo Study of the PB1 Domain of Ref(2)P
May 01, 2007; ... ABSTRACT Ref(2)P has been described as one of the Drosophila proteins that interacts with the sigma virus cycle. We generated alleles to identify critical residues involved in the restrictive (inhibiting viral multiplication) or permissive (allowing viral multiplication) character of ...
A Maximum-Likelihood Method for the Estimation of Pairwise Relatedness in Structured Populations
May 01, 2007; ... ABSTRACT A maximum-likelihood estimator for pairwise relatedness is presented for the situation in which the individuals under consideration come from a large outbred subpopulation of the population for which allele frequencies are known. We demonstrate via simulations that a variety of ...
Neutral Evolution of Multiple Quantitative Characters: A Genealogical Approach
May 01, 2007; ... ABSTRACT The G matrix measures the components of phenotypic variation that are genetically heritable. The structure of G, that is, its principal components and their associated variances, determines, in part, the direction and speed of multivariate trait evolution. In this article we ...
Adaptive Divergence in Experimental Populations of Pseudomonas fluorescens. III. Mutational Origins of Wrinkly Spreader Diversity
May 01, 2007; ... ABSTRACT Understanding the connections among genotype, phenotype, and fitness through evolutionary time is a central goal of evolutionary genetics. Wrinkly spreader (WS) genotypes evolve repeatedly in model Pseudomonas populations and show substantial morphological and fitness ...
Experimental Estimate of the Abundance and Effects of Nearly Neutral Mutations in the RNA Virus [straight phi]6
May 01, 2007; ... ABSTRACT Although the frequency and effects of neutral and nearly neutral mutations are critical to evolutionary patterns and processes governed by genetic drift, the small effects of such mutations make them difficult to study empirically. Here we present the results of a ...
Variance of the Parental Genome Contribution to Inbred Lines Derived From Biparental Crosses
May 01, 2007; ... ABSTRACT The expectation of the parental genome contribution to inbred lines derived from biparental crosses or backcrosses is well known, but no theoretical results exist for its variance. Our objective was to derive the variance of the parental genome contribution to inbred lines ...
Genetic Improvement of Traits Affected by Interactions Among Individuals: Sib Selection Schemes
May 01, 2007; ... ABSTRACT Livestock populations are usually kept in groups. As a consequence, social interactions among individuals affect productivity, health, and welfare. Current selection methods (individual selection), however, ignore those interactions and yield suboptimal or in some cases even ...
Evolution of Coadaptation in a Subdivided Population
May 01, 2007; ... ABSTRACT The interplay between population subdivision and epistasis is investigated by studying the fixation probability of a coadapted haplotype in a subdivided population. Analytical and simulation models are developed to study the evolutionary fate of two conditionally neutral ...
Evolution of DNA Double-Strand Break Repair by Gene Conversion: Coevolution Between a Phage and a Restriction-Modification System
May 01, 2007; ... ABSTRACT The necessity to repair genome damage has been considered to be an immediate factor responsible for the origin of sex. Indeed, attack by a cellular restriction enzyme of invading DNA from several bacteriophages initiates recombinational repair by gene conversion if there is ...
A Microsatellite-Based, Gene-Rich Linkage Map Reveals Genome Structure, Function and Evolution in Gossypium
May 01, 2007; ... ABSTRACT The mapping of functional genes plays an important role in studies of genome structure, function, and evolution, as well as allowing gene cloning and marker-assisted selection to improve agriculturally important traits. Simple sequence repeats (SSRs) developed from expressed ...
Nup96-Dependent Hybrid Lethality Occurs in a Subset of Species From the simulans Clade of Drosophila
May 01, 2007; ... ABSTRACT The cross of Drosophila melanogaster females to D. simulans males typically produces lethal F^sub 1^ hybrid males. F^sub 1^ male lethality is suppressed when the D. simulans Lhr^sup 1^ hybrid rescue strain is used. Viability of these F^sub 1^ males carrying Lhr^sup 1^ is in turn ...
Identifying Quantitative Trait Locus by Genetic Background Interactions in Association Studies
May 01, 2007; ... ABSTRACT Association studies are designed to identify main effects of alleles across a potentially wide range of genetic backgrounds. To control for spurious associations, effects of the genetic background itself are often incorporated into the linear model, either in the form of ...
Power to Detect Higher-Order Epistatic Interactions in a Metabolic Pathway Using a New Mapping Strategy
May 01, 2007; ... ABSTRACT Epistatic interactions among quantitative trait loci (QTL) contribute substantially to the variation in complex traits. The main objectives of this study were to (i) compare three- vs. four-step genome scans to identify three-way epistatic interactions among QTL belonging to a ...
Identification of Quantitative Trait loci and Environmental Interactions for Accumulation and Remobilization of Water-Soluble Carbohydrates in Wheat (Triticum aestivum L.) Stems
May 01, 2007; ... ABSTRACT Genetic analyses of nine traits associated with stem water-soluble carbohydrate (SWSC) accumulation and remobilization at grain-filling period under drought stress (DS) and well-watered (WW) conditions were undertaken using doubled haploid lines (DHLs) derived from two Chinese ...
Modeling Inheritance of Malignant Melanoma With DNA Markers in Sinclair Swine
May 01, 2007; ... ABSTRACT Cutaneous malignant melanoma in Sinclair swine is a hereditary disease that develops in utero or during the first 6 weeks of life. In many cases, the tumors regress and piglets survive the disease. Two different sets of gene(s) might be involved in the disease: tumor initiator ...
The FLOWERING LOCUS T-Like Gene Family in Barley (Hordeum vulgare)
May 01, 2007; ... ABSTRACT The FLOWERING LOCUS T (FT ) gene plays a central role in integrating flowering signals in Arabidopsis because its expression is regulated antagonistically by the photoperiod and vernalization pathways. FT belongs to a family of six genes characterized by a ...
Mapping Quantitative Trait Loci for Expression Abundance
May 01, 2007; ... ABSTRACT Mendelian loci that control the expression levels of transcripts are called expression quantitative trait loci (eQTL). When mapping eQTL, we often deal with thousands of expression traits simultaneously, which complicates the statistical model and data analysis. Two simple ...
Classical Genetic and Quantitative Trait Loci Analyses of Heterosis in a Maize Hybrid Between Two Elite Inbred Lines
May 01, 2007; ... ABSTRACT The exploitation of heterosis is one of the most outstanding advancements in plant breeding, although its genetic basis is not well understood yet. This research was conducted on the materials arising from the maize single cross B73 × H99 to study heterosis by procedures of ...
Precise Mapping of Quantitative Trait Loci for Resistance to Southern Leaf Blight, Caused by Cochliobolus heterostrophus Race O, and Flowering Time Using Advanced Intercross Maize Lines
May 01, 2007; ... ABSTRACT The intermated B73 × Mo17 (IBM) population, an advanced intercross recombinant inbred line population derived from a cross between the maize lines B73 (susceptible) and Mo17 (resistant), was evaluated in four environments for resistance to southern leaf blight (SLB) disease ...
The Genetic Basis of Zinc Tolerance in the Metallophyte Arabidopsis halleri ssp. halleri (Brassicaceae): An Analysis of Quantitative Trait Loci
May 01, 2007; ... ABSTRACT The species Arabidopsis halleri, an emerging model for the study of heavy metal tolerance and accumulation in plants, has evolved a high level of constitutive zinc tolerance. Mapping of quantitative trait loci (QTL) was used to investigate the genetic architecture of zinc ...
Genomewide Association Analysis in Diverse Inbred Mice: Power and Population Structure
May 01, 2007; ... ABSTRACT The discovery of quantitative trait loci (QTL) in model organisms has relied heavily on the ability to perform controlled breeding to generate genotypic and phenotypic diversity. Recently, we and others have demonstrated the use of an existing set of diverse inbred mice ...
A Soybean Transcript Map: Gene Distribution, Haplotype and Single-Nucleotide Polymorphism Analysis
May 01, 2007; ... ABSTRACT The first genetic transcript map of the soybean genome was created by mapping one SNP in each of 1141 genes in one or more of three recombinant inbred line mapping populations, thus providing a picture of the distribution of genic sequences across the mapped portion of the ...
An Unusual Pattern of Spontaneous Mutations Recovered in the Halophilic Archaeon Haloferax volcanii
May 01, 2007; ... ABSTRACT Spontaneous mutations in the orotate:phosphoribosyl transferase (pyrE2) gene of the halophilic archaeon Haloferax volcanii were selected by 5-fluoroorotic acid plus uracil at a rate of ~2 × 10^sup -8^/cell division in fluctuation and null-fraction tests but ~6 × 10^sup -8^/cell ...
Estimation of Population Heterozygosity and Library Construction-Induced Mutation Rate From Expressed Sequence Tag Collections
May 01, 2007; ... ABSTRACT Unigene alignments obtained from cDNA libraries made using multiple individuals are not currently used to estimate population heterozygosity, as they are known to harbor mutations created during library construction. We describe an estimator of population heterozygosity that ...
The Caenorhabditis elegans Rad17 Homolog HPR-17 Is Required for Telomere Replication
May 01, 2007; ... ABSTRACT Subunits of the Rad9/Rad1/Hus1 (9-1-1) proliferating cell nuclear antigen (PNCA)-like sliding clamp are required for DNA damage responses and telomerase-mediated telomere replication in the nematode Caenorhabditis elegans. PCNA sliding clamps are loaded onto DNA by a replication ...
Adaptation of a Quantitative Trait to a Moving Optimum
May 01, 2007; ... ABSTRACT We investigate adaptive evolution of a quantitative trait under stabilizing selection with a moving optimum. We characterize three regimes, depending on whether (1) the beneficial mutation rate, (2) the fixation time, or (3) the rate of environmental change is the limiting ...
Survival Quantitative Trait Locus Fine Mapping by Measuring and Testing for Hardy-Weinberg and Linkage Disequilibrium
May 01, 2007; ... ABSTRACT I show that fine-scale localization of a survival-related locus can be accomplished on the basis of deviations from Hardy-Weinberg equilibrium and linkage disequilibrium at closely linked marker loci. The method is based on χ^sup 2^-tests and they can be performed for ...
The Effect of Dominance on the Use of the Q^sub ST^ - F^sub ST^ Contrast to Detect Natural Selection on Quantitative Traits
May 01, 2007; ... THE comparison between Wright's among-population fixation index F^sub ST^ (a descriptor of the effect of the breeding structure on population diversity for neutral genes) and Spitze's quantitative index of population divergence Q^sub ST^ [defined as V^sub b^/(V^sub b^ + 2V^sub w^), where V^sub ...
Essential, Overlapping and Redundant Roles of the Drosophila Protein Phosphatase 1[alpha] and 1[beta] Genes
May 01, 2007; ... ABSTRACT Protein serine/threonine phosphatase type 1 (PP1) has been found in all eukaryotes examined to date and is involved in the regulation of many cellular functions, including glycogen metabolism, muscle contraction, and mitosis. In Drosophila, four genes code for the catalytic ...