Genetics back issues from August 2008:
Announcement
Aug 01, 2008; ... Dear Colleagues, Our journal has gone through some significant changes in the past few years. Most were planned, of course, and are decidedly positive; one was unexpected and tragic. We are now carrying the baton of progress handed to us by our esteemed and very dedicated ...
Tilting at Quixotic Trait Loci (QTL): An Evolutionary Perspective on Genetic Causation
Aug 01, 2008; ... ABSTRACT Recent years have seen great advances in generating and analyzing data to identify the genetic architecture of biological traits. Human disease has understandably received intense research focus, and the genes responsible for most Mendelian diseases have successfully been ...
Just and Unjust: E. E. Just (1883-1941)
Aug 01, 2008; ... Natur hat weder Kern Noch Schale Alles ist sie mit einem Male2 THIS year marks the 125th anniversary of the birth of Ernest Everett Just. He was one of the greatest biologists of the early 20th century, but being Afro-American, he never had a position that permitted full ...
Cytotype Regulation of P Transposable Elements in Drosophila melanogaster: Repressor Polypeptides or piRNAs?
Aug 01, 2008; ... ABSTRACT The telomeric P elements TP5 and TP6 are associated with the P cytotype, a maternally inherited condition that represses P-element-induced hybrid dysgenesis in the Drosophila germ line. To see if cytotype repression by TP5 and TP6 might be mediated by the polypeptides they could ...
Histone H3 K56 Hyperacetylation Perturbs Replisomes and Causes DNA Damage
Aug 01, 2008; ... ABSTRACT Deacetylation of histone H3 K56, regulated by the sirtuins Hst3p and Hst4p, is critical for maintenance of genomic stability. However, the physiological consequences of a lack of H3 K56 deacetylation are poorly understood. Here we show that cells lacking Hst3p and Hst4p, in ...
Mutants Defective in Rad1-Rad10-Slx4 Exhibit a Unique Pattern of Viability During Mating-Type Switching in Saccharomyces cerevisiae
Aug 01, 2008; ... ABSTRACT Efficient repair of DNA double-strand breaks (DSBs) requires the coordination of checkpoint signaling and enzymatic repair functions. To study these processes during gene conversion at a single chromosomal break, we monitored mating-type switching in Saccharomyces cerevisiae ...
Interplay of DNA Repair Pathways Controls Methylation Damage Toxicity in Saccharomyces cerevisiae
Aug 01, 2008; ... ABSTRACT Methylating agents of S^sub N^1 type are widely used in cancer chemotherapy, but their mode of action is poorly understood. In particular, it is unclear how the primary cytotoxic lesion, O^sup 6^-methylguanine (^sup Me^G), causes cell death. One hypothesis stipulates that ...
Natural Variation in Gene Expression Between Wild and Weedy Populations of Helianthus annuus
Aug 01, 2008; ... ABSTRACT The molecular genetic changes underlying the transformation of wild plants into agricultural weeds are poorly understood. Here we use a sunflower cDNA microarray to detect variation in gene expression between two wild (non-weedy) Helianthus annuus populations from Utah and ...
Developmental and Environmental Signals Induce Distinct Histone Acetylation Profiles on Distal and Proximal Promoter Elements of the C^sub 4^-Pepc Gene in Maize
Aug 01, 2008; ... ABSTRACT The maize C^sub 4^-Pepc gene is expressed in an organ- and cell-type-specific manner, inducible by light and modulated by nutrient availability and the metabolic state of the cell. We studied the contribution of histone acetylation at five lysine residues to the integration of ...
Maternal Phosphatase Inhibitor-2 Is Required for Proper Chromosome Segregation and Mitotic Synchrony During Drosophila Embryogenesis
Aug 01, 2008; ... ABSTRACT Protein phosphatase-1 (PP1) is a major Ser/Thr phosphatase conserved among all eukaryotes, present as the essential GLC7 gene in yeast. Inhibitor-2 (I-2) is an ancient PP1 regulator, named GLC8 in yeast, but its in vivo function is unknown. Unlike mammals with multiple I-2 ...
Identification of Amino Acid Residues in the Catalytic Domain of RNase E Essential for Survival of Escherichia coli: Functional Analysis of DNase I Subdomain
Aug 01, 2008; ... ABSTRACT RNase E is an essential Escherichia coli endoribonuclease that plays a major role in the decay and processing of a large fraction of RNAs in the cell. To better understand the molecular mechanisms of RNase E action, we performed a genetic screen for amino acid substitutions in ...
Differential Gene Expression of TRPM1, the Potential Cause of Congenital Stationary Night Blindness and Coat Spotting Patterns (LP) in the Appaloosa Horse (Equus caballus)
Aug 01, 2008; ... ABSTRACT The appaloosa coat spotting pattern in horses is caused by a single incomplete dominant gene (LP). Homozygosity for LP (LP/LP) is directly associated with congenital stationary night blindness (CSNB) in Appaloosa horses. LP maps to a 6-cM region on ECA1. We investigated the ...
Defective Break-Induced Replication Leads to Half-Crossovers in Saccharomyces cerevisiae
Aug 01, 2008; ... ABSTRACT Break-induced replication (BIR) is an important process of DNA metabolism that has been implicated in the restart of collapsed replication forks, as well as in various chromosomal instabilities, including loss of heterozygosity, translocations, and alternative telomere ...
Regulation of Apical Dominance in Aspergillus nidulans Hyphae by Reactive Oxygen Species
Aug 01, 2008; ... ABSTRACT In fungal hyphae, apical dominance refers to the suppression of secondary polarity axes in the general vicinity of a growing hyphal tip. The mechanisms underlying apical dominance remain largely undefined, although calcium signaling may play a role. Here, we describe the ...
Pervasive Sex-Linked Effects on Transcription Regulation As Revealed by Expression Quantitative Trait Loci Mapping in Lake Whitefish Species Pairs (Coregonus sp., Salmonidae)
Aug 01, 2008; ... ABSTRACT Mapping of expression quantitative trait loci (eQTL) is a powerful means for elucidating the genetic architecture of gene regulation. Yet, eQTL mapping has not been applied toward investigating the regulation architecture of genes involved in the process of population ...
Genomewide Screen for Negative Regulators of Sirtuin Activity in Saccharomyces cerevisiae Reveals 40 Loci and Links to Metabolism
Aug 01, 2008; ... ABSTRACT Sirtuins are conserved proteins implicated in myriad key processes including gene control, aging, cell survival, metabolism, and DNA repair. In Saccharomyces cerevisiae, the sirtuin Silent information regulator 2 (Sir2) promotes silent chromatin formation, suppresses ...
Synthetic Genetic Array Analysis in Saccharomyces cerevisiae Provides Evidence for an Interaction Between RAT8/DBP5 and Genes Encoding P-Body Components
Aug 01, 2008; ... ABSTRACT Coordination of the multiple steps of mRNA biogenesis helps to ensure proper regulation of gene expression. The Saccharomyces cerevisiae DEAD-box protein Rat8p/Dbp5p is an essential mRNA export factor that functions at the nuclear pore complex (NPC) where it is thought to ...
The Arp2/3 Activators WAVE and WASP Have Distinct Genetic Interactions With Rac GTPases in Caenorhabditis elegans Axon Guidance
Aug 01, 2008; ... ABSTRACT In the developing nervous system, axons are guided to their targets by the growth cone. Lamellipodial and filopodial protrusions from the growth cone underlie motility and guidance. Many molecules that control lamellipodia and filopodia formation, actin organization, and axon ...
Drosophila LIM-Only Is a Positive Regulator of Transcription During Thoracic Bristle Development
Aug 01, 2008; ... ABSTRACT The Drosophila LIM-only (LMO) protein DLMO functions as a negative regulator of transcription during development of the fly wing. Here we report a novel role of DLMO as a positive regulator of transcription during the development of thoracic sensory bristles. We isolated new ...
Dissection of Darkener of Apricot Kinase Isoform Functions in Drosophila
Aug 01, 2008; ... ABSTRACT The Darkener of apricot (Doa) locus of Drosophila encodes a LAMMER protein kinase affecting alterative splicing, and hence sex determination, via the phosphorylation of SR and SR-like proteins. Doa encodes 6 different kinases via alternative promoter usage. To provide further ...
Multiple Levels of Redundant Processes Inhibit Caenorhabditis elegans Vulval Cell Fates
Aug 01, 2008; ... ABSTRACT Many mutations cause obvious abnormalities only when combined with other mutations. Such synthetic interactions can be the result of redundant gene functions. In Caenorhabditis elegans, the synthetic multivulva (synMuv) genes have been grouped into multiple classes that ...
The Relationship Between Homozygosity and the Frequency of the Most Frequent Allele
Aug 01, 2008; ... ABSTRACT Homozygosity is a commonly used summary of allele-frequency distributions at polymorphic loci. Because high-frequency alleles contribute disproportionately to the homozygosity of a locus, it often occurs that most homozygotes are homozygous for the most frequent allele. To ...
The Population Genetics of Using Homing Endonuclease Genes in Vector and Pest Management
Aug 01, 2008; ... ABSTRACT Homing endonuclease genes (HEGs) encode proteins that in the heterozygous state cause double-strand breaks in the homologous chromosome at the precise position opposite the HEG. If the double-strand break is repaired using the homologous chromosome, the HEG becomes homozygous, ...
Molecular Basis of Spectral Tuning in the Red- and Green-Sensitive (M/LWS) Pigments in Vertebrates
Aug 01, 2008; ... ABSTRACT Vertebrate vision is mediated by five groups of visual pigments, each absorbing a specific wavelength of light between ultraviolet and red. Despite extensive mutagenesis analyses, the mechanisms by which contemporary pigments absorb variable wavelengths of light are poorly ...
A Theory of Age-Dependent Mutation and Senescence
Aug 01, 2008; ... ABSTRACT Laboratory experiments show us that the deleterious character of accumulated novel age-specific mutations is reduced and made less variable with increased age. While theories of aging predict that the frequency of deleterious mutations at mutation-selection equilibrium will ...
Comparative Genetic Mapping Between Octoploid and Diploid Fragaria Species Reveals a High Level of Colinearity Between Their Genomes and the Essentially Disomic Behavior of the Cultivated Octoploid Strawberry
Aug 01, 2008; ... ABSTRACT Macrosynteny and colinearity between Fragaria (strawberry) species showing extreme levels of ploidy have been studied through comparative genetic mapping between the octoploid cultivated strawberry (F. × ananassa) and its diploid relatives. A comprehensive map of the octoploid ...
Comparative Analysis of Testis Protein Evolution in Rodents
Aug 01, 2008; ... ABSTRACT Genes expressed in testes are critical to male reproductive success, affecting spermatogenesis, sperm competition, and sperm-egg interaction. Comparing the evolution of testis proteins at different taxonomic levels can reveal which genes and functional classes are targets of ...
Frequency-Dependent Selection and the Evolution of Assortative Mating
Aug 01, 2008; ... ABSTRACT A long-standing goal in evolutionary biology is to identify the conditions that promote the evolution of reproductive isolation and speciation. The factors promoting sympatric speciation have been of particular interest, both because it is notoriously difficult to prove ...
Segregation Models for Disomic, Tetrasomic and Intermediate Inheritance in Tetraploids: A General Procedure Applied to Rorippa (Yellow Cress) Microsatellite Data
Aug 01, 2008; ... ABSTRACT Tetraploid inheritance has two extremes: disomic in allotetraploids and tetrasomic in autotetraploids. The possibility of mixed, or intermediate, inheritance models has generally been neglected. These could well apply to newly formed hybrids or to diploidizing (auto)tetraploids ....
Loss of Least-Loaded Class in Asexual Populations Due to Drift and Epistasis
Aug 01, 2008; ... ABSTRACT We consider the dynamics of a nonrecombining haploid population of finite size that accumulates deleterious mutations irreversibly. This ratchet-like process occurs at a finite speed in the absence of epistasis, but it has been suggested that synergistic epistasis can halt the ...
Population Bottlenecks Increase Additive Genetic Variance But Do Not Break a Selection Limit in Rain Forest Drosophila
Aug 01, 2008; ... ABSTRACT According to neutral quantitative genetic theory, population bottlenecks are expected to decrease standing levels of additive genetic variance of quantitative traits. However, some empirical and theoretical results suggest that, if nonadditive genetic effects influence the ...
The Y Chromosome That Lost the Male-Determining Function Behaves as an X Chromosome in the Medaka Fish, Oryzias latipes
Aug 01, 2008; ... ABSTRACT The medaka, Oryzias latipes, has an XX/XY sex-determination system, and a Y-linked DM-domain gene, DMY, is the sex-determining gene in this species. Since DMY appears to have arisen from a duplicated copy of the autosomal DMRT1 gene ~10 million years ago, the medaka Y chromosome ...
Within-Generation Mutation Variance for Litter Size in Inbred Mice
Aug 01, 2008; ... ABSTRACT The mutational input of genetic variance per generation (σ^sup 2^^sub m^) is the lower limit of the genetic variability in inbred strains of mice, although greater values could be expected due to the accumulation of new mutations in successive generations. A mixed-model ...
An Empirical Test for Branch-Specific Positive Selection
Aug 01, 2008; ... ABSTRACT The use of phylogenetic analysis to predict positive selection specific to human genes is complicated by the very close evolutionary relationship with our nearest extant primate relatives, chimpanzees. To assess the power and limitations inherent in use of maximum-likelihood ...
Canine Polydactyl Mutations With Heterogeneous Origin in the Conserved Intronic Sequence of LMBR1
Aug 01, 2008; ... ABSTRACT Canine preaxial polydactyly (PPD) in the hind limb is a developmental trait that restores the first digit lost during canine evolution. Using a linkage analysis, we previously demonstrated that the affected gene in a Korean breed is located on canine chromosome 16. The candidate ...
Molecular Cytogenetic Evidence of Rearrangements on the Y Chromosome of the Threespine Stickleback Fish
Aug 01, 2008; ... ABSTRACT To identify the processes shaping vertebrate sex chromosomes during the early stages of their evolution, it is necessary to study systems in which genetic sex determination was recently acquired. Previous cytogenetic studies suggested that threespine stickleback fish ...
Experimental Estimation of Mutation Rates in a Wheat Population With a Gene Genealogy Approach
Aug 01, 2008; ... ABSTRACT Microsatellite markers are extensively used to evaluate genetic diversity in natural or experimental evolving populations. Their high degree of polymorphism reflects their high mutation rates. Estimates of the mutation rates are therefore necessary when characterizing diversity ...
Cut Thy Neighbor: Cyclic Birth and Death of Recombination Hotspots via Genetic Conflict
Aug 01, 2008; ... ABSTRACT Most recombination takes place in numerous, localized regions called hotspots. However, empirical evidence indicates that nascent hotspots are susceptible to removal due to biased gene conversion, so it is paradoxical that they should be so widespread. Previous modeling work has ...
Quantitative Trait Loci (QTL) Analysis For Rice Grain Width and Fine Mapping of an Identified QTL Allele gw-5 in a Recombination Hotspot Region on Chromosome 5
Aug 01, 2008; ... ABSTRACT Rice grain width and shape play a crucial role in determining grain quality and yield. The genetic basis of rice grain width was dissected into six additive quantitative trait loci (QTL) and 11 pairs of epistatic QTL using an F7 recombinant inbred line (RIL) population derived ...
A Complex Genetic Basis to X-Linked Hybrid Male Sterility Between Two Species of House Mice
Aug 01, 2008; ... ABSTRACT The X chromosome plays a central role in the evolution of reproductive isolation, but few studies have examined the genetic basis of X-linked incompatibilities during the early stages of speciation. We report the results of a large experiment focused on the reciprocal ...
Exchangeable Models of Complex Inherited Diseases
Aug 01, 2008; ... ABSTRACT A model of unlinked diallelic loci affecting the risk of a complex inherited disease is explored. The loci are equivalent in their effect on disease risk and are in Hardy-Weinberg and linkage equilibrium. The goal is to determine what assumptions about dependence of disease risk ...
The qSD12 Locus Controls Offspring Tissue-Imposed Seed Dormancy in Rice
Aug 01, 2008; ... ABSTRACT Seed component structures were grouped into maternal and offspring (embryo and endosperm) tissues to characterize a dormancy quantitative trait locus (QTL) for tissue-specific function using a marker-assisted genetic approach. The approach was devised to test if ...
A Recently Active Miniature Inverted-Repeat Transposable Element, Chunjie, Inserted Into an Operon Without Disturbing the Operon Structure in Geobacter uraniireducens Rf4
Aug 01, 2008; ... ABSTRACT Miniature inverted-repeat transposable elements (MITEs) are short DNA transposons with terminal inverted repeat (TIR) signals and have been extensively studied in plants and other eukaryotes. But little is known about them in eubacteria.We identified a novel and recently active ...
Bayesian Quantitative Trait Loci Mapping for Multiple Traits
Aug 01, 2008; ... ABSTRACT Most quantitative trait loci (QTL) mapping experiments typically collect phenotypic data on multiple correlated complex traits. However, there is a lack of a comprehensive genomewide mapping strategy for correlated traits in the literature. We develop Bayesian multiple-QTL ...
Incorporation of Y'-Ty1 cDNA Destabilizes Telomeres in Saccharomyces cerevisiae Telomerase-Negative Mutants
Aug 01, 2008; ... ABSTRACT Ty1 retrotransposons in Saccharomyces cerevisiae are activated by telomere erosion. Ty1-dependent reverse transcription of mRNA from subtelomeric Y' repeats generates chimeric Y'-Ty1 cDNA. Here, we show that Y'-Ty1 cDNA is incorporated at eroding telomeres in the absence of ...
Legume Anchor Markers Link Syntenic Regions Between Phaseolus vulgaris, Lotus japonicus, Medicago truncatula and Arachis
Aug 01, 2008; ... ABSTRACT We have previously described a bioinformatics pipeline identifying comparative anchor-tagged sequence (CATS) loci, combined with design of intron-spanning primers. The derived anchor markers defining the linkage position of homologous genes are essential for evaluating genome ...
Gene Dosage and Gene Duplicability
Aug 01, 2008; ... ABSTRACT The evolutionary process leading to the fixation of newly duplicated genes is not well understood. It was recently proposed that the fixation of duplicate genes is frequently driven by positive selection for increased gene dosage (i.e., the gene dosage hypothesis), because ...
Two New Y-Linked Genes in Drosophila melanogaster
Aug 01, 2008; ... ABSTRACT The Y chromosome and other heterochromatic regions present special challenges for genome sequencing and for the annotation of genes. Here we describe two new genes (ARY and WDY) on the Drosophila melanogaster Y, bringing its number of known single-copy genes to 12. WDY may ...
Functional Conservation of [beta]-Hairpin DNA Binding Domains in the Mcm Protein of Methanobacterium thermoautotrophicum and the Mcm5 protein of Saccharomyces cerevisiae
Aug 01, 2008; ... ABSTRACT Mcm proteins are an important family of evolutionarily conserved helicases required for DNA replication in eukaryotes. The eukaryotic Mcm complex consists of six paralogs that form a heterohexameric ring. Because the intact Mcm2-7 hexamer is inactive in vitro, it has been ...
Mutagenic and Recombinagenic Responses to Defective DNA Polymerase [delta] Are Facilitated by the Rev1 Protein in pol3-t Mutants of Saccharomyces cerevisiae
Aug 01, 2008; ... ABSTRACT Defective DNA replication can result in substantial increases in the level of genome instability. In the yeast Saccharomyces cerevisiae, the pol3-t allele confers a defect in the catalytic subunit of replicative DNA polymerase δ that results in increased rates of ...