Genetics

Professional journal providing news and analysis on field of genetics. Features special reports such as policy reviews and awards.

Articles from Vol. 180, No. 2, October

A Computational Approach to the Functional Clustering of Periodic Gene-Expression Profiles
ABSTRACTDNA microarray analysis has emerged as a leading technology to enhance our understanding of gene regulation and function in cellular mechanism controls on a genomic scale. This technology has advanced to unravel the genetic machinery of biological...
Adaptive Differentiation of Quantitative Traits in the Globally Distributed Weed, Wild Radish (Raphanus Raphanistrum)
ABSTRACTWeedy species with wide geographical distributions may face strong selection to adapt to new environments, which can lead to adaptive genetic differentiation among populations. However, genetic drift, particularly due to founder effects, will...
ADBP-1 Regulates an ADAR RNA-Editing Enzyme to Antagonize RNA-Interference-Mediated Gene Silencing in Caenorhabditis Elegans
ABSTRACTSmall interfering RNAs (siRNAs) and microRNAs (miRNAs) mediate gene silencing through evolutionarily conserved pathways. In Caenorhabditis elegans, the siRNA/miRNA pathways are also known to affect transgene expression. To identify genes that...
A Fundamental Relationship between Genotype Frequencies and Fitnesses
ABSTRACTThe set of possible postselection genotype frequencies in an infinite, randomly mating population is found. Geometric mean heterozygote frequency divided by geometric mean homozygote frequency equals two times the geometric mean heterozygote...
A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective
ABSTRACTIdentifying loci under natural selection from genomic surveys is of great interest in different research areas. Commonly used methods to separate neutral effects from adaptive effects are based on locus-specific population differentiation coefficients...
AMBIENCE: A Novel Approach and Efficient Algorithm for Identifying Informative Genetic and Environmental Associations with Complex Phenotypes
ABSTRACTWe developed a computationally efficient algorithm AMBIENCE, for identifying the informative variables involved in gene-gene (GGI) and gene-environment interactions (GEI) that are associated with disease phenotypes. The AMBIENCE algorithm uses...
A Role for Acp29AB, a Predicted Seminal Fluid Lectin, in Female Sperm Storage in Drosophila Melanogaster
ABSTRACTFemales of many animal species store sperm for taxon-specific periods of time, ranging from a few hours to years. Female sperm storage has important reproductive and evolutionary consequences, yet relatively little is known of its molecular basis....
A Two-Stage Pruning Algorithm for Likelihood Computation for a Population Tree
ABSTRACTWe have developed a pruning algorithm for likelihood estimation of a tree of populations. This algorithm enables us to compute the likelihood for large trees. Thus, it gives an efficient way of obtaining the maximum-likelihood estimate (MLE)...
BAM Receptors Regulate Stem Cell Specification and Organ Development through Complex Interactions with CLAVATA Signaling
ABSTRACTThe CLAVATA1 (CLV1) receptor kinase regulates stem cell specification at shoot and flower meristems of Arabidopsis. Most clv1 alleles are dominant negative, and clv1 null alleles are weak in phenotype, suggesting additional receptors functioning...
Bursicon Signaling Mutations Separate the Epithelial-Mesenchymal Transition from Programmed Cell Death during Drosophila Melanogaster Wing Maturation
ABSTRACTFollowing eclosion from the pupal case, wings of the immature adult fly unfold and expand to present a flat wing blade. During expansion the epithelia, which earlier produced the wing cuticle, delaminate from the cuticle, and the epithelial cells...
Chromosomal Regions Underlying Noncoagulation of Milk in Finnish Ayrshire Cows
ABSTRACTAbout 10% of Finnish Ayrshire cows produce noncoagulating milk, i.e., milk that does not form a curd in a standard 30-min testing time and is thus a poor raw material for cheese dairies. This phenomenon is associated with peak and midlactation,...
Chromosome Segmental Dosage Analysis of Maize Morphogenesis Using B-A-A Translocations
ABSTRACTThe B-A-A translocations have enabled us to simultaneously assess the possible dosage-sensitive interactions of two nonhomologous chromosome segments in affecting maize plant development. Maize B- A-A translocations contain segments of two nonhomologous...
Cohesin and Recombination Proteins Influence the G^sub 1^-to-S Transition in Azygotic Meiosis in Schizosaccharomyces Pombe
ABSTRACTTo determine whether recombination and/or sister-chromatid cohesion affect the timing of meiotic prophase events, the horsetail stage and S phase were analyzed in Schizosaccharomyces pombe strains carrying mutations in the cohesin genes rec8...
Domain-Specific Regulation of Recombination in Caenorhabditis Elegans in Response to Temperature, Age and Sex
ABSTRACTIt is generally considered that meiotic recombination rates increase with temperature, decrease with age, and differ between the sexes. We have reexamined the effects of these factors on meiotic recombination in the nematode Caenorhabditis elegans...
Dynamics and Differential Proliferation of Transposable Elements during the Evolution of the B and A Genomes of Wheat
ABSTRACTTransposable elements (TEs) constitute >80% of the wheat genome but their dynamics and contribution to size variation and evolution of wheat genomes (Triticum and Aegilops species) remain unexplored. In this study, 10 genomic regions have...
End Joining at Caenorhabditis Elegans Telomeres
ABSTRACTCritically shortened telomeres can be subjected to DNA repair events that generate end-to-end chromosome fusions. The resulting dicentric chromosomes can enter breakage-fusion-bridge cycles, thereby impeding elucidation of the structures of the...
From Hypo- to Hypersuppression: Effect of Amino Acid Substitutions on the RNA-Silencing Suppressor Activity of the Tobacco Etch Potyvirus HC-Pro
ABSTRACTRNA silencing participates in several important functions: from the regulation of cell metabolism and organism development to sequence-specific antiviral defense. Most plant viruses have evolved proteins that suppress RNA silencing and that in...
F^sub ST^ and Q^sub ST^ under Neutrality
ABSTRACTA commonly used test for natural selection has been to compare population differentiation for neutral molecular loci estimated by F^sub ST^ and for the additive genetic component of quantitative traits estimated by Q^sub ST^. Past analytical...
[gamma]Tub23C Interacts Genetically with Brahma Chromatin-Remodeling Complexes in Drosophila Melanogaster
ABSTRACTThe brahma gene encodes the catalytic subunit of the Drosophila melanogaster BRM chromatin-remodeling complexes. Screening for mutations that interact with brahma, we isolated the dominant-negative Pearl-2 allele of ?Tub23C. ?Tub23C encodes one...
Genetic Redundancy in Soybean Photoresponses Associated with Duplication of the Phytochrome A Gene
ABSTRACTGene and genome duplications underlie the origins of evolutionary novelty in plants. Soybean, Glycine max, is considered to be a paleopolyploid species with a complex genome. We found multiple homologs of the phytochrome A gene (phyA) in the...
Glo-3, a Novel Caenorhabditis Elegans Gene, Is Required for Lysosome-Related Organelle Biogenesis
ABSTRACTGut granules are specialized lysosome-related organelles that act as sites of fat storage in Caenorhabditis elegans intestinal cells. We identified mutations in a gene, glo-3, that functions in the formation of embryonic gut granules. Some glo-3(-)...
Impact of Transgene Inheritance on the Mitigation of Gene Flow between Crops and Their Wild Relatives: The Example of Foxtail Millet
ABSTRACTDeveloping genetically modified crop plants that are biologically contained could reduce significantly the potential spread of transgenes to conventional and organic crop plants and to wild or weedy relatives. Among several strategies, the hereditary...
Interactions between Markers Can Be Caused by the Dominance Effect of Quantitative Trait Loci
ABSTRACTF^sub 2^ populations are commonly used in genetic studies of animals and plants. For simplicity, most quantitative trait locus or loci (QTL) mapping methods have been developed on the basis of populations having two distinct genotypes at each...
Lethal Mutagenesis of Bacteria
ABSTRACTLethal mutagenesis, the killing of a microbial pathogen with a chemical mutagen, is a potential broad-spectrum antiviral treatment. It operates by raising the genomic mutation rate to the point that the deleterious load causes the population...
Metabolomic Signatures of Inbreeding at Benign and Stressful Temperatures in Drosophila Melanogaster
ABSTRACTWhile the population genetics of inbreeding is fairly well understood, the effects of inbreeding on the physiological and biochemical levels are not. Here we have investigated the effects of inbreeding on the Drosophila melanogaster metabolome....
Muller's Ratchet and the Degeneration of Y Chromosomes: A Simulation Study
ABSTRACTA typical pattern in sex chromosome evolution is that Y chromosomes are small and have lost many of their genes. One mechanism that might explain the degeneration of Y chromosomes is Muller's ratchet, the perpetual stochastic loss of linkage...
Natural Genetic Variation of Arabidopsis Thaliana Is Geographically Structured in the Iberian Peninsula
ABSTRACTTo understand the demographic history of Arabidopsis thaliana within its native geographical range, we have studied its genetic structure in the Iberian Peninsula region. We have analyzed the amount and spatial distribution of A. thaliana genetic...
On the Detection of Imprinted Quantitative Trait Loci in Line Crosses: Effect of Linkage Disequilibrium
ABSTRACTImprinted quantitative trait loci (QTL) are commonly reported in studies using line-cross designs, especially in livestock species. It was previously shown that such parent-of-origin effects might result from the nonfixation of QTL alleles in...
Patterns of Amino Acid Evolution in the Drosophila Ananassae Chimeric Gene, Siren, Parallel Those of Other Adh-Derived Chimeras
ABSTRACTsiren1 and siren2 are novel alcohol dehydrogenase (Adh)-derived chimeric genes in the Drosophila bipectinata complex. D. ananassae, however, harbors a single homolog of these genes. Like other Adh-derived chimeric genes, siren evolved adaptively...
Patterns of Molecular Evolution Associated with Two Selective Sweeps in the Tb1-Dwarf8 Region in Maize
ABSTRACTWe focused on a region encompassing a major maize domestication locus, Tb1, and a locus involved in the flowering time variation, Dwarf8 (D8), to investigate the consequences of two closely linked selective sweeps on nucleotide variation and...
Perils of Parsimony: Properties of Reduced-Rank Estimates of Genetic Covariance Matrices
ABSTRACTEigenvalues and eigenvectors of covariance matrices are important statistics for multivariate problems in many applications, including quantitative genetics. Estimates of these quantities are subject to different types of bias. This article reviews...
Pnc1p-Mediated Nicotinamide Clearance Modifies the Epigenetic Properties of rDNA Silencing in Saccharomyces Cerevisiae
ABSTRACTThe histone deacetylase activity of Sir2p is dependent on NAD^sup +^ and inhibited by nicotinamide (NAM). As a result, Sir2p-regulated processes in Saccharomyces cerevisiae such as silencing and replicative aging are susceptible to alterations...
Positive Selection at the Binding Sites of the Male-Specific Lethal Complex Involved in Dosage Compensation in Drosophila
ABSTRACTIn many taxa, males and females differ with respect to their sex chromosomes, and dosage compensation mechanisms have evolved to equalize X-linked gene transcription. In Drosophila, the male-specific lethal (MSL) complex binds to hundreds of...
Proteasomal Regulation of the Proliferation vs. Meiotic Entry Decision in the Caenorhabditis Elegans Germ Line
ABSTRACTReproductive fitness in many animals relies upon a tight balance between the number of cells that proliferate in the germ line and the number of cells that enter meiosis and differentiate as gametes. In the Caenorhabditis elegans germ line, the...
Quantitative Trait Loci Mapping of Genome Regions Controlling Permethrin Resistance in the Mosquito Aedes Aegypti
ABSTRACTThe mosquito Aedes aegypti is the principal vector of dengue and yellow fever flaviviruses. Permethrin is an insecticide used to suppress Ae. aegypti adult populations but metabolic and target site resistance to pyrethroids has evolved in many...
Secondary Mutations Correct Fitness Defects in Toxoplasma Gondii with Dinitroaniline Resistance Mutations
ABSTRACTDinitroanilines (oryzalin, trifluralin, ethafluralin) disrupt microtubules in protozoa but not in vertebrate cells, causing selective death of intracellular Toxoplasma gondii parasites without affecting host cells. Parasites containing a1-tubulin...
Selection at Work in Self-Incompatible Arabidopsis Lyrata. II. Spatial Distribution of S Haplotypes in Iceland
ABSTRACTWe survey the distribution of haplotypes at the self-incompatibility (SI) locus of Arabidopsis lyrata (Brassicaceae) at 12 locations spread over the species' natural distribution in Iceland. Previous investigations of the system have identified...
The Cellular, Developmental and Population-Genetic Determinants of Mutation-Rate Evolution
ABSTRACTAlthough the matter has been subject to considerable theoretical study, there are numerous open questions regarding the mechanisms driving the mutation rate in various phylogenetic lineages. Most notably, empirical evidence indicates that mutation...
The Chicken (Gallus Gallus) Z Chromosome Contains at Least Three Nonlinear Evolutionary Strata
ABSTRACTBirds have female heterogamety with Z and W sex chromosomes. These evolved from different autosomal precursor chromosomes than the mammalian X and Y. However, previous work has suggested that the pattern and process of sex chromosome evolution...
The Dominant Cold-Sensitive Out-Cold Mutants of Drosophila Melanogaster Have Novel Missense Mutations in the Voltage-Gated Sodium Channel Gene Paralytic
ABSTRACTHere we report the molecular characterization of Out-cold (Ocd) mutants of Drosophila melanogaster, which produce a dominant, X-linked, cold-sensitive paralytic phenotype. From its initial 1.5-Mb cytological location within 13F1-16A2, P-element...
The Genetic Architecture of Complex Traits in Teosinte (Zea Mays Ssp. Parviglumis): New Evidence from Association Mapping
ABSTRACTPrevious association analyses showed that variation at major regulatory genes contributes to standing variation for complex traits in Balsas teosinte, the progenitor of maize. This study expands our previous association mapping effort in teosinte...
The hisB463 Mutation and Expression of a Eukaryotic Protein in Escherichia Coli
CERTAINTY in science is never achieved and can only be approached asymptotically. How close to the asymptote and what kind of evidence is necessary to demonstrate a scientific point beyond reasonable doubt? How important is missing information that may...
The Influence of Gene Conversion on Linkage Disequilibrium around a Selective Sweep
ABSTRACTIn a 2007 article, McVean studied the effect of recombination on linkage disequilibrium (LD) between two neutral loci located near a third locus that has undergone a selective sweep. The results demonstrated that two loci on the same side of...
The Ku Complex in Silencing the Cryptic Mating-Type Loci of Saccharomyces Cerevisiae
ABSTRACTSir1 establishes transcriptional silencing at the cryptic mating-type loci HMR and HML (HM loci) by recruiting the three other Sir proteins, Sir2, -3, and -4, that function directly in silenced chromatin. However, SIR1-independent mechanisms...
The R2R3 MYB Transcription Factor GhMYB109 Is Required for Cotton Fiber Development
ABSTRACTCotton (Gossypium hirsutum L.) fibers are single highly elongated cells derived from the outer epidermis of ovules. A large number of genes are required for fiber differentiation and development, but so far, little is known about how these genes...
Transcriptional Control and Protein Specialization Have Roles in the Functional Diversification of Two Dicer-Like Proteins in Magnaporthe Oryzae
ABSTRACTQuantitative RT-PCR and overexpression studies of two Dicer-like proteins, MoDcl1 and MoDcl2, in Magnaporthe oryzae indicated that the functional diversification of the MoDcl1 and MoDcl2 proteins in RNA-mediated gene silencing pathways was likely...