Genetics back issues from November 2008:
A Tribute to Seymour Benzer, 1921-2007
Nov 01, 2008; ... NOVEMBER 2007 was marked by the loss of Seymour Benzer, long considered the father of the field of neurogenetics. Benzer's scientific contributions are broad and span from physics (his Ph.D. training) to molecular biology (defining the linearity of the gene) to behavioral genetics (establishing ...
Transmission Dynamics of Heritable Silencing Induced by Double-Stranded RNA in Caenorhabditis elegans
Nov 01, 2008; ... ABSTRACT Heritable silencing effects are gene suppression phenomena that can persist for generations after induction. In the majority of RNAi experiments conducted in Caenorhabditis elegans, the silencing response results in a hypomorphic phenotype where the effects recede after the ...
Molecular Marker Systems for Oenothera Genetics
Nov 01, 2008; ... ABSTRACT The genus Oenothera has an outstanding scientific tradition. It has been a model for studying aspects of chromosome evolution and speciation, including the impact of plastid nuclear co-evolution. A large collection of strains analyzed during a century of experimental work and ...
Chromatin Structure and Physical Mapping of Chromosome 6 of Potato and Comparative Analyses With Tomato
Nov 01, 2008; ... ABSTRACT Potato (Solanum tuberosum) has the densest genetic linkage map and one of the earliest established cytogenetic maps among all plant species. However, there has been limited effort to integrate these maps. Here, we report fluorescence in situ hybridization (FISH) mapping of 30 ...
Cross-Species Bacterial Artificial Chromosome-Fluorescence in Situ Hybridization Painting of the Tomato and Potato Chromosome 6 Reveals Undescribed Chromosomal Rearrangements
Nov 01, 2008; ... ABSTRACT Ongoing genomics projects of tomato (Solanum lycopersicum) and potato (S. tuberosum) are providing unique tools for comparative mapping studies in Solanaceae. At the chromosomal level, bacterial artificial chromosomes (BACs) can be positioned on pachytene complements by ...
A Genomewide Survey Argues That Every Zygotic Gene Product Is Dispensable for the Initiation of Somatic Homolog Pairing in Drosophila
Nov 01, 2008; ... ABSTRACT Studies from diverse organisms show that distinct interchromosomal interactions are associated with many developmental events. Despite recent advances in uncovering such phenomena, our understanding of how interchromosomal interactions are initiated and regulated is incomplete ....
Idaten Is a New Cold-Inducible Transposon of Volvox carteri That Can Be Used for Tagging Developmentally Important Genes
Nov 01, 2008; ... ABSTRACT A cold-inducible transposon called Jordan has previously been used to tag and recover genes controlling key aspects of Volvox development, including the process called inversion. In a search for additional genes, we isolated 17 new inversionless mutants from cultures grown at ...
Components of the RNAi Machinery That Mediate Long-Distance Chromosomal Associations Are Dispensable for Meiotic and Early Somatic Homolog Pairing in Drosophila melanogaster
Nov 01, 2008; ... ABSTRACT Homolog pairing is indispensable for the proper segregation of chromosomes in meiosis but the mechanism by which homologs uniquely pair with each other is poorly understood. In Drosophila, somatic chromosomes also undergo full homolog pairing by an unknown mechanism. It has been ...
Insulator and Ovo Proteins Determine the Frequency and Specificity of Insertion of the gypsy Retrotransposon in Drosophila melanogaster
Nov 01, 2008; ... ABSTRACT The gypsy retrovirus of Drosophila is quite unique among retroviruses in that it shows a strong preference for integration into specific sites in the genome. In particular, gypsy integrates with a frequency of >10% into the regulatory region of the ovo gene. We have used in ...
Evolution of Primate Gene Expression: Drift and Corrective Sweeps?
Nov 01, 2008; ... ABSTRACT Changes in gene expression play an important role in species' evolution. Earlier studies uncovered evidence that the effect of mutations on expression levels within the primate order is skewed, with many small downregulations balanced by fewer but larger upregulations. In ...
Nonsense-Mediated Decay of ash1 Nonsense Transcripts in Saccharomyces cerevisiae
Nov 01, 2008; ... ABSTRACT Nonsense-mediated mRNA decay (NMD) performs two functions in eukaryotes, one in controlling the expression level of a substantial subset of genes and the other in RNA surveillance. In the vast majority of genes, nonsense mutations render the corresponding transcripts prone to ...
The DNA End-Binding Protein Ku Regulates Silencing at the Internal HML and HMR Loci in Saccharomyces cerevisiae
Nov 01, 2008; ... ABSTRACT Heterochromatin resides near yeast telomeres and at the cryptic mating-type loci, HML and HMR, where it silences transcription of the α- and a-mating-type genes, respectively. Ku is a conserved DNA end-binding protein that binds telomeres and regulates silencing in yeast ....
A Targeted Deleterious Allele of the Splicing Factor SCNM1 in the Mouse
Nov 01, 2008; ... ABSTRACT The auxiliary spliceosomal protein SCNM1 contributes to recognition of nonconsensus splice donor sites. SCNM1 was first identified as a modifier of the severity of a sodium channelopathy in the mouse. The most severely affected strain, C57BL/6J, carries the variant allele ...
A Novel Septin-Associated Protein, Syp1p, Is Required for Normal Cell Cycle-Dependent Septin Cytoskeleton Dynamics in Yeast
Nov 01, 2008; ... ABSTRACT Septins are a family of GTP-binding proteins whose heterooligomeric complex is the basic structural element of the septin filaments found in many eukaryotic organisms. In budding yeast, septins are mainly confined at the mother-daughter junction and are required for cell ...
Genetic Analysis of MraY Inhibition by the [straight phi]X174 Protein E
Nov 01, 2008; ... ABSTRACT Protein E, the lysis protein of bacteriophage [straight phi]X174, is a specific inhibitor of MraY, the phospho-MurNAc-pentapeptide translocase that catalyzes the synthesis of lipid I in the conserved pathway for peptidoglycan biosynthesis. The original evidence for this ...
Suppression of Pleiotropic Effects of Functional CRYPTOCHROME Genes by TERMINAL FLOWER 1
Nov 01, 2008; ... ABSTRACT TERMINAL FLOWER 1 (TFL1) encodes a protein with similarity to animal phosphatidylethanolamine-binding proteins and is required for normal trafficking to the protein storage vacuole. In Arabidopsis thaliana the tfl1 mutation produces severe developmental abnormalities. Here we ...
The EGL-4 PKG Acts With KIN-29 Salt-Inducible Kinase and Protein Kinase A to Regulate Chemoreceptor Gene Expression and Sensory Behaviors in Caenorhabditis elegans
Nov 01, 2008; ... ABSTRACT The regulation of chemoreceptor (CR) gene expression by environmental signals and internal cues may contribute to the modulation of multiple physiological processes and behavior in Caenorhabditis elegans. We previously showed that KIN-29, a homolog of salt-inducible kinase, acts ...
EXPORTIN1 Genes Are Essential for Development and Function of the Gametophytes in Arabidopsis thaliana
Nov 01, 2008; ... ABSTRACT Gametes are produced in plants through mitotic divisions in the haploid gametophytes. We investigated the role of EXPORTIN1 (XPO1) genes during the development of both female and male gametophytes of Arabidopsis. Exportins exclude target proteins from the nucleus and are also ...
Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution
Nov 01, 2008; ... ABSTRACT Results of Nowak and collaborators concerning the onset of cancer due to the inactivation of tumor suppressor genes give the distribution of the time until some individual in a population has experienced two prespecified mutations and the time until this mutant phenotype becomes ...
Experimental Support for Multiple-Locus Complementary Sex Determination in the Parasitoid Cotesia vestalis
Nov 01, 2008; ... ABSTRACT Despite its fundamental role in development, sex determination is highly diverse among animals. Approximately 20% of all animals are haplodiploid, with haploid males and diploid females. Haplodiploid species exhibit diverse but poorly understood mechanisms of sex determination ....
Maximum-Likelihood Estimation of Site-Specific Mutation Rates in Human Mitochondrial DNA From Partial Phylogenetic Classification
Nov 01, 2008; ... ABSTRACT The mitochondrial DNA hypervariable segment I (HVS-I) is widely used in studies of human evolutionary genetics, and therefore accurate estimates of mutation rates among nucleotide sites in this region are essential. We have developed a novel maximum-likelihood methodology for ...
Identification of Selective Sweeps in Closely Related Populations of the House Mouse Based on Microsatellite Scans
Nov 01, 2008; ... ABSTRACT Genome scans of polymorphisms promise to provide insights into the patterns and frequencies of positive selection under natural conditions. The use of microsatellites as markers has the potential to focus on very recent events, since in contrast to SNPs, their high mutation ...
The Generation and Maintenance of Genetic Variation by Frequency-Dependent Selection: Constructing Polymorphisms Under the Pairwise Interaction Model
Nov 01, 2008; ... ABSTRACT Frequency-dependent selection remains the most commonly invoked heuristic explanation for the maintenance of genetic variation. For polymorphism to exist, new alleles must be both generated and maintained in the population. Here we use a construction approach to model ...
A Simple Method to Account for Natural Selection When Predicting Inbreeding Depression
Nov 01, 2008; ... ABSTRACT It has been widely appreciated that natural selection opposes the progress of inbreeding in small populations, thus limiting the actual inbreeding depression for fitness traits. However, no method to account for the consequences of this process has been given so far. I give a ...
Convergent Evolution in the Genetic Basis of Müllerian Mimicry in Heliconius Butterflies
Nov 01, 2008; ... ABSTRACT The neotropical butterflies Heliconius melpomene and H. erato are Müllerian mimics that display the same warningly colored wing patterns in local populations, yet pattern diversity between geographic regions. Linkage mapping has previously shown convergent red wing phenotypes in ...
Bayesian Comparisons of Codon Substitution Models
Nov 01, 2008; ... ABSTRACT In 1994, Muse and Gaut (MG) and Goldman and Yang (GY) proposed evolutionary models that recognize the coding structure of the nucleotide sequences under study, by defining a Markovian substitution process with a state space consisting of the 61 sense codons (assuming the ...
The Different Sources of Variation in Inbreeding Depression, Heterosis and Outbreeding Depression in a Metapopulation of Physa acuta
Nov 01, 2008; ... ABSTRACT Understanding how parental distance affects offspring fitness, i.e., the effects of inbreeding and outbreeding in natural populations, is a major goal in evolutionary biology. While inbreeding is often associated with fitness reduction (inbreeding depression), interpopulation ...
Distributions of Hardy-Weinberg Equilibrium Test Statistics
Nov 01, 2008; ... ABSTRACT It is well established that test statistics and P-values derived from discrete data, such as genetic markers, are also discrete. In most genetic applications, the null distribution for a discrete test statistic is approximated with a continuous distribution, but this ...
Role of Recombination in the Long-Term Retention of Transposable Elements in rRNA Gene Loci
Nov 01, 2008; ... ABSTRACT Multiple theoretical studies have focused on the concerted evolution of the tandemly repeated rRNA genes of eukaryotes; however, these studies did not consider the transposable elements that interrupt the rRNA genes in many organisms. For example, in insects, R1 and R2 have been ...
A General Extreme Value Theory Model for the Adaptation of DNA Sequences Under Strong Selection and Weak Mutation
Nov 01, 2008; ... ABSTRACT Recent theoretical studies of the adaptation of DNA sequences assume that the distribution of fitness effects among new beneficial mutations is exponential. This has been justified by using extreme value theory and, in particular, by assuming that the distribution of fitnesses ...
Selective Sweep at a Quantitative Trait Locus in the Presence of Background Genetic Variation
Nov 01, 2008; ... ABSTRACT We model selection at a locus affecting a quantitative trait (QTL) in the presence of genetic variance due to other loci. The dynamics at the QTL are related to the initial genotypic value and to the background genetic variance of the trait, assuming that background genetic ...
Sequential Elimination of Major-Effect Contributors Identifies Additional Quantitative Trait Loci Conditioning High-Temperature Growth in Yeast
Nov 01, 2008; ... ABSTRACT Several quantitative trait loci (QTL) mapping strategies can successfully identify major-effect loci, but often have poor success detecting loci with minor effects, potentially due to the confounding effects of major loci, epistasis, and limited sample sizes. To overcome such ...
Use of a Drosophila Model to Identify Genes Regulating Plasmodium Growth in the Mosquito
Nov 01, 2008; ... ABSTRACT We performed a forward genetic screen, using Drosophila as a surrogate mosquito, to identify host factors required for the growth of the avian malaria parasite, Plasmodium gallinaceum. We identified 18 presumed loss-of-function mutants that reduced the growth of the parasite in ...
Selective Transcriptional Profiling and Data Analysis Strategies for Expression Quantitative Trait Loci Mapping in Outbred F^sub 2^ Populations
Nov 01, 2008; ... ABSTRACT Genetic analysis of transcriptional profiling experiments is emerging as a promising approach for unraveling genes and pathways that underlie variation of complex biological traits. However, these genetical genomics approaches are currently limited by the high cost of ...
Optimal Design of Genetic Studies of Gene Expression With Two-Color Microarrays in Outbred Crosses
Nov 01, 2008; ... ABSTRACT Combining global gene-expression profiling and genetic analysis of natural allelic variation (genetical genomics) has great potential in dissecting the genetic pathways underlying complex phenotypes. Efficient use of microarrays is paramount in experimental design as the cost of ...
Identification of Single-Nucleotide Polymorphism in the Progesterone Receptor Gene and Its Association With Reproductive Traits in Rabbits
Nov 01, 2008; ... ABSTRACT A total of 598 F^sub 2^ does from a cross between the high and low lines selected divergently for uterine capacity during 10 generations were used in a candidate gene analysis. The presence of major genes affecting the number of implanted embryos and uterine capacity has been ...
Quantitative Trait Loci Mapping and The Genetic Basis of Heterosis in Maize and Rice
Nov 01, 2008; ... ABSTRACT Despite its importance to agriculture, the genetic basis of heterosis is still not well understood. The main competing hypotheses include dominance, overdominance, and epistasis. NC design III is an experimental design that has been used for estimating the average degree of ...
Dominance, Overdominance and Epistasis Condition the Heterosis in Two Heterotic Rice Hybrids
Nov 01, 2008; ... ABSTRACT Two recombinant inbred (RI) populations having 194 and 222 lines each, derived, respectively, from a highly heterotic inter- (IJ) and intrasubspecific (II) hybrid, were backcrossed to their respective parents. The RI and two backcross populations along with F^sub 1^ and its two ...
Mixed Effects Models for Quantitative Trait Loci Mapping With Inbred Strains
Nov 01, 2008; ... ABSTRACT Fixed effects models have dominated the statistical analysis of genetic crosses between inbred strains. In spite of their popularity, the traditional models ignore polygenic background and must be tailored to each specific cross. We reexamine the role of random effect models in ...
A Simple Polymerase Chain Reaction-Based Method for the Construction of Recombinase-Mediated Cassette Exchange Donor Vectors
Nov 01, 2008; ... ABSTRACT Here we describe a simple method for generating donor vectors suitable for targeted transgenesis via recombinase-mediated cassette exchange (RMCE) using the ΦC31 integrase. This PCR-based strategy employs small attB "tails" on the primers used to amplify a sequence of ...
Controlling Type-I Error of the McDonald-Kreitman Test in Genomewide Scans for Selection on Noncoding DNA
Nov 01, 2008; ... ABSTRACT Departures from the assumption of homogenously interdigitated neutral and putatively selected sites in the McDonald-Kreitman test can lead to false rejections of the neutral model in the presence of intermediate levels of recombination. This problem is exacerbated by small ...
A Simple Formula for Obtaining Markedly Improved Mutation Rate Estimates
Nov 01, 2008; ... ABSTRACT In previous work by M. E. Jones and colleagues, it was shown that mutation rate estimates can be improved and corresponding confidence intervals tightened by following a very easy modification of the standard fluctuation assay: cultures are grown to a larger-than-usual final ...
unc-44 Ankyrin and stn-2 [gamma]-Syntrophin Regulate sax-7 L1CAM Function in Maintaining Neuronal Positioning in Caenorhabditis elegans
Nov 01, 2008; ... ABSTRACT The L1 family of single-pass transmembrane cell adhesion molecules (L1CAMs) is conserved from Caenorhabditis elegans and Drosophila to vertebrates and is required for axon guidance, neurite outgrowth, and maintenance of neuronal positions. The extracellular region of L1CAMs ...