bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Suppressors ofCaenorhabditis elegans pha-4/FoxAIdentify the Predicted AAA Helicaseruvb-1/RuvB
Authors: Updike Dustin L , Mango Susan E 
Published: August 2007

AbstractFoxA transcription factors are critical regulators of gut development and function. FoxA proteins specify gut fate during early embryogenesis, drive gut differentiation and morphogenesis at later stages, and affect gut function to mediate nutritional responses. The level of FoxA is critical for these roles, yet we know relatively little about regulators for this family of proteins. To address this issue, we conducted a genetic screen for mutants that suppress a partial loss of pha-4, the sole FoxA factor of Caenorhabditis elegans. We identified 55 mutants using either chemical or insertional mutagenesis. Forty-two of these were informational suppressors that affected nonsense-mediated decay, while the remaining 13 were pha-4 suppressors. These 13 alleles defined at least six different loci. On the basis of mutational frequencies for C. elegans and the genetic dominance of four of the suppressors, we predict that many of the suppressors are either unusual loss-of-function mutations in negative regulators or rare gain-of-function mutations in positive regulators. We characterized one dominant suppressor molecularly and discovered the mutation alters a likely cis-regulatory region within pha-4 itself. A second suppressor defined a new locus, the predicted AAA+ helicase ruvb-1. These results indicate that our screen successfully found cis- or trans-acting regulators of pha-4.
A Genomewide Study of Reproductive Barriers Between Allopatric Populations of a Homosporous Fern,Ceratopteris richardii
Authors: Nakazato Takuya , Jung Min-Kyung , Housworth Elizabeth A , Rieseberg Loren H , Gastony Gerald J 
Published: August 2007

AbstractBiological factors involved in reproductive barriers between two divergent races of Ceratopteris richardii were investigated. We used a combination of spore germination rates, QTL analysis of spore germination rates, and transmission ratio distortion (TRD) of 729 RFLPs, AFLPs, and isozyme markers distributed across the genome on the basis of hybrid populations of 488 doubled haploid lines (DHLs) and 168 F2's. Substantial reproductive barriers were found between the parental races, predominantly in the form of spore inviability (23.7% F1 spore viability). Intrinsic genetic factors such as Bateson–Dobzhansky–Muller (BDM) incompatibilities involving both nuclear–nuclear and nuclear–cytoplasmic factors and chromosomal rearrangements appear to contribute to intrinsic postzygotic isolation. The genomewide distribution patterns of TRD loci support the hypothesis that reproductive barriers are a byproduct of divergence in allopatry and that the strong reproductive barriers are attributable to a small number of genetic elements scattered throughout the genome.
Stable Inheritance of Host Species-Derived Microchromosomes in the Gynogenetic Fish Poecilia formosa
Authors: Nanda Indrajit , Schlupp Ingo , Lamatsch Dunja K , Lampert Kathrin P , Schmid Michael , Schartl Manfred 
Published: August 2007

Abstract
B chromosomes are additional, usually unstable constituents of the genome of many organisms. Their origin, however, is often unclear and their evolutionary relevance is not well understood. They may range from being deleterious to neutral or even beneficial. We have followed the genetic fate of B chromosomes in the asexual, all-female fish Poecilia formosa over eight generations. In this species, B chromosomes come in the form of one to three tiny microchromosomes derived from males of the host species that serve as sperm donors for this gynogenetic species. All microchromosomes have centromeric heterochromatin but usually only one has a telomere. Such microchromosomes are stably inherited, while the telomereless are prone to be lost in both the soma and germline. In some cases the stable microchromosome carries a functional gene lending support to the hypothesis that the B chromosomes in P. formosa could increase the genetic diversity of the clonal lineage in this ameiotic organism and to some degree counteract the genomic decay that is supposed to be connected with the lack of recombination.
Gravity Force Transduced by the MEC-4/MEC-10 DEG/ENaC Channel Modulates DAF-16/FoxO Activity in Caenorhabditis elegans
Authors: Kim Nahui , Dempsey Catherine M , Kuan Chih-Jen , Zoval Jim V , O'Rourke Eyleen , Ruvkun Gary , Madou Marc J , Sze Ji Y 
Published: August 2007

Abstract
The gravity response is an array of behavioral and physiological plasticity elicited by changes in ambient mechanical force and is an evolutionarily ancient adaptive mechanism. We show in Caenorhabditis elegans that the force of hypergravity is translated into biological signaling via a genetic pathway involving three factors: the degenerin/epithelial Na+ channel (DEG/ENaC) class of mechanosensory channels of touch receptor neurons, the neurotransmitter serotonin, and the FoxO transcription factor DAF-16 known to regulate development, energy metabolism, stress responses, and aging. After worms were exposed to hypergravity for 3 hr, their muscular and neuronal functions were preserved, but they exhibited DAF-16∷GFP nuclear accumulation in cells throughout the body and accumulated excess fat. Mutations in MEC-4/MEC-10 DEG/ENaC or its partners MEC-6, MEC-7, and MEC-9 blocked DAF-16∷GFP nuclear accumulation induced by hypergravity but did not affect DAF-16 response to other stresses. We show that exogenous serotonin and the antidepressant fluoxetine can attenuate DAF-16∷GFP nuclear accumulation in WT animals exposed to hypergravity. These results reveal a novel physiological role of the mechanosensory channel, showing that the perception of mechanical stress controls FoxO signaling pathways and that inactivation of DEG/ENaC may decouple mechanical loading and physiological responses.
Contrasting Rates of Evolution inPm3Loci From Three Wheat Species and Rice
Authors: Wicker Thomas , Yahiaoui Nabila , Keller Beat 
Published: August 2007

AbstractThe Pm3 gene from wheat confers resistance against powdery mildew and recent studies have shown that it is a member of a multigene family in the wheat genome. We compared genomic sequences ranging from 178 to 332 kb containing six Pm3-like genes and five gene fragments from orthologous loci in the A genome of wheat at three different ploidy levels. We found that the wheat Pm3 loci display an extremely dynamic evolution where sequence conservation is minimal between species and basically limited to very short sequences containing the genetic markers that define the orthology. The Pm3-like genes and their up- and downstream regions were reshuffled by multiple rearrangements, resulting in a complex mosaic of conserved and unique sequences. Comparison with rice showed that the known wheat Pm3-like genes represent only one branch of a large superfamily with several clusters in rice and suggests the presence of additional similar genes in the wheat genome. Estimates of divergence times and transposable-element insertions indicate that the Pm3 locus in wheat has undergone more drastic changes in its recent evolution than its counterpart in rice. This indicates that loci containing homologous resistance gene analogs can evolve at highly variable speeds in different species.
Derivation of the Shrinkage Estimates of Quantitative Trait Locus Effects
Authors: Xu Shizhong 
Published: August 2007

AbstractThe shrinkage estimate of a quantitative trait locus (QTL) effect is the posterior mean of the QTL effect when a normal prior distribution is assigned to the QTL. This note gives the derivation of the shrinkage estimate under the multivariate linear model. An important lemma regarding the posterior mean of a normal likelihood combined with a normal prior is introduced. The lemma is then used to derive the Bayesian shrinkage estimates of the QTL effects.
Adaptive Evolution of Recently Duplicated Accessory Gland Protein Genes in Desert Drosophila
Authors: Wagstaff Bradley J , Begun David J 
Published: August 2007

AbstractThe relationship between animal mating system variation and patterns of protein polymorphism and divergence is poorly understood. Drosophila provides an excellent system for addressing this issue, as there is abundant interspecific mating system variation. For example, compared to D. melanogaster subgroup species, repleta group species have higher remating rates, delayed sexual maturity, and several other interesting differences. We previously showed that accessory gland protein genes (Acp's) of Drosophila mojavensis and D. arizonae evolve more rapidly than Acp's in the D. melanogaster subgroup and that adaptive Acp protein evolution is likely more common in D. mojavensis/D. arizonae than in D. melanogaster/D. simulans. These findings are consistent with the idea that greater postcopulatory selection results in more adaptive evolution of seminal fluid proteins in the repleta group flies. Here we report another interesting evolutionary difference between the repleta group and the D. melanogaster subgroup Acp's. Acp gene duplications are present in D. melanogaster, but their high sequence divergence indicates that the fixation rate of duplicated Acp's has been low in this lineage. Here we report that D. mojavensis and D. arizonae genomes contain several very young duplicated Acp's and that these Acp's have experienced very rapid, adaptive protein divergence. We propose that rapid remating of female desert Drosophila generates selection for continuous diversification of the male Acp complement to improve male fertilization potential. Thus, mating system variation may be associated with adaptive protein divergence as well as with duplication of Acp's in Drosophila.
The Number of Loci That Affect Milk Production Traits in Dairy Cattle
Authors: Chamberlain Amanda Jane , McPartlan Helen Clare , Goddard Michael Edward 
Published: August 2007

AbstractWe have used the results of an experiment mapping quantitative trait loci (QTL) affecting milk yield and composition to estimate the total number of QTL affecting these traits. We did this by estimating the number of segregating QTL within a half-sib daughter design using logic similar to that used to estimate the “false discovery rate” (FDR). In a half-sib daughter design with six sire families we estimate that the average sire was heterozygous for ∼5 QTL per trait. Also, in most cases only one sire was heterozygous for any one QTL; therefore at least 30 QTL were likely to be segregating for these milk production traits in this Holstein population.
Analysis of Litter Size and Average Litter Weight in Pigs Using a Recursive Model
Authors: Varona Luis , Sorensen Daniel , Thompson Robin 
Published: August 2007

Abstract
An analysis of litter size and average piglet weight at birth in Landrace and Yorkshire using a standard two-trait mixed model (SMM) and a recursive mixed model (RMM) is presented. The RMM establishes a one-way link from litter size to average piglet weight. It is shown that there is a one-to-one correspondence between the parameters of SMM and RMM and that they generate equivalent likelihoods. As parameterized in this work, the RMM tests for the presence of a recursive relationship between additive genetic values, permanent environmental effects, and specific environmental effects of litter size, on average piglet weight. The equivalent standard mixed model tests whether or not the covariance matrices of the random effects have a diagonal structure. In Landrace, posterior predictive model checking supports a model without any form of recursion or, alternatively, a SMM with diagonal covariance matrices of the three random effects. In Yorkshire, the same criterion favors a model with recursion at the level of specific environmental effects only, or, in terms of the SMM, the association between traits is shown to be exclusively due to an environmental (negative) correlation. It is argued that the choice between a SMM or a RMM should be guided by the availability of software, by ease of interpretation, or by the need to test a particular theory or hypothesis that may best be formulated under one parameterization and not the other.
A Hypothesis for How Chromosome 11 Translocations Cause Psychiatric Disorders
Authors: Singh Gurjeet , Klar Amar J S 
Published: August 2007

Abstract
Despite extensive effort for many years, the etiology of major psychiatric diseases remains unknown. A recent study by Baysal et al. has argued against the ALG9 gene variants in causing psychosis. Due to its disruption by a balanced t(9p24;11q23) translocation that segregates with the disorder in a family, it was proposed to be a primary candidate gene causing psychosis. In addition, a recent review article by Pickard et al., entitled “Cytogenetics and gene discovery in psychiatric disorders,” highlighted the importance of studies of chromosome rearrangements in finding disease-causing mutations. However, achieving the goal of finding genes by conventional association studies and by investigating chromosome rearrangements remains elusive. Here we discuss a fundamentally different explanation from the usual one considered by workers in the field concerning chromosome aberrations and psychoses etiology. We hypothesize how chromosome aberrations might cause disease but the gene at the rearrangement breakpoint is irrelevant for the etiology. Moreover, we discuss subsequently published findings that help scrutinize validity of the two very different hypotheses considered in the psychiatric genetics field. In sum, we alert the readers to the complexities of interpreting phenotypes associated with rearrangements.
Molecular Evolution of Pathogenicity-Island Genes in Pseudomonas viridiflava
Authors: Araki Hitoshi , Innan Hideki , Kreitman Martin , Bergelson Joy 
Published: August 2007

Abstract
The bacterial pathogen Pseudomonas viridiflava possesses two pathogenicity islands (PAIs) that share many gene homologs, but are structurally and phenotypically differentiated (T-PAI and S-PAI). These PAIs are paralogous, but only one is present in each isolate. While this dual presence/absence polymorphism has been shown to be maintained by balancing selection, little is known about the molecular evolution of individual genes on the PAIs. Here we investigate genetic variation of 12 PAI gene loci (7 on T-PAI and 5 on S-PAI) in 96 worldwide isolates of P. viridiflava. These genes include avirulence genes (hopPsyA and avrE), their putative chaperones (shcA and avrF), and genes encoding the type III outer proteins (hrpA, hrpZ, and hrpW). Average nucleotide diversities in these genes (π = 0.004–0.020) were close to those in the genetic background. Large numbers of recombination events were found within PAIs and a sign of positive selection was detected in avrE. These results suggest that the PAI genes are evolving relatively freely from each other on the PAIs, rather than as a single unit under balancing selection. Evolutionarily stable PAIs may be preferable in this species because preexisting genetic variation enables P. viridiflava to respond rapidly to natural selection.
Terminal Regions of Wheat Chromosomes Select Their Pairing Partners in Meiosis
Authors: Corredor Eduardo , Lukaszewski Adam J , Pachón Paula , Allen Diana C , Naranjo Tomás 
Published: August 2007

Abstract
Many plant species, including important crops like wheat, are polyploids that carry more than two sets of genetically related chromosomes capable of meiotic pairing. To safeguard a diploid-like behavior at meiosis, many polyploids evolved genetic loci that suppress incorrect pairing and recombination of homeologues. The Ph1 locus in wheat was proposed to ensure homologous pairing by controlling the specificity of centromere associations that precede chromosome pairing. Using wheat chromosomes that carry rye centromeres, we show that the centromere associations in early meiosis are not based on homology and that the Ph1 locus has no effect on such associations. Although centromeres indeed undergo a switch from nonhomologous to homologous associations in meiosis, this process is driven by the terminally initiated synapsis. The centromere has no effect on metaphase I chiasmate chromosome associations: homologs with identical or different centromeres, in the presence and absence of Ph1, pair the same. A FISH analysis of the behavior of centromeres and distal chromomeres in telocentric and bi-armed chromosomes demonstrates that it is not the centromeric, but rather the subtelomeric, regions that are involved in the correct partner recognition and selection.
The Flightless I Homolog, fli-1, Regulates Anterior/Posterior Polarity, Asymmetric Cell Division and Ovulation During Caenorhabditis elegans Development
Authors: Deng Hansong , Xia Dan , Fang Bin , Zhang Hong 
Published: August 2007

Abstract
Flightless I (Fli I) is an evolutionarily conserved member of the gelsolin family, containing actin-binding and severing activity in vitro. The physiological function of Fli I during animal development remains largely undefined. In this study, we reveal a key role of the Caenorhabditis elegans Fli I homolog, fli-1, in specifying asymmetric cell division and in establishing anterior–posterior polarity in the zygote. The fli-1 gene also regulates the cytokinesis of somatic cells and the development of germline and interacts with the phosphoinositol-signaling pathway in the regulation of ovulation. The fli-1 reporter gene shows that the localization of FLI-1 coincides with actin-rich regions and that the actin cytoskeleton is impaired in many tissues in the fli-1 mutants. Furthermore, the function of fli-1 in C. elegans can be functionally substituted by the Drosophila Fli I. Our studies demonstrate that fli-1 plays an important role in regulating the actin-dependent events during C. elegans development.
Joint Estimation of Migration Rate and Effective Population Size Using the Island Model
Authors: Skalski Garrick T 
Published: August 2007

AbstractUsing the island model of population demography, I report that the demographic parameters migration rate and effective population size can be jointly estimated with equilibrium probabilities of identity in state calculated using a sample of genotypes collected at a single point in time from a single generation. The method, which uses moment-type estimators, applies to dioecious populations in which females and males have identical demography and monoecious populations with no selfing and requires that offspring genotypes are sampled following reproduction and prior to migration. I illustrate the estimation procedure using the infinite-island model with no mutation and the finite-island model with three kinds of mutation models. In the infinite-island model with no mutation, the estimators can be expressed as simple functions of estimates of the F-statistic parameters FIT and FST. In the finite-island model with mutation among k alleles, mutation rate, migration rate, and effective population size can be simultaneously estimated. The estimates of migration rate and effective population size are somewhat robust to violations in assumptions that may arise in empirical applications such as different kinds of mutation models and deviations from temporal equilibrium.
A Single Nucleotide Polymorphism in the DNA Polymerase Gamma Gene of Saccharomyces cerevisiae Laboratory Strains Is Responsible for Increased Mitochondrial DNA Mutability
Authors: Baruffini Enrico , Lodi Tiziana , Dallabona Cristina , Foury Françoise 
Published: August 2007

Abstract
In the Saccharomyces cerevisiae strains used for genome sequencing and functional analysis, the mitochondrial DNA replicase Mip1p contains a single nucleotide polymorphism changing the strictly conserved threonine 661 to alanine. This substitution is responsible for the increased rate of mitochondrial DNA point mutations and deletions in these strains.
Association of Polymorphisms in Odorant-Binding Protein Genes With Variation in Olfactory Response to Benzaldehyde in Drosophila
Authors: Wang Ping , Lyman Richard F , Shabalina Svetlana A , Mackay Trudy F C , Anholt Robert R H 
Published: August 2007

Abstract
Adaptive evolution of animals depends on behaviors that are essential for their survival and reproduction. The olfactory system of Drosophila melanogaster has emerged as one of the best characterized olfactory systems, which in addition to a family of odorant receptors, contains an approximately equal number of odorant-binding proteins (OBPs), encoded by a multigene family of 51 genes. Despite their abundant expression, little is known about their role in chemosensation, largely due to the lack of available mutations in these genes. We capitalized on naturally occurring mutations (polymorphisms) to gain insights into their functions. We analyzed the sequences of 13 Obp genes in two chromosomal clusters in a population of wild-derived inbred lines, and asked whether polymorphisms in these genes are associated with variation in olfactory responsiveness. Four polymorphisms in 3 Obp genes exceeded the statistical permutation threshold for association with responsiveness to benzaldehyde, suggesting redundancy and/or combinatorial recognition by these OBPs of this odorant. Model predictions of alternative pre-mRNA secondary structures associated with polymorphic sites suggest that alterations in Obp mRNA structure could contribute to phenotypic variation in olfactory behavior.
Significance Thresholds for Quantitative Trait Locus Mapping Under Selective Genotyping
Authors: Manichaikul Ani , Palmer Abraham A , Sen Śaunak , Broman Karl W 
Published: August 2007

AbstractIn the case of selective genotyping, the usual permutation test to establish statistical significance for quantitative trait locus (QTL) mapping can give inappropriate significance thresholds, especially when the phenotype distribution is skewed. A stratified permutation test should be used, with phenotypes shuffled separately within the genotyped and ungenotyped individuals.
Design of a Portable Streamside Rearing Facility for Lake Sturgeon
Authors: Holtgren J Marty , Ogren Stephanie A , Paquet Aaron J , Fajfer Steve 
Published: August 2007

Abstract
A portable streamside rearing facility was designed and used by the Little River Band of Ottawa Indians during efforts to rehabilitate a remnant population of lake sturgeon Acipenser fulvescens in the Big Manistee River, Michigan, beginning in 2004. The streamside rearing facility facilitates rearing of wild-caught lake sturgeon larvae in their natal water. This rearing approach provides a cost-effective technique for small batch rearing, incorporates aspects of genetic conservation, and addresses concerns about imprinting and spawning site fidelity. This rearing method may be an important management tool for restoring remnant lake sturgeon populations. Successful rearing of lake sturgeon during the first 3 years of operation indicates that this portable design may be adapted and modified for other locations and fish species. Other management agencies in the Great Lakes basin are currently using this technology for lake sturgeon rehabilitation because of the demonstrated operational success of this facility.