bluuebunny/crossref_metadata_2025_split huggingface dataset:
TheSaccharomyces cerevisiaeActin Cytoskeletal Component Bsp1p Has an Auxiliary Role in Actomyosin Ring Function and in the Maintenance of Bud-Neck Structure
Authors: Wright Daniel J , Munro Ewen , Corbett Mark , Bentley Adam J , Fullwood Nigel J , Murray Stephen , Price Clive 
Published: April 2008

AbstractIqg1p is a component of the actomyosin contractile ring that is required for actin recruitment and septum deposition. Cells lacking Iqg1p function have an altered bud-neck structure and fail to form a functional actomyosin contractile ring resulting in a block to cytokinesis and septation. Here it is demonstrated that increased expression of the actin cytoskeleton associated protein Bsp1p bypasses the requirement for contractile ring function. This also correlates with reduced bud-neck width and remedial septum formation. Increased expression of this protein in a temperature-sensitive iqg1-1 background causes remedial septum formation at the bud neck that is reliant upon chitin synthase III activity and restores cell separation. The observed suppression correlates with a restoration of normal bud-neck structure. While Bsp1p is a component of the contractile ring, its recruitment to the bud neck is not required for the observed suppression. Loss of Bsp1p causes a brief delay in the redistribution of the actin cytoskeleton normally observed at the end of actin ring contraction. Compromise of Iqg1p function, in the absence of Bsp1p function, leads to a profound change in the distribution of actin and the pattern of cell growth accompanied by a failure to complete cytokinesis and cell separation.
Genetic Analysis of theCaenorhabditis elegansGLH Family of P-Granule Proteins
Authors: Spike Caroline , Meyer Nicole , Racen Erica , Orsborn April , Kirchner Jay , Kuznicki Kathleen , Yee Christopher , Bennett Karen , Strome Susan 
Published: April 2008

AbstractThe Vasa DEAD-box helicases are widespread markers of germ cells across species, and in some organisms have been shown to be essential for germ-cell formation and development. In contrast to the single Vasa gene in most systems analyzed, Caenorhabditis elegans has four Vasa family members, the germline helicases GLH-1, GLH-2, GLH-3, and GLH-4. Our analysis of deletion alleles of each glh gene demonstrates that GLH-1 is the key member of the family: loss of GLH-1 function causes sterility that is mainly maternal effect, is manifested predominantly at elevated temperature, and is due to reduced germ-cell proliferation and impaired formation of both sperm and oocytes. The other GLHs are not essential. However, GLH-4 serves redundant roles with GLH-1: loss of both genes' function causes glh-1-like sterility at all temperatures. Molecular epistasis analysis demonstrates that GLH-1 and GLH-4 are required for proper association of the PGL family of proteins with P granules, suggesting a pathway of P-granule assembly in which the GLHs are upstream of the PGL proteins and the mRNA cap-binding protein IFE-1. While loss of some P-granule components causes worms to be defective in RNA interference, loss of GLH-1 and GLH-4 does not compromise RNAi. Thus, RNAi likely does not require intact P granules but instead relies on particular P-granule factors. We discuss the evolution of the Vasa/GLH genes and current views of their functions and the assembly and roles of germ granules among species.
Quantitative Trait Loci Mapping in Five New Large Recombinant Inbred Line Populations of Arabidopsis thaliana Genotyped With Consensus Single-Nucleotide Polymorphism Markers
Authors: Simon Matthieu , Loudet Olivier , Durand Stéphanie , Bérard Aurélie , Brunel Dominique , Sennesal François-Xavier , Durand-Tardif Mylène , Pelletier Georges , Camilleri Christine 
Published: April 2008

Abstract
Quantitative approaches conducted in a single mapping population are limited by the extent of genetic variation distinguishing the parental genotypes. To overcome this limitation and allow a more complete dissection of the genetic architecture of complex traits, we built an integrated set of 15 new large Arabidopsis thaliana recombinant inbred line (RIL) populations optimized for quantitative trait loci (QTL) mapping, having Columbia as a common parent crossed to distant accessions. Here we present 5 of these populations that were validated by investigating three traits: flowering time, rosette size, and seed production as an estimate of fitness. The large number of RILs in each population (between 319 and 377 lines) and the high density of evenly spaced genetic markers scored ensure high power and precision in QTL mapping even under a minimal phenotyping framework. Moreover, the use of common markers across the different maps allows a direct comparison of the QTL detected within the different RIL sets. In addition, we show that following a selective phenotyping strategy by performing QTL analyses on genotypically chosen subsets of 164 RILs (core populations) does not impair the power of detection of QTL with phenotypic contributions &gt;7%.
Rapid Evolution of Yeast Centromeres in the Absence of Drive
Authors: Bensasson Douda , Zarowiecki Magdalena , Burt Austin , Koufopanou Vassiliki 
Published: April 2008

AbstractTo find the most rapidly evolving regions in the yeast genome we compared most of chromosome III from three closely related lineages of the wild yeast Saccharomyces paradoxus. Unexpectedly, the centromere appears to be the fastest-evolving part of the chromosome, evolving even faster than DNA sequences unlikely to be under selective constraint (i.e., synonymous sites after correcting for codon usage bias and remnant transposable elements). Centromeres on other chromosomes also show an elevated rate of nucleotide substitution. Rapid centromere evolution has also been reported for some plants and animals and has been attributed to selection for inclusion in the egg or the ovule at female meiosis. But Saccharomyces yeasts have symmetrical meioses with all four products surviving, thus providing no opportunity for meiotic drive. In addition, yeast centromeres show the high levels of polymorphism expected under a neutral model of molecular evolution. We suggest that yeast centromeres suffer an elevated rate of mutation relative to other chromosomal regions and they change through a process of “centromere drift,” not drive.
Adaptive Plasmid Evolution Results in Host-Range Expansion of a Broad-Host-Range Plasmid
Authors: De Gelder Leen , Williams Julia J , Ponciano José M , Sota Masahiro , Top Eva M 
Published: April 2008

Abstract
Little is known about the range of hosts in which broad-host-range (BHR) plasmids can persist in the absence of selection for plasmid-encoded traits, and whether this “long-term host range” can evolve over time. Previously, the BHR multidrug resistance plasmid pB10 was shown to be highly unstable in Stenotrophomonas maltophilia P21 and Pseudomonas putida H2. To investigate whether this plasmid can adapt to such unfavorable hosts, we performed evolution experiments wherein pB10 was maintained in strain P21, strain H2, and alternatingly in P21 and H2. Plasmids that evolved in P21 and in both hosts showed increased stability and decreased cost in ancestral host P21. However, the latter group showed higher variability in stability patterns, suggesting that regular switching between distinct hosts hampered adaptive plasmid evolution. The plasmids evolved in P21 were also equally or more stable in other hosts compared to pB10, which suggested true host-range expansion. The complete genome sequences of four evolved plasmids with improved stability showed only one or two genetic changes. The stability of plasmids evolved in H2 improved only in their coevolved hosts, not in the ancestral host. Thus a BHR plasmid can adapt to an unfavorable host and thereby expand its long-term host range.
Distinct Functions of MLH3 at Recombination Hot Spots in the Mouse
Authors: Svetlanov Anton , Baudat Frederic , Cohen Paula E , de Massy Bernard 
Published: April 2008

Abstract
The four mammalian MutL homologs (MLH1, MLH3, PMS1, and PMS2) participate in a variety of events, including postreplicative DNA repair, prevention of homeologous recombination, and crossover formation during meiosis. In this latter role, MLH1–MLH3 heterodimers predominate and are essential for prophase I progression. Previous studies demonstrated that mice lacking Mlh1 exhibit a 90% reduction in crossing over at the Psmb9 hot spot while noncrossovers, which do not result in exchange of flanking markers but arise from the same double-strand break event, are unaffected. Using a PCR-based strategy that allows for detailed analysis of crossovers and noncrossovers, we show here that Mlh3−/− exhibit a 85–94% reduction in the number of crossovers at the Psmb9 hot spot. Most of the remaining crossovers in Mlh3−/− meiocytes represent simple exchanges similar to those seen in wild-type mice, with a small fraction (6%) representing complex events that can extend far from the initiation zone. Interestingly, we detect an increase of noncrossovers in Mlh3−/− spermatocytes. These results suggest that MLH3 functions predominantly with MLH1 to promote crossovers, while noncrossover events do not require these activities. Furthermore, these results indicate that ∼10% of crossovers in the mouse are independent of MLH3, suggesting the existence of alternative crossover pathways in mammals.
Key Impact of Vgt1 on Flowering Time Adaptation in Maize: Evidence From Association Mapping and Ecogeographical Information
Authors: Ducrocq Sébastien , Madur Delphine , Veyrieras Jean-Baptiste , Camus-Kulandaivelu Létizia , Kloiber-Maitz Monika , Presterl Thomas , Ouzunova Milena , Manicacci Domenica , Charcosset Alain 
Published: April 2008

Abstract
An association study conducted on 375 maize inbred lines indicates a strong relationship between Vgt1 polymorphisms and flowering time, extending former quantitative trait loci (QTL) mapping results. Analysis of allele frequencies in a landrace collection supports a key role of Vgt1 in maize altilatitudinal adaptation.
Genetic Expectations of Quantitative Trait Loci Main and Interaction Effects Obtained With the Triple Testcross Design and Their Relevance for the Analysis of Heterosis
Authors: Melchinger A E , Utz H F , Schön C C 
Published: April 2008

Abstract
Interpretation of experimental results from quantitative trait loci (QTL) mapping studies on the predominant type of gene action can be severely affected by the choice of statistical model, experimental design, and provision of epistasis. In this study, we derive quantitative genetic expectations of (i) QTL effects obtained from one-dimensional genome scans with the triple testcross (TTC) design and (ii) pairwise interactions between marker loci using two-way analyses of variance (ANOVA) under the F2- and the F∞-metric model. The theoretical results show that genetic expectations of QTL effects estimated with the TTC design are complex, comprising both main and epistatic effects, and that genetic expectations of two-way marker interactions are not straightforward extensions of effects estimated in one-dimensional scans. We also demonstrate that the TTC design can partially overcome the limitations of the design III in separating QTL main effects and their epistatic interactions in the analysis of heterosis and that dominance × additive epistatic interactions of individual QTL with the genetic background can be estimated with a one-dimensional genome scan. Furthermore, we present genetic expectations of variance components for the analysis of TTC progeny tested in a split-plot design, assuming digenic epistasis and arbitrary linkage.
Exploring Population Genetic Models With Recombination Using Efficient Forward-Time Simulations
Authors: Padhukasahasram Badri , Marjoram Paul , Wall Jeffrey D , Bustamante Carlos D , Nordborg Magnus 
Published: April 2008

Abstract
We present an exact forward-in-time algorithm that can efficiently simulate the evolution of a finite population under the Wright–Fisher model. We used simulations based on this algorithm to verify the accuracy of the ancestral recombination graph approximation by comparing it to the exact Wright–Fisher scenario. We find that the recombination graph is generally a very good approximation for models with complete outcrossing, whereas, for models with self-fertilization, the approximation becomes slightly inexact for some combinations of selfing and recombination parameters.
Genetic Variation Affecting Host–Parasite Interactions: Different Genes Affect Different Aspects of Sigma Virus Replication and Transmission in Drosophila melanogaster
Authors: Bangham Jenny , Kim Kang-Wook , Webster Claire L , Jiggins Francis M 
Published: April 2008

Abstract
In natural populations, genetic variation affects resistance to disease. Knowing how much variation exists, and understanding the genetic architecture of this variation, is important for medicine, for agriculture, and for understanding evolutionary processes. To investigate the extent and nature of genetic variation affecting resistance to pathogens, we are studying a tractable model system: Drosophila melanogaster and its natural pathogen the vertically transmitted sigma virus. We show that considerable genetic variation affects transmission of the virus from parent to offspring. However, maternal and paternal transmission of the virus is affected by different genes. Maternal transmission is a simple Mendelian trait: most of the genetic variation is explained by a polymorphism in ref(2)P, a gene already well known to affect resistance to sigma. In contrast, there is considerable genetic variation in paternal transmission that cannot be explained by ref(2)P and is caused by other loci on chromosome 2. Furthermore, we found no genetic correlation between paternal transmission of the virus and resistance to infection by the sigma virus following injection. This suggests that different loci affect viral replication and paternal transmission.
The Role of Regulatory Genes During Maize Domestication: Evidence From Nucleotide Polymorphism and Gene Expression
Authors: Zhao Qiong , Thuillet Anne-Céline , Uhlmann Nathan K , Weber Allison , Rafalski J Antoni , Allen Stephen M , Tingey Scott , Doebley John 
Published: April 2008

Abstract
We investigated DNA sequence variation in 72 candidate genes in maize landraces and the wild ancestor of maize, teosinte. The candidate genes were chosen because they exhibit very low sequence diversity among maize inbreds and have sequence homology to known regulatory genes. We observed signatures of selection in 17 candidate genes, indicating that they were potential targets of artificial selection during domestication. In addition, 21 candidate genes were identified as potential targets of natural selection in teosinte. A comparison of the proportion of selected genes between our regulatory genes and genes unfiltered for their potential function (but also with very low sequence diversity among maize inbreds) provided some weak evidence that regulatory genes are overrepresented among selected genes. We detected no significant association between the positions of genes identified as potential targets of selection during domestication and quantitative trait loci (QTL) responsible for maize domestication traits. However, a subset of these genes, those identified by sequence homology as kinase/phosphatase genes, significantly cluster with the domestication QTL. We also analyzed expression profiles of genes in distinct maize tissues and observed that domestication genes are expressed on average at a significantly higher level than neutral genes in reproductive organs, including kernels.
The Rad52 Homologs Rad22 and Rti1 ofSchizosaccharomyces pombeAre Not Essential for Meiotic Interhomolog Recombination, but Are Required for Meiotic Intrachromosomal Recombination and Mating-Type-Related DNA Repair
Authors: Octobre Guillaume , Lorenz Alexander , Loidl Josef , Kohli Jürg 
Published: April 2008

AbstractProteins of the RAD52 epistasis group play an essential role in repair of some types of DNA damage and genetic recombination. In Schizosaccharomyces pombe, Rad22 (a Rad52 ortholog) has been shown to be as necessary for repair and recombination events during vegetative growth as its Saccharomyces cerevisiae counterpart. This finding contrasts with previous reports where, due to suppressor mutations in the fbh1 gene, rad22 mutants did not display a severe defect. We have analyzed the roles of Rad22 and Rti1, another Rad52 homolog, during meiotic recombination and meiosis in general. Both proteins play an important role in spore viability. During meiotic prophase I, they partially colocalize and partially localize to Rad51 foci and linear elements. Genetic analysis showed that meiotic interchromosomal crossover and conversion events were unexpectedly not much affected by deletion of either or both genes. A strong decrease of intrachromosomal recombination assayed by a gene duplication construct was observed. Therefore, we propose that the most important function of Rad22 and Rti1 in S. pombe meiosis is repair of double-strand breaks with involvement of the sister chromatids. In addition, a novel mating-type-related repair function of Rad22 specific to meiosis and spore germination is described.
Schizosaccharomyces pombe Hsp90/Git10 Is Required for Glucose/cAMP Signaling
Authors: Alaamery Manal A , Hoffman Charles S 
Published: April 2008

Abstract
The fission yeast Schizosaccharomyces pombe senses environmental glucose through a cAMP-signaling pathway. Elevated cAMP levels activate protein kinase A (PKA) to inhibit transcription of genes involved in sexual development and gluconeogenesis, including the fbp1+ gene, which encodes fructose-1,6-bisphosphatase. Glucose-mediated activation of PKA requires the function of nine glucose-insensitive transcription (git) genes, encoding adenylate cyclase, the PKA catalytic subunit, and seven “upstream” proteins required for glucose-triggered adenylate cyclase activation. We describe the cloning and characterization of the git10+ gene, which is identical to swo1+ and encodes the S. pombe Hsp90 chaperone protein. Glucose repression of fbp1+ transcription is impaired by both git10− and swo1− mutant alleles of the hsp90+ gene, as well as by chemical inhibition of Hsp90 activity and temperature stress to wild-type cells. Unlike the swo1− mutant alleles, the git10-201 allele supports cell growth at 37°, while severely reducing glucose repression of an fbp1-lacZ reporter, suggesting a separation-of-function defect. Sequence analyses of three swo1− alleles and the one git10− allele indicate that swo1− mutations alter core functional domains of Hsp90, while the git10− mutation affects the Hsp90 central domain involved in client protein binding. These results suggest that Hsp90 plays a specific role in the S. pombe glucose/cAMP pathway.
RNAi ofmet1Reduces DNA Methylation and Induces Genome-Specific Changes in Gene Expression and Centromeric Small RNA Accumulation in Arabidopsis Allopolyploids
Authors: Chen Meng , Ha Misook , Lackey Erika , Wang Jianlin , Chen Z Jeffrey 
Published: April 2008

AbstractChanges in genome structure and gene expression have been documented in both resynthesized and natural allopolyploids that contain two or more divergent genomes. The underlying mechanisms for rapid and stochastic changes in gene expression are unknown. Arabidopsis suecica is a natural allotetraploid derived from the extant A. thaliana and A. arenosa genomes that are homeologous in the allotetraploid. Here we report that RNAi of met1 reduced DNA methylation and altered the expression of ∼200 genes, many of which encode transposons, predicted proteins, and centromeric and heterochromatic RNAs. Reduced DNA methylation occurred frequently in promoter regions of the upregulated genes, and an En/Spm-like transposon was reactivated in met1-RNAi A. suecica lines. Derepression of transposons, heterochromatic repeats, and centromeric small RNAs was primarily derived from the A. thaliana genome, and A. arenosa homeologous loci were less affected by methylation defects. A high level of A. thaliana centromeric small RNA accumulation was correlated with hypermethylation of A. thaliana centromeres. The greater effects of reduced DNA methylation on transposons and centromeric repeats in A. thaliana than in A. arenosa are consistent with the repression of many genes that are expressed at higher levels in A. thaliana than in A. arenosa in the resynthesized allotetraploids. Moreover, non-CG (CC) methylation in the promoter region of A. thaliana At2g23810 remained in the resynthesized allotetraploids, and the methylation spread within the promoter region in natural A. suecica, leading to silencing of At2g23810. At2g23810 was demethylated and reactivated in met1-RNAi A. suecica lines. We suggest that many A. thaliana genes are transcriptionally repressed in resynthesized allotetraploids, and a subset of A. thaliana loci including transposons and centromeric repeats are heavily methylated and subjected to homeologous genome-specific RNA-mediated DNA methylation in natural allopolyploids.
Nearly Neutrality and the Evolution of Codon Usage Bias in Eukaryotic Genomes
Authors: Subramanian Sankar 
Published: April 2008

Abstract
Here I show that the mean codon usage bias of a genome, and of the lowly expressed genes in a genome, is largely similar across eukaryotes ranging from unicellular protists to vertebrates. Conversely, this bias in housekeeping genes and in highly expressed genes has a remarkable inverse relationship with species generation time that varies by more than four orders of magnitude. The relevance of these results to the nearly neutral theory of molecular evolution is discussed.
Basolateral Junctions Utilize Warts Signaling to Control Epithelial-Mesenchymal Transition and Proliferation Crucial For Migration and Invasion of Drosophila Ovarian Epithelial Cells
Authors: Zhao Min , Szafranski Przemyslaw , Hall Chad Albert , Goode Scott 
Published: April 2008

Abstract
Fasciclin2 (Fas2) and Discslarge (Dlg) localize to the basolateral junction (BLJ) of Drosophila follicle epithelial cells and inhibit their proliferation and invasion. To identify a BLJ signaling pathway we completed a genomewide screen for mutants that enhance dlg tumorigenesis. We identified two genes that encode known BLJ scaffolding proteins, lethal giant larvae (lgl) and scribble (scrib), and several not previously associated with BLJ function, including warts (wts) and roughened eye (roe), which encode a serine–threonine kinase and a transcription factor, respectively. Like scrib, wts and roe also enhance Fas2 and lgl tumorigenesis. Further, scrib, wts, and roe block border cell migration, and cause noninvasive tumors that resemble dlg partial loss of function, suggesting that the BLJ utilizes Wts signaling to repress EMT and proliferation, but not motility. Apicolateral junction proteins Fat (Ft), Expanded (Ex), and Merlin (Mer) either are not involved in these processes, or have highly spatio-temporally restricted roles, diminishing their significance as upstream inputs to Wts in follicle cells. This is further indicated in that Wts targets, CyclinE and DIAP1, are elevated in Fas2, dlg, lgl, wts, and roe cells, but not Fat, ex, or mer cells. Thus, the BLJ appears to regulate epithelial polarity and dynamics not only as a localized scaffold, but also by communicating signals to the nucleus. Wts may be regulated by distinct junction inputs depending on developmental context.