bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intragenic Spatial Patterns of Codon Usage Bias in Prokaryotic and Eukaryotic Genomes
Authors: Qin Hong , Wu Wei Biao , Comeron Josep M , Kreitman Martin , Li Wen-Hsiung 
Published: December 2004

Abstract
To study the roles of translational accuracy, translational efficiency, and the Hill-Robertson effect in codon usage bias, we studied the intragenic spatial distribution of synonymous codon usage bias in four prokaryotic (Escherichia coli, Bacillus subtilis, Sulfolobus tokodaii, and Thermotoga maritima) and two eukaryotic (Saccharomyces cerevisiae and Drosophila melanogaster) genomes. We generated supersequences at each codon position across genes in a genome and computed the overall bias at each codon position. By quantitatively evaluating the trend of spatial patterns using isotonic regression, we show that in yeast and prokaryotic genomes, codon usage bias increases along translational direction, which is consistent with purifying selection against nonsense errors. Fruit fly genes show a nearly symmetric M-shaped spatial pattern of codon usage bias, with less bias in the middle and both ends. The low codon usage bias in the middle region is best explained by interference (the Hill-Robertson effect) between selections at different codon positions. In both yeast and fruit fly, spatial patterns of codon usage bias are characteristically different from patterns of GC-content variations. Effect of expression level on the strength of codon usage bias is more conspicuous than its effect on the shape of the spatial distribution.
A Pseudohitchhiking Model of X vs. Autosomal Diversity
Authors: Betancourt Andrea J , Kim Yuseob , Orr H Allen 
Published: December 2004

Abstract
We study levels of X-linked vs. autosomal diversity using a model developed to analyze the hitchhiking effect. Repeated bouts of hitchhiking are thought to lower X-linked diversity for two reasons: first, because sojourn times of beneficial mutations are shorter on the X, and second, because adaptive substitutions may be more frequent on the X. We investigate whether each of these effects does, in fact, cause reduced X-linked diversity under hitchhiking. We study the strength of the hitchhiking effect on the X vs. autosomes when there is no recombination and under two different recombination schemes. When recombination occurs in both sexes, X-linked vs. autosomal diversity is reduced by hitchhiking under a broad range of conditions, but when there is no recombination in males, as in Drosophila, the required conditions are considerably more restrictive.
High-Resolution Fine Mapping and Fluorescence in Situ Hybridization Analysis of sun, a Locus Controlling Tomato Fruit Shape, Reveals a Region of the Tomato Genome Prone to DNA Rearrangements
Authors: van der Knaap E , Sanyal A , Jackson S A , Tanksley S D 
Published: December 2004

Abstract
The locus sun on the short arm of tomato chromosome 7 controls morphology of the fruit. Alleles from wild relatives impart a round shape, while alleles from certain cultivated varieties impart an oval shape typical of roma-type tomatoes. We fine mapped the locus in two populations and investigated the genome organization of the region spanning and flanking sun. The first high-resolution genetic map of the sun locus was constructed using a nearly isogenic F2 population derived from a cross between Lycopersicon pennellii introgression line IL7-4 and L. esculentum cv Sun1642. The mapping combined with results from pachytene FISH experiments demonstrated that the top of chromosome 7 is inverted in L. pennellii accession LA716. sun was located close to the chromosomal breakpoint and within the inversion, thereby precluding map-based cloning of the gene using this population. The fruit-shape locus was subsequently fine mapped in a population derived from a cross between L. esculentum Sun1642 and L. pimpinellifolium LA1589. Chromosome walking using clones identified from several large genomic insert libraries resulted in two noncontiguous contigs flanking sun. Fiber-FISH analysis showed that distance between the two contigs measured 68 kb in L. esculentum Sun1642 and 38 kb in L. pimpinellifolium LA1589, respectively. The sun locus mapped between the two contigs, suggesting that allelic variation at this locus may be due to an insertion/deletion event. The results demonstrate that sun is located in a highly dynamic region of the tomato genome.
Bile-Induced DNA Damage in Salmonella enterica
Authors: Prieto Ana I , Ramos-Morales Francisco , Casadesús Josep 
Published: December 2004

Abstract
In the absence of DNA adenine methylase, growth of Salmonella enterica serovar Typhimurium is inhibited by bile. Mutations in any of the mutH, mutL, and mutS genes suppress bile sensitivity in a Dam− background, indicating that an active MutHLS system renders Dam− mutants bile sensitive. However, inactivation of the MutHLS system does not cause bile sensitivity. An analogy with Escherichia coli, in which the MutHLS system sensitizes Dam− mutants to DNA-injuring agents, suggested that bile might cause DNA damage. In support of this hypothesis, we show that bile induces the SOS response in S. enterica and increases the frequency of point mutations and chromosomal rearrangements. Mutations in mutH, mutL, or mutS cause partial relief of virulence attenuation in a Dam− background (50- to 100-fold by the oral route and 10-fold intraperitoneally), suggesting that an active MutHLS system reduces the ability of Salmonella Dam− mutants to cope with DNA-damaging agents (bile and others) encountered during the infection process. The DNA-damaging ability of bile under laboratory conditions raises the possibility that the phenomenon may be relevant in vivo, since high bile concentrations are found in the gallbladder, the niche for chronic Salmonella infections.
DNA Methylation Affects Meiotic trans-sensing, Not Meiotic Silencing, in Neurospora
Authors: Pratt Robert J , Lee Dong W , Aramayo Rodolfo 
Published: December 2004

Abstract
During the early stages of meiosis in Neurospora, the symmetry of homologous chromosomal regions is carefully evaluated by actively trans-sensing their identity. If a DNA region cannot be detected on the opposite homologous chromosome, then this lack of “sensing” activates meiotic silencing, a post-transcriptional gene silencing-like mechanism that silences all genes in the genome with homology to the loop of unpaired DNA, whether they are paired or unpaired. In this work, we genetically dissected the meiotic trans-sensing step from meiotic silencing by demonstrating that DNA methylation affects sensing without interfering with silencing. We also determined that DNA sequence is an important parameter considered during meiotic trans-sensing. Altogether, these observations assign a previously undescribed role for DNA methylation in meiosis and, on the basis of studies in other systems, we speculate the existence of an intimate connection among meiotic trans-sensing, meiotic silencing, and meiotic recombination.
Inferring the Population Structure and Demography of Drosophila ananassae From Multilocus Data
Authors: Das Aparup , Mohanty Sujata , Stephan Wolfgang 
Published: December 2004

AbstractInferring the origin, population structure, and demographic history of a species is a major objective of population genetics. Although many organisms have been analyzed, the genetic structures of subdivided populations are not well understood. Here we analyze Drosophila ananassae, a highly substructured, cosmopolitan, and human-commensal species distributed in the tropical, subtropical, and mildly temperate regions of the world. We adopt a multilocus approach (with 10 neutral loci) using 16 population samples covering almost the entire species range (Asia, Australia, and America). Analyzed with our recently developed Bayesian method, 5 populations in Southeast Asia are found to be central, while the other 11 are peripheral. These 5 central populations were sampled from localities that belonged to a single landmass (“Sundaland”) during the late Pleistocene (∼18,000 years ago), when sea level was ∼120 m below the present level. The inferred migration routes of D. ananassae out of Sundaland seem to parallel those of humans in this region. Strong evidence for a population size expansion is seen particularly in the ancestral populations.
Oligosyndactylism Mice Have an Inversion of Chromosome 8
Authors: Wise Thomas L , Pravtcheva Dimitrina D 
Published: December 2004

Abstract
The radiation-induced mutation Oligosyndactylism (Os) is associated with limb and kidney defects in heterozygotes and with mitotic arrest and embryonic lethality in homozygotes. We reported that the cell cycle block in Os and in the 94-A/K transgene-induced mutations is due to disruption of the Anapc10 (Apc10/Doc1) gene. To understand the genetic basis of the limb and kidney abnormalities in Os mice we characterized the structural changes of chromosome 8 associated with this mutation. We demonstrate that the Os chromosome 8 has suffered two breaks that are 5 cM (∼10 Mb) apart and the internal fragment delineated by the breaks is in an inverted orientation on the mutant chromosome. While sequences in proximity to the distal break are present in an abnormal Os-specific Anapc10 hybrid transcript, transcription of these sequences in normal mice is low and difficult to detect. Transfer of the Os mutation onto an FVB/N background indicated that the absence of dominant effects in 94-A/K mice is not due to strain background effects on the mutation. Further analysis of this mutation will determine if a gene interrupted by the break or a long-range effect of the rearrangement on neighboring genes is responsible for the dominant effects of Os.
Deletion of a Disease Resistance Nucleotide-Binding-Site Leucine-Rich- Repeat-like Sequence Is Associated With the Loss of the Phytophthora Resistance Gene Rps4 in Soybean
Authors: Sandhu Devinder , Gao Hongyu , Cianzio Silvia , Bhattacharyya Madan K 
Published: December 2004

Abstract
Resistance of soybean against the oomycete pathogen Phytophthora sojae is conferred by a series of Rps genes. We have characterized a disease resistance gene-like sequence NBSRps4/6 that was introgressed into soybean lines along with Rps4 or Rps6. High-resolution genetic mapping established that NBSRps4/6 cosegregates with Rps4. Two mutants, M1 and M2, showing rearrangements in the NBSRps4/6 region were identified from analyses of 82 F1's and 201 selfed HARO4272 plants containing Rps4. Fingerprints of these mutants are identical to those of HARO4272 for 176 SSR markers representing the whole genome except the NBSRps4/6 region. Both mutants showed a gain of race specificities, distinct from the one encoded by Rps4. To investigate the possible mechanism of gain of Phytophthora resistance in M1, the novel race specificity was mapped. Surprisingly, the gene encoding this resistance mapped to the Rps3 region, indicating that this gene could be either allelic or linked to Rps3. Recombinant analyses have shown that deletion of NBSRps4/6 in M1 is associated with the loss of Rps4 function. The NBSRps4/6 sequence is highly transcribed in etiolated hypocotyls expressing the Phytophthora resistance. It is most likely that a copy of the NBSRps4/6 sequence is the Rps4 gene. Possible mechanisms of the deletion in the NBSRps4/6 region and introgression of two unlinked Rps genes into Harosoy are discussed.
The Changing Tails of a Novel Short Interspersed Element in Aedes aegypti
Authors: Tu Zhijian , Li Song , Mao Chunhong 
Published: December 2004

Abstract
A novel family of tRNA-related SINEs named gecko was discovered in the yellow fever mosquito, Aedes aegypti. Approximately 7200 copies of gecko were distributed in the A. aegypti genome with a significant bias toward A + T-rich regions. The 3′ end of gecko is similar in sequence and identical in secondary structure to the 3′ end of MosquI, a non-LTR retrotransposon in A. aegypti. Nine conserved substitutions and a deletion separate gecko into two groups. Group I includes all gecko that end with poly(dA) and a copy that ends with AGAT repeats. Group II comprises gecko elements that end with CCAA or CAAT repeats. Members within each group cannot be differentiated when the 3′ repeats are excluded in phylogenetic and sequence analyses, suggesting that the alterations of 3′ tails are recent. Imperfect poly(dA) tail was recorded in group I and partial replication of the 3′ tandem repeats was frequently observed in group II. Genomic evidence underscores the importance of slippage retrotransposition in the alteration and expansion of the tandem repeat during the evolution of gecko sequences, although we do not rule out postinsertion mechanisms that were previously invoked to explain the evolution of Alu-associated microsatellites. We propose that the 3′ tandem repeats and the poly(dA) tail may be generated by similar mechanisms during retrotransposition of both SINEs and non-LTR retrotransposons and thus the distinction between poly(dA) retrotransposons such as L1 and non-poly(dA) retrotransposons such as I factor may not be informative.
Population Genetics of the Developmental Gene optomotor-blind (omb) in Drosophila polymorpha
Authors: Brisson Jennifer A , Templeton Alan R , Duncan Ian 
Published: December 2004

AbstractThe developmental gene optomotor-blind (omb) encodes a T-box-containing transcription factor that has multiple roles in Drosophila development. Previous genetic analyses established that omb plays a key role in establishing the abdominal pigmentation pattern of Drosophila melanogaster. In this report we examine patterns of omb nucleotide variation in D. polymorpha, a species that is highly polymorphic for the phenotype of abdominal pigmentation. Haplotypes at this locus fall into two classes that are separated by six mutational steps; five of these mutational events result in amino acid changes. Two lines of evidence are consistent with a role for omb in the abdominal pigmentation polymorphism of D. polymorpha. First, we find that haplotype classes of omb are correlated with abdominal pigmentation phenotypes, as are microsatellite repeat numbers in the region. Second, tests of selection reveal that the two haplotype classes have been maintained by balancing selection. Within each class there is a significantly low amount of diversity, indicative of previous selective sweeps. An analysis including D. polymorpha's closest relatives (members of the cardini group) provides evidence for directional selection across species. Selection at this locus is expected if omb contributes to variation in abdominal pigmentation, since this trait is likely of ecological importance.
Fitness Costs of Mutations Affecting the Systemic Acquired Resistance Pathway in Arabidopsis thaliana
Authors: Heidel Andrew J , Clarke Joseph D , Antonovics Janis , Dong Xinnian 
Published: December 2004

Abstract
This study investigated the fitness effects of four mutations (npr1, cpr1, cpr5, and cpr6) and two transgenic genotypes (NPR1-L and NPR1-H) affecting different points of the systemic acquired resistance (SAR) signaling pathway associated with pathogen defense in Arabidopsis thaliana. The npr1 mutation, which resulted in a failure to express SAR, had no effect on fitness under growth chamber conditions, but decreased fitness in the field. The expression of NPR1 positively correlated with the fitness in the field. Constitutive activation of SAR by cpr1, cpr5, and cpr6 generally decreased fitness in the field and under two nutrient levels in two growth chamber conditions. At low-nutrient levels, fitness differences between wild type and the constitutive mutants were unchanged or reduced (especially in cpr5). The reduced fitness of the constitutive mutants suggests that this pathway is costly, with the precise fitness consequences highly dependent on the environmental context.
In Vivo Activation of Protein Kinase A in Schizosaccharomyces pombe Requires Threonine Phosphorylation at Its Activation Loop and Is Dependent on PDK1
Authors: Tang Yi , McLeod Maureen 
Published: December 2004

Abstract
Phosphoinositide-dependent protein kinase 1 (PDK1) plays a central role in cellular signaling by phosphorylating members of the AGC family of kinases. This family includes protein kinase C (PKC), protein kinase B (PKB), p70/p90 ribosomal S6 kinases (RSK and S6K), and the catalytic subunit of cAMP-dependent protein kinase (PKA). Although PDK1 phosphorylates and activates PKC, PKB, and RSK in vivo, PDK1 regulation of PKA remains controversial. We isolated ksg1, the fission yeast ortholog of mammalian PDK1, as a suppressor of growth defects caused by loss of the stress-activated MAP kinase, Spc1. Here, we demonstrate that Ksg1 is required for activation of PKA. Cells containing the ksg1.12 thermolabile allele exhibit pleiotropic phenotypes, including the failure to arrest in G1 and an inability to conjugate. The ksg1.12 allele strongly suppresses defects associated with unregulated PKA. Pka1, the catalytic subunit of cAMP-dependent protein kinase, is phosphorylated in vivo at Thr-356, which is located in the activation loop of the kinase and corresponds to Thr-197 in mammalian PKA. Phosphorylation of Thr-356 is required for in vivo activation of Pka1 and is dependent upon Ksg1. These data provide experimental evidence that PKA is a physiological substrate for PDK1.
Genetic and Biochemical Interactions Among Yar1, Ltv1 and RpS3 Define Novel Links Between Environmental Stress and Ribosome Biogenesis in Saccharomyces cerevisiae
Authors: Loar Jesse W , Seiser Robert M , Sundberg Alexandra E , Sagerson Holly J , Ilias Nasreen , Zobel-Thropp Pamela , Craig Elizabeth A , Lycan Deborah E 
Published: December 2004

AbstractIn the yeast S. cerevisiae, ribosome assembly is linked to environmental conditions by the coordinate transcriptional regulation of genes required for ribosome biogenesis. In this study we show that two nonessential stress-responsive genes, YAR1 and LTV1, function in 40S subunit production. We provide genetic and biochemical evidence that Yar1, a small ankyrin-repeat protein, physically interacts with RpS3, a component of the 40S subunit, and with Ltv1, a protein recently identified as a substoichiometric component of a 43S preribosomal particle. We demonstrate that cells lacking YAR1 or LTV1 are hypersensitive to particular protein synthesis inhibitors and exhibit aberrant polysome profiles, with a reduced absolute number of 40S subunits and an excess of free 60S subunits. Surprisingly, both mutants are also hypersensitive to a variety of environmental stress conditions. Overexpression of RPS3 suppresses both the stress sensitivity and the ribosome biogenesis defect of Δyar1 mutants, but does not suppress either defect in Δltv1 mutants. We propose that YAR1 and LTV1 play distinct, nonessential roles in 40S subunit production. The stress-sensitive phenotypes of strains lacking these genes reveal a hitherto unknown link between ribosome biogenesis factors and environmental stress sensitivity.
Genetic Analysis of Yeast Yip1p Function Reveals a Requirement for Golgi-Localized Rab Proteins and Rab-Guanine Nucleotide Dissociation Inhibitor
Authors: Chen Catherine Z , Calero Monica , DeRegis Carol J , Heidtman Matthew , Barlowe Charles , Collins Ruth N 
Published: December 2004

Abstract
Yip1p is the first identified Rab-interacting membrane protein and the founder member of the YIP1 family, with both orthologs and paralogs found in all eukaryotic genomes. The exact role of Yip1p is unclear; YIP1 is an essential gene and defective alleles severely disrupt membrane transport and inhibit ER vesicle budding. Yip1p has the ability to physically interact with Rab proteins and the nature of this interaction has led to suggestions that Yip1p may function in the process by which Rab proteins translocate between cytosol and membranes. In this study we have investigated the physiological requirements for Yip1p action. Yip1p function requires Rab-GDI and Rab proteins, and several mutations that abrogate Yip1p function lack Rab-interacting capability. We have previously shown that Yip1p in detergent extracts has the capability to physically interact with Rab proteins in a promiscuous manner; however, a genetic analysis that covers every yeast Rab reveals that the Rab requirement in vivo is exclusively confined to a subset of Rab proteins that are localized to the Golgi apparatus.
The Effect of Sequence Divergence on Recombination Between Direct Repeats in Arabidopsis
Authors: Opperman Roy , Emmanuel Eyal , Levy Avraham A 
Published: December 2004

Abstract
It is well established that sequence divergence has an inhibitory effect on homologous recombination. However, a detailed analysis of this relationship is missing for most higher eukaryotes. We have measured the rate of somatic recombination between direct repeats as a function of the number, type, and position of divergent nucleotides in Arabidopsis. We show that a minor divergence level of 0.16% (one mutation in otherwise identical 618 bp) has a profound effect, decreasing the recombination rate approximately threefold. A further increase in the divergence level affects the recombination rate to a smaller extent until a “divergence saturation” effect is reached at relatively low levels of divergence (∼0.5%). The type of mismatched nucleotide does not affect recombination rates. The decrease in the rate of recombination caused by a single mismatch was not affected by the position of the mismatch along the repeat. This suggests that most recombination intermediate tracts contain a mismatch and thus are as long as the full length of the 618-bp repeats. Finally, we could deduce an antirecombination efficiency of ∼66% for the first mismatch in the repeat. Altogether, this work shows some degree of conservation across kingdoms when compared to previous reports in yeast; it also provides new insight into the effect of sequence divergence on homologous recombination.
Competing Crossover Pathways Act During Meiosis in Saccharomyces cerevisiae
Authors: Argueso Juan Lucas , Wanat Jennifer , Gemici Zekeriyya , Alani Eric 
Published: December 2004

Abstract
In Saccharomyces cerevisiae the MSH4-MSH5, MLH1-MLH3, and MUS81-MMS4 complexes act to promote crossing over during meiosis. MSH4-MSH5, but not MUS81-MMS4, promotes crossovers that display interference. A role for MLH1-MLH3 in crossover control is less clear partly because mlh1Δ mutants retain crossover interference yet display a decrease in crossing over that is only slightly less severe than that seen in msh4Δ and msh5Δ mutants. We analyzed the effects of msh5Δ, mlh1Δ, and mms4Δ single, double, and triple mutants on meiotic crossing over at four consecutive genetic intervals on chromosome XV using newly developed computer software. mlh1Δ mms4Δ double mutants displayed the largest decrease in crossing over (13- to 15-fold) of all mutant combinations, yet these strains displayed relatively high spore viability (42%). In contrast, msh5Δ mms4Δ and msh5Δ mms4Δ mlh1Δ mutants displayed smaller decreases in crossing over (4- to 6-fold); however, spore viability (18–19%) was lower in these strains than in mlh1Δ mms4Δ strains. These data suggest that meiotic crossing over can occur in yeast through three distinct crossover pathways. In one pathway, MUS81-MMS4 promotes interference-independent crossing over; in a second pathway, both MSH4-MSH5 and MLH1-MLH3 promote interference-dependent crossovers. A third pathway, which appears to be repressed by MSH4-MSH5, yields deleterious crossovers.