bluuebunny/crossref_metadata_2025 huggingface dataset:
SepBCTF4 Is Required for the Formation of DNA-Damage-Induced UvsCRAD51 Foci in Aspergillus nidulans
Authors: Gygax Scott E , Semighini Camile P , Goldman Gustavo H , Harris Steven D
Published: January 2005

SepB is an essential, conserved protein required for chromosomal DNA metabolism in Aspergillus nidulans. Homologs of SepB include yeast Ctf4p and human hAnd-1. Molecular and bioinformatic characterization of these proteins suggests that they act as molecular scaffolds. Furthermore, recent observations implicate the yeast family members in lagging-strand replication and the establishment of sister-chromatid cohesion. Here, we demonstrate that SepB functions in the A. nidulans DNA damage response. In particular, analysis of double mutants reveals that SepB is a member of the UvsCRAD51 epistasis group. In accord with this prediction, we show that UvsCRAD51 forms DNA-damage-induced nuclear foci in a manner that requires SepB function. We also provide evidence that implicates SepB in sister-chromatid cohesion, thereby suggesting that cohesion may play a role in regulating the localization and/or assembly of UvsCRAD51 complexes.
Mapping Quantitative Trait Loci in Multiple Populations of Arabidopsis thaliana Identifies Natural Allelic Variation for Trichome Density
Authors: Symonds V Vaughan , Godoy A Veronica , Alconada Teresa , Botto Javier F , Juenger Thomas E , Casal Jorge J , Lloyd Alan M
Published: January 2005

The majority of biological traits are genetically complex. Mapping the quantitative trait loci (QTL) that determine these phenotypes is a powerful means for estimating many parameters of the genetic architecture for a trait and potentially identifying the genes responsible for natural variation. Typically, such experiments are conducted in a single mapping population and, therefore, have only the potential to reveal genomic regions that are polymorphic between the progenitors of the population. What remains unclear is how well the QTL identified in any one mapping experiment characterize the genetics that underlie natural variation in traits. Here we provide QTL mapping data for trichome density from four recombinant inbred mapping populations of Arabidopsis thaliana. By aligning the linkage maps for these four populations onto a common physical map, the results from each experiment were directly compared. Seven of the nine QTL identified are population specific while two were mapped in all four populations. Our results show that many lineage-specific alleles that either increase or decrease trichome density persist in natural populations and that most of this genetic variation is additive. More generally, these findings suggest that the use of multiple populations holds great promise for better understanding the genetic architecture of natural variation.
Detecting Amino Acid Sites Under Positive Selection and Purifying Selection
Authors: Massingham Tim , Goldman Nick
Published: January 2005

An excess of nonsynonymous over synonymous substitution at individual amino acid sites is an important indicator that positive selection has affected the evolution of a protein between the extant sequences under study and their most recent common ancestor. Several methods exist to detect the presence, and sometimes location, of positively selected sites in alignments of protein-coding sequences. This article describes the “sitewise likelihood-ratio” (SLR) method for detecting nonneutral evolution, a statistical test that can identify sites that are unusually conserved as well as those that are unusually variable. We show that the SLR method can be more powerful than currently published methods for detecting the location of positive selection, especially in difficult cases where the strength of selection is low. The increase in power is achieved while relaxing assumptions about how the strength of selection varies over sites and without elevated rates of false-positive results that have been reported with some other methods. We also show that the SLR method performs well even under circumstances where the results from some previous methods can be misleading.
Statistical Tests of the Coalescent Model Based on the Haplotype Frequency Distribution and the Number of Segregating Sites
Authors: Innan Hideki , Zhang Kangyu , Marjoram Paul , Tavaré Simon , Rosenberg Noah A
Published: January 2005

Several tests of neutral evolution employ the observed number of segregating sites and properties of the haplotype frequency distribution as summary statistics and use simulations to obtain rejection probabilities. Here we develop a “haplotype configuration test” of neutrality (HCT) based on the full haplotype frequency distribution. To enable exact computation of rejection probabilities for small samples, we derive a recursion under the standard coalescent model for the joint distribution of the haplotype frequencies and the number of segregating sites. For larger samples, we consider simulation-based approaches. The utility of the HCT is demonstrated in simulations of alternative models and in application to data from Drosophila melanogaster.
Serotonin (5HT), Fluoxetine, Imipramine and Dopamine Target Distinct 5HT Receptor Signaling to Modulate Caenorhabditis elegans Egg-Laying Behavior
Authors: Dempsey Catherine M , Mackenzie Scott M , Gargus Andrew , Blanco Gabriela , Sze Ji Ying
Published: January 2005

Drugs that target the serotonergic system are the most commonly prescribed therapeutic agents and are used for treatment of a wide range of behavioral and neurological disorders. However, the mechanism of the drug action remain a conjecture. Here, we dissect the genetic targets of serotonin (5HT), the selective 5HT reuptake inhibitor (SSRI) fluoxetine (Prozac), the tricyclic antidepressant imipramine, and dopamine. Using the well-established serotonergic response in C. elegans egg-laying behavior as a paradigm, we show that action of fluoxetine and imipramine at the 5HT reuptake transporter (SERT) and at 5HT receptors are separable mechanisms. Even mutants completely lacking 5HT or SERT can partially respond to fluoxetine and imipramine. Furthermore, distinct mechanisms for each drug can be recognized to mediate these responses. Deletion of SER-1, a 5HT1 receptor, abolishes the response to 5HT but has only a minor effect on the response to imipramine and no effect on the response to fluoxetine. In contrast, deletion of SER-4, a 5HT2 receptor, confers significant resistance to imipramine while leaving the responses to 5HT or fluoxetine intact. Further, fluoxetine can stimulate egg laying via the Gq protein EGL-30, independent of SER-1, SER-4, or 5HT. We also show that dopamine antagonizes the 5HT action via the 5HT-gated ion channel MOD-1 signaling, suggesting that this channel activity couples 5HT and dopamine signaling. These results suggest that the actions of these drugs at specific receptor subtypes could determine their therapeutic efficacy. SSRIs and tricyclic antidepressants may regulate 5HT outputs independently of synaptic levels of 5HT.
Segregation Distortion in Hybrids Between the Bogota and USA Subspecies of Drosophila pseudoobscura
Authors: Orr H Allen , Irving Shannon
Published: January 2005

We show that, contrary to claims in the literature, “sterile” males resulting from the cross of the Bogota and USA subspecies of Drosophila pseudoobscura are weakly fertile. Surprisingly, these hybrid males produce almost all daughters when crossed to females of any genotype (pure Bogota, pure USA, hybrid F1). Several lines of evidence suggest that this sex ratio distortion is caused by sex chromosome segregation distortion in hybrid males. We genetically analyze this normally cryptic segregation distortion and show that it involves several regions of the Bogota X chromosome that show strong epistatic interactions with each other. We further show that segregation distortion is normally masked within the Bogota subspecies by autosomal suppressors. Our analysis shows that the genetic basis of hybrid segregation distortion is similar to that of hybrid male sterility between the same subspecies. Indeed the severity of segregation distortion is correlated with the severity of sterility among hybrids. We discuss the possibility that hybrid sterility in this paradigmatic case of incipient speciation is caused by segregation distortion.
The WD40 Repeat Protein Fritz Links Cytoskeletal Planar Polarity to Frizzled Subcellular Localization in the Drosophila Epidermis
Authors: Collier Simon , Lee Haeryun , Burgess Rosemary , Adler Paul
Published: January 2005

Much of our understanding of the genetic mechanisms that control planar cell polarity (PCP) in epithelia has derived from studies of the formation of polarized cell hairs during Drosophila wing development. The correct localization of an F-actin prehair to the distal vertex of the pupal wing cell has been shown to be dependent upon the polarized subcellular localization of Frizzled and other core PCP proteins. However, the core PCP proteins do not organize actin cytoskeletal polarity directly but require PCP effector proteins such as Fuzzy and Inturned to mediate this process. Here we describe the characterization of a new PCP effector gene, fritz, that encodes a novel but evolutionarily conserved coiled-coil WD40 protein. We show that the fritz gene product functions cell-autonomously downstream of the core PCP proteins to regulate both the location and the number of wing cell prehair initiation sites.
MLH1 and MSH2 Promote the Symmetry of Double-Strand Break Repair Events at the HIS4 Hotspot in Saccharomyces cerevisiae
Authors: Hoffmann Eva R , Eriksson Emma , Herbert Benjamin J , Borts Rhona H
Published: January 2005

Double-strand breaks (DSBs) initiate meiotic recombination. The DSB repair model predicts that both genetic markers spanning the DSB should be included in heteroduplex DNA and be detectable as non-Mendelian segregations (NMS). In experiments testing this, a significant fraction of events do not conform to this prediction, as only one of the markers displays NMS (one-sided events). Two explanations have been proposed to account for the discrepancies between the predictions and experimental observations. One suggests that two-sided events are the norm but are “hidden” as heteroduplex repair frequently restores the parental configuration of one of the markers. Another explanation posits that one-sided events reflect events in which heteroduplex is formed predominantly on only one side of the DSB. In the absence of heteroduplex repair, the first model predicts that two-sided events would be revealed at the expense of one-sided events, while the second predicts no effect on the distribution of events when heteroduplex repair is lost. We tested these predictions by deleting the DNA mismatch repair genes MSH2 or MLH1 and analyzing the proportion of two-sided events. Unexpectedly, the results do not match the predictions of either model. In both mlh1Δ and msh2Δ, the proportion of two-sided events is significantly decreased relative to wild type. These observations can be explained in one of two ways. Either Msh2p/Mlh1p-independent mispair removal leads to restoration of one of the markers flanking the DSB site or Msh2p/Mlh1p actively promote two-sided events.
Trans Events Associated With Crossovers Are Revealed in the Absence of Mismatch Repair Genes in Saccharomyces cerevisiae
Authors: Hoffmann Eva R , Borts Rhona H
Published: January 2005

Genetic analysis of recombination in Saccharomyces cerevisiae has revealed products with structures not predicted by the double-strand break repair model of meiotic recombination. A particular type of recombinant containing trans heteroduplex DNA has been observed at two loci. Trans events were originally identified only in tetrads in which the non-Mendelian segregations were not associated with a crossover. Because of this, these events were proposed to have arisen from the unwinding of double Holliday junctions. Previous studies used palindromes, refractory to mismatch repair, as genetic markers whereas we have used a complementary approach of deleting mismatch repair proteins to identify heteroduplex DNA. We found that the markers occurred in trans and were associated with crossovers. In both mlh1Δ and msh2Δ strains, the frequency of trans events associated with a crossover exceeded that predicted from the random association of crossovers with noncrossover trans events. We propose two different models to account for trans events associated with crossovers and discuss the relevance to wild-type DSB repair.
A Multilocus Sequence Survey in Arabidopsis thaliana Reveals a Genome-Wide Departure From a Neutral Model of DNA Sequence Polymorphism
Authors: Schmid Karl J , Ramos-Onsins Sebastian , Ringys-Beckstein Henriette , Weisshaar Bernd , Mitchell-Olds Thomas
Published: January 2005

The simultaneous analysis of multiple genomic loci is a powerful approach to studying the effects of population history and natural selection on patterns of genetic variation of a species. By surveying nucleotide sequence polymorphism at 334 randomly distributed genomic regions in 12 accessions of Arabidopsis thaliana, we examined whether a standard neutral model of nucleotide sequence polymorphism is consistent with observed data. The average nucleotide diversity was 0.0071 for total sites and 0.0083 for silent sites. Although levels of diversity are variable among loci, no correlation with local recombination rate was observed, but polymorphism levels were correlated for physically linked loci (<250 kb). We found that observed distributions of Tajima's D- and D/Dmin- and of Fu and Li's D-, D*- and F-, F*-statistics differed significantly from the expected distributions under a standard neutral model due to an excess of rare polymorphisms and high variances. Observed and expected distributions of Fay and Wu's H were not different, suggesting that demographic processes and not selection at multiple loci are responsible for the deviation from a neutral model. Maximum-likelihood comparisons of alternative demographic models like logistic population growth, glacial refugia, or past bottlenecks did not produce parameter estimates that were more consistent with observed patterns. However, exclusion of highly polymorphic “outlier loci” resulted in a fit to the logistic growth model. Various tests of neutrality revealed a set of candidate loci that may evolve under selection.
Combining Data From Multiple Inbred Line Crosses Improves the Power and Resolution of Quantitative Trait Loci Mapping
Authors: Li Renhua , Lyons Malcolm A , Wittenburg Henning , Paigen Beverly , Churchill Gary A
Published: January 2005

Rodent inbred line crosses are widely used to map genetic loci associated with complex traits. This approach has proven to be powerful for detecting quantitative trait loci (QTL); however, the resolution of QTL locations, typically ∼20 cM, means that hundreds of genes are implicated as potential candidates. We describe analytical methods based on linear models to combine information available in two or more inbred line crosses. Our strategy is motivated by the hypothesis that common inbred strains of the laboratory mouse are derived from a limited ancestral gene pool and thus QTL detected in multiple crosses are likely to represent shared ancestral polymorphisms. We demonstrate that the combined-cross analysis can improve the power to detect weak QTL, can narrow support intervals for QTL regions, and can be used to separate multiple QTL that colocalize by chance. Moreover, combined-cross analysis can establish the allelic states of a QTL among a set of parental lines, thus providing critical information for narrowing QTL regions by haplotype analysis.
Sex-Linked Differentiation Between Incipient Species of Anopheles gambiae
Authors: Stump Aram D , Shoener Jennifer A , Costantini Carlo , Sagnon N'Fale , Besansky Nora J
Published: January 2005

Emerging species within the primary malaria vector Anopheles gambiae show different ecological preferences and significant prezygotic reproductive isolation. They are defined by fixed sequence differences in X-linked rDNA, but most previous studies have failed to detect large and significant differentiation between these taxa elsewhere in the genome, except at two other loci on the X chromosome near the rDNA locus. Hypothesizing that this pericentromeric region of the X chromosome may be accumulating differences faster than other regions of the genome, we explored the pattern and extent of differentiation between A. gambiae incipient species and a sibling species, A. arabiensis, from Burkina Faso, West Africa, at 17 microsatellite loci spanning the X chromosome. Interspecific differentiation was large and significant across the entire X chromosome. Among A. gambiae incipient species, we found some of the highest levels of differentiation recorded in a large region including eight independent loci near the centromere of the X chromosome. Outside of this region, no significant differentiation was detected. This pattern suggests that selection is playing a role in the emergence of A. gambiae incipient species. This process, associated with efficient exploitation of anthropogenic modifications to the environment, has public health implications as it fosters the spread of malaria transmission both spatially and temporally.
The Genetic Basis for Inflorescence Variation Between Foxtail and Green Millet (Poaceae)
Authors: Doust Andrew N , Devos Katrien M , Gadberry Mike D , Gale Mike D , Kellogg Elizabeth A
Published: January 2005

Grass species differ in many aspects of inflorescence architecture, but in most cases the genetic basis of the morphological difference is unknown. To investigate the genes underlying the morphology in one such instance, we undertook a developmental and QTL analysis of inflorescence differences between the cereal grain foxtail millet and its presumed progenitor green millet. Inflorescence differences between these two species are the result of changes in primary branch number and density, spikelet number, and bristle (sterile branchlet) number; these differences also account for inflorescence variation within the clade of 300+ species that share the presence of bristles in the inflorescence. Fourteen replicated QTL were detected for the four inflorescence traits, and these are suggested to represent genes that control differences between the species. Comparative mapping using common markers from rice and maize allowed a number of candidate genes from maize to be localized to QTL regions in the millet genome. Searches of regions of the sequenced rice genome orthologous to QTL regions on foxtail millet identified a number of transcription factors and hormone pathway genes that may be involved in control of inflorescence branching.
Genetic Structure and Diversity in Oryza sativa L.
Authors: Garris Amanda J , Tai Thomas H , Coburn Jason , Kresovich Steve , McCouch Susan
Published: January 2005

The population structure of domesticated species is influenced by the natural history of the populations of predomesticated ancestors, as well as by the breeding system and complexity of the breeding practices exercised by humans. Within Oryza sativa, there is an ancient and well-established divergence between the two major subspecies, indica and japonica, but finer levels of genetic structure are suggested by the breeding history. In this study, a sample of 234 accessions of rice was genotyped at 169 nuclear SSRs and two chloroplast loci. The data were analyzed to resolve the genetic structure and to interpret the evolutionary relationships between groups. Five distinct groups were detected, corresponding to indica, aus, aromatic, temperate japonica, and tropical japonica rices. Nuclear and chloroplast data support a closer evolutionary relationship between the indica and the aus and among the tropical japonica, temperate japonica, and aromatic groups. Group differences can be explained through contrasting demographic histories. With the availability of rice genome sequence, coupled with a large collection of publicly available genetic resources, it is of interest to develop a population-based framework for the molecular analysis of diversity in O. sativa.
Modeling Quantitative Trait Loci and Interpretation of Models
Authors: Zeng Zhao-Bang , Wang Tao , Zou Wei
Published: January 2005

A quantitative genetic model relates the genotypic value of an individual to the alleles at the loci that contribute to the variation in a population in terms of additive, dominance, and epistatic effects. This partition of genetic effects is related to the partition of genetic variance. A number of models have been proposed to describe this relationship: some are based on the orthogonal partition of genetic variance in an equilibrium population. We compare a few representative models and discuss their utility and potential problems for analyzing quantitative trait loci (QTL) in a segregating population. An orthogonal model implies that estimates of the genetic effects are consistent in a full or reduced model in an equilibrium population and are directly related to the partition of the genetic variance in the population. Linkage disequilibrium does not affect the estimation of genetic effects in a full model, but would in a reduced model. Certainly linkage disequilibrium would complicate the detection of QTL and epistasis. Using different models does not influence the detection of QTL and epistasis. However, it does influence the estimation and interpretation of genetic effects.
Gene Clusters for Insecticidal Loline Alkaloids in the Grass-Endophytic Fungus Neotyphodium uncinatum
Authors: Spiering Martin J , Moon Christina D , Wilkinson Heather H , Schardl Christopher L
Published: January 2005

Loline alkaloids are produced by mutualistic fungi symbiotic with grasses, and they protect the host plants from insects. Here we identify in the fungal symbiont, Neotyphodium uncinatum, two homologous gene clusters (LOL-1 and LOL-2) associated with loline-alkaloid production. Nine genes were identified in a 25-kb region of LOL-1 and designated (in order) lolF-1, lolC-1, lolD-1, lolO-1, lolA-1, lolU-1, lolP-1, lolT-1, and lolE-1. LOL-2 contained the homologs lolC-2 through lolE-2 in the same order and orientation. Also identified was lolF-2, but its possible linkage with either cluster was undetermined. Most lol genes were regulated in N. uncinatum and N. coenophialum, and all were expressed concomitantly with loline-alkaloid biosynthesis. A lolC-2 RNA-interference (RNAi) construct was introduced into N. uncinatum, and in two independent transformants, RNAi significantly decreased lolC expression (P < 0.01) and loline-alkaloid accumulation in culture (P < 0.001) compared to vector-only controls, indicating involvement of lolC in biosynthesis of lolines. The predicted LolU protein has a DNA-binding site signature, and the relationships of other lol-gene products indicate that the pathway has evolved from various different primary and secondary biosynthesis pathways.
Variogram Analysis of the Spatial Genetic Structure of Continuous Populations Using Multilocus Microsatellite Data
Authors: Wagner Helene H , Holderegger Rolf , Werth Silke , Gugerli Felix , Hoebee Susan E , Scheidegger Christoph
Published: January 2005

A geostatistical perspective on spatial genetic structure may explain methodological issues of quantifying spatial genetic structure and suggest new approaches to addressing them. We use a variogram approach to (i) derive a spatial partitioning of molecular variance, gene diversity, and genotypic diversity for microsatellite data under the infinite allele model (IAM) and the stepwise mutation model (SMM), (ii) develop a weighting of sampling units to reflect ploidy levels or multiple sampling of genets, and (iii) show how variograms summarize the spatial genetic structure within a population under isolation-by-distance. The methods are illustrated with data from a population of the epiphytic lichen Lobaria pulmonaria, using six microsatellite markers. Variogram-based analysis not only avoids bias due to the underestimation of population variance in the presence of spatial autocorrelation, but also provides estimates of population genetic diversity and the degree and extent of spatial genetic structure accounting for autocorrelation.
Genetic Control of Temperature Preference in the Nematode Caenorhabditis elegans
Authors: Mohri Akiko , Kodama Eiji , Kimura Koutarou D , Koike Mizuho , Mizuno Takafumi , Mori Ikue
Published: January 2005

Animals modify behavioral outputs in response to environmental changes. C. elegans exhibits thermotaxis, where well-fed animals show attraction to their cultivation temperature on a thermal gradient without food. We show here that feeding-state-dependent modulation of thermotaxis is a powerful behavioral paradigm for elucidating the mechanism underlying neural plasticity, learning, and memory in higher animals. Starved experience alone could induce aversive response to cultivation temperature. Changing both cultivation temperature and feeding state simultaneously evoked transient attraction to or aversion to the previous cultivation temperature: recultivation of starved animals with food immediately induced attraction to the temperature associated with starvation, although the animals eventually exhibited thermotaxis to the new temperature associated with food. These results suggest that the change in feeding state quickly stimulates the switch between attraction and aversion for the temperature in memory and that the acquisition of new temperature memory establishes more slowly. We isolated aho (abnormal hunger orientation) mutants that are defective in starvation-induced cultivation-temperature avoidance. Some aho mutants responded normally to changes in feeding state with respect to locomotory activity, implying that the primary thermosensation followed by temperature memory formation remains normal and the modulatory aspect of thermotaxis is specifically impaired in these mutants.
Systematic, RNA-Interference-Mediated Identification of mus-101 Modifier Genes in Caenorhabditis elegans
Authors: Holway Antonia H , Hung Crystal , Michael W Matthew
Published: January 2005

The Mus101 family of chromosomal proteins, identified initially in Drosophila, is widely conserved and has been shown to function in a variety of DNA metabolic processes. Such functions include DNA replication, DNA damage repair, postreplication repair, damage checkpoint activation, chromosome stability, and chromosome condensation. Despite its conservation and widespread involvement in chromosome biogenesis, very little is known about how Mus101 is regulated and what other proteins are required for Mus101 to exert its functions. To learn more about Mus101, we have initiated an analysis of the protein in C. elegans. Here, we show that C. elegans mus-101 is an essential gene, that it is required for DNA replication, and that it also plays an important role in the DNA damage response. Furthermore, we use RNA interference (RNAi)-mediated reverse genetics to screen for genes that modify a mus-101 partial loss-of-function RNAi phenotype. Using a systematic approach toward modifier gene discovery, we have found five chromosome I genes that modify the mus-101 RNAi phenotype, and we go on to show that one of them encodes an E3 SUMO ligase that promotes SUMO modification of MUS-101 in vitro. These results expand our understanding of MUS-101 regulation and show that genetic interactions can be uncovered using screening strategies that rely solely on RNAi.
Bayesian Analysis of an Admixture Model With Mutations and Arbitrarily Linked Markers
Authors: Excoffier Laurent , Estoup Arnaud , Cornuet Jean-Marie
Published: January 2005

We introduce here a Bayesian analysis of a classical admixture model in which all parameters are simultaneously estimated. Our approach follows the approximate Bayesian computation (ABC) framework, relying on massive simulations and a rejection-regression algorithm. Although computationally intensive, this approach can easily deal with complex mutation models and partially linked loci, and it can be thoroughly validated without much additional computation cost. Compared to a recent maximum-likelihood (ML) method, the ABC approach leads to similarly accurate estimates of admixture proportions in the case of recent admixture events, but it is found superior when the admixture is more ancient. All other parameters of the admixture model such as the divergence time between parental populations, the admixture time, and the population sizes are also well estimated, unlike the ML method. The use of partially linked markers does not introduce any particular bias in the estimation of admixture, but ML confidence intervals are found too narrow if linkage is not specifically accounted for. The application of our method to an artificially admixed domestic bee population from northwest Italy suggests that the admixture occurred in the last 10–40 generations and that the parental Apis mellifera and A. ligustica populations were completely separated since the last glacial maximum.
Infrequent Co-conversion of Markers Flanking a Meiotic Recombination Initiation Site in Saccharomyces cerevisiae
Authors: Jessop Lea , Allers Thorsten , Lichten Michael
Published: January 2005

To study the mechanism of meiotic recombination in Saccharomyces cerevisiae, we examined recombination in an interval where the majority of events are initiated at a single hotspot for DNA double-strand breaks (DSBs), with little or no expected contribution by outside initiation events. This interval contained infrequently corrected palindromic markers 300 bp to the left and 600 bp to the right of the DSB hotspot. Conversion of single markers occurred frequently, while conversion of both markers occurred rarely, and many of the tetrads in which both markers converted were the products of multiple events. These data indicate that most meiotic recombination intermediates are asymmetrically positioned around the initiating DSB, with a short (<300 bp) tract of heteroduplex DNA (hDNA) to one side and hDNA on the other side frequently extending 600 bp or more. One consequence of this asymmetry is the preferential concentration of crossovers in the vicinity of the initiating DSB.
Seizure Suppression by Gain-of-Function escargot Mutations
Authors: Hekmat-Scafe Daria S , Dang Kim N , Tanouye Mark A
Published: January 2005

Suppressor mutations provide potentially powerful tools for examining mechanisms underlying neurological disorders and identifying novel targets for pharmacological intervention. Here we describe mutations that suppress seizures in a Drosophila model of human epilepsy. A screen utilizing the Drosophila easily shocked (eas) “epilepsy” mutant identified dominant suppressors of seizure sensitivity. Among several mutations identified, neuronal escargot (esg) reduced eas seizures almost 90%. The esg gene encodes a member of the snail family of transcription factors. Whereas esg is normally expressed in a limited number of neurons during a defined period of nervous system development, here normal esg was expressed in all neurons and throughout development. This greatly ameliorated both the electrophysiological and the behavioral epilepsy phenotypes of eas. Neuronal esg appears to act as a general seizure suppressor in the Drosophila epilepsy model as it reduces the susceptibility of several seizure-prone mutants. We observed that esg must be ectopically expressed during nervous system development to reduce seizure susceptibility in adults. Furthermore, induction of esg in a small subset of neurons (interneurons) will reduce seizure susceptibility. A combination of microarray and computational analyses revealed 100 genes that represent possible targets of neuronal esg. We anticipate that some of these genes may ultimately serve as targets for novel antiepileptic drugs.
A Genetic Screen for top3 Suppressors in Saccharomyces cerevisiae Identifies SHU1, SHU2, PSY3 and CSM2
Authors: Shor Erika , Weinstein Justin , Rothstein Rodney
Published: January 2005

Helicases of the RecQ family and topoisomerase III are evolutionarily conserved proteins important for maintenance of genome stability. In Saccharomyces cerevisiae, loss of the TOP3 gene, encoding topoisomerase III, results in a phenotype of slow growth, DNA damage sensitivity, meiotic defects, and hyperrecombination. The sole RecQ helicase in budding yeast, Sgs1, interacts with Top3 both physically and genetically, and the two proteins are thought to act in concert in vivo. Much recent genetic and biochemical evidence points to the role of RecQ helicases and topoisomerase III in regulating homologous recombination (HR) during DNA replication. Previously, we found that mutations in HR genes partially suppress top3 slow growth. Here, we describe the analysis of four additional mutational suppressors of top3 defects: shu1, shu2, psy3, and csm2. These genes belong to one epistasis group and their protein products interact with each other, strongly suggesting that they function as a complex in vivo. Their mutant phenotype indicates that they are important for error-free repair of spontaneous and induced DNA lesions, protecting the genome from mutation. These mutants exhibit an epistatic relationship with rad52 and show altered dynamics of Rad52-YFP foci, suggesting a role for these proteins in recombinational repair.
The Heme Activator Protein Hap1 Represses Transcription by a Heme-Independent Mechanism in Saccharomyces cerevisiae
Authors: Hon Thomas , Lee Hee Chul , Hu Zhanzhi , Iyer Vishwanath R , Zhang Li
Published: January 2005

The yeast heme activator protein Hap1 binds to DNA and activates transcription of genes encoding functions required for respiration and for controlling oxidative damage, in response to heme. Hap1 contains a DNA-binding domain with a C6 zinc cluster motif, a coiled-coil dimerization element, typical of the members of the yeast Gal4 family, and an acidic activation domain. The regulation of Hap1 transcription-activating activity is controlled by two classes of Hap1 elements, repression modules (RPM1–3) and heme-responsive motifs (HRM1–7). Previous indirect evidence indicates that Hap1 may repress transcription directly. Here we show, by promoter analysis, by chromatin immunoprecipitation, and by electrophoretic mobility shift assay, that Hap1 binds directly to DNA and represses transcription of its own gene by at least 20-fold. We found that Hap1 repression of the HAP1 gene occurs independently of heme concentrations. While DNA binding is required for transcriptional repression by Hap1, deletion of Hap1 activation domain and heme-regulatory elements has varying effects on repression. Further, we found that repression by Hap1 requires the function of Hsp70 (Ssa), but not Hsp90. These results show that Hap1 binds to its own promoter and represses transcription in a heme-independent but Hsp70-dependent manner.
A Novel Recombination Pathway Initiated by the Mre11/Rad50/Nbs1 Complex Eliminates Palindromes During Meiosis in Schizosaccharomyces pombe
Authors: Farah Joseph A , Cromie Gareth , Steiner Walter W , Smith Gerald R
Published: January 2005

DNA palindromes are rare in humans but are associated with meiosis-specific translocations. The conserved Mre11/Rad50/Nbs1 (MRN) complex is likely directly involved in processing palindromes through the homologous recombination pathway of DNA repair. Using the fission yeast Schizosaccharomyces pombe as a model system, we show that a 160-bp palindrome (M-pal) is a meiotic recombination hotspot and is preferentially eliminated by gene conversion. Importantly, this hotspot depends on the MRN complex for full activity and reveals a new pathway for generating meiotic DNA double-strand breaks (DSBs), separately from the Rec12 (ortholog of Spo11) pathway. We show that MRN-dependent DSBs are formed at or near the M-pal in vivo, and in contrast to the Rec12-dependent breaks, they appear early, during premeiotic replication. Analysis of mrn mutants indicates that the early DSBs are generated by the MRN nuclease activity, demonstrating the previously hypothesized MRN-dependent breakage of hairpins during replication. Our studies provide a genetic and physical basis for frequent translocations between palindromes in human meiosis and identify a conserved meiotic process that constantly selects against palindromes in eukaryotic genomes.
Insertion/Deletion and Nucleotide Polymorphism Data Reveal Constraints in Drosophila melanogaster Introns and Intergenic Regions
Authors: Ometto Lino , Stephan Wolfgang , De Lorenzo David
Published: January 2005

Our study of nucleotide sequence and insertion/deletion polymorphism in Drosophila melanogaster noncoding DNA provides evidence for selective pressures in both intergenic regions and introns (of the large size class). Intronic and intergenic sequences show a similar polymorphic deletion bias. Insertions have smaller sizes and higher frequencies than deletions, supporting the hypothesis that insertions are selected to compensate for the loss of DNA caused by deletion bias. Analysis of a simple model of selective constraints suggests that the blocks of functional elements located in intergenic sequences are on average larger than those in introns, while the length distribution of relatively unconstrained sequences interspaced between these blocks is similar in intronic and intergenic regions.
Characterization of Mos1-Mediated Mutagenesis in Caenorhabditis elegans
Authors: Williams Daniel C , Boulin Thomas , Ruaud Anne-Françoise , Jorgensen Erik M , Bessereau Jean-Louis
Published: January 2005

Insertional mutagenesis with a heterologous transposon provides a method to rapidly determine the molecular identity of mutated genes. The Drosophila transposon Mos1 can be mobilized to cause mutations in Caenorhabditis elegans (Bessereau  et al. 2001); however, the mutagenic rate was initially too low for use in most forward genetic screens. To increase the effectiveness of Mos1-mediated mutagenesis we examined the conditions influencing Mos1 transposition. First, optimal transposition occurs 24 hr after expression of the transposase and is unlikely to occur in differentiated sperm or oocytes. Second, transposition is limited to germ-cell nuclei that contain donor elements, but the transposase enzyme can diffuse throughout the gonad syncytium. Third, silencing of transposition is caused by changes in the donor array that occur over time. Finally, multiple transposition events occur in individual germ cells. By using screening techniques based on these results, Mos1 mutagenicity was increased to within an order of magnitude of chemical mutagens.
The Integration of Recombination and Physical Maps in a Large-Genome Monocot Using Haploid Genome Analysis in a Trihybrid Allium Population
Authors: Khrustaleva L I , de Melo P E , van Heusden A W , Kik C
Published: January 2005

Integrated mapping in large-genome monocots has been carried out on a limited number of species. Furthermore, integrated maps are difficult to construct for these species due to, among other reasons, the specific plant populations needed. To fill these gaps, Alliums were chosen as target species and a new strategy for constructing suitable populations was developed. This strategy involves the use of trihybrid genotypes in which only one homeolog of a chromosome pair is recombinant due to interspecific recombination. We used genotypes from a trihybrid Allium cepa × (A. roylei × A. fistulosum) population. Recombinant chromosomes 5 and 8 from the interspecific parent were analyzed using genomic in situ hybridization visualization of recombination points and the physical positions of recombination were integrated into AFLP linkage maps of both chromosomes. The integrated maps showed that in Alliums recombination predominantly occurs in the proximal half of chromosome arms and that 57.9% of PstI/MseI markers are located in close proximity to the centromeric region, suggesting the presence of genes in this region. These findings are different from data obtained on cereals, where recombination rate and gene density tends to be higher in distal regions.
Quantification of polycyclic aromatic hydrocarbons (PAHs) in human hair by HPLC with fluorescence detection: a biological monitoring method to evaluate the exposure to PAHs
Authors: Toriba Akira , Kuramae Yayoi , Chetiyanukornkul Thaneeya , Kizu Ryoichi , Makino Tsunehisa , Nakazawa Hiroyuki , Hayakawa Kazuichi
Published: January 2005

A high‐performance liquid chromatographic (HPLC) method with fluorescence detection was developed for the quantification of polycyclic aromatic hydrocarbons (PAHs) in human hair. Fifteen kinds of PAHs classified as priority pollutants by the US EPA were quantified with four perdeuterated PAHs as internal standards. After 50 mg hair samples were washed with n‐hexane to remove external contamination of PAHs, the samples were digested in 2.5 M sodium hydroxide. The digests were extracted with n‐hexane and then analyzed by HPLC. Eleven kinds of PAHs were identified in hair samples of 20 subjects, and 10 kinds of PAHs were eventually quantified using the internal standards. For anthracene, chrysene and benzo[k]fluoranthene, significant differences were observed between smokers and non‐smokers. Although benzo[b]fluoranthene, dibenz[a,h]anthracene, benzo[ghi]perylene and indeno[1,2,3‐cd]pyrene were observed in the particulates of indoor and outdoor air, they were not detected in all hair samples. The analysis of PAHs in human hair should be useful as a new biomarker to evaluate the exposure to PAHs. Copyright ­© 2003 John Wiley & Sons, Ltd.
Analysis of perchlorate in difficult matrices by LC/MS
Authors: Di Rienzo Robert P. , Lin Kham , McKay Thomas T. , Wade Richard W.
Published: January 2005

A method has been developed and validated for the determination of perchlorate in drinking water, soil, biota, groundwater, and saline water using highperformance liquid chromatography/mass spectrometry (LC/MS) without sample pretreatment. Mass spectrometry is used to monitor perchlorate at mass 83. The 83/85 isotopic ratio is used for additional identification of perchlorate, along with an internal standard containing Oxygen‐18 isotopic labeled perchlorate. The method can achieve a method detection limit in aqueous samples of 0.05 μg/L and can easily quantify perchlorate at 0.2 μg/L in any aqueous environmental sample matrix. This method uses simple determinative techniques available to LC/MS technologies and does not require any instrumentation additions or systematic pretreatment of samples. Inadequacies of current EPA Method 314.0 caused by matrix interference, high dissolved solids, and conductivity are eliminated and confirmation of perchlorate is accomplished with this new method. © 2005 Wiley Periodicals, Inc.
Investigation of nickel suppression and cytocompatibility of surface‐treated nickel‐titanium shape memory alloys by using plasma immersion ion implantation
Authors: Yeung K. W. K. , Poon R. W. Y. , Liu X. Y. , Ho J. P. Y. , Chung C. Y. , Chu P. K. , Lu W. W. , Chan D. , Cheung K. M. C.
Published: January 2005

Nickel‐titanium (NiTi) shape memory alloys are increasingly being used in orthopedic applications. However, there is a concern that Ni is harmful to the human body. We have recently investigated the use of nitrogen, or oxygen plasma immersion ion implantation to mitigate this deleterious effect. Our results reveal that the near‐surface Ni concentration in all the treated samples is significantly suppressed. In addition, our in vitro tests show that the plasma‐treated surfaces are cytologically compatible allowing the attachment and proliferation of osteoblasts. Among the two types of samples, the best biological effects are found on the samples with nitrogen implantation. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res 72A: 238–245, 2005
One‐Minute Wear‐Rate Measurement
Authors: Schaake Richard P. , den Toonder Jaap M. J. , Vellinga Willem‐Pier , Meijer Han E. H.
Published: January 2005

Summary: Single‐asperity wear measurements were performed on small quantities of polyethylene with different molecular weights. Experiments could be performed on a surface area of 25 × 3000 μm2. A quantitative value of wear rate could be obtained that was proportional to macroscopic results relating the wear rate to the molecular weight. Material transfer limited the maximum sliding velocity to 1 μm · s−1. Possible solutions for this problem have been identified and will be a subject of further investigation.

Indentation profile for high‐molecular‐weight polyethylene (PE‐H).

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Indentation profile for high‐molecular‐weight polyethylene (PE‐H).
Comparison of Hyperbranched and Linear Polyglycidol Unimolecular Reverse Micelles as Nanoreactors and Nanocapsules
Authors: Kumar Kainthan Rajesh , Brooks Donald E.
Published: January 2005

Summary: Amphiphilic‐hyperbranched polyglycidols and a linear analogue were tested for their ability to act as nanoreactors for the unimolecular elimination (E1) reactions of tert‐alkyl iodides. Their encapsulation properties were also compared. The linear polymer was found to have very good “unimolecular reverse micellar” characteristics as well, even though the results showed the advantages of a hyperbranched nature over a linear one. Our results stress the need for a direct comparison of branched and linear polymers for any application.

Amphiphilic polyglycidol unimolecular reverse micelles.

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Amphiphilic polyglycidol unimolecular reverse micelles.
Repellency and toxicity of aromatic plant extracts against the mosquito Culex pipiens molestus (Diptera: Culicidae)
Authors: Traboulsi Abdallah F , El‐Haj Samih , Tueni Marie , Taoubi Khalil , Nader Natalie Abi , Mrad Abir
Published: January 2005

The insecticidal activities of essential oil extracts from leaves, flowers and roots of aromatic plants against fourth‐instar larvae of the mosquito Culex pipiens molestus Forskål were determined. Extracts of Foeniculum vulgare Mill were the most toxic, followed by those of Ferula hermonis Boiss, Citrus sinensis Osbeck, Pinus pinea L, Laurus nobilis L and Eucalyptus spp with LC50 values of 24.5, 44.0, 60.0, 75.0, 117.0 and 120.0 mg litre−1, respectively. Combination tests between the LC50 and the maximum sub‐lethal concentration (MSLC) were determined. Over 20 major components were identified in extracts from each plant species tested. Five essential oils and nine pure components were studied for their repellency against mosquito bites. Terpineol and 1,8‐cineole were the most effective against Culex pipiens molestus bites offering complete protection for 1.6 and 2 h, respectively. Copyright © 2005 Society of Chemical Industry
Unconventional density wave as possible explanation of the Nernst signal in CeCoIn5
Authors: Dóra Balázs , Maki Kazumi , Virosztek Attila , Ványolos András
Published: January 2005

Recently large Nernst effect and Seebeck effect were observed above the superconducting transition temperature 2.3 K in a heavy fermion superconductor CeCoIn5. We interpret this large Nernst effect in terms of unconventional density wave (UDW), which appears around T = 18 K. In the presence of magnetic field, Landau levels are formed in UDW, and the transport is dominated by thermally excited quasiparticles across the levels. Our theory describes successfully the available experimental data, and the deduced fitting parameters are in accordance with what is expected in the vicinity of a quantum critical point. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electron ionization mass spectral fragmentation of C19 isoprenoid aldehydes and carboxylic acid methyl and trimethylsilyl esters
Authors: Rontani J.‐F. , Aubert C.
Published: January 2005

The electron ionization (EI) mass spectra of saturated and α,β‐unsaturated C19 isoprenoid aldehydes and carboxylic acid methyl and trimethylsilyl esters are reported. Different pathways are proposed in order to explain the main fragmentations observed. The conjugated double bond migrates more or less readily before γ‐hydrogen rearrangement according to the structure of the considered compound. Configurations of the double bond of α,β‐unsaturated C19 isoprenoid aldehydes and fatty acid methyl and trimethylsilyl esters can be easily determined thanks to the peaks at m/z 97, 127 and 185, respectively, which are much more abundant in the mass spectra of the Z isomers owing to the formation of a cyclic ion. In the case of trimethylsilyl esters, subsequent fragmentation of the cyclic ion at m/z 185 affords two other diagnostic ions at m/z 95 and 169. Copyright © 2003 John Wiley & Sons, Ltd.