bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self-Fertilization and the Evolution of Recombination
Authors: Roze Denis , Lenormand Thomas 
Published: March 2005

Abstract
In this article, we study the effect of self-fertilization on the evolution of a modifier allele that alters the recombination rate between two selected loci. We consider two different life cycles: under gametophytic selfing, a given proportion of fertilizations involves gametes produced by the same haploid individual, while under sporophytic selfing, a proportion of fertilizations involves gametes produced by the same diploid individual. Under both life cycles, we derive approximations for the change in frequency of the recombination modifier when selection is weak relative to recombination, so that the population reaches a state of quasi-linkage equilibrium. We find that gametophytic selfing increases the range of epistasis under which increased recombination is favored; however, this effect is substantial only for high selfing rates. Moreover, gametophytic selfing affects the relative influence of different components of epistasis (additive × additive, additive × dominance, dominance × dominance) on the evolution of the modifier. Sporophytic selfing has much stronger effects: even a small selfing rate greatly increases the parameter range under which recombination is favored, when there is negative dominance × dominance epistasis. This effect is due to the fact that selfing generates a correlation in homozygosity at linked loci, which is reduced by recombination.
Intron Size and Exon Evolution in Drosophila
Authors: Marais Gabriel , Nouvellet Pierre , Keightley Peter D , Charlesworth Brian 
Published: March 2005

Abstract
We have found a negative correlation between evolutionary rate at the protein level (as measured by dN) and intron size in Drosophila. Although such a relation is expected if introns reduce Hill-Robertson interference within genes, it seems more likely to be explained by the higher abundance of cis-regulatory elements in introns (especially first introns) in genes under strong selective constraints.
Saccharomyces cerevisiae Histone H2A Ser122 Facilitates DNA Repair
Authors: Harvey Anne C , Jackson Stephen P , Downs Jessica A 
Published: March 2005

Abstract
DNA repair takes place in the context of chromatin. Recently, it has become apparent that proteins that make up and modulate chromatin structure are involved in the detection and repair of DNA lesions. We previously demonstrated that Ser129 in the carboxyl-terminal tail of yeast histone H2A is important for double-strand-break responses. By undertaking a systematic site-directed mutagenesis approach, we identified another histone H2A serine residue (Ser122) that is important for survival in the presence of DNA-damaging agents. We show that mutation of this residue does not affect DNA damage-dependent Rad53 phosphorylation or G2/M checkpoint responses. Interestingly, we find that yeast lacking H2A S122 are defective in their ability to sporulate. Finally, we demonstrate that H2A S122 provides a function distinct from that of H2A S129. These data demonstrate a role for H2A S122 in facilitating survival in the presence of DNA damage and suggest a potential role in mediating homologous recombination. The distinct roles of H2A S122 and S129 in mediating these responses suggest that chromatin components can provide specialized functions for distinct DNA repair and survival mechanisms and point toward the possibility of a complex DNA damage responsive histone code.
Quantitative Trait Locus Study Design From an Information Perspective
Authors: Sen Śaunak , Satagopan Jaya M , Churchill Gary A 
Published: March 2005

AbstractWe examine the efficiency of different genotyping and phenotyping strategies in inbred line crosses from an information perspective. This provides a mathematical framework for the statistical aspects of QTL experimental design, while guiding our intuition. Our central result is a simple formula that quantifies the fraction of missing information of any genotyping strategy in a backcross. It includes the special case of selectively genotyping only the phenotypic extreme individuals. The formula is a function of the square of the phenotype and the uncertainty in our knowledge of the genotypes at a locus. This result is used to answer a variety of questions. First, we examine the cost-information trade-off varying the density of markers and the proportion of extreme phenotypic individuals genotyped. Then we evaluate the information content of selective phenotyping designs and the impact of measurement error in phenotyping. A simple formula quantifies the information content of any combined phenotyping and genotyping design. We extend our results to cover multigenotype crosses, such as the F2 intercross, and multiple QTL models. We find that when the QTL effect is small, any contrast in a multigenotype cross benefits from selective genotyping in the same manner as in a backcross. The benefit remains in the presence of a second unlinked QTL with small effect (explaining &lt;20% of the variance), but diminishes if the second QTL has a large effect. Software for performing power calculations for backcross and F2 intercross incorporating selective genotyping and marker spacing is available from http://www.biostat.ucsf.edu/sen.
A Gene(s) for All-trans-Retinoic Acid-Induced Forelimb Defects Mapped and Confirmed to Murine Chromosome 11
Authors: Lee Grace S , Cantor Rita M , Abnoosian Arin , Park Euisun , Yamamoto Mitsuko L , Hovland David N , Collins Michael D 
Published: March 2005

AbstractAll-trans-retinoic acid (RA) induces various anatomical limb dysmorphologies in mice dependent on the time of exposure. During early limb development, RA induces forelimb ectrodactyly (digital absence) with varying susceptibilities for different inbred mouse strains; C57BL/6N are highly susceptible while SWV are resistant. To isolate the genetic basis of this defect, a full-genome scan was performed in 406 backcross fetuses of F1 males to C57BL/6N females. Fetuses were exposed via a maternal injection of 75 mg of RA per kilogram of body weight on gestational day 9.25. The genome-wide analysis revealed significant linkage to a chromosome 11 locus near D11Mit39 with a maximum LOD score of 9.0 and to a chromosome 4 locus near D4Mit170. An epistatic interaction was detected between loci on chromosome 11 (D11Mit39) and chromosome 18 (D18Mit64). Linkage to the chromosome 11 locus (D11Mit39) was confirmed in RA-treated backcross fetuses of F1 females to C57BL/6N males. Loci associated with bone density/mass in both human and mouse were previously detected in the same region, suggesting a mechanistic linkage with bone homeostasis. The human syntenic region of this locus has been previously linked to Meckel syndrome; the phenotype includes postaxial polydactyly, an ectopic digital defect hypothesized to be induced by a common molecular pathway with ectrodactyly.
Transmission Ratio Distortion in Intraspecific Hybrids of Mimulus guttatus
Authors: Hall Megan C , Willis John H 
Published: March 2005

Abstract
We constructed a genetic linkage map between two divergent populations of Mimulus guttatus. We genotyped an F2 mapping population (N = 539) at 154 AFLP, microsatellite, and gene-based markers. A framework map was constructed consisting of 112 marker loci on 14 linkage groups with a total map length of 1518 cM Kosambi. Nearly half of all markers (48%) exhibited significant transmission ratio distortion (α = 0.05). By using a Bayesian multipoint mapping method and visual inspection of significantly distorted markers, we detected 12 transmission ratio distorting loci (TRDL) throughout the genome. The high degree of segregation distortion detected in this intraspecific map indicates substantial genomic divergence that perhaps suggests genomic incompatibilities between these two populations. We compare the pattern of transmission ratio distortion in this map to an interspecific map constructed between M. guttatus and M. nasutus. A similar level of segregation distortion is detected in both maps. Collinear regions between maps are compared to determine if there are shared genetic patterns of non-Mendelian segregation distortion within and among Mimulus species.
Characterization of Active R2 Retrotransposition in the rDNA Locus of Drosophila simulans
Authors: Zhang Xian , Eickbush Thomas H 
Published: March 2005

Abstract
The rRNA gene (rDNA) loci of all arthropod lineages contain non-LTR retrotransposable elements that have evolved to specifically insert into the 28S rRNA genes. Extensive in vitro experiments have been conducted to investigate the mechanism of R2 retrotransposition but little is known of the insertion frequency or cellular factors that might regulate R2 activity. In this article, isofemale lines obtained from a population of Drosophila simulans were surveyed for recent R2 insertions. Within most lines, all individuals showed the same collection of R2 insertions, providing no evidence for recent R2 activity. However, in a few of the isofemale lines, virtually all individuals differed in their R2 insertion profiles. The descendants of individual pairs of flies from these “active lines” rapidly accumulated new insertions. The frequent insertion of new R2 elements was associated with the elimination of old R2 elements from the rDNA locus. The existence of lines in which R2 retrotransposes frequently and lines in which the elements appear dormant suggests that cellular mechanisms that can regulate the activity of R2 exist. Retrotransposition activity was correlated with the number of full-length R2 elements but not with the size of the rDNA locus or the number of uninserted units.
The Structure and Population Genetics of the Breakpoints Associated With the Cosmopolitan Chromosomal Inversion In(3R)Payne in Drosophila melanogaster
Authors: Matzkin Luciano M , Merritt Thomas J S , Zhu Chen-Tseh , Eanes Walter F 
Published: March 2005

Abstract
We report here the breakpoint structure and sequences of the Drosophila melanogaster cosmopolitan chromosomal inversion In(3R)P. Combining in situ hybridization to polytene chromosomes and long-range PCR, we have identified and sequenced the distal and proximal breakpoints. The breakpoints are not simple cut-and-paste structures; gene fragments and small duplications of DNA are associated with both breaks. The distal breakpoint breaks the tolkin (tok) gene and the proximal breakpoint breaks CG31279 and the tolloid (tld) gene. Functional copies of all three genes are found at the opposite breakpoints. We sequenced a representative sample of standard (St) and In(3R)P karyotypes for a 2-kb portion of the tok gene, as well as the same 2 kb from the pseudogene tok fragment found at the distal breakpoint of In(3R)P chromosomes. The tok gene in St arrangements possesses levels of polymorphism typical of D. melanogaster genes. The functional tok gene associated with In(3R)P shows little polymorphism. Numerous single-base changes, as well as deletions and duplications, are associated with the truncated copy of tok. The overall pattern of polymorphism is consistent with a recent origin of In(3R)P, on the order of Ne generations. The identification of these breakpoint sequences permits a simple PCR-based screen for In(3R)P.
Bayesian Shrinkage Estimation of Quantitative Trait Loci Parameters
Authors: Wang Hui , Zhang Yuan-Ming , Li Xinmin , Masinde Godfred L , Mohan Subburaman , Baylink David J , Xu Shizhong 
Published: March 2005

AbstractMapping multiple QTL is a typical problem of variable selection in an oversaturated model because the potential number of QTL can be substantially larger than the sample size. Currently, model selection is still the most effective approach to mapping multiple QTL, although further research is needed. An alternative approach to analyzing an oversaturated model is the shrinkage estimation in which all candidate variables are included in the model but their estimated effects are forced to shrink toward zero. In contrast to the usual shrinkage estimation where all model effects are shrunk by the same factor, we develop a Bayesian method that allows the shrinkage factor to vary across different effects. The new shrinkage method forces marker intervals that contain no QTL to have estimated effects close to zero whereas intervals containing notable QTL have estimated effects subject to virtually no shrinkage. We demonstrate the method using both simulated and real data for QTL mapping. A simulation experiment with 500 backcross (BC) individuals showed that the method can localize closely linked QTL and QTL with effects as small as 1% of the phenotypic variance of the trait. The method was also used to map QTL responsible for wound healing in a family of a (MRL/MPJ × SJL/J) cross with 633 F2 mice derived from two inbred lines.
Genetical Genomics Analysis of a Yeast Segregant Population for Transcription Network Inference
Authors: Bing Nan , Hoeschele Ina 
Published: March 2005

Abstract
Genetic analysis of gene expression in a segregating population, which is expression profiled and genotyped at DNA markers throughout the genome, can reveal regulatory networks of polymorphic genes. We propose an analysis strategy with several steps: (1) genome-wide QTL analysis of all expression profiles to identify eQTL confidence regions, followed by fine mapping of identified eQTL; (2) identification of regulatory candidate genes in each eQTL region; (3) correlation analysis of the expression profiles of the candidates in any eQTL region with the gene affected by the eQTL to reduce the number of candidates; (4) drawing directional links from retained regulatory candidate genes to genes affected by the eQTL and joining links to form networks; and (5) statistical validation and refinement of the inferred network structure. Here, we apply an initial implementation of this strategy to a segregating yeast population. In 65, 7, and 28% of the identified eQTL regions, a single candidate regulatory gene, no gene, or more than one gene was retained in step 3, respectively. Overall, 768 putative regulatory links were retained, 331 of which are the strongest candidate links, as they were retained in the expression correlation analysis and were located within or near an eQTL subregion identified by a multimarker analysis separating multiple linked QTL. One or several biological processes were statistically significantly overrepresented in independent network structures or in highly interconnected subnetworks. Most of the transcription factors found in the inferred network had a putative regulatory link to only one other gene or exhibited cis-regulation.
Effect of soilborne wheat mosaic virus on winter wheat yield and yield components
Authors: Altay F. , Bolat N. 
Published: March 2005

Soil-borne wheat mosaic virus (SBWMV) is an important disease of wheat production areas throughout the world, causing a great reduction in wheat and barley yields. The most effective way of controlling the disease is the use of resistant varieties in infested areas. In this study, the effects of SBWMV on yields and some yield components of eight susceptible, one moderately susceptible/resistant and nine resistant varieties were evaluated using data from 9 virus-infested and 6 non-infested sites in Eskisehir, Turkey over 6 years. The susceptible varieties yielded 5.35% more than resistant varieties in non-infested sites, while they gave 28.98% lower yield in infested sites. Significant yield loss differences were observed between the varieties in infested sites. Decreases were also observed in yield components at various levels. This study showed that SBWMV is an important disease, which survives in soil for long periods and causes significant yield decreases in wheat. Recently developed varieties have good resistance to the disease and are recommended to farmers in infested areas. Abbreviations: SBWMV, soil-borne wheat mosaic virus
Effect of cadmium on growth and oxidative metabolism of faba bean plants
Authors: Moussa H. R. 
Published: March 2005

The effect of CdCl2(0-50 µM) on the growth, physiological parametersand leaf antioxidative enzymes of faba bean plants was studied in order toinvestigate the possible involvement of this metal in the generationof oxidative stress. In the roots and leaves of faba bean plants Cd produceda significant inhibition of growth, as well as a reduction inthe transpiration rate, photosynthetic efficiency (14CO2-fixation), ribulose-1,5-bisphosphate-carboxylase/oxygenase (Rubisco) activity and leaf pigment content, and an alteration in the nutrient status in booth roots and leaves. an increased level of free proline was also detected. The results suggest thatthe treatment of faba bean plants with CdCl2 induced a concentration-dependentoxidative stress situation in the leaves, characterized by an accumulationof H2O2, as a result of theinhibition of the antioxidant enzymes glutathione reductase (GR) and catalase (CAT). These results point to the possible inductionof leaf senescence by cadmium.
Talajfizikai tulajdonságok becslése és alkalmazásuk modellekben
Authors: Fodor Nándor , Rajkai Kálmán 
Published: March 2005

A talajban végbemeno vízáramlás leírásához két talajfizikai összefüggés, a víztartóképesség- és a vízvezetoképesség-függvény szükséges. A talaj vízforgalmának modellezése elvileg akkor a legpontosabb, ha bemeno adatként a talajfizikai függvényeket a mérési adatokra illesztett függvényekkel adjuk meg. A vizsgálatokhoz a Szilas-patak árterén található öntés réti talajszelvény mért víztartóképesség- és vízvezetoképesség-függvényeit használtuk. A mért víztartóképesség-értékekre Brutsaert-, illetve van Genuchten-függvényeket, a mért vízvezetoképesség-értékekre pedig Mualem-van Genuchten-függvényeket illesztettünk. Az illesztett függvényeket tekintettük referenciának. Feltételeztük, hogy a 4M modell ezekkel a függvényparaméterekkel szimulálja a vizsgált talajszelvény nedvességforgalmát a legvalósághubb módon. Különbözo becslo módszerekkel (Mualem-van Genuchten módszer: M-vG; grafikus módszer: B-vG; pedotranszfer függvények: PTF-vG) számított víz-tartóképesség-, illetve vízvezetoképesség-függvényeket alkalmaztunk és hasonlítottunk össze a mért víztartóképesség- illetve vízvezetoképesség-értékekkel. Ezt követoen a referencia függvényekkel és a becsült függvényekkel kapott 4M modelleredményeket (kumET) hasonlítottuk össze és értékeltük. Fobb megállapításainkat az alábbiakban foglaljuk össze: - Esetünkben a grafikus módszer eredményesen használható a vízvezeto-képesség-függvény víztartóképesség-függvénybol történo becslésére. - A pedotranszfer függvényekkel kapott víztartóképesség-függvények illeszkedése, az elfogadható, ±2,5%-os hibahatáron belüli volt mindhárom talajmintára. - A vízvezetoképesség-függvény becslésében mindhárom becslo módszer elfogadható hibájú volt, a B-szintet kivéve, ahol a PTF-vG módszer jelentosen alábecsülte a mért értékeket. - Esetünkben a M-vG és B-vG, illetve PTF-vG módszerekkel becsült függvényekkel szimulált kumET-értékek következetesen alulbecsülték, illetve felülbecsülték a referencia függvényekkel számított kumulált evapotranszspirációt. - A M-vG és a PTF-vG módszer kielégíto eredménnyel használható a 4M növénytermesztési modell talajfizikai függvényeinek meghatározására, amennyiben az evapotranszspiráció számítása a modellhasználat célja. Tervezzük a vizsgálatok kiterjesztését heterogénebb talajtani és éghajlati körülményekre.
Enzimaktivitások és a fluoreszkáló pszeudomonasz csíraszámok változása a fehér lóhere (Trifolium repens L.) rizoszférájában sókezelés (NaCl) hatására
Authors: Khalif A. A. , Abdorhim H. , Bayoumi Hosam E. H. T. , Füzy Anna , Kecskés Mihály 
Published: March 2005

Üvegházi körülmények között savanyú barna erdotalajban nevelt fehér here (Trifolium repensL.) növények rizoszférájának sókezelés hatására bekövetkezo változását ellenoriztük. Megvizsgáltuk a különbözo sókoncentrációknak (0, 0,2, 0,4, 0,6 és 0,8 tömeg %) a baktériumnépesség összetételére és a különbözo talajenzimek aktivitására gyakorolt hatását. Megállapítottuk, hogy a talaj sótartalma közvetlenül befolyásolta a rizoszférában található fluoreszkáló pszeudomonaszok csíraszámát. A legsurubb populáció a 0,2% NaCl-ot tartalmazó talajban volt mérheto, ahol a fluoreszkáló pszeudomonaszok között aPseudomonas putidaés aP. fluorescensfordultak elo a legnagyobb számban. A pszeudomonaszok ily módon jól tolerálják a talaj magas NaCl-tartalmát, és gyökérkolonizáló tevékenységet képesek kifejteni a magas NaCl-tartalmú talajban is. A sókoncentráció növelésével kezdetben (a 0,2-0,4%-os tartományban) jelentosen növekedett a dehidrogenáz, kataláz, és ureáz enzimek aktivitása. A proteáz enzimek aktivitásmaximuma a 0,1-0,2% NaCl-koncentráció tartományba esett. A 0,4%-nál magasabb koncentrációkban a kontrollhoz hasonló mértékure csökkent mind a négy enzim aktivitása, és a baktériumok száma is. A foszfatáz- és a b-glükozidáz-tevékenység viszont a NaCl-dózis növelése következtében a koncentrációval arányosan, jelentosen csökkent a kontrollhoz viszonyítva. Feltételezésünk szerint az enzimaktivitások változását is a sókezelés hatására bekövetkezo mikrobióta összetételének megváltozása okozta.
A viselkedésben megjelenő interakciós szinkronitás vizsgálatának módszertani problémái
Authors: Biró Eszter 
Published: March 2005

A cikk az interakciós szinkronitás egyik részterületére, a viselkedéses jelenségekben megfigyelhető összehangolódási folyamatokra vonatkozó kutatások főbb módszertani irányzatait tekinti át. Az 1960-as évektől alkalmazott mikroelemzéses eljárások érvényességét kiterjedt kutatások igazolják, az utóbbi másfél évtizedben mégis sok kritikát kaptak elementarizmusuk és redukcionizmusuk miatt. A mikroelemzéses eljárások alternatívájaként kidolgozott - gyorsabban és egyszerűbben alkalmazható, naiv megítéléseken alapuló - globális módszer megbízhatósági és érvényességi eredményei azt mutatják, hogy ez a módszer is alkalmas lehet az interakciós szinkronitás sokrétű szociális folyamatainak megragadására, a mikroelemzéses eljárások kiegészítésére, sőt akár kiváltására. A mikroelemzés és a globális megközelítés adatai közötti kapcsolat vizsgálata a globális módszer egyik alapvető érvényességi kérdése. A globális megítélési adatok és a raport, az expresszivitás és a mosolygás közötti összefüggések ellentmondásainak tisztázása a további kutatások legfontosabb feladatai közé tartozik.