bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Fitness Cost Associated With the Antibiotic Resistance Enzyme SME-1 β-Lactamase
Authors: Marciano David C , Karkouti Omid Y , Palzkill Timothy 
Published: June 2007

Abstract
The blaTEM-1 β-lactamase gene has become widespread due to the selective pressure of β-lactam use and its stable maintenance on transferable DNA elements. In contrast, blaSME-1 is rarely isolated and is confined to the chromosome of carbapenem-resistant Serratia marcescens strains. Dissemination of blaSME-1 via transfer to a mobile DNA element could hinder the use of carbapenems. In this study, blaSME-1 was determined to impart a fitness cost upon Escherichia coli in multiple genetic contexts and assays. Genetic screens and designed SME-1 mutants were utilized to identify the source of this fitness cost. These experiments established that the SME-1 protein was required for the fitness cost but also that the enzyme activity of SME-1 was not associated with the fitness cost. The genetic screens suggested that the SME-1 signal sequence was involved in the fitness cost. Consistent with these findings, exchange of the SME-1 signal sequence for the TEM-1 signal sequence alleviated the fitness cost while replacing the TEM-1 signal sequence with the SME-1 signal sequence imparted a fitness cost to TEM-1 β-lactamase. Taken together, these results suggest that fitness costs associated with some β-lactamases may limit their dissemination.
On the Utility of Linkage Disequilibrium as a Statistic for Identifying Targets of Positive Selection in Nonequilibrium Populations
Authors: Jensen Jeffrey D , Thornton Kevin R , Bustamante Carlos D , Aquadro Charles F 
Published: June 2007

AbstractA critically important challenge in empirical population genetics is distinguishing neutral nonequilibrium processes from selective forces that produce similar patterns of variation. We here examine the extent to which linkage disequilibrium (i.e., nonrandom associations between markers) improves this discrimination. We show that patterns of linkage disequilibrium recently proposed to be unique to hitchhiking models are replicated under nonequilibrium neutral models. We also demonstrate that jointly considering spatial patterns of association among variants alongside the site-frequency spectrum is nonetheless of value. Through a comparison of models of equilibrium neutrality, nonequilibrium neutrality, equilibrium hitchhiking, nonequilibrium hitchhiking, and recurrent hitchhiking, we evaluate a linkage disequilibrium (LD) statistic (ωmax) that appears to have power to identify regions recently shaped by positive selection. Most notably, for demographic parameters relevant to non-African populations of Drosophila melanogaster, we demonstrate that selected loci are distinguishable from neutral loci using this statistic.
Intraspecific Genetic Variations, Fitness Cost and Benefit of RPW8, A Disease Resistance Locus in Arabidopsis thaliana
Authors: Orgil Undral , Araki Hitoshi , Tangchaiburana Samantha , Berkey Robert , Xiao Shunyuan 
Published: June 2007

Abstract
The RPW8 locus of Arabidopsis thaliana confers broad-spectrum resistance to powdery mildew pathogens. In many A. thaliana accessions, this locus contains two homologous genes, RPW8.1 and RPW8.2. In some susceptible accessions, however, these two genes are replaced by HR4, a homolog of RPW8.1. Here, we show that RPW8.2 from A. lyrata conferred powdery mildew resistance in A. thaliana, suggesting that RPW8.2 might have gained the resistance function before the speciation of A. thaliana and A. lyrata. To investigate how RPW8 has been maintained in A. thaliana, we examined the nucleotide sequence polymorphisms in RPW8 from 51 A. thaliana accessions, related disease reaction phenotypes to the evolutionary history of RPW8.1 and RPW8.2, and identified mutations that confer phenotypic variations. The average nucleotide diversities were high at RPW8.1 and RPW8.2, showing no sign of selective sweep. Moreover, we found that expression of RPW8 incurs fitness benefits and costs on A. thaliana in the presence and absence of the pathogens, respectively. Our results suggest that polymorphisms at the RPW8 locus in A. thaliana may have been maintained by complex selective forces, including those from the fitness benefits and costs both associated with RPW8.
Multipoint Identity-by-Descent Prediction Using Dense Markers to Map Quantitative Trait Loci and Estimate Effective Population Size
Authors: Meuwissen Theo H E , Goddard Mike E 
Published: June 2007

AbstractA novel multipoint method, based on an approximate coalescence approach, to analyze multiple linked markers is presented. Unlike other approximate coalescence methods, it considers all markers simultaneously but only two haplotypes at a time. We demonstrate the use of this method for linkage disequilibrium (LD) mapping of QTL and estimation of effective population size. The method estimates identity-by-descent (IBD) probabilities between pairs of marker haplotypes. Both LD and combined linkage and LD mapping rely on such IBD probabilities. The method is approximate in that it considers only the information on a pair of haplotypes, whereas a full modeling of the coalescence process would simultaneously consider all haplotypes. However, full coalescence modeling is computationally feasible only for few linked markers. Using simulations of the coalescence process, the method is shown to give almost unbiased estimates of the effective population size. Compared to direct marker and haplotype association analyses, IBD-based QTL mapping showed clearly a higher power to detect a QTL and a more realistic confidence interval for its position. The modeling of LD could be extended to estimate other LD-related parameters such as recombination rates.
A Covariance Structure Model for the Admixture of Binary Genetic Variation
Authors: Grote Mark N 
Published: June 2007

Abstract
I derive a covariance structure model for pairwise linkage disequilibrium (LD) between binary markers in a recently admixed population and use a generalized least-squares method to fit the model to two different data sets. Both linked and unlinked marker pairs are incorporated in the model. Under the model, a pairwise LD matrix is decomposed into two component matrices, one containing LD attributable to admixture, and another containing, in an aggregate form, LD specific to the populations forming the mixture. I use population genetics theory to show that the latter matrix has block-diagonal structure. For the data sets considered here, I show that the number of source populations can be determined by statistical inference on the canonical correlations of the sample LD matrix.
Postprocessing of Genealogical Trees
Authors: Meligkotsidou Loukia , Fearnhead Paul 
Published: June 2007

Abstract
We consider inference for demographic models and parameters based upon postprocessing the output of an MCMC method that generates samples of genealogical trees (from the posterior distribution for a specific prior distribution of the genealogy). This approach has the advantage of taking account of the uncertainty in the inference for the tree when making inferences about the demographic model and can be computationally efficient in terms of reanalyzing data under a wide variety of models. We consider a (simulation-consistent) estimate of the likelihood for variable population size models, which uses importance sampling, and propose two new approximate likelihoods, one for migration models and one for continuous spatial models.
Linkage Disequilibrium and Recombination Rate Estimates in the Self-Incompatibility Region ofArabidopsis lyrata
Authors: Kamau Esther , Charlesworth Brian , Charlesworth Deborah 
Published: June 2007

AbstractGenetic diversity is unusually high at loci in the S-locus region of the self-incompatible species of the flowering plant, Arabidopsis lyrata, not just in the S loci themselves, but also at two nearby loci. In a previous study of a single natural population from Iceland, we attributed this elevated polymorphism to linkage disequilibrium (LD) between variants at loci close to the S locus and the S alleles, which are maintained in the population by balancing selection. With the four S-flanking loci whose diversity we previously studied, we could not determine the extent of the region linked to the S loci in which neutral sites are affected. We also could not exclude the possibility of a population bottleneck, or of admixture, as causes of the LD. We have now studied four more distant loci flanking the S-locus region, and more populations, and we analyze the results using a theoretical model of the effect of balancing selection on diversity at linked neutral sites within and between different functional S-allelic classes. In the model, diversity is a function of the number of selectively maintained alleles and the recombination distances from the selectively maintained sites. We use the model to estimate the number of different functional S alleles, their turnover rate, and recombination rates between the S-locus region and other loci. Our estimates suggest that there is a small region of very low recombination surrounding the S-locus region.
SYP-3 Restricts Synaptonemal Complex Assembly to Bridge Paired Chromosome Axes During Meiosis in Caenorhabditis elegans
Authors: Smolikov Sarit , Eizinger Andreas , Schild-Prufert Kristina , Hurlburt Allison , McDonald Kent , Engebrecht JoAnne , Villeneuve Anne M , Colaiácovo Mónica P 
Published: June 2007

Abstract
Synaptonemal complex (SC) formation must be regulated to occur only between aligned pairs of homologous chromosomes, ultimately ensuring proper chromosome segregation in meiosis. Here we identify SYP-3, a coiled-coil protein that is required for assembly of the central region of the SC and for restricting its loading to occur only in an appropriate context, forming structures that bridge the axes of paired meiotic chromosomes in Caenorhabditis elegans. We find that inappropriate loading of central region proteins interferes with homolog pairing, likely by triggering a premature change in chromosome configuration during early prophase that terminates the search for homologs. As a result, syp-3 mutants lack chiasmata and exhibit increased chromosome missegregation. Altogether, our studies lead us to propose that SYP-3 regulates synapsis along chromosomes, contributing to meiotic progression in early prophase.
The flare Gene, Which Encodes the AIP1 Protein of Drosophila, Functions to Regulate F-Actin Disassembly in Pupal Epidermal Cells
Authors: Ren Nan , Charlton Jeannette , Adler Paul N 
Published: June 2007

Abstract
Adult Drosophila are decorated with several types of polarized cuticular structures, such as hairs and bristles. The morphogenesis of these takes place in pupal cells and is mediated by the actin and microtubule cytoskeletons. Mutations in flare (flr) result in grossly abnormal epidermal hairs. We report here that flr encodes the Drosophila actin interacting protein 1 (AIP1). In other systems this protein has been found to promote cofilin-mediated F-actin disassembly. In Drosophila cofilin is encoded by twinstar (tsr). We show that flr mutations result in increased levels of F-actin accumulation and increased F-actin stability in vivo. Further, flr is essential for cell proliferation and viability and for the function of the frizzled planar cell polarity system. All of these phenotypes are similar to those seen for tsr mutations. This differs from the situation in yeast where cofilin is essential while aip1 mutations result in only subtle defects in the actin cytoskeleton. Surprisingly, we found that mutations in flr and tsr also result in greatly increased tubulin staining, suggesting a tight linkage between the actin and microtubule cytoskeleton in these cells.
Phenotypic and Transcriptomic Changes Associated With Potato Autopolyploidization
Authors: Stupar Robert M , Bhaskar Pudota B , Yandell Brian S , Rensink Willem A , Hart Amy L , Ouyang Shu , Veilleux Richard E , Busse James S , Erhardt Robert J , Buell C Robin , Jiang Jiming 
Published: June 2007

AbstractPolyploidy is remarkably common in the plant kingdom and polyploidization is a major driving force for plant genome evolution. Polyploids may contain genomes from different parental species (allopolyploidy) or include multiple sets of the same genome (autopolyploidy). Genetic and epigenetic changes associated with allopolyploidization have been a major research subject in recent years. However, we know little about the genetic impact imposed by autopolyploidization. We developed a synthetic autopolyploid series in potato (Solanum phureja) that includes one monoploid (1x) clone, two diploid (2x) clones, and one tetraploid (4x) clone. Cell size and organ thickness were positively correlated with the ploidy level. However, the 2x plants were generally the most vigorous and the 1x plants exhibited less vigor compared to the 2x and 4x individuals. We analyzed the transcriptomic variation associated with this autopolyploid series using a potato cDNA microarray containing ∼9000 genes. Statistically significant expression changes were observed among the ploidies for ∼10% of the genes in both leaflet and root tip tissues. However, most changes were associated with the monoploid and were within the twofold level. Thus, alteration of ploidy caused subtle expression changes of a substantial percentage of genes in the potato genome. We demonstrated that there are few genes, if any, whose expression is linearly correlated with the ploidy and can be dramatically changed because of ploidy alteration.
Meta-analysis of Polyploid Cotton QTL Shows Unequal Contributions of Subgenomes to a Complex Network of Genes and Gene Clusters Implicated in Lint Fiber Development
Authors: Rong Junkang , Feltus F Alex , Waghmare Vijay N , Pierce Gary J , Chee Peng W , Draye Xavier , Saranga Yehoshua , Wright Robert J , Wilkins Thea A , May O Lloyd , Smith C Wayne , Gannaway John R , Wendel Jonathan F , Paterson Andrew H 
Published: June 2007

Abstract
QTL mapping experiments yield heterogeneous results due to the use of different genotypes, environments, and sampling variation. Compilation of QTL mapping results yields a more complete picture of the genetic control of a trait and reveals patterns in organization of trait variation. A total of 432 QTL mapped in one diploid and 10 tetraploid interspecific cotton populations were aligned using a reference map and depicted in a CMap resource. Early demonstrations that genes from the non-fiber-producing diploid ancestor contribute to tetraploid lint fiber genetics gain further support from multiple populations and environments and advanced-generation studies detecting QTL of small phenotypic effect. Both tetraploid subgenomes contribute QTL at largely non-homeologous locations, suggesting divergent selection acting on many corresponding genes before and/or after polyploid formation. QTL correspondence across studies was only modest, suggesting that additional QTL for the target traits remain to be discovered. Crosses between closely-related genotypes differing by single-gene mutants yield profoundly different QTL landscapes, suggesting that fiber variation involves a complex network of interacting genes. Members of the lint fiber development network appear clustered, with cluster members showing heterogeneous phenotypic effects. Meta-analysis linked to synteny-based and expression-based information provides clues about specific genes and families involved in QTL networks.
Quantitative Trait Locus Analysis of the Early Domestication of Sunflower
Authors: Wills David M , Burke John M 
Published: June 2007

Abstract
Genetic analyses of the domestication syndrome have revealed that domestication-related traits typically have a very similar genetic architecture across most crops, being conditioned by a small number of quantitative trait loci (QTL), each with a relatively large effect on the phenotype. To date, the domestication of sunflower (Helianthus annuus L.) stands as the only counterexample to this pattern. In previous work involving a cross between wild sunflower (also H. annuus) and a highly improved oilseed cultivar, we found that domestication-related traits in sunflower are controlled by numerous QTL, typically of small effect. To provide insight into the minimum genetic changes required to transform the weedy common sunflower into a useful crop plant, we mapped QTL underlying domestication-related traits in a cross between a wild sunflower and a primitive Native American landrace that has not been the target of modern breeding programs. Consistent with the results of the previous study, our data indicate that the domestication of sunflower was driven by selection on a large number of loci, most of which had small to moderate phenotypic effects. Unlike the results of the previous study, however, nearly all of the QTL identified herein had phenotypic effects in the expected direction, with the domesticated allele producing a more crop-like phenotype and the wild allele producing a more wild-like phenotype. Taken together, these results are consistent with the hypothesis that selection during the post-domestication era has resulted in the introduction of apparently maladaptive alleles into the modern sunflower gene pool.
Saccharomyces cerevisiae Sae2- and Tel1-Dependent Single-Strand DNA Formation at DNA Break Promotes Microhomology-Mediated End Joining
Authors: Lee Kihoon , Lee Sang Eun 
Published: June 2007

Abstract
Microhomology-mediated end joining (MMEJ) joins DNA ends via short stretches [5–20 nucleotides (nt)] of direct repeat sequences, yielding deletions of intervening sequences. Non-homologous end joining (NHEJ) and single-strand annealing (SSA) are other error prone processes that anneal single-stranded DNA (ssDNA) via a few bases (&lt;5 nt) or extensive direct repeat homologies (&gt;20 nt). Although the genetic components involved in MMEJ are largely unknown, those in NHEJ and SSA are characterized in some detail. Here, we surveyed the role of NHEJ or SSA factors in joining of double-strand breaks (DSBs) with no complementary DNA ends that rely primarily on MMEJ repair. We found that MMEJ requires the nuclease activity of Mre11/Rad50/Xrs2, 3′ flap removal by Rad1/Rad10, Nej1, and DNA synthesis by multiple polymerases including Pol4, Rad30, Rev3, and Pol32. The mismatch repair proteins, Rad52 group genes, and Rad27 are dispensable for MMEJ. Sae2 and Tel1 promote MMEJ but inhibit NHEJ, likely by regulating Mre11-dependent ssDNA accumulation at DNA break. Our data support the role of Sae2 and Tel1 in MMEJ and genome integrity.
Könyvismertetések
Authors: Fekete István , Gósy Mária , Ivády Rozália Eszter , Kardos Péter 
Published: June 2007

DianePecherés
RolfA. Zwaan(szerk.):
Grounding cognition: The role of perception and
action in memory, language, and thinking
(Fekete
István) 253
CsépeValéria:
Az olvasó agy
(Gósy Mária) 256 Kormos, Judit:
Speech production and second language acquisition
(Ivády Rozália Eszter) 260 MarosánGyörgy:
Hogyan készül a történelem?
(Kardos Péter) 263
The Drama of 2005 and the Future of German Politics
Authors: Langenbacher Eric 
Published: June 2007

I recall a conversation from a while back with a colleague. He wasdisdainful of German politics, stating that they are ponderous, lackluster,even boring. He prefers to follow Italian politics because ofthe intrigue, emotion, and, most of all, the drama. Although forcedto agree at the time that the contrast between the two countriescould not be greater, I was also immediately reminded of the old(apocryphal) Chinese curse, “may you live in interesting times.”
Änderung der Waldinventurmethode im Kanton Graubünden | Modification of the Forest Inventory Method in the Canton of Grisons, Switzerland
Authors: Gordon Riet , Bühler Ueli , Zinggeler Jürg 
Published: June 2007

The new planning concept in the canton of Grisons, consisting of regional development plans and local management plans, affects information needs and thus the previous inventory method. Information on forest condition and forest dynamics is needed both at the regional and at the management level. Where the management level is concerned, the information needed is gained by means of a detailed description of each stand.
To support the decision on the future inventory method at the regional level, a pilot inventory was conducted, using the method of the second National Forest Inventory (NFI 2).
The given cost framework enabled a survey in a sample grid of 500 × 500 m to be conducted. The software and the recording equipment of the NFI 2 were used. The variable list of the NFI 2, however, was reduced according to the needs of the canton. In order to reduce the costs, no tariff sample trees were assessed.
The field work for assessing one plot required 8.4 person hours or CHF. 680.–. These values are within the expected range. For the entire area, the costs amounted to CHF. 27.30 per hectare.
The standard error for the total forest area was between 6.0% (Schanfigg) and 6.8% (Val Mustair) and thus rather high. The standard error for the growing stock, the most important variable, was 7.0% and thus within the desired range. The pilot inventory also gave satisfactory results for the growing stock of the main tree species. Based on the sample grid of the NF11, the increase in growing stock could, already with the first regional inventory, be determined more reliably than by the use of the previous sampling design with temporary plots.
The pilot inventory also showed that, with the conditions prevailing in the canton of Grisons, an additional interpretation of aerial photographs is only useful if the variables assessed on the photographs enable a better stratification than the variable tree height class alone.
The experience and the results gained from the pilot inventory are positive. From now on, the canton of Grisons will conduct an inventory on permanent plots in a 500 × 500 m grid, and drop the surveys of temporary sampling plots.
Betriebsergebnisse 1992 bis 2000 der öffentlichen Forstbetriebe im Kanton Appenzell Ausserrhoden | Annual Financial Results 1992–2000 of Public Forest Enterprises in the Canton Appenzell Ausserrhoden
Authors: Burri Roland , Sommerhalder Robert 
Published: June 2007

For some years forest enterprises have had an instrument at their disposal to make costs transparent with the accounting model, BAR, developed at the ETH Zurich. After 1989 the Swiss Forestry Union introduced the BAR programme in many forest enterprises. It enables the directors to manage the enterprises on economical lines and enables them to justify costs to the public administration. A good accounting system helps management decisions. As a management and planning instrument,forestry accounting will become even more important in the future.
The public forestry administration in the canton of Appenzell Ausserrhoden have been using the BAR programme since 1992. Financial results for the years 1992 to 2000 are shown and commented on in the paper. Costs were considerably lower in the area of wood production. The cost for other charges, such as forest duties, advice to private forest owners,protection, charity etc., led to a considerable increase in overall costs.