bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anti-microfouling activities in extracts of two invasive algae:Grateloupia turuturuandSargassum muticum
Authors: Plouguerné Erwan , Hellio Claire , Deslandes Eric , Véron Benoît , Stiger-Pouvreau Valérie 
Published: June 2008

AbstractMarine macroalgae are particularly prone to epiphytism. The colonisation of their surface may lead to severe perturbations and sometimes to the death of the host. To protect themselves against settling and/or competing organisms, many algae have developed defences against fouling by producing a wide variety of chemically active metabolites. The goal of this study was to investigate potential anti-microfouling activities of two introduced algal species from the Brittany coast (France),Sargassum muticum(Phaeophyceae) andGrateloupia turuturu(Rhodophyceae). Thus, a complete study of the antimicrobial activities of extracts (aqueous, acetone, chloroform, dichloromethane, diethyl-ether, ethyl acetate, ethanol 96°, hexane and methanol) fromS. muticumandG. turuturuagainst marine fouling bacteria (5 strains), fungi (5 strains) and biofilm-associated microphytobenthic strains (5) were performed. The most active extract ofG. turuturuwas the dichloromethane fraction, while the chloroform extract fromS. muticumshowed some good results. Our data suggest that these macroalgae can provide useful compounds or templates for industrial anti-microfouling applications.
Testing for Neutrality in Samples With Sequencing Errors
Authors: Achaz Guillaume 
Published: June 2008

AbstractMany data sets one could use for population genetics contain artifactual sites, i.e., sequencing errors. Here, we first explore the impact of such errors on several common summary statistics, assuming that sequencing errors are mostly singletons. We thus show that in the presence of those errors, estimators of θ can be strongly biased. We further show that even with a moderate number of sequencing errors, neutrality tests based on the frequency spectrum reject neutrality. This implies that analyses of data sets with such errors will systematically lead to wrong inferences of evolutionary scenarios. To avoid to these errors, we propose two new estimators of θ that ignore singletons as well as two new tests Y and Y* that can be used to test neutrality despite sequencing errors. All in all, we show that even though singletons are ignored, these new tests show some power to detect deviations from a standard neutral model. We therefore advise the use of these new tests to strengthen conclusions in suspicious data sets.
Functional Characterization of the dRYBP Gene in Drosophila
Authors: González Inma , Aparicio Ricardo , Busturia Ana 
Published: June 2008

Abstract
The Drosophila dRYBP gene has been described to function as a Polycomb-dependent transcriptional repressor. To determine the in vivo function of the dRYBP gene, we have generated mutations and analyzed the associated phenotypes. Homozygous null mutants die progressively throughout development and present phenotypes variable both in their penetrance and in their expressivity, including disrupted oogenesis, a disorganized pattern of the syncytial nuclear divisions, defects in pattern formation, and decreased wing size. Although dRYBP mutations do not show the homeotic-like phenotypes typical of mutations in the PcG and trxG genes, they enhance the phenotypes of mutations of either the Sex comb extra gene (PcG) or the trithorax gene (trxG). Finally, the dRYBP protein interacts physically with the Sex comb extra and the Pleiohomeotic proteins, and the homeotic-like phenotypes produced by the high levels of the dRYBP protein are mediated through its C-terminal domain. Our results indicate that the dRYBP gene functions in the control of cell identity together with the PcG/trxG proteins. Furthermore, they also indicate that dRYBP participates in the control of cell proliferation and cell differentiation and we propose that its functional requirement may well depend on the robustness of the animal.
Comparative Genetics of Hybrid Incompatibility: Sterility in Two Solanum Species Crosses
Authors: Moyle Leonie C , Nakazato Takuya 
Published: June 2008

AbstractThe genetic basis of hybrid sterility can provide insight into the genetic and evolutionary origins of species barriers. We examine the genetics of hybrid incompatibility between two diploid plant species in the plant clade Solanum sect. Lycopersicon. Using a set of near-isogenic lines (NILs) representing the wild species Solanum pennellii (formerly Lycopersicon pennellii) in the genetic background of the cultivated tomato S. lycopersicum (formerly L. esculentum), we found that hybrid pollen and seed infertility are each based on a modest number of loci, male (pollen) and other (seed) incompatibility factors are roughly comparable in number, and seed-infertility QTL act additively or recessively. These findings are remarkably consistent with our previous analysis in a different species pair, S. lycopersicum × S. habrochaites. Data from both studies contrast strongly with data from Drosophila. Finally, QTL for pollen and seed sterility from the two Solanum studies were chromosomally colocalized, indicating a shared evolutionary history for these QTL, a nonrandom genomic distribution of loci causing sterility, and/or a proclivity of certain genes to be involved in hybrid sterility. We show that comparative mapping data can delimit the probable timing of evolution of detected QTL and discern which sterility loci likely evolved earliest among species.
The Temporal Dynamics of Processes Underlying Y Chromosome Degeneration
Authors: Bachtrog Doris 
Published: June 2008

Abstract
Y chromosomes originate from ordinary autosomes and degenerate by accumulating deleterious mutations. This accumulation results from a lack of recombination on the Y and is driven by interference among deleterious mutations (Muller's ratchet and background selection) and the fixation of beneficial alleles (genetic hitchhiking). Here I show that the relative importance of these processes is expected to vary over the course of Y chromosome evolution due to changes in the number of active genes. The dominant mode of degeneration on a newly formed gene-rich Y chromosome is expected to be Muller's ratchet and/or background selection due to the large numbers of deleterious mutations arising in active genes. However, the relative importance of these modes of degeneration declines rapidly as active genes are lost. In contrast, the rate of degeneration due to hitchhiking is predicted to be highest on Y chromosomes containing an intermediate number of active genes. The temporal dynamics of these processes imply that a gradual restriction of recombination, as inferred in mammals, will increase the importance of genetic hitchhiking relative to Muller's ratchet and background selection.
Quantitative Trait Locus-by-Environment Interaction for Milk Yield Traits on Bos taurus Autosome 6
Authors: Lillehammer Marie , Goddard Mike E , Nilsen Heidi , Sehested Erling , Olsen Hanne Gro , Lien Sigbjørn , Meuwissen Theo H E 
Published: June 2008

Abstract
Genotype-by-environment interactions for production traits in dairy cattle have often been observed, while QTL analyses have focused on detecting genes with general effects on production traits. In this study, a QTL search for genes with environmental interaction for the traits milk yield, protein yield, and fat yield were performed on Bos taurus autosome 6 (BTA6), also including information about the previously investigated candidate genes ABCG2 and OPN. The animals in the study were Norwegian Red. Eighteen grandsires and 716 sires were genotyped for 362 markers on BTA6. Every marker bracket was regarded as a putative QTL position. The effects of the candidate genes and the putative QTL were modeled as a regression on an environmental parameter (herd year), which is based on the predicted herd-year effect for the trait. Two QTL were found to have environmentally dependent effects on milk yield. These QTL were located 3.6 cM upstream and 9.1 cM downstream from ABCG2. No environmentally dependent QTL was found to significantly affect protein or fat yield.
The Direction of Linkage Disequilibrium: A New Measure Based on the Ancestral-Derived Status of Segregating Alleles
Authors: Takahasi K Ryo , Innan Hideki 
Published: June 2008

Abstract
A new measure of directional linkage disequilibrium is developed for detecting epistatic selection on interacting genes. Simulations show that by orienting the direction of linkage disequilibrium on the basis of the ancestral-derived status of alleles, the new measure indeed improves the power to detect a positive fitness interaction between two new mutations.
The Molecular Basis for Relative Physiological Functionality of the ADP/ATP Carrier Isoforms in Saccharomyces cerevisiae
Authors: Smith Christopher P , Thorsness Peter E 
Published: June 2008

Abstract
AAC2 is one of three paralogs encoding mitochondrial ADP/ATP carriers in the yeast Saccharomyces cerevisiae, and because it is required for respiratory growth it has been the most extensively studied. To comparatively examine the relative functionality of Aac1, Aac2, and Aac3 in vivo, the gene encoding each isoform was expressed from the native AAC2 locus in aac1Δ aac3Δ yeast. Compared to Aac2, Aac1 exhibited reduced capacity to support growth of yeast lacking mitochondrial DNA or of yeast lacking the ATP/Mg-Pi carrier, both conditions requiring ATP import into the mitochondrial matrix through the ADP/ATP carrier. Sixteen AAC1/AAC2 chimeric genes were constructed and analyzed to determine the key differences between residues or sections of Aac1 and Aac2. On the basis of the growth rate differences of yeast expressing different chimeras, the C1 and M2 loops of the ADP/ATP carriers contain divergent residues that are responsible for the difference(s) between Aac1 and Aac2. One chimeric gene construct supported growth on nonfermentable carbon sources but failed to support growth of yeast lacking mitochondrial DNA. We identified nine independent intragenic mutations in this chimeric gene that suppressed the growth phenotype of yeast lacking mitochondrial DNA, identifying regions of the carrier important for nucleotide exchange activities.
DNA Damage Differentially Activates Regional Chromosomal Loci for Tn7 Transposition in Escherichia coli
Authors: Shi Qiaojuan , Parks Adam R , Potter Benjamin D , Safir Ilan J , Luo Yun , Forster Brian M , Peters Joseph E 
Published: June 2008

Abstract
The bacterial transposon Tn7 recognizes replicating DNA as a target with a preference for the region where DNA replication terminates in the Escherichia coli chromosome. It was previously shown that DNA double-strand breaks in the chromosome stimulate Tn7 transposition where transposition events occur broadly around the point of the DNA break. We show that individual DNA breaks actually activate a series of small regional hotspots in the chromosome for Tn7 insertion. These hotspots are fixed and become active only when a DNA break occurs in the same region of the chromosome. We find that the distribution of insertions around the break is not explained by the exonuclease activity of RecBCD moving the position of the DNA break, and stimulation of Tn7 transposition is not dependent on RecBCD. We show that other forms of DNA damage, like exposure to UV light, mitomycin C, or phleomycin, also stimulate Tn7 transposition. However, inducing the SOS response does not stimulate transposition. Tn7 transposition is not dependent on any known specific pathway of replication fork reactivation as a means of recognizing DNA break repair. Our results are consistent with the idea that Tn7 recognizes DNA replication involved in DNA repair and reveals discrete regions of the chromosome that are differentially activated as transposition targets.
A Genetic Screen for Increased Loss of Heterozygosity inSaccharomyces cerevisiae
Authors: Andersen Marguerite P , Nelson Zara W , Hetrick Elizabeth D , Gottschling Daniel E 
Published: June 2008

AbstractLoss of heterozygosity (LOH) can be a driving force in the evolution of mitotic/somatic diploid cells, and cellular changes that increase the rate of LOH have been proposed to facilitate this process. In the yeast Saccharomyces cerevisiae, spontaneous LOH occurs by a number of mechanisms including chromosome loss and reciprocal and nonreciprocal recombination. We performed a screen in diploid yeast to identify mutants with increased rates of LOH using the collection of homozygous deletion alleles of nonessential genes. Increased LOH was quantified at three loci (MET15, SAM2, and MAT) on three different chromosomes, and the LOH events were analyzed as to whether they were reciprocal or nonreciprocal in nature. Nonreciprocal LOH was further characterized as chromosome loss or truncation, a local mutational event (gene conversion or point mutation), or break-induced replication (BIR). The 61 mutants identified could be divided into several groups, including ones that had locus-specific effects. Mutations in genes involved in DNA replication and chromatin assembly led to LOH predominantly via reciprocal recombination. In contrast, nonreciprocal LOH events with increased chromosome loss largely resulted from mutations in genes implicated in kinetochore function, sister chromatid cohesion, or relatively late steps of DNA recombination. Mutants of genes normally involved in early steps of DNA damage repair and signaling produced nonreciprocal LOH without an increased proportion of chromosome loss. Altogether, this study defines a genetic landscape for the basis of increased LOH and the processes by which it occurs.
Genetic Analysis of Heterosis for Yield and Yield Components in Rapeseed (Brassica napus L.) by Quantitative Trait Locus Mapping
Authors: Radoev Mladen , Becker Heiko C , Ecke Wolfgang 
Published: June 2008

Abstract
The main objective in this research was the genetic analysis of heterosis in rapeseed at the QTL level. A linkage map comprising 235 SSR and 144 AFLP markers covering 2045 cM was constructed in a doubled-haploid population from a cross between the cultivar “Express” and the resynthesized line “R53.” In field experiments at four locations in Germany 250 doubled-haploid (DH) lines and their corresponding testcrosses with Express were evaluated for grain yield and three yield components. The heterosis ranged from 30% for grain yield to 0.7% for kernel weight. QTL were mapped using three different data sets, allowing the estimation of additive and dominance effects as well as digenic epistatic interactions. In total, 33 QTL were detected, of which 10 showed significant dominance effects. For grain yield, mainly complete dominance or overdominance was observed, whereas the other traits showed mainly partial dominance. A large number of epistatic interactions were detected. It was concluded that epistasis together with all levels of dominance from partial to overdominance is responsible for the expression of heterosis in rapeseed.
Detection of Larval Remains after Consumption by Fishes
Authors: Schooley Jason D. , Karam Abraham P. , Kesner Brian R. , Marsh Paul C. , Pacey Carol A. , Thornbrugh Darren J. 
Published: June 2008

AbstractIn southwestern North America, consumption of native fish larvae by nonnative predators has imperiled native populations. Field‐acquired dietary analyses have provided little evidence of this cause‐effect relationship. In this study, small, nonnative green sunfish Lepomis cyanellus, bluegills L. macrochirus, red shiners Cyprinella lutrensis, fathead minnow Pimephales promelas, and yellow bullheads Ameiurus natalis were each fed a single larva of the native razorback sucker Xyrauchen texanus. Gut content analysis revealed that prey detection generally became increasingly difficult over a short postconsumption time period under laboratory conditions. For green sunfish, bluegills, and yellow bullheads, significant relationships between prey detection and time were revealed; the probability of prey identification was initially 50% or greater for about 30 min postconsumption, whereas few prey (3%) were identifiable at 60 min postconsumption. For red shiners and fathead minnow (pooled for analysis), no relationship was evident; these two species completely masticated their prey, thus hindering identification. Green sunfish and bluegills swallowed prey whole, and yellow bullheads damaged larvae during consumption. Many larvae were discovered in the foregut, and 25% were regurgitated during predator fixation. Use of gut content analysis as evidence of predation on native fish larvae by small, nonnative fish is problematic and unreliable due to rapid mechanical and chemical digestion of fragile larval tissues.
Effect of processing parameters on the cellular morphology and mechanical properties of thermoplastic polyolefin (TPO) microcellular foams
Authors: Wong Steven , Naguib Hani E. , Park Chul B. 
Published: June 2008

AbstractIn this study, the effects of processing parameters on the cellular morphologies and mechanical properties of thermoplastic polyolefin (TPO) microcellular foams are investigated. Microcellular closed cell TPO foams were prepared using a two‐stage batch process method. The microstructure of these foamed samples was controlled by carefully altering the processing parameters such as saturation pressure, foaming temperature, and foaming time. Foam morphologies were characterized in terms of the cell density, foam density, and average cell size. Elastic modulus, tensile strength, and elongation at break of the foamed TPO samples were measured for different cell morphologies. The findings show that the mechanical properties are significantly affected by the foaming parameters that varied with the cell morphologies. The experimental results can be used to predict the microstructure and mechanical properties of microcellular polymeric TPO foams prepared with different processing parameters. © 2008 Wiley Periodicals, Inc. Adv Polym Techn 26:232–246, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/adv.20104
Genomic investigation of α‐synuclein multiplication and parkinsonism
Authors: Ross Owen A. , Braithwaite Adam T. , Skipper Lisa M. , Kachergus Jennifer , Hulihan Mary M. , Middleton Frank A. , Nishioka Kenya , Fuchs Julia , Gasser Thomas , Maraganore Demetrius M. , Adler Charles H. , Larvor Lydie , Chartier‐Harlin Marie‐Christine , Nilsson Christer , Langston J. William , Gwinn Katrina , Hattori Nobutaka , Farrer Matthew J. 
Published: June 2008

AbstractObjectiveCopy number variation is a common polymorphic phenomenon within the human genome. Although the majority of these events are non‐deleterious they can also be highly pathogenic. Herein we characterize five families with parkinsonism that have been identified to harbor multiplication of the chromosomal 4q21 locus containing the α‐synuclein gene (SNCA).MethodsA methodological approach using fluorescent in situ hybridization and Affymetrix (Santa Clara, CA) 250K SNP microarrays was used to characterize the multiplication in each family and to identify the genes encoded within the region. The telomeric and centromeric breakpoints of each family were further narrowed using semiquantitative polymerase chain reaction with microsatellite markers and then screened for transposable repeat elements.ResultsThe severity of clinical presentation is correlated with SNCA dosage and does not appear to be overtly affected by the presence of other genes in the multiplicated region. With the exception of the Lister kindred, in each family the multiplication event appears de novo. The type and position of Alu/LINE repeats are also different at each breakpoint. Microsatellite analysis demonstrates two genomic mechanisms are responsible for chromosome 4q21 multiplications, including both SNCA duplication and recombination.InterpretationSNCA dosage is responsible for parkinsonism, autonomic dysfunction, and dementia observed within each family. We hypothesize dysregulated expression of wild‐type α‐synuclein results in parkinsonism and may explain the recent association of common SNCA variants in sporadic Parkinson's disease. SNCA genomic duplication results from intraallelic (segmental duplication) or interallelic recombination with unequal crossing over, whereas both mechanisms appear to be required for genomic SNCA triplication. Ann Neurol 2008
Different features of histopathological subtypes of pediatric focal cortical dysplasia
Authors: Krsek Pavel , Maton Bruno , Korman Brandon , Pacheco‐Jacome Esperanza , Jayakar Prasanna , Dunoyer Catalina , Rey Gustavo , Morrison Glenn , Ragheb John , Vinters Harry V. , Resnick Trevor , Duchowny Michael 
Published: June 2008

AbstractObjectiveFocal cortical dysplasia (FCD) is the most frequent pathological finding in pediatric epilepsy surgery patients. Several histopathological types of FCD are distinguished. The aim of the study was to define distinctive features of FCD subtypes.MethodsWe retrospectively reviewed clinical, electroencephalographic, magnetic resonance imaging, neuropsychological, and surgical variables, and seizure outcome data in 200 children. Cortical malformations were histopathologically confirmed in all patients, including mild malformation of cortical development type II (mMCD) in 36, FCD type Ia in 55, FCD type Ib in 39, FCD type IIa in 35, and FCD type IIb in 35 subjects.ResultsPerinatal risk factors were more frequent in mMCD/FCD type I than FCD type II. Children with FCD type IIb had more localized ictal electroencephalographic patterns and magnetic resonance imaging changes. Increased cortical thickness, abnormal gyral/sulcal patterns, gray/white matter junction blurring, and gray matter signal abnormality in fluid‐attenuated inversion recovery and T2‐weighted sequences occurred more often in FCD type II, were infrequent in FCD type I, and rare in mMCD. Lobar hypoplasia/atrophy was common in FCD type I. Hippocampal sclerosis was most frequent in FCD type I. Neuropsychological testing demonstrated no significant differences between the groups. There was a trend toward better surgical outcomes in FCD type II compared with FCD type I patients.InterpretationDifferent histopathological types of mMCD/FCD have distinct clinical and imaging characteristics. The ability to predict the subtype before surgery could influence surgical planning. Invasive electroencephalographic study should be considered when mMCD/FCD type I is expected based on noninvasive tests. Ann Neurol 2008;63:758–769