bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variability of Gene Expression After Polyhaploidization in Wheat (Triticum aestivumL.)
Authors: Wang Jiali , Liu Dongcheng , Guo Xiaoli , Yang Wenlong , Wang XiuJie , Zhan Kehui , Zhang Aimin 
Published: December 2011

AbstractInterspecific hybridization has a much greater effect than chromosome doubling on gene expression; however, the associations between homeologous gene expression changes and polyhaploidization had rarely been addressed. In this study, cDNA–single strand conformation polymorphism analysis was applied to measure the expression of 30 homeologous transcripts in naturally occurring haploid (ABD, 2n = 21) and its polyploid maternal parent Yumai 21A (AABBDD, 2n = 42) in wheat. Only one gene (TC251989) showed preferentially silenced homoeoalleles in haploids. Further analyses of 24 single-copy genes known to be silenced in the root and/or leaf also found no evidence of homeologous silencing in 1-month-old haploids and two ESTs (BF484100 and BF473379) exhibit different expression patterns between 4-month-old haploids and hexaploids. Global analysis of the gene expression patterns using the Affymetrix GeneChip showed that of the 55,052 genes probed, only about 0.11% in the shoots and 0.25% in the roots were activated by polyhaploidization. The results demonstrate that activation and silencing of homoeoalleles were not widespread in haploid seedlings.
High-Resolution Genotyping of Wild Barley Introgression Lines and Fine-Mapping of the Threshability Locus thresh-1 Using the Illumina GoldenGate Assay
Authors: Schmalenbach Inga , March Timothy J , Bringezu Thomas , Waugh Robbie , Pillen Klaus 
Published: December 2011

Abstract
Genetically well-characterized mapping populations are a key tool for rapid and precise localization of quantitative trait loci (QTL) and subsequent identification of the underlying genes. In this study, a set of 73 introgression lines (S42ILs) originating from a cross between the spring barley cultivar Scarlett (Hordeum vulgare ssp. vulgare) and the wild barley accession ISR42-8 (H. v. ssp. spontaneum) was subjected to high-resolution genotyping with an Illumina 1536-SNP array. The array enabled a precise localization of the wild barley introgressions in the elite barley background. Based on 636 informative SNPs, the S42IL set represents 87.3% of the wild barley genome, where each line contains on average 3.3% of the donor genome. Furthermore, segregating high-resolution mapping populations (S42IL-HRs) were developed for 70 S42ILs in order to facilitate QTL fine-mapping and cloning. As a case study, we used the developed genetic resources to rapidly identify and fine-map the novel locus thresh-1 on chromosome 1H that controls grain threshability. Here, the recessive wild barley allele confers a difficult to thresh phenotype, suggesting that thresh-1 played an important role during barley domestication. Using a S42IL-HR population, thresh-1 was fine-mapped within a 4.3cM interval that was predicted to contain candidate genes involved in regulation of plant cell wall composition. The set of wild barley introgression lines and derived high-resolution populations are ideal tools to speed up the process of mapping and further dissecting QTL, which ultimately clears the way for isolating the genes behind QTL effects.
Sequence Analysis of the Segmental Duplication Responsible for ParisSex-RatioDrive inDrosophila simulans
Authors: Fouvry Lucie , Ogereau David , Berger Anne , Gavory Frederick , Montchamp-Moreau Catherine 
Published: December 2011

AbstractSex-ratio distorters are X-linked selfish genetic elements that facilitate their own transmission by subverting Mendelian segregation at the expense of the Y chromosome. Naturally occurring cases of sex-linked distorters have been reported in a variety of organisms, including several species of Drosophila; they trigger genetic conflict over the sex ratio, which is an important evolutionary force. However, with a few exceptions, the causal loci are unknown. Here, we molecularly characterize the segmental duplication involved in the Paris sex-ratio system that is still evolving in natural populations of Drosophila simulans. This 37.5 kb tandem duplication spans six genes, from the second intron of the Trf2 gene (TATA box binding protein-related factor 2) to the first intron of the org-1 gene (optomotor-blind-related-gene-1). Sequence analysis showed that the duplication arose through the production of an exact copy on the template chromosome itself. We estimated this event to be less than 500 years old. We also detected specific signatures of the duplication mechanism; these support the Duplication-Dependent Strand Annealing model. The region at the junction between the two duplicated segments contains several copies of an active transposable element, Hosim1, alternating with 687 bp repeats that are noncoding but transcribed. The almost-complete sequence identity between copies made it impossible to complete the sequencing and assembly of this region. These results form the basis for the functional dissection of Paris sex-ratio drive and will be valuable for future studies designed to better understand the dynamics and the evolutionary significance of sex chromosome drive.
A Synthetic Human Kinase Can Control Cell Cycle Progression in Budding Yeast
Authors: Davey Megan J , Andrighetti Heather J , Ma Xiaoli , Brandl Christopher J 
Published: December 2011

Abstract
The DDK kinase complex, composed of Cdc7 and Dbf4, is required for S-phase progression. The two component proteins show different degrees of sequence conservation between human and yeast. Here, we determine that Saccharomyces cerevisiae bearing human CDC7 and DBF4 grows comparably to cells with yeast DDK under standard growth conditions. HsDrf1 (a second human Dbf4-like protein) does not support growth, suggesting that HsDbf4 is the true ortholog of ScDbf4. Both human subunits are required to complement yeast cdc7Δ or dbf4Δ due to the inability of human Cdc7 or Dbf4 to interact with the corresponding yeast protein. Flow cytometry indicates normal cell cycle progression for yeast containing human DDK. However, yeast containing human DDK is sensitive to long-term exposure to hydroxyurea and fails to sporulate, suggesting that human DDK substitutes for some, but not all, of yeast DDK’s functions. We mapped the region of Cdc7 required for species-specific function of DDK to the C-terminus of Cdc7 by substituting the yeast C-terminal 55 amino acid residues in place of the equivalent human residues. The resulting hybrid protein supported growth of a cdc7Δ strain only in the presence of ScDBF4. The strain supported by the hybrid CDC7 was not sensitive to HU and formed tetrads. Together, our data indicate that DDK’s targeting of its essential substrate is conserved between species, whereas the interactions within DDK are species specific.
High-Resolution SNP/CGH Microarrays Reveal the Accumulation of Loss of Heterozygosity in Commonly UsedCandida albicansStrains
Authors: Abbey Darren , Hickman Meleah , Gresham David , Berman Judith 
Published: December 2011

AbstractPhenotypic diversity can arise rapidly through loss of heterozygosity (LOH) or by the acquisition of copy number variations (CNV) spanning whole chromosomes or shorter contiguous chromosome segments. In Candida albicans, a heterozygous diploid yeast pathogen with no known meiotic cycle, homozygosis and aneuploidy alter clinical characteristics, including drug resistance. Here, we developed a high-resolution microarray that simultaneously detects ∼39,000 single nucleotide polymorphism (SNP) alleles and ∼20,000 copy number variation loci across the C. albicans genome. An important feature of the array analysis is a computational pipeline that determines SNP allele ratios based upon chromosome copy number. Using the array and analysis tools, we constructed a haplotype map (hapmap) of strain SC5314 to assign SNP alleles to specific homologs, and we used it to follow the acquisition of loss of heterozygosity (LOH) and copy number changes in a series of derived laboratory strains. This high-resolution SNP/CGH microarray and the associated hapmap facilitated the phasing of alleles in lab strains and revealed detrimental genome changes that arose frequently during molecular manipulations of laboratory strains. Furthermore, it provided a useful tool for rapid, high-resolution, and cost-effective characterization of changes in allele diversity as well as changes in chromosome copy number in new C. albicans isolates.
Physical Mapping in a Triplicated Genome: Mapping the Downy Mildew Resistance LocusPp523inBrassica oleraceaL.
Authors: Carlier Jorge D , Alabaça Claudia S , Sousa Nelson H , Coelho Paula S , Monteiro António A , Paterson Andrew H , Leitão José M 
Published: December 2011

AbstractWe describe the construction of a BAC contig and identification of a minimal tiling path that encompass the dominant and monogenically inherited downy mildew resistance locus Pp523 of Brassica oleracea L. The selection of BAC clones for construction of the physical map was carried out by screening gridded BAC libraries with DNA overgo probes derived from both genetically mapped DNA markers flanking the locus of interest and BAC-end sequences that align to Arabidopsis thaliana sequences within the previously identified syntenic region. The selected BAC clones consistently mapped to three different genomic regions of B. oleracea. Although 83 BAC clones were accurately mapped within a ∼4.6 cM region surrounding the downy mildew resistance locus Pp523, a subset of 33 BAC clones mapped to another region on chromosome C8 that was ∼60 cM away from the resistance gene, and a subset of 63 BAC clones mapped to chromosome C5. These results reflect the triplication of the Brassica genomes since their divergence from a common ancestor shared with A. thaliana, and they are consonant with recent analyses of the C genome of Brassica napus. The assembly of a minimal tiling path constituted by 13 (BoT01) BAC clones that span the Pp523 locus sets the stage for map-based cloning of this resistance gene.
A Geographically Diverse Collection ofSchizosaccharomyces pombeIsolates Shows Limited Phenotypic Variation but Extensive Karyotypic Diversity
Authors: Brown William R A , Liti Gianni , Rosa Carlos , James Steve , Roberts Ian , Robert Vincent , Jolly Neil , Tang Wen , Baumann Peter , Green Carter , Schlegel Kristina , Young Jonathan , Hirchaud Fabienne , Leek Spencer , Thomas Geraint , Blomberg Anders , Warringer Jonas 
Published: December 2011

AbstractThe fission yeast Schizosaccharomyces pombe has been widely used to study eukaryotic cell biology, but almost all of this work has used derivatives of a single strain. We have studied 81 independent natural isolates and 3 designated laboratory strains of Schizosaccharomyces pombe. Schizosaccharomyces pombe varies significantly in size but shows only limited variation in proliferation in different environments compared with Saccharomyces cerevisiae. Nucleotide diversity, π, at a near neutral site, the central core of the centromere of chromosome II is approximately 0.7%. Approximately 20% of the isolates showed karyotypic rearrangements as detected by pulsed field gel electrophoresis and filter hybridization analysis. One translocation, found in 6 different isolates, including the type strain, has a geographically widespread distribution and a unique haplotype and may be a marker of an incipient speciation event. All of the other translocations are unique. Exploitation of this karyotypic diversity may cast new light on both the biology of telomeres and centromeres and on isolating mechanisms in single-celled eukaryotes.
Genotype Imputation with Thousands of Genomes
Authors: Howie Bryan , Marchini Jonathan , Stephens Matthew 
Published: December 2011

AbstractGenotype imputation is a statistical technique that is often used to increase the power and resolution of genetic association studies. Imputation methods work by using haplotype patterns in a reference panel to predict unobserved genotypes in a study dataset, and a number of approaches have been proposed for choosing subsets of reference haplotypes that will maximize accuracy in a given study population. These panel selection strategies become harder to apply and interpret as sequencing efforts like the 1000 Genomes Project produce larger and more diverse reference sets, which led us to develop an alternative framework. Our approach is built around a new approximation that uses local sequence similarity to choose a custom reference panel for each study haplotype in each region of the genome. This approximation makes it computationally efficient to use all available reference haplotypes, which allows us to bypass the panel selection step and to improve accuracy at low-frequency variants by capturing unexpected allele sharing among populations. Using data from HapMap 3, we show that our framework produces accurate results in a wide range of human populations. We also use data from the Malaria Genetic Epidemiology Network (MalariaGEN) to provide recommendations for imputation-based studies in Africa. We demonstrate that our approximation improves efficiency in large, sequence-based reference panels, and we discuss general computational strategies for modern reference datasets. Genome-wide association studies will soon be able to harness the power of thousands of reference genomes, and our work provides a practical way for investigators to use this rich information. New methodology from this study is implemented in the IMPUTE2 software package.
Are Entry Threats Always Credible?
Authors: Dasgupta Utteeyo 
Published: December 2011

Abstract
This paper studies the efficacy of entry threats in a contestable environment using experiments. It is hypothesized here that the entrant firm’s home market profits influence the entrant’s competitive behavior even when entry is costless and completely reversible. In the experiment, entrants and incumbents tacitly collude when each has its own monopoly market. In contrast, an entrant from a competitive market practices hit-and-run entry whenever such opportunities exist, forcing the incumbent monopolist to price at average cost. The experiment results suggest that the usefulness of hit-and-run competitive threat in a contestable environment depends crucially on the relative profits in the entrant’s and the incumbent’s home and entry markets.
PCAOB Inspections and Large Accounting Firms
Authors: Church Bryan K. , Shefchik Lori B. 
Published: December 2011

SYNOPSIS
The purpose of this paper is to analyze the PCAOB's inspection reports of large, annually inspected accounting firms. The inspection reports identify audit deficiencies that have implications for audit quality. By examining the inspection reports in detail, we can identify the nature and severity of audit deficiencies; we can track the total number of deficiencies over time; and we can pinpoint common, recurring audit deficiencies. We focus on large accounting firms because they play a dominant role in the marketplace (i.e., they audit public companies that comprise approximately 99 percent of U.S.-based issuer market capitalization). We document a significant, downward linear trend in the number of deficiencies from 2004 to 2009. We also identify common, recurring audit deficiencies, determine the financial statement accounts most often impacted by audit deficiencies, and isolate the primary emphasis of the financial statement impacted. Our findings generally are consistent comparing Big 4 and second-tier accounting firms, though a few differences emerge. In addition, we make comparisons with findings that have been documented for small, triennially inspected firms.
Data Availability: The data are available from public sources.
Negative-Book-Value Firms and Their Valuation
Authors: Jan Ching-Lih , Ou Jane A. 
Published: December 2011

SYNOPSIS
We document a phenomenon that, along with the increasing trend of negative earnings, the frequency and the magnitude of negative book value of equity have also grown substantially over time. Although negative-book-value firms are commonly perceived as financially distressed, we find that the majority of these firms survive for a long time, and that many continue to report negative book value for several years. Over the most recent decade of our 30-year test period, 1976–2005, we find that based on per-dollar of assets, the market, on average, prices negative-book-value firms higher than positive-book-value firms. In addition, we discover that the correlation between market value and book value for negative-book-value firms is negative. Searching for explanations of these phenomena, we examine R&D expenditures of negative-book-value firms. Our results indicate that R&D, especially R&D accumulated over time, not only contributes to the increasing trend of negative-book-value incidences, but also plays an important role in the market's valuation of firms that concurrently report negative earnings and negative book value.
Data Availability: The authors will make their data available for use by others in extending or replicating results reported in this article.
Measuring Accounting Professionals' Attitudes Regarding Alternative Work Arrangements
Authors: Johnson Eric N. , Lowe D. Jordan , Reckers Philip M. J. 
Published: December 2011

ABSTRACT
Drawing on the work-life balance and organizational justice literatures, we developed a 20-item scale of individual attitudes and beliefs regarding alternative work arrangements (AWAs) in public accounting. We administered the scale to 412 highly experienced accounting professionals (primarily managers) from two Big 4 firms and two large national firms. Principal components analysis of scale responses yielded three identifiable dimensions regarding AWA attitudes and beliefs: (1) ideals and benefits of AWAs, (2) costs and inequities related to AWAs at the office level (organization-level or procedural justice issues), and (3) costs and inequities related to individuals' use of AWAs (person-level or distributive justice issues). Scale responses were significantly influenced by gender and AWA participation. In addition, the principal components were related in a predictable pattern to hypothetical performance evaluation judgments related to AWA use. Implications of these findings for the accounting profession and future research are discussed.
Data Availability: Data used in this study are available from the authors upon request.
In GAAP We Trust: Examining How Trust Influences Nonprofessional Investor Decisions Under Rules-Based and Principles-Based Standards
Authors: Bailey Wendy J. , Sawers Kimberly M. 
Published: December 2011

ABSTRACT
In this study, we investigate whether and how trust in our current, more rules-based financial reporting system and type of accounting standard affects nonprofessional investor decision making. In an experiment, 151 nonprofessional investors analyzed two companies that were economically identical except for a single underlying financial reporting difference that allowed one company to more positively report its financial results. By itself, the type of standard (rules-based, principles-based) did not affect investment choices or allocation decisions. However, when trust was considered, nonprofessional investors who are less trusting of our current financial reporting system chose to invest in a company with more positive financial results only when evaluating principles-based financial statements. Conversely, the type of standard did not affect investor decision making for nonprofessional investors who trust our current financial reporting system. These results have implications for standard setters as we move to a more principles-based accounting system.
Data Availability: Available on request.
Phylogenetic analyses using molecular markers reveal ecological lineages inMedetera(Diptera: Dolichopodidae)
Authors: Pollet Marc , Germann Christoph , Bernasconi Marco Valerio 
Published: December 2011

AbstractMedeteraFischer von Waldheim is the most speciose genus in the Medeterinae, with a nearly ubiquitous global distribution. Phylogenetic relationships withinMedeteraand betweenMedeteraand four other medeterine genera were investigated using mitochondrial (COI, 16S) and nuclear (18S) markers to test morphological hypotheses. Our results confirm most of Bickel's hypotheses.ThrypticusGerstäcker shows a sister-group relationship withMedetera+DolichophorusLichtwardt. TheMedeteraspecies included here split into two clades. One clade corresponds to theM. diademaL. –velesLoew species groupsensuBickel. The second clade is largely composed of theM. apicalis(Zetterstedt) species groupsensuBickel and theM. aberransWheeler species groupsensuBickel +Dolichophorus. Although most Medeterinae are associated with plants (mainly trees), species in at least two separate lineages demonstrate a secondary return to terrestrial habitats. The implication of this evolutionary phenomenon is briefly discussed.
Efferia okanagana, a new species of robber fly (Diptera: Asilidae) from the grasslands of southern British Columbia, Canada, with notes on taxonomy, biology, distribution, and conservation status
Authors: Cannings Robert A. 
Published: December 2011

AbstractEfferia okanagana sp. nov. is described from specimens collected in the grasslands of the southern Interior of British Columbia, Canada, mainly the Okanagan Valley. The male and female genitalia are described and illustrated. The existing key to species of Efferia Coquillett is modified to enable identification of male and female E. okanagana. The species belongs to the E. arida species group and perhaps is most closely related to E. arida (Williston) and E. pinali Wilcox. Efferia coulei Wilcox is the closest sympatric relative. Sequences of the cytochrome oxidase I gene (DNA barcode) for E. okanagana and E. coulei show distinct clusters for each species that are approximately 7.0% divergent (uncorrected p distance). Efferia okanagana has an early flight period (May and June) and lives in low-elevation grasslands dominated by bluebunch wheatgrass (Pseudoroegneria spicata (Pursh) Á. Löve) (Poaceae), especially where the soil is gravelly. It is considered a potential species at risk by the Committee on the Status of Endangered Wildlife in Canada.
The genus Calamoncosis in the Nearctic region (Diptera: Chloropidae)
Authors: Taillefer Amélie Grégoire , Wheeler Terry A. 
Published: December 2011

AbstractThe Nearctic fauna of the genus Calamoncosis Enderlein is reviewed. Five species are present in eastern North America: C. carncrossi Nartshuk was recently described from New York; the Palearctic species C. aprica (Meigen) and C. glyceriae Nartshuk are newly recorded, and two new species, C. brooksi and C. munda, are described from eastern North America. A sixth species present in the Nearctic Region is represented by one female specimen and is not identifiable. Most Nearctic specimens were collected in peatlands or marshes in Quebec, but there are scattered records from other grass-dominated habitats in Ontario, Manitoba, New York, and Texas. A key to the described species of Calamoncosis in the Nearctic Region is given.