bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two Zinc-Cluster Transcription Factors Control Induction of Alternative Oxidase in Neurospora crassa
Authors: Chae Michael S , Nargang Cheryl E , Cleary Ian A , Lin Colin C , Todd Andrea T , Nargang Frank E 
Published: December 2007

Abstract
The alternative oxidase transfers electrons from ubiquinol to molecular oxygen, providing a mechanism for bypassing the later steps of the standard cytochrome-mediated electron transport chain. The enzyme is found in an array of organisms and in many cases is known to be produced in response to perturbations of the standard chain. Alternative oxidase is encoded in the nucleus but functions in the inner mitochondrial membrane. This implies the existence of a retrograde regulation pathway for communicating from the mitochondrion to the nucleus to induce alternative oxidase expression. Previous studies on alternative oxidase in fungi and plants have shown that a number of genes are required for expression of the enzyme, but the identity of these genes has remained elusive. By gene rescue we have now shown that the aod-2 and aod-5 genes of Neurospora crassa encode transcription factors of the zinc-cluster family. Electrophoretic mobility shift assays show that the DNA-binding domains of the AOD2 and AOD5 proteins act in tandem to bind a sequence element in the alternative oxidase gene promoter that is required for expression. Both proteins contain potential PAS domains near their C terminus, which are found primarily in proteins involved in signal transduction.
Nucleotide Variation in Wild and Inbred Mice
Authors: Salcedo Tovah , Geraldes Armando , Nachman Michael W 
Published: December 2007

Abstract
The house mouse is a well-established model organism, particularly for studying the genetics of complex traits. However, most studies of mice use classical inbred strains, whose genomes derive from multiple species. Relatively little is known about the distribution of genetic variation among these species or how variation among strains relates to variation in the wild. We sequenced intronic regions of five X-linked loci in large samples of wild Mus domesticus and M. musculus, and we found low levels of nucleotide diversity in both species. We compared these data to published data from short portions of six X-linked and 18 autosomal loci in wild mice. We estimate that M. domesticus and M. musculus diverged &lt;500,000 years ago. Consistent with this recent divergence, some gene genealogies were reciprocally monophyletic between these species, while others were paraphyletic or polyphyletic. In general, the X chromosome was more differentiated than the autosomes. We resequenced classical inbred strains for all 29 loci and found that inbred strains contain only a small amount of the genetic variation seen in wild mice. Notably, the X chromosome contains proportionately less variation among inbred strains than do the autosomes. Moreover, variation among inbred strains derives from differences between species as well as from differences within species, and these proportions differ in different genomic regions. Wild mice thus provide a reservoir of additional genetic variation that may be useful for mapping studies. Together these results suggest that wild mice will be a valuable complement to laboratory strains for studying the genetics of complex traits.
Genomewide Spatial Correspondence Between Nonsynonymous Divergence and Neutral Polymorphism Reveals Extensive Adaptation in Drosophila
Authors: Macpherson J Michael , Sella Guy , Davis Jerel C , Petrov Dmitri A 
Published: December 2007

AbstractThe effect of recurrent selective sweeps is a spatially heterogeneous reduction in neutral polymorphism throughout the genome. The pattern of reduction depends on the selective advantage and recurrence rate of the sweeps. Because many adaptive substitutions responsible for these sweeps also contribute to nonsynonymous divergence, the spatial distribution of nonsynonymous divergence also reflects the distribution of adaptive substitutions. Thus, the spatial correspondence between neutral polymorphism and nonsynonymous divergence may be especially informative about the process of adaptation. Here we study this correspondence using genomewide polymorphism data from Drosophila simulans and the divergence between D. simulans and D. melanogaster. Focusing on highly recombining portions of the autosomes, at a spatial scale appropriate to the study of selective sweeps, we find that neutral polymorphism is both lower and, as measured by a new statistic QS, less homogeneous where nonsynonymous divergence is higher and that the spatial structure of this correlation is best explained by the action of strong recurrent selective sweeps. We introduce a method to infer, from the spatial correspondence between polymorphism and divergence, the rate and selective strength of adaptation. Our results independently confirm a high rate of adaptive substitution (∼1/3000 generations) and newly suggest that many adaptations are of surprisingly great selective effect (∼1%), reducing the effective population size by ∼15% even in highly recombining regions of the genome.
Large-Scale Survey of Cytosine Methylation of Retrotransposons and the Impact of Readout Transcription From Long Terminal Repeats on Expression of Adjacent Rice Genes
Authors: Kashkush Khalil , Khasdan Vadim 
Published: December 2007

Abstract
Transposable elements (TEs) represent ∼45% of the human genome and 50–90% of some grass genomes. While most elements contain inactivating mutations, others are reversibly inactivated (silenced) by epigenetic mechanisms, including cytosine methylation. Previous studies have shown that retrotransposons can influence the expression of adjacent host genes. In this study, the methylation patterns of TEs and their flanking sequences in different tissues were undertaken using a novel technique called transposon methylation display (TMD). TMD was successfully applied on a highly copied (∼1000 copies), newly amplified LTR retrotransposon family in rice called Dasheng. We determined that the methylation status of a subset of LTRs varies in leaves vs. roots. In addition, we determined that tissue-specific LTR methylation correlated with tissue-specific expression of the flanking rice gene. Genes showing tissue-specific expression were in opposite orientation relative to the LTR. Antisense transcripts were detected in the tissue where the sense transcripts from that gene were not detected. Comparative analysis of Dasheng LTR methylation in the two subspecies, japonica vs. indica revealed LTR-mediated differences in subspecies gene expression. Subspecies-specific expression was due either to polymorphic Dasheng insertion sites between the two subspecies or to subspecies-specific methylation of LTRs at the same locus accounted for observed differences in the expression of adjacent genes.
Joint Inference of the Distribution of Fitness Effects of Deleterious Mutations and Population Demography Based on Nucleotide Polymorphism Frequencies
Authors: Keightley Peter D , Eyre-Walker Adam 
Published: December 2007

Abstract
The distribution of fitness effects of new mutations (DFE) is important for addressing several questions in genetics, including the nature of quantitative variation and the evolutionary fate of small populations. Properties of the DFE can be inferred by comparing the distributions of the frequencies of segregating nucleotide polymorphisms at selected and neutral sites in a population sample, but demographic changes alter the spectrum of allele frequencies at both neutral and selected sites, so can bias estimates of the DFE if not accounted for. We have developed a maximum-likelihood approach, based on the expected allele-frequency distribution generated by transition matrix methods, to estimate parameters of the DFE while simultaneously estimating parameters of a demographic model that allows a population size change at some time in the past. We tested the method using simulations and found that it accurately recovers simulated parameter values, even if the simulated demography differs substantially from that assumed in our analysis. We use our method to estimate parameters of the DFE for amino acid-changing mutations in humans and Drosophila melanogaster. For a model of unconditionally deleterious mutations, with effects sampled from a gamma distribution, the mean estimate for the distribution shape parameter is ∼0.2 for human populations, which implies that the DFE is strongly leptokurtic. For Drosophila populations, we estimate that the shape parameter is ∼0.35. Differences in the shape of the distribution and the mean selection coefficient between humans and Drosophila result in significantly more strongly deleterious mutations in Drosophila than in humans, and, conversely, nearly neutral mutations are significantly less frequent.
Flowering Time Quantitative Trait Loci Analysis of Oilseed Brassica in Multiple Environments and Genomewide Alignment with Arabidopsis
Authors: Long Y , Shi J , Qiu D , Li R , Zhang C , Wang J , Hou J , Zhao J , Shi L , Park Beom-Seok , Choi S R , Lim Y P , Meng J 
Published: December 2007

Abstract
Most agronomical traits exhibit quantitative variation, which is controlled by multiple genes and are environmentally dependent. To study the genetic variation of flowering time in Brassica napus, a DH population and its derived reconstructed F2 population were planted in 11 field environments. The flowering time varied greatly with environments; 60% of the phenotypic variation was attributed to genetic effects. Five to 18 QTL at a statistically significant level (SL-QTL) were detected in each environment and, on average, two new SL-QTL were discovered with each added environment. Another type of QTL, micro-real QTL (MR-QTL), was detected repeatedly from at least 2 of the 11 environments; resulting in a total of 36 SL-QTL and 6 MR-QTL. Sixty-three interacting pairs of loci were found; 50% of them were involved in QTL. Hundreds of floral transition genes in Arabidopsis were aligned with the linkage map of B. napus by in silico mapping; 28% of them aligned with QTL regions and 9% were consistent with interacting loci. One locus, BnFLC10, in N10 and a QTL cluster in N16 were specific to spring- and winter-cropped environments respectively. The number of QTL, interacting loci, and aligned functional genes revealed a complex genetic network controlling flowering time in B. napus.
The Impact of Genetic Relationship Information on Genome-Assisted Breeding Values
Authors: Habier D , Fernando R L , Dekkers J C M 
Published: December 2007

Abstract
The success of genomic selection depends on the potential to predict genome-assisted breeding values (GEBVs) with high accuracy over several generations without additional phenotyping after estimating marker effects. Results from both simulations and practical applications have to be evaluated for this potential, which requires linkage disequilibrium (LD) between markers and QTL. This study shows that markers can capture genetic relationships among genotyped animals, thereby affecting accuracies of GEBVs. Strategies to validate the accuracy of GEBVs due to LD are given. Simulations were used to show that accuracies of GEBVs obtained by fixed regression–least squares (FR–LS), random regression–best linear unbiased prediction (RR–BLUP), and Bayes-B are nonzero even without LD. When LD was present, accuracies decrease rapidly in generations after estimation due to the decay of genetic relationships. However, there is a persistent accuracy due to LD, which can be estimated by modeling the decay of genetic relationships and the decay of LD. The impact of genetic relationships was greatest for RR–BLUP. The accuracy of GEBVs can result entirely from genetic relationships captured by markers, and to validate the potential of genomic selection, several generations have to be analyzed to estimate the accuracy due to LD. The method of choice was Bayes-B; FR–LS should be investigated further, whereas RR–BLUP cannot be recommended.
Gene-Based Sequence Diversity Analysis of Field Pea (Pisum)
Authors: Jing Runchun , Johnson Richard , Seres Andrea , Kiss Gyorgy , Ambrose Mike J , Knox Maggie R , Ellis T H Noel , Flavell Andrew J 
Published: December 2007

Abstract
Sequence diversity of 39 dispersed gene loci was analyzed in 48 diverse individuals representative of the genus Pisum. The different genes show large variation in diversity parameters, suggesting widely differing levels of selection and a high overall diversity level for the species. The data set yields a genetic diversity tree whose deep branches, involving wild samples, are preserved in a tree derived from a polymorphic retrotransposon insertions in an identical sample set. Thus, gene regions and intergenic “junk DNA” share a consistent picture for the genomic diversity of Pisum, despite low linkage disequilibrium in wild and landrace germplasm, which might be expected to allow independent evolution of these very different DNA classes. Additional lines of evidence indicate that recombination has shuffled gene haplotypes efficiently within Pisum, despite its high level of inbreeding and widespread geographic distribution. Trees derived from individual gene loci show marked differences from each other, and genetic distance values between sample pairs show high standard deviations. Sequence mosaic analysis of aligned sequences identifies nine loci showing evidence for intragenic recombination. Lastly, phylogenetic network analysis confirms the non-treelike structure of Pisum diversity and indicates the major germplasm classes involved. Overall, these data emphasize the artificiality of simple tree structures for representing genomic sequence variation within Pisum and emphasize the need for fine structure haplotype analysis to accurately define the genetic structure of the species.
Characterization of New Spt3 and TATA-Binding Protein Mutants of Saccharomyces cerevisiae: Spt3–TBP Allele-Specific Interactions and Bypass of Spt8
Authors: Laprade Lisa , Rose David , Winston Fred 
Published: December 2007

Abstract
The Spt-Ada-Gcn5-acetyltransferase (SAGA) complex of Saccharomyces cerevisiae is a multifunctional coactivator complex that has been shown to regulate transcription by distinct mechanisms. Previous results have shown that the Spt3 and Spt8 components of SAGA regulate initiation of transcription of particular genes by controlling the level of TATA-binding protein (TBP/Spt15) associated with the TATA box. While biochemical evidence exists for direct Spt8–TBP interactions, similar evidence for Spt3–TBP interactions has been lacking. To learn more about Spt3–TBP interactions in vivo, we have isolated a new class of spt3 mutations that cause a dominant-negative phenotype when overexpressed. These mutations all cluster within a conserved region of Spt3. The isolation of extragenic suppressors of one of these spt3 mutations has identified two new spt15 mutations that show allele-specific interactions with spt3 mutations with respect to transcription and the recruitment of TBP to particular promoters. In addition, these new spt15 mutations partially bypass an spt8 null mutation. Finally, we have examined the level of SAGA–TBP physical interaction in these mutants. While most spt3, spt8, and spt15 mutations do not alter SAGA–TBP interactions, one spt3 mutation, spt3-401, causes a greatly increased level of SAGA–TBP physical association. These results, taken together, suggest that a direct Spt3–TBP interaction is required for normal TBP levels at Spt3-dependent promoters in vivo.
Avalanche Safety Practices in Utah
Authors: Silverton Natalie A. , McIntosh Scott E. , Kim Han S. 
Published: December 2007

Objective Avalanche fatalities occur on a yearly basis in Utah. The purpose of this study was to assess avalanche safety practices of different backcountry users in Utah and to identify groups that can be targeted for avalanche safety education. Methods We surveyed 353 winter backcountry users to determine the percentage of participants in each group who were traveling with one or more partners; the percentage who were carrying avalanche transceivers, shovels, probes, or AvaLungs; and the percentage who had taken an avalanche safety course. A measure of minimum safe practice was defined as 1) traveling with a partner, 2) carrying an avalanche transceiver, and 3) carrying a shovel. Participants in this study were backcountry skiers, snowboarders, snowshoers, snowmobilers, and out-of-bounds resort skiers/snowboarders traveling in the Wasatch and Uinta Mountains of Utah during the winter of 2005–06. Results The percentage of backcountry recreationists traveling with one or more partners was not significantly different ( P = .0658) among backcountry skiers, snowboarders, snowshoers, snowmobilers, and out-of-bounds resort skiers/snowboarders. These groups did, however, differ in the percentage who carried avalanche transceivers ( P < .0001), shovels ( P < .0001), probes ( P < .0001), and AvaLungs ( P = .0020), as well as in the percentage who had taken an avalanche safety course ( P < .0001) and the percentage who were carrying out minimum safe practices ( P < .0001). Backcountry skiers showed the highest level of avalanche preparedness, with 98% carrying avalanche transceivers, 98% carrying shovels, 77% carrying probes, 86% having taken an avalanche safety course, and 88% carrying out minimum safe practices. Out of bounds snowboarders were the least prepared with 9% carrying avalanche transceivers, 9% carrying shovels, 7% carrying probes, 33% having taken an avalanche safety course, and 2% carrying out minimum safe practices. Conclusions There are significant differences in the avalanche safety practices of the various groups of backcountry travelers in Utah. Backcountry skiers and snowboarders were the most prepared, while snowmobilers, snowshoers, and out-of-bounds skiers/snowboarders were relatively less prepared.
New-Onset Anxiety Disorders at High Altitude
Authors: Fagenholz Peter J. , Murray Alice F. , Gutman Jonathan A. , Findley John K. , Harris N. Stuart 
Published: December 2007

Objective Studies on the neurologic effects of high-altitude travel have focused on psychometric and cognitive testing and the long-term effects of hypoxia on memory and cognition. Few authors have discussed overt clinical psychiatric illness during high-altitude travel, and those few have focused on patients with preexisting psychiatric diagnoses. We describe a series of patients with new-onset anxiety disorders at high altitude treated at the Himalayan Rescue Association (HRA) clinic in Pheriche, Nepal (4240 m) in the spring season of 2006. Methods We report on all 6 cases of anxiety-related illness diagnosed at the HRA Pheriche Clinic during the spring season, 2006. Three cases, representing the 3 discrete types of illness we encountered, are described in detail. Results Six of 76 foreign patients and none of the 224 Nepalis seen during the season had anxiety-related primary diagnoses. None of the 6 patients had a history of psychiatric disorders or anxiety-related problems at low altitude. Three of the 6 patients were seen after hours, and all 6 required multiple visits. We describe 3 types of anxiety-related disorders: limited-symptom panic attacks induced by nocturnal periodic breathing, excessive health-related anxiety, and excessive emotionality. Conclusions Anxiety-related illness requires significant use of medical resources by high-altitude travelers. Further research is needed to define the epidemiology of anxiety-related disorders at high altitude, to quantify the contributions of various etiologic factors, and to identify safe, effective treatments.
Differences in the Role of Job-Relevant Information in the Budget Participation-Performance Relationship among U.S. and Mexican Managers: A Question of Culture or Communication
Authors: Leach-López Maria A. , Stammerjohan William W. , McNair Frances M. 
Published: December 2007

This study extends the stream of participative budgeting literature and, specifically, the work of Frucot and Shearon (1991). This study employs an expanded version of the path model introduced to this literature by Kren (1992) to examine and compare the budget participation-performance relationship for U.S. and Mexican mid-level managers. The expanded path model allows the examination of both the direct effects of budget participation on performance and the indirect effects of budget participation on performance that run through job satisfaction and job-relevant information.
The primary findings of this study are that while there are strong associations between budget participation and performance for both U.S. managers working in the U.S. and Mexican managers working for U.S.-controlled maquiladoras in Mexico, the causal mechanisms connecting budget participation to performance are quite different between these two groups. The information-communication aspect of the budget participation-performance relationship is much stronger among our Mexican managers and strongest among our Mexican managers who may face the greatest psychic distance from their U.S. parent companies: those who are not bilingual, and/or those who are supervised by U.S. nationals.
Product Costing for Decision Making in Certain Variable-Proportion Technologies
Authors: Dhavale Dileep G. 
Published: December 2007

Most methods and techniques in management accounting assume that a production technology consumes inputs in a fixed proportion. This paper develops product-costing measures for pricing and decision-making purposes for homogeneous variable-proportion technologies using first-order conditions and Euler's theorem. The results developed in this paper show that relevant costs under these circumstances are conventional full costs adjusted by a factor that is a function of returns to scale of a variable-proportion technology.
In the development of the above results, it is shown that, for any technology, the price of a product is a linear function of its full cost only for a certain type of demand function. For all other demand functions, the relationship between the price and the full cost is nonlinear.
The fixed- and the variable-proportion technologies are compared using a Monte Carlo simulation to determine the relative magnitudes of errors in product costs and prices, and differences in profit resulting from inappropriate use of a fixed-proportion model in a variable-proportion technology environment. The simulation results indicate that the costs are about 3 percent higher for fixed-proportion technology over a range of returns to scale values. The pricing error, on the other hand, is significant and varies from 70 percent lower to 50 percent higher compared to the correct prices. Variance analyses of difference in profits under the two technologies indicate that the errors in costing and pricing under fixed-proportion technology result in significantly lower profits.