bluuebunny/crossref_metadata_2025_split huggingface dataset:
Positional Cloning of a Bombyx Wingless Locus flügellos (fl) Reveals a Crucial Role for fringe That Is Specific for Wing Morphogenesis
Authors: Sato Kaoru , Matsunaga Tomoko Matsuoka , Futahashi Ryo , Kojima Tetsuya , Mita Kazuei , Banno Yutaka , Fujiwara Haruhiko 
Published: May 2008

Abstract
Mutations at the flügellos (fl) locus in Bombyx mori produce wingless pupae and moths because of the repressed response of wing discs to ecdysteroid. Four recessive fl alleles occurred spontaneously and were mapped at 13.0 of the silkworm genetic linkage group 10. By positional cloning, we confirmed that the gene responsible for fl is fringe (fng) encoding Fng glycosyltransferase, which is involved in regulating the Notch signaling pathway. In four different fl alleles, we detected a large deletion of the fng gene in flk and nonsense mutations in fl, flo, and fln. In the wild-type (WT) silkworm, fng is expressed actively in the wing discs, brain, and reproductive organs from the fourth to final instars but barely in the other tissues tested. In situ hybridization showed that fng mRNA is expressed in the dorsal layer of the WT wing discs. The wingless (wg) mRNA, a downstream marker of Fng-mediated Notch signaling, is localized at the dorsoventral boundary in the WT wing discs but repressed markedly in the fl wing discs. Although null mutants of Drosophila fng result in postembryonic lethality, loss of fng function in Bombyx affects only wing morphogenesis, suggesting different essential roles for fng in tissue differentiation among insects.
Identification of Mutations in Caenorhabditis elegans That Cause Resistance to High Levels of Dietary Zinc and Analysis Using a Genomewide Map of Single Nucleotide Polymorphisms Scored by Pyrosequencing
Authors: Bruinsma Janelle J , Schneider Daniel L , Davis Diana E , Kornfeld Kerry 
Published: May 2008

Abstract
Zinc plays many critical roles in biological systems: zinc bound to proteins has structural and catalytic functions, and zinc is proposed to act as a signaling molecule. Because zinc deficiency and excess result in toxicity, animals have evolved sophisticated mechanisms for zinc metabolism and homeostasis. However, these mechanisms remain poorly defined. To identify genes involved in zinc metabolism, we conducted a forward genetic screen for chemically induced mutations that cause Caenorhabditis elegans to be resistant to high levels of dietary zinc. Nineteen mutations that confer significant resistance to supplemental dietary zinc were identified. To determine the map positions of these mutations, we developed a genomewide map of single nucleotide polymorphisms (SNPs) that can be scored by the high-throughput method of DNA pyrosequencing. This map was used to determine the approximate chromosomal position of each mutation, and the accuracy of this approach was verified by conducting three-factor mapping experiments with mutations that cause visible phenotypes. This is a generally applicable mapping approach that can be used to position a wide variety of C. elegans mutations. The mapping experiments demonstrate that the 19 mutations identify at least three genes that, when mutated, confer resistance to toxicity caused by supplemental dietary zinc. These genes are likely to be involved in zinc metabolism, and the analysis of these genes will provide insights into mechanisms of excess zinc toxicity.
An Approximate Bayesian Computation Approach to Overcome Biases That Arise When Using Amplified Fragment Length Polymorphism Markers to Study Population Structure
Authors: Foll Matthieu , Beaumont Mark A , Gaggiotti Oscar 
Published: May 2008

Abstract
There is great interest in using amplified fragment length polymorphism (AFLP) markers because they are inexpensive and easy to produce. It is, therefore, possible to generate a large number of markers that have a wide coverage of species genomes. Several statistical methods have been proposed to study the genetic structure using AFLPs but they assume Hardy–Weinberg equilibrium and do not estimate the inbreeding coefficient, FIS. A Bayesian method has been proposed by Holsinger and colleagues that relaxes these simplifying assumptions but we have identified two sources of bias that can influence estimates based on these markers: (i) the use of a uniform prior on ancestral allele frequencies and (ii) the ascertainment bias of AFLP markers. We present a new Bayesian method that avoids these biases by using an implementation based on the approximate Bayesian computation (ABC) algorithm. This new method estimates population-specific FIS and FST values and offers users the possibility of taking into account the criteria for selecting the markers that are used in the analyses. The software is available at our web site (http://www-leca.ujf-grenoble.fr/logiciels.htm). Finally, we provide advice on how to avoid the effects of ascertainment bias.
Delimiting the Frequency of Paternal Leakage of Mitochondrial DNA in Chinook Salmon
Authors: Wolff Jonci N , Gandre Sandra , Kalinin Aleksander , Gemmell Neil J 
Published: May 2008

Abstract
We analyzed embryos of a wild-return hatchery population of chinook salmon for the presence of paternal mtDNA. None of the 10,082 offspring examined revealed paternally transmitted DNA, delimiting the maximum frequency of paternal leakage in this system to 0.03% (power of 0.95) and 0.05% (power of 0.99).
High DNA Sequence Diversity in Pericentromeric Genes of the Plant Arabidopsis lyrata
Authors: Kawabe Akira , Forrest Alan , Wright Stephen I , Charlesworth Deborah 
Published: May 2008

Abstract
Differences in neutral diversity at different loci are predicted to arise due to differences in mutation rates and from the “hitchhiking” effects of natural selection. Consistent with hitchhiking models, Drosophila melanogaster chromosome regions with very low recombination have unusually low nucleotide diversity. We compared levels of diversity from five pericentromeric regions with regions of normal recombination in Arabidopsis lyrata, an outcrossing close relative of the highly selfing A. thaliana. In contrast with the accepted theoretical prediction, and the pattern in Drosophila, we found generally high diversity in pericentromeric genes, which is consistent with the observation in A. thaliana. Our data rule out balancing selection in the pericentromeric regions, suggesting that hitchhiking is more strongly reducing diversity in the chromosome arms than the pericentromere regions.
Bayesian LASSO for Quantitative Trait Loci Mapping
Authors: Yi Nengjun , Xu Shizhong 
Published: May 2008

AbstractThe mapping of quantitative trait loci (QTL) is to identify molecular markers or genomic loci that influence the variation of complex traits. The problem is complicated by the facts that QTL data usually contain a large number of markers across the entire genome and most of them have little or no effect on the phenotype. In this article, we propose several Bayesian hierarchical models for mapping multiple QTL that simultaneously fit and estimate all possible genetic effects associated with all markers. The proposed models use prior distributions for the genetic effects that are scale mixtures of normal distributions with mean zero and variances distributed to give each effect a high probability of being near zero. We consider two types of priors for the variances, exponential and scaled inverse-χ2 distributions, which result in a Bayesian version of the popular least absolute shrinkage and selection operator (LASSO) model and the well-known Student's t model, respectively. Unlike most applications where fixed values are preset for hyperparameters in the priors, we treat all hyperparameters as unknowns and estimate them along with other parameters. Markov chain Monte Carlo (MCMC) algorithms are developed to simulate the parameters from the posteriors. The methods are illustrated using well-known barley data.
Schizosaccharomyces pombe Histone Acetyltransferase Mst1 (KAT5) Is an Essential Protein Required for Damage Response and Chromosome Segregation
Authors: Gómez Eliana B , Nugent Rebecca L , Laria Sebastián , Forsburg Susan L 
Published: May 2008

Abstract
Schizosaccharomyces pombe Mst1 is a member of the MYST family of histone acetyltransferases and is the likely ortholog of Saccharomyces cerevisiae Esa1 and human Tip60 (KAT5). We have isolated a temperature-sensitive allele of this essential gene. mst1 cells show a pleiotropic phenotype at the restrictive temperature. They are sensitive to a variety of DNA-damaging agents and to the spindle poison thiabendazole. mst1 has an increased frequency of Rad22 repair foci, suggesting endogenous damage. Two-hybrid results show that Mst1 interacts with a number of proteins involved in chromosome integrity and centromere function, including the methyltransferase Skb1, the recombination mediator Rad22 (Sc Rad52), the chromatin assembly factor Hip1 (Sc Hir1), and the Msc1 protein related to a family of histone demethylases. mst1 mutant sensitivity to hydroxyurea suggests a defect in recovery following HU arrest. We conclude that Mst1 plays essential roles in maintenance of genome stability and recovery from DNA damage.
Recurrent Events of Positive Selection in Independent Drosophila Lineages at the Spermatogenesis Gene roughex
Authors: Llopart Ana , Comeron Josep M 
Published: May 2008

Abstract
Our understanding of the role of positive selection in the evolution of genes with male-biased expression can be hindered by two observations. First, male-biased genes tend to be overrepresented among lineage-specific genes. Second, novel genes are prone to experience bursts of adaptive evolution shortly after their formation. A thorough study of the forces acting on male-biased genes therefore would benefit from phylogenywide analyses that could distinguish evolutionary trends associated with gene formation and later events, while at the same time tackling the interesting question of whether adaptive evolution is indeed idiosyncratic. Here we investigate the roughex (rux) gene, a dose-dependent regulator of Drosophila spermatogenesis with a C-terminal domain responsible for nuclear localization that shows a distinct amino acid sequence in the melanogaster subgroup. We collected polymorphism and divergence data in eight populations of six Drosophila species, for a total of 99 rux sequences, to study rates and patterns of evolution at this male-biased gene. Our results from two phylogeny-based methods (PAML and HyPhy) as well as from population genetics analyses (McDonald–Kreitman-based tests) indicate that amino acid replacements have contributed disproportionately to divergence, consistent with adaptive evolution at the Rux protein. Analyses based on extant variation show also the signature of recent selective sweeps in several of the populations surveyed. Most important, we detect the significant and consistent signature of positive selection in several independent Drosophila lineages, which evidences recurrent and concurrent events of adaptive evolution after rux formation.
Phenotypic Plasticity and Genotype by Environment Interaction for Olfactory Behavior inDrosophila melanogaster
Authors: Sambandan Deepa , Carbone Mary Anna , Anholt Robert R H , Mackay Trudy F C 
Published: May 2008

AbstractGenotype by environment interactions (GEI) play a major part in shaping the genetic architecture of quantitative traits and are confounding factors in genetic studies, for example, in attempts to associate genetic variation with disease susceptibility. It is generally not known what proportion of phenotypic variation is due to GEI and how many and which genes contribute to GEI. Behaviors are complex traits that mediate interactions with the environment and, thus, are ideally suited for studies of GEI. Olfactory behavior in Drosophila melanogaster presents an opportunity to systematically dissect GEI, since large numbers of genetically identical individuals can be reared under defined environmental conditions and the olfactory system of Drosophila and its behavioral response to odorants have been well characterized. We assessed variation in olfactory behavior in a population of 41 wild-derived inbred lines and asked to what extent different larval-rearing environments would influence adult olfactory behavior and whether GEI is a minor or major contributing source of phenotypic variation. We found that ∼50% of phenotypic variation in adult olfactory behavior is attributable to GEI. In contrast, transcriptional analysis revealed that only 20 genes show GEI at the level of gene expression [false discovery rate (FDR) &lt; 0.05], some of which are associated with physiological responses to environmental chemicals. Quantitative complementation tests with piggyBac-tagged mutants for 2 of these genes (CG9664 and Transferrin 1) demonstrate that genes that show transcriptional GEI are candidate genes for olfactory behavior and that GEI at the level of gene expression is correlated with GEI at the level of phenotype.
A Fast and Reliable Computational Method for Estimating Population Genetic Parameters
Authors: Vasco Daniel A 
Published: May 2008

AbstractThe estimation of ancestral and current effective population sizes in expanding populations is a fundamental problem in population genetics. Recently it has become possible to scan entire genomes of several individuals within a population. These genomic data sets can be used to estimate basic population parameters such as the effective population size and population growth rate. Full-data-likelihood methods potentially offer a powerful statistical framework for inferring population genetic parameters. However, for large data sets, computationally intensive methods based upon full-likelihood estimates may encounter difficulties. First, the computational method may be prohibitively slow or difficult to implement for large data. Second, estimation bias may markedly affect the accuracy and reliability of parameter estimates, as suggested from past work on coalescent methods. To address these problems, a fast and computationally efficient least-squares method for estimating population parameters from genomic data is presented here. Instead of modeling genomic data using a full likelihood, this new approach uses an analogous function, in which the full data are replaced with a vector of summary statistics. Furthermore, these least-squares estimators may show significantly less estimation bias for growth rate and genetic diversity than a corresponding maximum-likelihood estimator for the same coalescent process. The least-squares statistics also scale up to genome-sized data sets with many nucleotides and loci. These results demonstrate that least-squares statistics will likely prove useful for nonlinear parameter estimation when the underlying population genomic processes have complex evolutionary dynamics involving interactions between mutation, selection, demography, and recombination.
When Parameters in Dynamic Models Become Phenotypes: A Case Study on Flesh Pigmentation in the Chinook Salmon (Oncorhynchus tshawytscha)
Authors: Rajasingh Hannah , Gjuvsland Arne B , Våge Dag Inge , Omholt Stig W 
Published: May 2008

Abstract
The Pacific chinook salmon occurs as both white- and red-fleshed populations, with the flesh color type (red or white) seemingly under strong genetic influence. Previously published data on crosses between red- and white-fleshed individuals cannot be reconciled with a simple Mendelian two-locus, two-allele model, pointing to either a more complex inheritance pattern or the existence of gene interactions. Here we show that a standard single-locus, three-allele model can fully explain these data. Moreover, by implementing the single-locus model at the parameter level of a previously developed mathematical model describing carotenoid dynamics in salmon, we show that variation at a single gene involved in the muscle uptake of carotenoids is able to explain the available data. This illustrates how such a combined approach can generate biological understanding that would not be possible in a classical population genetic explanatory structure. An additional asset of this approach is that by allowing parameters to become phenotypes obeying a given genetic model, biological interpretations of mechanisms involved at a resolution level far beyond what is built into the original dynamic model are made possible. These insights can in turn be exploited in experimental studies as well as in construction of more detailed models.
The T-Box Gene tbx-2, the Homeobox Gene egl-5 and the Asymmetric Cell Division Gene ham-1 Specify Neural Fate in the HSN/PHB Lineage
Authors: Singhvi Aakanksha , Frank C Andrew , Garriga Gian 
Published: May 2008

Abstract
Understanding how neurons adopt particular fates is a fundamental challenge in developmental neurobiology. To address this issue, we have been studying a Caenorhabditis elegans lineage that produces the HSN motor neuron and the PHB sensory neuron, sister cells produced by the HSN/PHB precursor. We have previously shown that the novel protein HAM-1 controls the asymmetric neuroblast division in this lineage. In this study we examine tbx-2 and egl-5, genes that act in concert with ham-1 to regulate HSN and PHB fate. In screens for mutants with abnormal HSN development, we identified the T-box protein TBX-2 as being important for both HSN and PHB differentiation. TBX-2, along with HAM-1, regulates the migrations of the HSNs and prevents the PHB neurons from adopting an apoptotic fate. The homeobox gene egl-5 has been shown to regulate the migration and later differentiation of the HSN. While mutations that disrupt its function show no obvious role for EGL-5 in PHB development, loss of egl-5 in a ham-1 mutant background leads to PHB differentiation defects. Expression of EGL-5 in the HSN/PHB precursor but not in the PHB neuron suggests that EGL-5 specifies precursor fate. These observations reveal a role for both EGL-5 and TBX-2 in neural fate specification in the HSN/PHB lineage.
Overdispersion of the Molecular Clock Varies Between Yeast, Drosophila and Mammals
Authors: Bedford Trevor , Wapinski Ilan , Hartl Daniel L 
Published: May 2008

Abstract
Although protein evolution can be approximated as a “molecular evolutionary clock,” it is well known that sequence change departs from a clock-like Poisson expectation. Through studying the deviations from a molecular clock, insight can be gained into the forces shaping evolution at the level of proteins. Generally, substitution patterns that show greater variance than the Poisson expectation are said to be “overdispersed.” Overdispersion of sequence change may result from temporal variation in the rate at which amino acid substitutions occur on a phylogeny. By comparing the genomes of four species of yeast, five species of Drosophila, and five species of mammals, we show that the extent of overdispersion shows a strong negative correlation with the effective population size of these organisms. Yeast proteins show very little overdispersion, while mammalian proteins show substantial overdispersion. Additionally, X-linked genes, which have reduced effective population size, have gene products that show increased overdispersion in both Drosophila and mammals. Our research suggests that mutational robustness is more pervasive in organisms with large population sizes and that robustness acts to stabilize the molecular evolutionary clock of sequence change.
Scaling Mitigation and Strategy for First Full Field Steam Injection X Field Oman: History Matching and Modelling
Authors: Nengkoda Ardian , John Walsh , Ahmed Dilshad , Busaidy Ali , Shuely Nasser , Sariry Sameer , Putra Pristiwanto 
Published: May 2008

Abstract
The X Field steam-injection project is the world's first full-field steam-injection project based on thermally assisted gas/oil gravity drainage (TAGOGD) in a fractured carbonate field. The project scope includes drilling some wells and installing facilities to treat water and generate around 18,000 tonnes per day of steam. Additional facilities will be built to process the incremental oil and gas produced at the field as well as disposing of excess produced water in deep reservoirs. The EOR recovery process being applied TAGOGD is based on injecting steam into the formation's fractures to heat the low-permeability oil-bearing rock. This feature of the project allows the number of wells, and hence development costs, to be kept to a minimum. In other hand, the flow assurance issue across the facilities will be challenging, and managing scaling issues and inhibition require a host of solutions especially on the economics of scale management. A history of scaling as a lesson learnt had been gathered during Pilot steam back to a couple years ago and current cold production experiences is captured. At the moment, the incompatibility of various water stream indicated scaling deposition are majority dominated by carbonate and less sulphate. The strategy of integrated mitigation for all possible scaling for the next facilities scenario whether from water treatment and oil production facilities have been implemented and assessed during engineering design, while the type of inhibitor have been identified base on dynamic tube blocking tests and the potential risk have been registered. In the end, win-win economics approach is modeled base on water and fluid composition, various pressure and temperature.
Innovative Use of Kaolinite in Downhole Scale Management: Squeeze Life Enhancement and Water Shutoff
Authors: Fleming Niall , Ramstad Kari , Mathisen Anne-Mette , Nelson Alex , Kidd Sam 
Published: May 2008

Abstract
Applied research has been undertaken to examine the potential of kaolinite combined with a kaolinite fixation agent to; Increase squeeze lifetime through alteration of near wellbore surface characteristics and mineralogy and,Provide water shut off control.
With respect to enhancing squeeze lifetime, it is documented that kaolinite increases the quantity of inhibitor adsorbed. Conversely, clean sandstone with low clay content commonly provides a poor substrate for adsorption. Furthermore, in reservoirs that experience near wellbore formation damage due to kaolinite mobilisation, it has been shown that use of a fixation agent as part of a squeeze treatment can increase squeeze lifetime. Using these facts, research has assessed the feasibility of injecting microcrystalline kaolinite (average particle size 2 μm) combined with the fixation agent and scale inhibitor as a means of mechanically altering near wellbore mineralogy and surface property characteristics within clean, high permeability sandstones. The testing has been designed to mimic the squeeze procedure used in the field for performing such a job and involves no additional steps to that used in a normal squeeze, i.e. Pre-Flush → Main Treatment → Over-Flush. The paper presents the results of coreflood experiments that have been undertaken to demonstrate "proof of concept" for the above along with examples of potential field applications.
A further concept, born from the initial idea, was the use of kaolinite and fixation agent for efficient, low cost, environmentally friendly water shutoff. There are several available products for water shutoff but the disadvantage of these is that they are not acceptable for use in Norway due to poor environmental characteristics. Hence, there was a need to fill this gap by developing water shutoff technology to meet country specific environmental legislation. The paper provides details of coreflood testing, where an excess of kaolinite has been used to form an internal and external filter cake that is attached to the wellbore face and within the near wellbore using the fixation agent.
The paper draws on data from StatoilHydro operated fields in order to highlight the potential of this innovative approach to downhole scale management and water control.