bluuebunny/crossref_metadata_2025_split huggingface dataset:
Approximating Identity-by-Descent Matrices Using Multiple Haplotype Configurations on Pedigrees
Authors: Gao Guimin , Hoeschele Ina 
Published: June 2005

Abstract
Identity-by-descent (IBD) matrix calculation is an important step in quantitative trait loci (QTL) analysis using variance component models. To calculate IBD matrices efficiently for large pedigrees with large numbers of loci, an approximation method based on the reconstruction of haplotype configurations for the pedigrees is proposed. The method uses a subset of haplotype configurations with high likelihoods identified by a haplotyping method. The new method is compared with a Markov chain Monte Carlo (MCMC) method (Loki) in terms of QTL mapping performance on simulated pedigrees. Both methods yield almost identical results for the estimation of QTL positions and variance parameters, while the new method is much more computationally efficient than the MCMC approach for large pedigrees and large numbers of loci. The proposed method is also compared with an exact method (Merlin) in small simulated pedigrees, where both methods produce nearly identical estimates of position-specific kinship coefficients. The new method can be used for fine mapping with joint linkage disequilibrium and linkage analysis, which improves the power and accuracy of QTL mapping.
Gene Arrays atPneumocystis cariniiTelomeres
Authors: Keely Scott P , Renauld Hubert , Wakefield Ann E , Cushion Melanie T , Smulian A George , Fosker Nigel , Fraser Audrey , Harris David , Murphy Lee , Price Claire , Quail Michael A , Seeger Kathy , Sharp Sarah , Tindal Carolyn J , Warren Tim , Zuiderwijk Eduard , Barrell Barclay G , Stringer James R , Hall Neil 
Published: June 2005

AbstractIn the fungus Pneumocystis carinii, at least three gene families (PRT1, MSR, and MSG) have the potential to generate high-frequency antigenic variation, which is likely to be a strategy by which this parasitic fungus is able to prolong its survival in the rat lung. Members of these gene families are clustered at chromosome termini, a location that fosters recombination, which has been implicated in selective expression of MSG genes. To gain insight into the architecture, evolution, and regulation of these gene clusters, six telomeric segments of the genome were sequenced. Each of the segments began with one or more unique genes, after which were members of different gene families, arranged in a head-to-tail array. The three-gene repeat PRT1-MSR-MSG was common, suggesting that duplications of these repeats have contributed to expansion of all three families. However, members of a gene family in an array were no more similar to one another than to members in other arrays, indicating rapid divergence after duplication. The intergenic spacers were more conserved than the genes and contained sequence motifs also present in subtelomeres, which in other species have been implicated in gene expression and recombination. Long mononucleotide tracts were present in some MSR genes. These unstable sequences can be expected to suffer frequent frameshift mutations, providing P. carinii with another mechanism to generate antigen variation.
Modeling Linkage Disequilibrium in Natural Populations: The Example of the Soay Sheep Population of St. Kilda, Scotland
Authors: McRae Allan F , Pemberton Josephine M , Visscher Peter M 
Published: June 2005

Abstract
The use of linkage disequilibrium to localize the genes underlying quantitative traits has received considerable attention in the livestock genetics community over the past few years. This has resulted in the investigation of linkage disequilibrium structures of several domestic livestock populations to assess their potential use in fine-mapping efforts. However, the linkage disequilibrium structure of free-living populations has been less well investigated. As the direct evaluation of linkage disequilibrium can be both time consuming and expensive the use of simulations that include as many aspects of population history as possible is advocated as an alternative. A simulation of the linkage disequilibrium structure of the Soay sheep population of St. Kilda, Scotland, is provided as an example. The simulated population showed significant decline of linkage disequilibrium with genetic distance and low levels of background linkage disequilibrium, indicating that the Soay sheep population is a viable resource for linkage disequilibrium fine mapping of quantitative trait loci.
The Drosophila Meiotic Mutant mei-352 Is an Allele of klp3A and Reveals a Role for a Kinesin-like Protein in Crossover Distribution
Authors: Page Scott L , Hawley R Scott 
Published: June 2005

Abstract
The semisterile meiotic mutant mei-352 alters the distribution of meiotic exchanges without greatly affecting their total frequency. We show that the mei-352 mutation is an allele of the klp3A gene, which encodes a kinesin-like protein of the Kinesin-4 family. The semisterility observed in mei-352 females results from a known defect of klp3A oocytes in mediating pronuclear fusion. Interestingly, other klp3A alleles also exhibit defects in meiotic recombination similar to those of mei-352. Finally, we show that the Klp3A protein localizes within the oocyte nucleus during meiotic prophase, the time at which exchange distribution is established, and extensively colocalizes with DNA. The parallel of the klp3A phenotype with a meiotic defect observed for kar3 mutants in yeast suggests a role for kinesins in early meiosis and might reflect a previously suggested role for this class of kinesins in chromosome condensation.
Positive Assortative Mating With Family Size as a Function of Predicted Parental Breeding Values
Authors: Lstibůrek M , Mullin T J , Mackay T F C , Huber D , Li B 
Published: June 2005

Abstract
While other investigations have described benefits of positive assortative mating (PAM) for forest tree breeding, the allocation of resources among mates in these studies was either equal or varied, using schemes corresponding only to parental rank (i.e., more resources invested in higher-ranking parents). In this simulation study, family sizes were proportional to predicted midparent BLUP values. The distribution of midparent BLUP values was standardized by a constant, which was varied to study the range of distributions of family size. Redistributing progenies from lower- to higher-ranking families to a point where an equal number of progenies were still selected out of each family to the next generation caused minimal change in group coancestry and inbreeding in the breeding population (BP), while the additive genetic response and variance in the BP were both greatly enhanced. This generated additional genetic gains for forest plantations by selecting more superior genotypes from the BP (compared to PAM with equal family sizes) for production of improved regeneration materials. These conclusions were verified for a range of heritability under a polygenic model and under a mixed-inheritance model with a QTL contributing to the trait variation.
A Novel Markov Chain Monte Carlo Approach for Constructing Accurate Meiotic Maps
Authors: George Andrew W 
Published: June 2005

AbstractMapping markers from linkage data continues to be a task performed in many genetic epidemiological studies. Data collected in a study may be used to refine published map estimates and a study may use markers that do not appear in any published map. Furthermore, inaccuracies in meiotic maps can seriously bias linkage findings. To make best use of the available marker information, multilocus linkage analyses are performed. However, two computational issues greatly limit the number of markers currently mapped jointly; the number of candidate marker orders increases exponentially with marker number and computing exact multilocus likelihoods on general pedigrees is computationally demanding. In this article, a new Markov chain Monte Carlo (MCMC) approach that solves both these computational problems is presented. The MCMC approach allows many markers to be mapped jointly, using data observed on general pedigrees with unobserved individuals. The performance of the new mapping procedure is demonstrated through the analysis of simulated and real data. The MCMC procedure performs extremely well, even when there are millions of candidate orders, and gives results superior to those of CRI-MAP.
Haplotype Diversity in 11 Candidate Genes Across Four Populations
Authors: Beaty T H , Fallin M D , Hetmanski J B , McIntosh I , Chong S S , Ingersoll R , Sheng X , Chakraborty R , Scott A F 
Published: June 2005

Abstract
Analysis of haplotypes based on multiple single-nucleotide polymorphisms (SNP) is becoming common for both candidate gene and fine-mapping studies. Before embarking on studies of haplotypes from genetically distinct populations, however, it is important to consider variation both in linkage disequilibrium (LD) and in haplotype frequencies within and across populations, as both vary. Such diversity will influence the choice of “tagging” SNPs for candidate gene or whole-genome association studies because some markers will not be polymorphic in all samples and some haplotypes will be poorly represented or completely absent. Here we analyze 11 genes, originally chosen as candidate genes for oral clefts, where multiple markers were genotyped on individuals from four populations. Estimated haplotype frequencies, measures of pairwise LD, and genetic diversity were computed for 135 European-Americans, 57 Chinese-Singaporeans, 45 Malay-Singaporeans, and 46 Indian-Singaporeans. Patterns of pairwise LD were compared across these four populations and haplotype frequencies were used to assess genetic variation. Although these populations are fairly similar in allele frequencies and overall patterns of LD, both haplotype frequencies and genetic diversity varied significantly across populations. Such haplotype diversity has implications for designing studies of association involving samples from genetically distinct populations.
Molecular Genetic Analysis of the Nested Drosophila melanogaster Lamin C Gene
Authors: Schulze Sandra R , Curio-Penny Beatrice , Li Yuhong , Imani Reza A , Rydberg Lena , Geyer Pamela K , Wallrath Lori L 
Published: June 2005

Abstract
Lamins are intermediate filaments that line the inner surface of the nuclear envelope, providing structural support and making contacts with chromatin. There are two types of lamins, A- and B-types, which differ in structure and expression. Drosophila possesses both lamin types, encoded by the LamC (A-type) and lamin Dm0 (B-type) genes. LamC is nested within an intron of the essential gene ttv. We demonstrate that null mutations in LamC are lethal, and expression of a wild-type LamC transgene rescues lethality of LamC but not ttv mutants. Mutations in the human A-type lamin gene lead to diseases called laminopathies. To determine if Drosophila might serve as a useful model to study lamin biology and disease mechanisms, we generated transgenic flies expressing mutant LamC proteins modeled after human disease-causing lamins. These transgenic animals display a nuclear lamin aggregation phenotype remarkably similar to that observed when human mutant A-type lamins are expressed in mammalian cells. LamC aggregates also cause disorganization of lamin Dm0, indicating interdependence of both lamin types for proper lamina assembly. Taken together, these data provide the first detailed genetic analysis of the LamC gene and support using Drosophila as a model to study the role of lamins in disease.
qUVR-10, a Major Quantitative Trait Locus for Ultraviolet-B Resistance in Rice, Encodes Cyclobutane Pyrimidine Dimer Photolyase
Authors: Ueda Tadamasa , Sato Tadashi , Hidema Jun , Hirouchi Tokuhisa , Yamamoto Kazuo , Kumagai Tadashi , Yano Masahiro 
Published: June 2005

AbstractRice qUVR-10, a quantitative trait locus (QTL) for ultraviolet-B (UVB) resistance on chromosome 10, was cloned by map-based strategy. It was detected in backcross inbred lines (BILs) derived from a cross between the japonica variety Nipponbare (UV resistant) and the indica variety Kasalath (UV sensitive). Plants homozygous for the Nipponbare allele at the qUVR-10 locus were more resistant to UVB compared with the Kasalath allele. High-resolution mapping using 1850 F2 plants enabled us to delimit qUVR-10 to a &lt;27-kb genomic region. We identified a gene encoding the cyclobutane pyrimidine dimer (CPD) photolyase in this region. Activity of CPD photorepair in Nipponbare was higher than that of Kasalath and nearly isogenic with qUVR-10 [NIL(qUVR-10)], suggesting that the CPD photolyase of Kasalath was defective. We introduced a genomic fragment containing the CPD photolyase gene of Nipponbare to NIL(qUVR-10). Transgenic plants showed the same level of resistance as Nipponbare did, indicating that the qUVR-10 encoded the CPD photolyase. Comparison of the qUVR-10 sequence in the Nipponbare and Kasalath alleles revealed one probable candidate for the functional nucleotide polymorphism. It was indicated that single-base substitution in the CPD photolyase gene caused the alteration of activity of CPD photorepair and UVB resistance. Furthermore, we were able to develop a UV-hyperresistant plant by overexpression of the photolyase gene.
Interaction Between Genetic Background and the Mating-Type Locus in Cryptococcus neoformans Virulence Potential
Authors: Nielsen Kirsten , Marra Robert E , Hagen Ferry , Boekhout Teun , Mitchell Thomas G , Cox Gary M , Heitman Joseph 
Published: June 2005

Abstract
The study of quantitative traits provides a window on the interactions between multiple unlinked genetic loci. The interaction between hosts and pathogenic microbes, such as fungi, involves aspects of quantitative genetics for both partners in this dynamic equilibrium. One important pathogenic fungus is Cryptococcus neoformans, a basidiomycete yeast that can infect the human brain and whose mating system has two mating type alleles, a and α. The α mating-type allele has previously been linked to increased virulence potential. Here congenic C. neoformans strains were generated in the two well-characterized genetic backgrounds B3501α and NIH433a to examine the potential influence of genes outside of the mating-type locus on the virulence potential of mating type. The congenic nature of these new strain pairs was established by karyotyping, amplified fragment length polymorphism genotyping, and whole-genome molecular allele mapping (congenicity mapping). Virulence studies revealed that virulence was equivalent between the B3501 a and α congenic strains but the α strain was more virulent than its a counterpart in the NIH433 genetic background. These results demonstrate that genomic regions outside the mating type locus contribute to differences in virulence between a and α cells. The congenic strains described here provide a foundation upon which to elucidate at genetic and molecular levels how mating-type and other unlinked loci interact to enable microbial pathogenesis.
Intermediate Mutation Frequencies Favor Evolution of Multidrug Resistance in Escherichia coli
Authors: Denamur Erick , Tenaillon Olivier , Deschamps Catherine , Skurnik David , Ronco Esthel , Gaillard Jean Louis , Picard Bertrand , Branger Catherine , Matic Ivan 
Published: June 2005

Abstract
In studying the interplay between mutation frequencies and antibiotic resistance among Escherichia coli natural isolates, we observed that modest modifications of mutation frequency may significantly influence the evolution of antibiotic resistance. The strains having intermediate mutation frequencies have significantly more antibiotic resistances than strains having low and high mutation frequencies.
Application of a method for the mathematical experimental statistical modeling approach to analyze physical–chemical properties of interpenetrating polymer network of polyurethane and unsaturated polyester
Authors: Król Piotr , Wojturska Joanna , Statyukha Gennadiy A. , Skladannyy Denis M. 
Published: June 2005

AbstractModern statistical analysis methods were employed to investigate and evaluate the effect of chemical composition on mechanical properties of interpenetrating polymer network (IPN) formulations that had been synthesized of polyurethane and unsaturated polyester resin (cross‐linked with styrene). Experiments run according to the mathematical plan made a basis for empirical models derived from the Sheffe polynomials. The models were utilized to optimize the chemical composition of IPN from the viewpoint of achievable mechanical parameters, to assess changes of those properties over the whole theoretically possible scope of quantitative compositions, and to investigate the effects of individual components and their possible interactions. The findings supported a thesis on complex interactions between polymeric components of IPN; they can be the reason for tangled polyurethane, unsaturated polyester, and linear polystyrene polymer networks, and ultimately they can be responsible for the formation of immiscible phases within the plastics produced. Data were also obtained which make it possible to evaluate potential mechanical properties of synthesized IPN compounds as coating materials and engineering plastics. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 97: 1855–1867, 2005
Novel high dielectric constant nanocomposites of polyaniline dispersed with γ‐Fe2O3 nanoparticles
Authors: Mallikarjuna N. N. , Manohar S. K. , Kulkarni P. V. , Venkataraman A. , Aminabhavi T. M. 
Published: June 2005

AbstractNovel nanocomposites of polyaniline dispersed with γ‐Fe2O3 nanoparticles were prepared by the in situ polymerization of aniline in the presence of ammonium peroxysulfate as an oxidizing agent. Dielectric constants of the derived composites varied with the composition of γ‐Fe2O3 present in the matrix. A maximum dielectric constant of ∼5500 was achieved when 10 mass % γ‐Fe2O3 nanoparticles were present. Nanocomposites were characterized by X‐ray diffraction, Fourier transform infrared, scanning electron microscopy, and thermal analytical techniques. Conductivity increased marginally by increasing the amount of γ‐Fe2O3 in the matrix. Dielectric constants increased 100–150 times compared to plain polyaniline matrix and were 20–40 times higher than that of γ‐Fe2O3 nanoparticles. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 97: 1868–1874, 2005
Effects of the properties of blowing agents on the processing and performance of extruded starch acetate
Authors: Zhou Jiahua , Hanna Milford A. 
Published: June 2005

AbstractThe extrusion of polysaccharide‐based polymers, such as starch acetate, is quite different from that of ordinary synthetic polymers. To understand how the physiochemical properties of blowing agents affect plasticization and expansion processes, starch acetate was extruded with water, ethanol, and ethyl acetate. The studied properties and factors were the evaporation rate, surface tension, boiling point, solubility index, latent heat of vaporization of blowing agents, extrusion temperature, and nucleating‐ and blowing‐agent concentrations. The properties of the blowing agents and operating conditions affected the solubility of the matrix polymer, the nucleation process, and cell growth, which affected the foam density and specific volume. A high temperature increased the cell density and specific volume when water and ethanol were used because a high temperature increased the solubility of starch acetate in water and ethanol and promoted nucleation. Ethyl acetate already had high solvency to starch acetate and a high evaporation rate. A high temperature reduced the melting strength, thereby reducing the cell density and specific volume. Water evaporation was greater, despite a high latent heat of evaporation (hr) and boiling point, than the average volumes of ethanol and ethyl acetate that evaporated. The blowing‐agent efficiency was a function of the solvency, blowing‐agent evaporation rate, and operating conditions. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 97: 1880–1890, 2005
CO2 foaming of poly(ethylene glycol)/polystyrene blends: Relationship of the blend morphology, CO2 mass transfer, and cellular structure
Authors: Taki Kentaro , Nitta Kouei , Kihara Shin‐Ichi , Ohshima Masahiro 
Published: June 2005

AbstractWhen polymer blends are foamed by physical foaming agents, such as CO2 or N2, not only the morphology and viscosity of the blend polymers but also the solubility and diffusivity of the physical foaming agents in the polymers determine the cellular structure: closed cell or open cell and monomodal or bimodal. The foam of poly(ethylene glycol) (PEG)/polystyrene (PS) blends shows a unique bimodal (large and small) cellular structure, in which the large‐size cells embrace a PEG particle. Depending on the foaming condition, the average size of the large cells ranges from 40 to 500 μm, whereas that of small cells becomes less than 20 μm, which is smaller than that of neat PS foams. The formation mechanism of the cellular structure has been investigated from the viewpoint of the morphology and viscosity of the blend polymer and the mass‐transfer rate of the physical foaming agent in each polymer phase. The solubility and diffusivity of CO2, which determine the mass‐transfer rate of CO2 from the matrix to the bubbles, were measured by a gravimetric measurement, that is, a magnetic suspension balance. The solubility and diffusivity of CO2 in PS differed from those in PEG: the diffusion coefficient of CO2 in PEG at 110°C was 3.36 × 10−9 m2/s, and that in PS was 2.38 × 10−10 m2/s. Henry's constant in PEG was 5600 cm3 (STP)/(kg MPa) at 110°C, and that in PS was 3100 cm3 (STP)/(kg MPa). These differences in the transport properties, morphology of the blend, and CO2‐induced viscosity depression are the control factors for creating the unique cellular structure in PEG/PS blends. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 97: 1899–1906, 2005
Preparation and characterization of pH‐ and temperature‐responsive semi–interpenetrating polymer network hydrogels based on linear sodium alginate and crosslinked poly(N‐isopropylacrylamide)
Authors: Zhang Gao Qi , Zha Liu Sheng , Zhou Mei Hua , Ma Jing Hong , Liang Bo Run 
Published: June 2005

AbstractIn this study, pH‐ and temperature‐responsive hydrogels based on linear sodium alginate (SA) and crosslinked poly(N‐isopropylacrylamide) (PNIPAAm) were prepared by semi‐interpenetrating network (semi‐IPN) technique. The dually responsive hydrogels were characterized by FTIR, DSC, and SEM, and their temperature‐ and pH‐responsive behaviors were investigated by measuring equilibrium swelling ratios and pulsatile swelling experiments. The results showed that these hydrogels underwent volume phase transition at around 33°C irrespective of the pH value of the medium, but their pH sensitivity was evident only below their volume phase transition temperature. Under basic conditions, the swelling ratios of SA/PNIPAAm semi‐IPN hydrogels were greater than that of pure PNIPAAm hydrogel and increased with increasing SA content incorporated into the hydrogels, but the case was inverse under acidic conditions. The pulsatile swelling experiments indicated that the higher the SA content in SA/PNIPAAm semi‐IPN hydrogels, the faster the response rate to both pH and temperature change. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 97: 1931–1940, 2005