bluuebunny/crossref_metadata_2025_split huggingface dataset:
Testing for Archaic Hominin Admixture on the X Chromosome: Model Likelihoods for the Modern Human RRM2P4 Region From Summaries of Genealogical Topology Under the Structured Coalescent
Authors: Cox Murray P , Mendez Fernando L , Karafet Tatiana M , Pilkington Maya Metni , Kingan Sarah B , Destro-Bisol Giovanni , Strassmann Beverly I , Hammer Michael F 
Published: January 2008

Abstract
A 2.4-kb stretch within the RRM2P4 region of the X chromosome, previously sequenced in a sample of 41 globally distributed humans, displayed both an ancient time to the most recent common ancestor (e.g., a TMRCA of ∼2 million years) and a basal clade composed entirely of Asian sequences. This pattern was interpreted to reflect a history of introgressive hybridization from archaic hominins (most likely Asian Homo erectus) into the anatomically modern human genome. Here, we address this hypothesis by resequencing the 2.4-kb RRM2P4 region in 131 African and 122 non-African individuals and by extending the length of sequence in a window of 16.5 kb encompassing the RRM2P4 pseudogene in a subset of 90 individuals. We find that both the ancient TMRCA and the skew in non-African representation in one of the basal clades are essentially limited to the central 2.4-kb region. We define a new summary statistic called the minimum clade proportion (pmc), which quantifies the proportion of individuals from a specified geographic region in each of the two basal clades of a binary gene tree, and then employ coalescent simulations to assess the likelihood of the observed central RRM2P4 genealogy under two alternative views of human evolutionary history: recent African replacement (RAR) and archaic admixture (AA). A molecular-clock-based TMRCA estimate of 2.33 million years is a statistical outlier under the RAR model; however, the large variance associated with this estimate makes it difficult to distinguish the predictions of the human origins models tested here. The pmc summary statistic, which has improved power with larger samples of chromosomes, yields values that are significantly unlikely under the RAR model and fit expectations better under a range of archaic admixture scenarios.
The Fixation of Locally Beneficial Alleles in a Metapopulation
Authors: Vuilleumier Séverine , Yearsley Jon M , Perrin Nicolas 
Published: January 2008

Abstract
Extinction, recolonization, and local adaption are common in natural spatially structured populations. Understanding their effect upon genetic variation is important for systems such as genetically modified organism management or avoidance of drug resistance. Theoretical studies on the effect of extinction and recolonization upon genetic variance started appearing in the 1970s, but the role of local adaption still has no good theoretical basis. Here we develop a model of a haploid species in a metapopulation in which a locally adapted beneficial allele is introduced. We study the effect of different spatial patterns of local adaption, and different metapopulation dynamics, upon the fixation probability of the beneficial allele. Controlling for the average selection pressure, we find that a small area of positive selection can significantly increase the global probability of fixation. However, local adaption becomes less important as extinction rate increases. Deme extinction and recolonization have a spatial smoothing effect that effectively reduces spatial variation in fitness.
Identification of Novel Activation Mechanisms for FLO11 Regulation in Saccharomyces cerevisiae
Authors: Barrales Ramón R , Jimenez Juan , Ibeas José I 
Published: January 2008

Abstract
Adhesins play a central role in the cellular response of eukaryotic microorganisms to their host environment. In pathogens such as Candida spp. and other fungi, adhesins are responsible for adherence to mammalian tissues, and in Saccharomyces spp. yeasts also confer adherence to solid surfaces and to other yeast cells. The analysis of FLO11, the main adhesin identified in Saccharomyces cerevisiae, has revealed complex mechanisms, involving both genetic and epigenetic regulation, governing the expression of this critical gene. We designed a genomewide screen to identify new regulators of this pivotal adhesin in budding yeasts. We took advantage of a specific FLO11 allele that confers very high levels of FLO11 expression to wild “flor” strains of S. cerevisiae. We screened for mutants that abrogated the increased FLO11 expression of this allele using the loss of the characteristic fluffy-colony phenotype and a reporter plasmid containing GFP controlled by the same FLO11 promoter. Using this approach, we isolated several genes whose function was essential to maintain the expression of FLO11. In addition to previously characterized activators, we identified a number of novel FLO11 activators, which reveal the pH response pathway and chromatin-remodeling complexes as central elements involved in FLO11 activation.
Few Mendelian Genes Underlie the Quantitative Response of a Forest Tree, Eucalyptus globulus, to a Natural Fungal Epidemic
Authors: Freeman Jules S , Potts Brad M , Vaillancourt René E 
Published: January 2008

Abstract
Foliar fungal pathogens from the genus Mycosphaerella affect eucalypts in natural forests and plantations worldwide. QTL analysis was conducted to dissect the genetic control of resistance in Eucalyptus globulus to a natural infection by Mycosphaerella leaf disease, using a clonally replicated outbred F2 family (112 genotypes) planted in a field trial. Two major QTL, with high LOD support (20.2 and 10.9) and high genomewide significance, explained a large proportion (52%) of the phenotypic variance in the severity of damage by Mycosphaerella cryptica, which may be indicative of oligogenic control. Both QTL were validated in a second F2 family and one was validated in a third F2 family. The mean values of different genotype classes at both major QTL argue for Mendelian inheritance with resistance dominant over susceptibility. There were strong correlations between the levels of Mycosphaerella damage in related genetic material planted in three widely separated locations in Tasmania. These findings together provide evidence that the genes controlling resistance to Mycosphaerella damage are stable in different genetic backgrounds and across different environments.
Empirical Tests of the Reliability of Phylogenetic Trees Constructed With Microsatellite DNA
Authors: Takezaki Naoko , Nei Masatoshi 
Published: January 2008

Abstract
Microsatellite DNA loci or short tandem repeats (STRs) are abundant in eukaryotic genomes and are often used for constructing phylogenetic trees of closely related populations or species. These phylogenetic trees are usually constructed by using some genetic distance measure based on allele frequency data, and there are many distance measures that have been proposed for this purpose. In the past the efficiencies of these distance measures in constructing phylogenetic trees have been studied mathematically or by computer simulations. Recently, however, allele frequencies of 783 STR loci have been compiled from various human populations. We have therefore used these empirical data to investigate the relative efficiencies of different distance measures in constructing phylogenetic trees. The results showed that (1) the probability of obtaining the correct branching pattern of a tree (PC) is generally highest for DA distance; (2) FST*, standard genetic distance (DS), and $\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(F_{\mathrm{ST}}/(1{-}F_{\mathrm{ST}})\) \end{document}$ give similar PC-values, FST* being slightly better than the other two; and (3) (δμ)2 shows PC-values much lower than the other distance measures. To have reasonably high PC-values for trees similar to ours, at least 30 loci with a minimum of 15 individuals are required when DA distance is used.
A Bayesian Method for Simultaneously Detecting Mendelian and Imprinted Quantitative Trait Loci in Experimental Crosses of Outbred Species
Authors: Hayashi Takeshi , Awata Takashi 
Published: January 2008

Abstract
Genomic imprinting is interpreted as a phenomenon, in which some genes inherited from one parent are not completely expressed due to modification of the genome caused during gametogenesis. Subsequently, the expression level of an allele at the imprinted gene is changed dependent on the parental origin, which is referred to as the parent-of-origin effect. In livestock, some QTL for reproductive performance and meat productivity have been reported to be imprinted. So far, methods detecting imprinted QTL have been proposed on the basis of interval mapping, where only a single QTL was tested at a time. In this study, we developed a Bayesian method for simultaneously mapping multiple QTL, allowing the inference about expression modes of QTL in an outbred F2 family. The inference about whether a QTL is Mendelian or imprinted was made using Markov chain Monte Carlo estimation by comparing the goodness-of-fits between models, assuming the presence and the absence of parent-of-origin effect at a QTL. We showed by the analyses of simulated data sets that the Bayesian method can effectively detect both Mendelian QTL and imprinted QTL.
Population Genetics of Speciation in Two Closely Related Wild Tomatoes (Solanum Section Lycopersicon)
Authors: Städler Thomas , Arunyawat Uraiwan , Stephan Wolfgang 
Published: January 2008

Abstract
We present a multilocus sequencing study to assess patterns of polymorphism and divergence in the closely related wild tomato species, Solanum peruvianum and S. chilense (Solanum section Lycopersicon, Solanaceae). The data set comprises seven mapped nuclear loci (≈9.3 kb of analyzed sequence across loci) and four local population samples per species that cover much of the species' range (between 80 and 88 sequenced alleles across both species). We employ the analytical framework of divergence population genetics (DPG) in evaluating the utility of the “isolation” model of speciation to explain observed patterns of polymorphism and divergence. Whereas the isolation model is not rejected by goodness-of-fit criteria established via coalescent simulations, patterns of intragenic linkage disequilibrium provide evidence for postdivergence gene flow at two of the seven loci. These results suggest that speciation occurred under residual gene flow, implying that natural selection is one of the evolutionary forces driving the divergence of these tomato species. This inference is fully consistent with their recent divergence, conservatively estimated to be ≤0.55 million years. We discuss possible biases in the demographic parameter estimates due to the current restriction of DPG algorithms to panmictic species.
Dual Involvement of CbrAB and NtrBC in the Regulation of Histidine Utilization inPseudomonas fluorescensSBW25
Authors: Zhang Xue-Xian , Rainey Paul B 
Published: January 2008

AbstractPseudomonas fluorescens SBW25 is capable of growing on histidine as a sole source of carbon and/or nitrogen. Previous work showed that the two-component regulatory system CbrAB is required for expression of the histidine utilization (hut) locus when histidine is the sole source of carbon and nitrogen. Here, using mutational analysis and transcriptional assays, we demonstrate involvement of a second two-component system, NtrBC. When histidine is the sole carbon source, transcription of the hutU operon is initiated from a σ54-type promoter and requires CbrB (an enhancer binding protein for σ54-recruitment). However, when histidine is the sole nitrogen source, the hutU operon is transcribed from a σ70-type promoter and requires either CbrB or the nitrogen regulator, NtrC. No role was found for the SBW25 homolog of the nitrogen assimilation control protein (NAC). Biolog phenotypic microarray analysis of the ability of the three mutants (ΔcbrB, ΔntrC, and ΔcbrB ΔntrC) to utilize 190 carbon and 95 nitrogen substrates confirmed the central regulatory roles of CbrAB and NtrBC in cellular carbon and nitrogen catabolism: deletion of cbrB abolished growth on 20 carbon substrates; deletion of ntrC eliminated growth on 28 nitrogen substrates. A double cbrB–ntrC mutant was unable to utilize a further 14 nitrogen substrates (including histidine, proline, leucine, isoleucine, and valine). Our data show that CbrAB plays a role in regulation of both carbon and nitrogen catabolism and maintains activity of catabolic pathways under different C:N ratios.
Chromatin-Associated Genes Protect the Yeast Genome From Ty1 Insertional Mutagenesis
Authors: Nyswaner Katherine M , Checkley Mary Ann , Yi Ming , Stephens Robert M , Garfinkel David J 
Published: January 2008

Abstract
Chromosomal genes modulate Ty retrotransposon movement in the genome of Saccharomyces cerevisiae. We have screened a collection of 4739 deletion mutants to identify those that increase Ty1 mobility (Ty1 restriction genes). Among the 91 identified mutants, 80% encode products involved in nuclear processes such as chromatin structure and function, DNA repair and recombination, and transcription. However, bioinformatic analyses encompassing additional Ty1 and Ty3 screens indicate that 264 unique genes involved in a variety of biological processes affect Ty mobility in yeast. Further characterization of 33 of the mutants identified here show that Ty1 RNA levels increase in 5 mutants and the rest affect mobility post-transcriptionally. RNA and cDNA levels remain unchanged in mutants defective in transcription elongation, including ckb2Δ and elf1Δ, suggesting that Ty1 integration may be more efficient in these strains. Insertion-site preference at the CAN1 locus requires Ty1 restriction genes involved in histone H2B ubiquitination by Paf complex subunit genes, as well as BRE1 and RAD6, histone H3 acetylation by RTT109 and ASF1, and transcription elongation by SPT5. Our results indicate that multiple pathways restrict Ty1 mobility and histone modifications may protect coding regions from insertional mutagenesis.
The Telotype Defines the Telomere State inSaccharomyces cerevisiaeand Is Inherited as a Dominant Non-Mendelian Characteristic in Cells Lacking Telomerase
Authors: Makovets Svetlana , Williams Tanya L , Blackburn Elizabeth H 
Published: January 2008

AbstractTelomeres are an unusual component of the genome because they do not encode genes, but their structure and cellular maintenance machinery (which we define as “telotype”) are essential for chromosome stability. Cells can switch between different phenotypic states. One such example is when they switch from maintenance mediated by telomerase (TERT telotype) to one of the two alternative mechanisms of telomere preservation (ALT I and ALT II telotype). The nature of this switch is largely unknown. Reintroduction of telomerase into ALT II, but not ALT I, yeast led to the loss of their ability to survive a second round of telomerase withdrawal. Mating-based genetic analysis of ALT I and II revealed that both types of telomerase-independent telomere maintenance are inherited as a non-Mendelian trait dominant over senescence (SEN telotype). Additionally, inheritance of ALT I and ALT II did not depend on either the mitochondrial genome or a prion-based mechanism. Type I, but not type II, survivor cells exhibited impaired gene silencing, potentially connecting the switch to the ALT telotype epigenetic changes. These data provide evidence that nonprion epigenetic-like mechanisms confer flexibility on cells as a population to adjust to the life-threatening situation of telomerase loss, allowing cells to switch from TERT to ALT telotypes that can sustain viable populations.
Molecular Population Genetics of Drosophila Subtelomeric DNA
Authors: Anderson Jennifer A , Song Yun S , Langley Charles H 
Published: January 2008

Abstract
DNA sequence surveys in yeast and humans suggest that the forces shaping telomeric polymorphism and divergence are distinctly more dynamic than those in the euchromatic, gene-rich regions of the chromosomes. However, the generality of this pattern across outbreeding, multicellular eukaryotes has not been determined. To characterize the structure and evolution of Drosophila telomeres, we collected and analyzed molecular population genetics data from the X chromosome subtelomere in 58 lines of North American Drosophila melanogaster and 29 lines of African D. melanogaster. We found that Drosophila subtelomeres exhibit high levels of both structural and substitutional polymorphism relative to linked euchromatic regions. We also observed strikingly different patterns of variation in the North American and African samples. Moreover, our analyses of the polymorphism data identify a localized hotspot of recombination in the most-distal portion of the X subtelomere. While the levels of polymorphism decline sharply and in parallel with rates of crossing over per physical length over the distal first euchromatic megabase pairs of the X chromosome, our data suggest that they rise again sharply in the subtelomeric region (≈80 kbp). These patterns of historical recombination and geographic differentiation indicate that, similar to yeast and humans, Drosophila subtelomeric DNA is evolving very differently from euchromatic DNA.
Inhibition of Transcription by the Caenorhabditis elegans Germline Protein PIE-1: Genetic Evidence for Distinct Mechanisms Targeting Initiation and Elongation
Authors: Ghosh Dolan , Seydoux Geraldine 
Published: January 2008

Abstract
In Caenorhabditis elegans embryos, specification of the germ lineage depends on PIE-1, a maternal protein that blocks mRNA transcription in germline blastomeres. Studies in mammalian cell culture have suggested that PIE-1 inhibits P-TEFb, a kinase that phosphorylates serine 2 in the carboxyl-terminal domain (CTD) repeats of RNA polymerase II during transcriptional elongation. We have tested this hypothesis using an in vivo complementation assay for PIE-1 function. Our results support the view that PIE-1 inhibits P-TEFb using the CTD-like motif YAPMAPT. This activity is required to block serine 2 phosphorylation in germline blastomeres, but unexpectedly is not essential for transcriptional repression or specification of the germline. We find that sequences outside of the YAPMAPT are required to inhibit serine 5 phosphorylation, and that this second inhibitory mechanism is essential for transcriptional repression and specification of the germ lineage. Our results suggest that PIE-1 uses partially redundant mechanisms to block transcription by targeting both the initiation and elongation phases of the transcription cycle.
1H, 13C, 15N NMR and 13C, 15N CPMAS studies of cobalt(III)-chloride-pyridine complexes, spontaneous py → Cl substitution in trans-[Co(py)4Cl2]Cl, and a new synthesis of mer-[Co(py)3Cl3]
Authors: Pazderski Leszek , Surdykowski Andrzej , Pazderska-Szabłowicz Małgorzata , Sitkowski Jerzy , Kozerski Lech , Kamieński Bohdan , Szłyk Edward 
Published: January 2008

Abstract
trans-[Co(py)4Cl2]Cl·6H2O, mer-[Co(py)3Cl3] and mer-[Co(py)3(CO3)Cl] were studied by UV-Vis, far-IR and 1H, 13C, 15N NMR. The formation of Co-N bonds lead to variable in sign and magnitude changes of 1H NMR chemical shifts, heavily dependent on proton position, coordination sphere geometry and character of auxiliary ligands. 13C nuclei were deshielded upon Co(III) coordination, while 15N NMR studies exhibited ca. 85–110 ppm shielding effects (ca. 15–25 ppm more expressed for nitrogens trans to N than trans to Cl or O). 13C and 15N CPMAS spectra revealed a slight inequivalency of formally identical Co-py bonds in trans-[Co(py)4Cl2]Cl·6H2O and mer-[Co(py)3Cl3], suggesting for the latter complex an existence of distortion isomers. In chloroform, a spontaneous trans-[Co(py)4Cl2]Cl → mer-[Co(py)3Cl3] + py reaction was monitored by 1H NMR and UV-Vis. This process of py → Cl substitution allowed the design of a more convenient and efficient method of mer-[Co(py)3Cl3] preparation.
Influence of surfactants on the fading of malachite green
Authors: Raducan Adina , Olteanu Alexandra , Puiu Mihaela , Oancea Dumitru 
Published: January 2008

Abstract
The kinetics of the reaction between malachite green (MG) and sodium hydroxide (MG fading) was studied using a spectrophotometric method in the presence of two cationic surfactants, cetyl-benzyl-dimethyl-ammonium chloride (CBDAC) and hexadecyl-trimethylammonium bromide (HTAB) and one anionic surfactant, sodium dodecyl sulphate (SDS) at concentrations below and above critical micellar concentrations. The cationic surfactants have a catalytic effect, while the anionic surfactant has an inhibitory effect on the reaction. A kinetic model describing the influence of surfactant on reaction rate was developed. The results are discussed on the basis of electrostatic and hydrophobic interactions between the kinetic micelles and malachite green.
Oxidation of UO2(s) in aqueous solution
Authors: Roth Olivia , Jonsson Mats 
Published: January 2008

Abstract
In this review the kinetics and mechanism of oxidative dissolution of UO2(s), mainly under conditions of relevance for the safety assessment of a deep geological repository for spent nuclear fuel, are discussed. Rate constants for the elementary processes involved (oxidation of UO2 and dissolution of oxidized UO2) are used to calculate the rates of oxidative UO2(s) dissolution under various conditions (type of oxidant, oxidant concentration and HCO3−/CO32− concentration) for which experimental data are also available. The calculated rates are compared to the corresponding experimental values under the assumption that the experimental numbers reflect the steady-state conditions of the system. The agreement between the calculated rates and the corresponding experimental ones is very good, in particular for the higher rates. In general, the calculated rates are somewhat higher than the experimental numbers. This can be due partly to the use of initial concentrations rather than steady-state concentrations in the calculations. The kinetic data are also used to quantitatively discuss the dynamics of spent nuclear fuel dissolution under deep geological repository conditions.
Aminophosphine complex as a catalyst precursor in Suzuki coupling reactions
Authors: Zhao Dongbin , Fei Zhaofu , Ang Wee 
Published: January 2008

Abstract
A palladium complex with an aminophosphine ligand has been prepared and investigated as a catalyst precursor in Suzuki coupling reactions in toluene. Nanoparticles composed of elemental palladium have been isolated from the reaction media and analyzed using transmission electroscopic microscope (TEM), which shows the essential catalysts palladium nanoparticles to have a size of ca. 3.0 nm.
Microwave-induced combustion synthesis and characterization of NixCo1−xFe2O4 nanocrystals (x = 0.0, 0.4, 0.6, 0.8, 1.0)
Authors: Baykal Abdülhadi , Kasapoğlu Nermin , Köseoğlu Yüksel , Başaran Ali , Kavas Hüseyin , Toprak Muhammet 
Published: January 2008

Abstract
A series of Ni-doped cobalt ferrites NixCo1−xFe2O4 (x = 0.0, 0.4, 0.6, 0.8, and 1.0) were prepared using microwave-induced combustion. Nickel, cobalt, and ferric nitrates were used as starting materials and glycine as fuel. The influence of Ni content on the lattice parameter, stretching vibrations, and magnetization was studied. XRD, FTIR, and SEM were used for structure, composition, and morphology investigation. A porous network structure was observed with average particle size 60–67 nm. All samples had a cubic spinel structure. The unit cell parameter “a” decreases linearly with nickel concentration due to the smaller ionic radius of nickel. Magnetization measurements showed that coercivity decreased as Ni content increased; it increased with decreasing temperature.