bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergence of DNA Polymerase ε Antimutators That Escape Error-Induced Extinction in Yeast
Authors: Williams Lindsey N , Herr Alan J , Preston Bradley D 
Published: January 2013

AbstractDNA polymerases (Pols) ε and δ perform the bulk of yeast leading- and lagging-strand DNA synthesis. Both Pols possess intrinsic proofreading exonucleases that edit errors during polymerization. Rare errors that elude proofreading are extended into duplex DNA and excised by the mismatch repair (MMR) system. Strains that lack Pol proofreading or MMR exhibit a 10- to 100-fold increase in spontaneous mutation rate (mutator phenotype), and inactivation of both Pol δ proofreading (pol3-01) and MMR is lethal due to replication error-induced extinction (EEX). It is unclear whether a similar synthetic lethal relationship exists between defects in Pol ε proofreading (pol2-4) and MMR. Using a plasmid-shuffling strategy in haploid Saccharomyces cerevisiae, we observed synthetic lethality of pol2-4 with alleles that completely abrogate MMR (msh2Δ, mlh1Δ, msh3Δ msh6Δ, or pms1Δ mlh3Δ) but not with partial MMR loss (msh3Δ, msh6Δ, pms1Δ, or mlh3Δ), indicating that high levels of unrepaired Pol ε errors drive extinction. However, variants that escape this error-induced extinction (eex mutants) frequently emerged. Five percent of pol2-4 msh2Δ eex mutants encoded second-site changes in Pol ε that reduced the pol2-4 mutator phenotype between 3- and 23-fold. The remaining eex alleles were extragenic to pol2-4. The locations of antimutator amino-acid changes in Pol ε and their effects on mutation spectra suggest multiple mechanisms of mutator suppression. Our data indicate that unrepaired leading- and lagging-strand polymerase errors drive extinction within a few cell divisions and suggest that there are polymerase-specific pathways of mutator suppression. The prevalence of suppressors extragenic to the Pol ε gene suggests that factors in addition to proofreading and MMR influence leading-strand DNA replication fidelity.
Detecting Signatures of Selection Through Haplotype Differentiation Among Hierarchically Structured Populations
Authors: Fariello María Inés , Boitard Simon , Naya Hugo , SanCristobal Magali , Servin Bertrand 
Published: January 2013

AbstractThe detection of molecular signatures of selection is one of the major concerns of modern population genetics. A widely used strategy in this context is to compare samples from several populations and to look for genomic regions with outstanding genetic differentiation between these populations. Genetic differentiation is generally based on allele frequency differences between populations, which are measured by FST or related statistics. Here we introduce a new statistic, denoted hapFLK, which focuses instead on the differences of haplotype frequencies between populations. In contrast to most existing statistics, hapFLK accounts for the hierarchical structure of the sampled populations. Using computer simulations, we show that each of these two features—the use of haplotype information and of the hierarchical structure of populations—significantly improves the detection power of selected loci and that combining them in the hapFLK statistic provides even greater power. We also show that hapFLK is robust with respect to bottlenecks and migration and improves over existing approaches in many situations. Finally, we apply hapFLK to a set of six sheep breeds from Northern Europe and identify seven regions under selection, which include already reported regions but also several new ones. We propose a method to help identifying the population(s) under selection in a detected region, which reveals that in many of these regions selection most likely occurred in more than one population. Furthermore, several of the detected regions correspond to incomplete sweeps, where the favorable haplotype is only at intermediate frequency in the population(s) under selection.
The Mechanism of Nucleotide Excision Repair-Mediated UV-Induced Mutagenesis in Nonproliferating Cells
Authors: Kozmin Stanislav G , Jinks-Robertson Sue 
Published: January 2013

Abstract
Following the irradiation of nondividing yeast cells with ultraviolet (UV) light, most induced mutations are inherited by both daughter cells, indicating that complementary changes are introduced into both strands of duplex DNA prior to replication. Early analyses demonstrated that such two-strand mutations depend on functional nucleotide excision repair (NER), but the molecular mechanism of this unique type of mutagenesis has not been further explored. In the experiments reported here, an ade2 adeX colony-color system was used to examine the genetic control of UV-induced mutagenesis in nondividing cultures of Saccharomyces cerevisiae. We confirmed a strong suppression of two-strand mutagenesis in NER-deficient backgrounds and demonstrated that neither mismatch repair nor interstrand crosslink repair affects the production of these mutations. By contrast, proteins involved in the error-prone bypass of DNA damage (Rev3, Rev1, PCNA, Rad18, Pol32, and Rad5) and in the early steps of the DNA-damage checkpoint response (Rad17, Mec3, Ddc1, Mec1, and Rad9) were required for the production of two-strand mutations. There was no involvement, however, for the Pol η translesion synthesis DNA polymerase, the Mms2-Ubc13 postreplication repair complex, downstream DNA-damage checkpoint factors (Rad53, Chk1, and Dun1), or the Exo1 exonuclease. Our data support models in which UV-induced mutagenesis in nondividing cells occurs during the Pol ζ-dependent filling of lesion-containing, NER-generated gaps. The requirement for specific DNA-damage checkpoint proteins suggests roles in recruiting and/or activating factors required to fill such gaps.
Meiotic Sex Chromosome Inactivation Is Disrupted in Sterile Hybrid Male House Mice
Authors: Campbell Polly , Good Jeffrey M , Nachman Michael W 
Published: January 2013

Abstract
In male mammals, the X and Y chromosomes are transcriptionally silenced in primary spermatocytes by meiotic sex chromosome inactivation (MSCI) and remain repressed for the duration of spermatogenesis. Here, we test the longstanding hypothesis that disrupted MSCI might contribute to the preferential sterility of heterogametic hybrid males. We studied a cross between wild-derived inbred strains of Mus musculus musculus and M. m. domesticus in which sterility is asymmetric: F1 males with a M. m. musculus mother are sterile or nearly so while F1 males with a M. m. domesticus mother are normal. In previous work, we discovered widespread overexpression of X-linked genes in the testes of sterile but not fertile F1 males. Here, we ask whether this overexpression is specifically a result of disrupted MSCI. To do this, we isolated cells from different stages of spermatogenesis and measured the expression of several genes using quantitative PCR. We found that X overexpression in sterile F1 primary spermatocytes is coincident with the onset of MSCI and persists in postmeiotic spermatids. Using a series of recombinant X genotypes, we then asked whether X overexpression in hybrids is controlled by cis-acting loci across the X chromosome. We found that it is not. Instead, one large interval in the proximal portion of the M. m. musculus X chromosome is associated with both overexpression and the severity of sterility phenotypes in hybrids. These results demonstrate a strong association between X-linked hybrid male sterility and disruption of MSCI and suggest that trans-acting loci on the X are important for the transcriptional regulation of the X chromosome during spermatogenesis.
Systems Genetics Implicates Cytoskeletal Genes in Oocyte Control of Cloned Embryo Quality
Authors: Cheng Yong , Gaughan John , Midic Uros , Han Zhiming , Liang Cheng-Guang , Patel Bela G , Latham Keith E 
Published: January 2013

AbstractCloning by somatic cell nuclear transfer is an important technology, but remains limited due to poor rates of success. Identifying genes supporting clone development would enhance our understanding of basic embryology, improve applications of the technology, support greater understanding of establishing pluripotent stem cells, and provide new insight into clinically important determinants of oocyte quality. For the first time, a systems genetics approach was taken to discover genes contributing to the ability of an oocyte to support early cloned embryo development. This identified a primary locus on mouse chromosome 17 and potential loci on chromosomes 1 and 4. A combination of oocyte transcriptome profiling data, expression correlation analysis, and functional and network analyses yielded a short list of likely candidate genes in two categories. The major category—including two genes with the strongest genetic associations with the traits (Epb4.1l3 and Dlgap1)—encodes proteins associated with the subcortical cytoskeleton and other cytoskeletal elements such as the spindle. The second category encodes chromatin and transcription regulators (Runx1t1, Smchd1, and Chd7). Smchd1 promotes X chromosome inactivation, whereas Chd7 regulates expression of pluripotency genes. Runx1t1 has not been associated with these processes, but acts as a transcriptional repressor. The finding that cytoskeleton-associated proteins may be key determinants of early clone development highlights potential roles for cytoplasmic components of the oocyte in supporting nuclear reprogramming. The transcriptional regulators identified may contribute to the overall process as downstream effectors.
Characterizing individual Au25(SG)18 clusters within a nanopore detector
Authors: Angevine Christopher E. , Kothalawala Nuwan , Dass Amala , Reiner Joseph E. 
Published: January 2013

ABSTRACTMetallic quantum clusters are stable structures that can exhibit many useful properties. Clusters can be ligand stabilized in aqueous environments to expand their usefulness as biosensors. There are some limitations in characterizing the physical and chemical properties of individual water soluble clusters. This report describes initial results of a new approach for detecting and characterizing individual gold nanoclusters (Au25(SG)18) in an aqueous solution with nanopore-based resistive pulse sensing. Here the nanopore is a single alpha hemolysin from Staphylococcus aureus. Clusters that enter through the cis side of the pore (large vestibule) usually create shallow current blockades with a mean residence time of several milliseconds. Clusters that enter through the trans side of the pore (narrow lumen) create deeper blockades that are either very short (∼200 μs), long lived (∼50 ms) or trapped (>10s). The short and long lived blockades yield sufficient statistics to help characterize the clusters and the trapped state events may allow for additional analysis and controlled delivery of individual clusters. We demonstrate the possibility of this additional analysis by performing I-V measurements on individually trapped clusters. These show an optimal voltage for confining a cluster within the pore.
Influence of Addition of Alumina Nanoparticles on Thermoelectric Properties of Higher Manganese Silicide
Authors: Itoh Takashi , Ono Naoki 
Published: January 2013

ABSTRACTHigher manganese silicide (HMS) is a low-cost and eco-friendly thermoelectric material available for recovering waste heat of 500 to 900 K. In this research, we tried to uniformly disperse the alumina nanoparticles (ANPs) in the HMS matrix to reduce the thermal conductivity and to improve the thermoelectric performance. Influence of addition of ANPs on the thermoelectric properties was investigated. It was confirmed that ANPs were uniformly dispersed in the HMS grain boundary. The lattice thermal conductivity was reduced by adding ANPs. As a result, the maximum thermoelectric performance of ZT=0.58 was achieved at about 800 K by adding 1 vol% of ANPs. The performance of ANPs-added HMS was improved about 25 %.
Microstructural and Optical Properties of Nitrogen Doped ZnO Nanowires
Authors: Souissi Ahmed , Hanèche Nadia , Sartel Corinne , Meftah Abdel , Lusson Alain , Oueslati Meherzi , Bluet Jean-Marie , Masenelli Bruno , Sallet Vincent , Galtier Pierre 
Published: January 2013

ABSTRACTNanowires with different nitrogen concentrations were grown by Metal-Organic Chemical Vapor Deposition (MOCVD) using DEZn, N2O and NH3as zinc, oxygen and nitrogen doping sources respectively. Low temperature photoluminescence, Raman spectroscopy and Transmission Electron Microscopy are combined to study the incorporation of nitrogen in the wires. The observation of donor-acceptor pair band confirms that the incorporation nitrogen in ZnO nanowires is responsible for the creation of acceptor centers. The additional peaks observed in Raman are correlated to nano-sized inter-atomic distance fluctuations observed in TEM. These domains combined with a resonance effect are probably the explanation of the huge Raman cross section observed for the impurity related peaks.
Deposition of tin oxides by Ion-Beam-Sputtering
Authors: Becker Martin , Polity Angelika , Feili Davar , Meyer Bruno K. 
Published: January 2013

ABSTRACTSynthesis of both p-type and n-type oxide semiconductors is required to develop oxide-based electronic devices. Tin monoxide (SnO) recently has received increasing attention as an alternative p-type oxide semiconductor because it is a simple binary compound consisting of abundant elements. Another phase of the tin oxygen system, SnO2, is of great technological interest as transparent electrodes and as heat-reflecting filters. The preparation of tin oxide thin films has been performed by many different procedures. Radio-frequency (RF) ion-thrusters, as designed for propulsion applications, are also qualified for thin film deposition and surface etching, because different gas mixtures, extraction voltages and RF power can be applied. Tin oxide thin films were grown by ion beam sputtering (IBS) using a 3” metallic tin target. Different aspects of the thin film growth and properties of the tin oxide phases were investigated in relation to flux of oxygen fed into the gas discharge in the ion thruster. Results on thin film growth by IBS will be presented, structural, vibrational and optical properties of the films will be discussed.
Metal Oxide Nanowire Growth via Intermediate Hydroxide Formation:A Thermochemical Assessment
Authors: Shalav Avi , Elliman Robert G. 
Published: January 2013

ABSTRACTIn this study we apply reaction thermodynamics to show that a significant volatile hydroxide vapor partial pressure forms at a metal-oxide interface and is a likely precursor source for nanowire growth. The growth of WO3 and CuO nanowires are used as examples for reactions dependent on only H2O and O2+H2O, respectively. Optimal temperatures, H2O (and O2) partial pressures for volatile hydroxide formation are calculated and experimentally investigated. We conclude that metal oxide nanowires can be readily grown at relatively low temperatures (close to or less than 500oC) over short anneal times (tens of minutes). The growth of these metal oxide nanowires, with many oxidation states, by this simple thermal technique is readily suited for a range of emergent large surface area nanostructured optical and electrical applications, including sensing, photocatalysis and ultracapacitors.
Fabrication, Properties and Electrochemical Applications of Diamond Nanostructures
Authors: Yang Nianjun , Smirnov Waldemar , Nebel Christoph E. 
Published: January 2013

ABSTRACTWe summarized in this paper the fabrication, properties, and electrochemical applications of diamond nanostructures, mainly diamond nanotextures and diamond nanowires. The characterizations of nanostructures were introduced with different techniques. As example of applications, electrochemical DNA sensing and protein trapping on diamond nanotextures are shown.
Ultra thin transition metal oxide coatings on diamond for thermionic applications
Authors: Tiwari Amit K. , Goss Jonathan P. , Briddon Patrick R. , Wright Nick G. , Horsfall Alton B. , Rayson Mark J. 
Published: January 2013

ABSTRACTWe have investigated, using density functional simulations, the energetics and the electronic properties of oxides of selected transition metals, TMs, adsorbed onto a dia-mond (001) surface. We find that stoichiometric oxides of TMs, particularly Ti and Zn,influence the electron affinity of diamond strongly. The electron affinities of stoichiomet-ric oxides of Ti and Zn are calculated to be around −3 eV, significantly higher than 1.9 eV of commonly used H–termination. The reactions of TMs with an oxygenated diamond are found to be highly exothermic. Based upon the energetics and the electronic properties, we propose that in the regime of ultra thin films, oxides of TMs are promising options for surface coating of diamond–based electron emitters, as these coatings are compatible with semiconductor device fabrication processes, while having the benefit of inducing a large negative electron affinity.
Future species composition will affect forest water use after loss of eastern hemlock from southern Appalachian forests
Authors: Brantley Steven , Ford Chelcy R. , Vose James M. 
Published: January 2013

Infestation of eastern hemlock (Tsuga canadensis (L.) Carr.) with hemlock woolly adelgid (HWA, Adelges tsugae) has caused widespread mortality of this key canopy species throughout much of the southern Appalachian Mountains in the past decade. Because eastern hemlock is heavily concentrated in riparian habitats, maintains a dense canopy, and has an evergreen leaf habit, its loss is expected to have a major impact on forest processes, including transpiration (Et). Our goal was to estimate changes in stand‐level Et since HWA infestation, and predict future effects of forest regeneration on forest Et in declining eastern hemlock stands where hemlock represented 50–60% of forest basal area. We used a combination of community surveys, sap flux measurements, and empirical models relating sap flux‐scaled leaf‐level transpiration (EL) to climate to estimate the change in Et after hemlock mortality and forecast how forest Et will change in the future in response to eastern hemlock loss.From 2004 to 2011, eastern hemlock mortality reduced annual forest Et by 22% and reduced winter Et by 74%. As hemlock mortality increased, growth of deciduous tree species—especially sweet birch (Betula lenta L.), red maple (Acer rubrum L.), yellow poplar (Liriodendron tulipifera L.), and the evergreen understory shrub rosebay rhododendron (Rhododendron maximum L.)— also increased, and these species will probably dominate post‐hemlock riparian forests. All of these species have higher daytime EL rates than hemlock, and replacement of hemlock with species that have less conservative transpiration rates will result in rapid recovery of annual stand Et. Further, we predict that annual stand Et will eventually surpass Et levels observed before hemlock was infested with HWA. This long‐term increase in forest Et may eventually reduce stream discharge, especially during the growing season. However, the dominance of deciduous species in the canopy will result in a permanent reduction in winter Et and possible increase in winter stream discharge. The effects of hemlock die‐off and replacement with deciduous species will have a significant impact on the hydrologic flux of forest transpiration, especially in winter. These results highlight the impact that invasive species can have on landscape‐level ecosystem fluxes.
New Attempts to Modify Periodontal Risk Assessment for Generalized Aggressive Periodontitis: A Retrospective Study
Authors: Lü Da , Meng Huanxin , Xu Li , Lu Ruifang , Zhang Li , Chen Zhibin , Feng Xianghui , Shi Dong , Tian Yu , Wang Xian'e 
Published: January 2013

Background: Periodontal risk assessment (PRA) model was designed for risk evaluation of treated patients with periodontal disease. However, its use on generalized aggressive periodontitis (GAgP) had been scarcely reported. This study aims to investigate the association of original PRA/modified PRA (MPRA) and compliance of periodontal maintenance with long‐term treatment outcomes of Chinese patients with GAgP.Methods: Eighty‐eight patients from a GAgP cohort, who completed active periodontal treatment (APT) and accepted reevaluation 3 to 11 years (mean of 5.5 years) afterward, were enrolled. PRA was modified (three strategies involving replacement of bleeding on probing with bleeding index >2, counting sites with probing depth ≥6 mm and changing method of bone loss [BL] calculation) to classify patients into different risk groups based on data at the first recall after APT. PRA and three MPRA models were investigated regarding long‐term association with tooth loss (TL) and alteration of bone level (∆BL).Results: Based on original PRA, 87 patients (98.8%) had a high‐risk profile. According to three MPRA models, annual TL per patient values were greater in high‐risk groups than in low‐to‐moderate risk groups (MPRA‐1, 0.20 ± 0.33 versus 0.04 ± 0.14; MPRA‐2, 0.18 ± 0.32 versus 0.05 ± 0.14; MPRA‐3, 0.17 ± 0.32 versus 0.05 ± 0.15; P <0.05). By MPRA‐1, irregular compliers with low‐to‐moderate risk profile had greater ∆BL (0.027 ± 0.031, indicating bone increment) than those with high risk (−0.012 ± 0.064, tendency for BL). For regular compliers, no significant differences of annual TL or ∆BL were found between risk groups.Conclusions: MPRA models could be used for evaluating the long‐term outcomes of Chinese patients with severe GAgP, especially irregular compliers. High‐risk patients of MPRAs exhibited more TL and less bone fill than low‐to‐moderate risk ones.
Comparative Evaluation of HIV-1 Neutralization in External Secretions and Sera of HIV-1-Infected Women
Authors: Wei Qing , Moldoveanu Zina , Huang Wen-Qiang , Alexander Rashada C , Goepfert Paul A , Mestecky Jiri 
Published: January 2013

Objectives:Although human immunodeficiency virus type 1 (HIV-1)-specific antibodies are detectable in external secretions by ELISA and western blot (WB), the presence of HIV-1 neutralizing antibodies is difficult to evaluate due to the low levels of immunoglobulins (Ig) and the presence of humoral factors of innate immunity. The objective of this study was to determine virus neutralization activity and the relative contribution of HIV-1-specific antibodies of various isotypes to virus neutralization in serum/plasma samples, cervicovaginal lavages (CVL), and rectal lavages (RL).Design:Serum/plasma, CVL, and RL samples were examined by ELISA, WB and HIV-1 neutralization assays. Selected samples were Ig depleted and analyzed for virus neutralization.Results:IgG specific for three HIV-1 ENV antigens was detected in all serum/plasma samples, while IgA to at least one ENV glycoprotein was found at the low levels in 95% samples. Serum/plasma samples had the ability to neutralize at least one of three clade B and two clade C viruses. The neutralizing titers were reduced significantly or became undetectable after IgG removal. In corresponding CVL and RL, HIV-1 ENV-specific IgG antibodies were readily detected compared to IgA. Furthermore, IgG in CVL had greater ability than IgA to reduce virus infectivity. The difference in HIV-1 neutralization before and after Ig depletion was not observed in RL, implying that innate humoral factors were involved in anti-HIV-1 activity.Conclusions:Results demonstrate that HIV-1-specific neutralizing antibodies are almost exclusively of the IgG isotype in serum/plasma and CVL samples. HIV-1-specific binding antibodies detected in RL are not responsible for neutralization activity, suggesting that the antibody-mediated virus neutralization in external secretions should be verified by means of a selective depletion of Ig.