bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pol32, a Subunit of Saccharomyces cerevisiae DNA Polymerase δ, Suppresses Genomic Deletions and Is Involved in the Mutagenic Bypass Pathway
Authors: Huang Meng-Er , Rio Anne-Gaëlle , Galibert Marie-Dominique , Galibert Francis 
Published: April 2021

Abstract
The Pol32 subunit of S. cerevisiae DNA polymerase (Pol) δ plays an important role in replication and mutagenesis. Here, by measuring the CAN1 forward mutation rate, we found that either POL32 or REV3 (which encodes the Pol ζ catalytic subunit) inactivation produces overlapping antimutator effects against rad mutators belonging to three epistasis groups. In contrast, the msh2Δ pol32Δ double mutant exhibits a synergistic mutator phenotype. Canr mutation spectrum analysis of pol32Δ strains revealed a substantial increase in the frequency of deletions and duplications (primarily deletions) of sequences flanked by short direct repeats, which appears to be RAD52 and RAD10 independent. To better understand the pol32Δ and rev3Δ antimutator effects in rad backgrounds and the pol32Δ mutator effect in a msh2Δ background, we determined Canr mutation spectra for rad5Δ, rad5Δ pol32Δ, rad5Δ rev3Δ, msh2Δ, msh2Δ pol32Δ, and msh2Δ rev3Δ strains. Both rad5Δ pol32Δ and rad5Δ rev3Δ mutants exhibit a reduction in frameshifts and base substitutions, attributable to antimutator effects conferred by the pol32Δ and rev3Δ mutations. In contrast, an increase in these two types of alterations is attributable to a synergistic mutator effect between the pol32Δ and msh2Δ mutations. Taken together, these observations indicate that Pol32 is important in ensuring genome stability and in mutagenesis.
A Genetic Map of Gibberella zeae (Fusarium graminearum)
Authors: Jurgenson J E , Bowden R L , Zeller K A , Leslie J F , Alexander N J , Plattner R D 
Published: April 2021

Abstract
We constructed a genetic linkage map of Gibberella zeae (Fusarium graminearum) by crossing complementary nitrate-nonutilizing (nit) mutants of G. zeae strains R-5470 (from Japan) and Z-3639 (from Kansas). We selected 99 nitrate-utilizing (recombinant) progeny and analyzed them for amplified fragment length polymorphisms (AFLPs). We used 34 pairs of two-base selective AFLP primers and identified 1048 polymorphic markers that mapped to 468 unique loci on nine linkage groups. The total map length is ~1300 cM with an average interval of 2.8 map units between loci. Three of the nine linkage groups contain regions in which there are high levels of segregation distortion. Selection for the nitrate-utilizing recombinant progeny can explain two of the three skewed regions. Two linkage groups have recombination patterns that are consistent with the presence of intercalary inversions. Loci governing trichothecene toxin amount and type (deoxynivalenol or nivalenol) map on linkage groups IV and I, respectively. The locus governing the type of trichothecene produced (nivalenol or deoxynivalenol) cosegregated with the TRI5 gene (which encodes trichodiene synthase) and probably maps in the trichothecene gene cluster. This linkage map will be useful in population genetic studies, in map-based cloning, for QTL (quantitative trait loci) analysis, for ordering genomic libraries, and for genomic comparisons of related species.
Improved Confidence Intervals in Quantitative Trait Loci Mapping by Permutation Bootstrapping
Authors: Bennewitz Jörn , Reinsch Norbert , Kalm Ernst 
Published: April 2021

Abstract
The nonparametric bootstrap approach is known to be suitable for calculating central confidence intervals for the locations of quantitative trait loci (QTL). However, the distribution of the bootstrap QTL position estimates along the chromosome is peaked at the positions of the markers and is not tailed equally. This results in conservativeness and large width of the confidence intervals. In this study three modified methods are proposed to calculate nonparametric bootstrap confidence intervals for QTL locations, which compute noncentral confidence intervals (uncorrected method I), correct for the impact of the markers (weighted method I), or both (weighted method II). Noncentral confidence intervals were computed with an analog of the highest posterior density method. The correction for the markers is based on the distribution of QTL estimates along the chromosome when the QTL is not linked with any marker, and it can be obtained with a permutation approach. In a simulation study the three methods were compared with the original bootstrap method. The results showed that it is useful, first, to compute noncentral confidence intervals and, second, to correct the bootstrap distribution of the QTL estimates for the impact of the markers. The weighted method II, combining these two properties, produced the shortest and less biased confidence intervals in a large number of simulated configurations.
Volatile Anesthetics Affect Nutrient Availability in Yeast
Authors: Palmer Laura K , Wolfe Darren , Keeley Jessica L , Keil Ralph L 
Published: April 2021

Abstract
Volatile anesthetics affect all cells and tissues tested, but their mechanisms and sites of action remain unknown. To gain insight into the cellular activities of anesthetics, we have isolated genes that, when overexpressed, render Saccharomyces cerevisiae resistant to the volatile anesthetic isoflurane. One of these genes, WAK3/TAT1, encodes a permease that transports amino acids including leucine and tryptophan, for which our wild-type strain is auxotrophic. This suggests that availability of amino acids may play a key role in anesthetic response. Multiple lines of evidence support this proposal: (i) Deletion or overexpression of permeases that transport leucine and/or tryptophan alters anesthetic response; (ii) prototrophic strains are anesthetic resistant; (iii) altered concentrations of leucine and tryptophan in the medium affect anesthetic response; and (iv) uptake of leucine and tryptophan is inhibited during anesthetic exposure. Not all amino acids are critical for this response since we find that overexpression of the lysine permease does not affect anesthetic sensitivity. These findings are consistent with models in which anesthetics have a physiologically important effect on availability of specific amino acids by altering function of their permeases. In addition, we show that there is a relationship between nutrient availability and ubiquitin metabolism in this response.
Expression-State Boundaries in the Mating-Type Region of Fission Yeast
Authors: Thon Geneviève , Bjerling Pernilla , Bünner Camilla Marie , Verhein-Hansen Janne 
Published: April 2021

Abstract
A transcriptionally silent chromosomal domain is found in the mating-type region of fission yeast. Here we show that this domain is delimited by 2-kb inverted repeats, IR-L and IR-R. IR-L and IR-R prevent the expansion of transcription-permissive chromatin into the silenced region and that of silenced chromatin into the expressed region. Their insulator activity is partially orientation dependent. The silencing defects that follow deletion or inversion of IR-R are suppressed by high dosage of the chromodomain protein Swi6. Combining chromosomal deletions and Swi6 overexpression shows that IR-L and IR-R provide firm borders in a region where competition between silencing and transcriptional competence occurs. IR-R possesses autonomously replicating sequence (ARS) activity, leading to a model where replication factors, or replication itself, participate in boundary formation.
Mutational Analysis of the Gephyrin-Related Molybdenum Cofactor Biosynthetic Gene cnxE From the Lower Eukaryote Aspergillus nidulans
Authors: Heck Immanuel S , Schrag Joseph D , Sloan Joan , Millar Lindsey J , Kanan Ghassan , Kinghorn James R , Unkles Shiela E 
Published: April 2021

Abstract
We report the identification of a number of mutations that result in amino acid replacements (and their phenotypic characterization) in either the MogA-like domain or domains 2 and 3 of the MoeA-like region of the Aspergillus nidulans cnxE gene. These domains are functionally required since mutations that result in amino acid substitutions in any one domain lead to the loss or to a substantial reduction in all three identified molybdoenzyme activities (i.e., nitrate reductase, xanthine dehydrogenase, and nicotinate hydroxylase). Certain cnxE mutants that show partial growth with nitrate as the nitrogen source in contrast do not grow on hypoxanthine or nicotinate. Complementation between mutants carrying lesions in the MogA-like domain or the MoeA-like region, respectively, most likely occurs at the protein level. A homology model of CnxE based on the dimeric structure of E. coli MoeA is presented and the position of inactivating mutations (due to amino acid replacements) in the MoeA-like functional region of the CnxE protein is mapped to this model. Finally, the activity of nicotinate hydroxylase, unlike that of nitrate reductase and xanthine dehydrogenase, is not restored in cnxE mutants grown in the presence of excess molybdate.
Transposon Insertions in the Promoter of the Zea mays a1 Gene Differentially Affect Transcription by the Myb Factors P and C1
Authors: Pooma Wilailak , Gersos Christos , Grotewold Erich 
Published: April 2021

Abstract
The understanding of control of gene regulation in higher eukaryotes relies heavily on results derived from non-in vivo studies, but rarely can the significance of these approximations be established in vivo. Here, we investigated the effect of Mutator and Spm insertions on the expression of the flavonoid biosynthetic gene a1, independently regulated by the transcription factors C1 and P. The a1-mum2 and a1-m2 alleles carry Mu1 and Spm insertions, respectively, in a cis-element (ARE) of unknown function located between the P- and C1-binding sites. We show that the insertions of Mu1 and Spm similarly influence the expression of a1 controlled by C1 or P. The P-controlled a1 expression in a1-m2 is Spm dependent, and the mutant phenotype of a1-mum2 is suppressed in the pericarp in the absence of the autonomous MuDR element. Footprints within the ARE affect the regulation of a1 by C1 and P differently, providing evidence that these factors control a1 expression using distinct cis-acting regulatory elements. Together, our findings contribute significantly to one of the best-described plant regulatory systems, while stressing the need to complement with in vivo experiments current approaches used for the study of control of gene expression.
Comparing Relative Rates of Pollen and Seed Gene Flow in the Island Model Using Nuclear and Organelle Measures of Population Structure
Authors: Hamilton Matthew B , Miller Judith R 
Published: April 2021

Abstract
We describe a method for comparing nuclear and organelle population differentiation (FST) in seed plants to test the hypothesis that pollen and seed gene flow rates are equal. Wright’s infinite island model is used, with arbitrary levels of self-fertilization and biparental organelle inheritance. The comparison can also be applied to gene flow in animals. Since effective population sizes are smaller for organelle genomes than for nuclear genomes and organelles are often uniparentally inherited, organelle FST is expected to be higher at equilibrium than nuclear FST even if pollen and seed gene flow rates are equal. To reject the null hypothesis of equal seed and pollen gene flow rates, nuclear and organelle FST’s must differ significantly from their expected values under this hypothesis. Finite island model simulations indicate that infinite island model expectations are not greatly biased by finite numbers of populations (≥100 subpopulations). The power to distinguish dissimilar rates of pollen and seed gene flow depends on confidence intervals for fixation index estimates, which shrink as more subpopulations and loci are sampled. Using data from the tropical tree Corythophora alta, we rejected the null hypothesis that seed and pollen gene flow rates are equal but cannot reject the alternative hypothesis that pollen gene flow is 200 times greater than seed gene flow.
Marker-Assisted Introgression of Favorable Alleles at Quantitative Trait Loci Between Maize Elite Lines
Authors: Bouchez Agnès , Hospital Frédéric , Causse Mathilde , Gallais André , Charcosset Alain 
Published: April 2021

Abstract
This article reports the marker-assisted introgression of favorable alleles at three quantitative trait loci (QTL) for earliness and grain yield among maize elite lines. The QTL were originally detected in 1992 by means of ANOVA in a population of 96 recombinant inbred lines (RILs). Introgression started from a selected RIL, which was crossed three times to one of the original parents and then self-fertilized, leading to BC3S1 progenies. Markers were used to assist both foreground and background selection at each generation. At the end of the program, the effect of introgression was assessed phenotypically in agronomic trials, and QTL detection was performed by composite interval mapping among BC3S1 progenies. The marker-assisted introgression proved successful at the genotypic level, as analyzed by precision graphical genotypes, although no emphasis was put on the reduction of linkage drag around QTL. Also, QTL positions were generally sustained in the introgression background. For earliness, the magnitude and sign of the QTL effects were in good agreement with those expected from initial RIL analyses. Conversely, for yield, important discrepancies were observed in the magnitude and sign of the QTL effects observed after introgression, when compared to those expected from initial RIL analyses. These discrepancies are probably due to important genotype-by-environment interactions.
Quantitative Trait Loci for Susceptibility to Tapeworm Infection in the Red Flour Beetle
Authors: Zhong Daibin , Pai Aditi , Yan Guiyun 
Published: April 2021

Abstract
Parasites have profound effects on host ecology and evolution, and the effects of parasites on host ecology are often influenced by the magnitude of host susceptibility to parasites. Many parasites have complex life cycles that require intermediate hosts for their transmission, but little is known about the genetic basis of the intermediate host's susceptibility to these parasites. This study examined the genetic basis of susceptibility to a tapeworm (Hymenolepis diminuta) in the red flour beetle (Tribolium castaneum) that serves as an intermediate host in its transmission. Quantitative trait loci (QTL) mapping experiments were conducted with two independent segregating populations using amplified fragment length polymorphism (AFLP) markers and randomly amplified polymorphic DNA (RAPD) markers. A total of five QTL that significantly affected beetle susceptibility were identified in the two reciprocal crosses. Two common QTL on linkage groups 3 and 6 were identified in both crosses with similar effects on the phenotype, and three QTL were unique to each cross. In one cross, the three main QTL accounted for 29% of the total phenotypic variance and digenic epistasis explained 39% of the variance. In the second cross, the four main QTL explained 62% of the variance and digenic epistasis accounted for only 5% of the variance. The actions of these QTL were either overdominance or underdominance. Our results suggest that the polygenic nature of beetle susceptibility to the parasites and epistasis are important genetic mechanisms for the maintenance of variation within or among beetle strains in susceptibility to tapeworm infection.
Targeted Gene Expression Using the GAL4/UAS System in the Silkworm Bombyx mori
Authors: Imamura Morikazu , Nakai Junichi , Inoue Satoshi , Quan Guo Xing , Kanda Toshio , Tamura Toshiki 
Published: April 2021

Abstract
The silkworm Bombyx mori is one of the most well-studied insects in terms of both genetics and physiology and is recognized as the model lepidopteran insect. To develop an efficient system for analyzing gene function in the silkworm, we investigated the feasibility of using the GAL4/UAS system in conjunction with piggyBac vector-mediated germ-line transformation for targeted gene expression. To drive the GAL4 gene, we used two endogenous promoters that originated from the B. mori actin A3 (BmA3) and fibroin light-chain (FiL) genes and the artificial promoter 3xP3. GFP was used as the reporter. In initial tests of the function of the GAL4/UAS system, we generated transgenic animals that carried the UAS-GFP construct plus either BmA3-GAL4 or 3xP3-GAL4. GFP fluorescence was observed in the tissues of GFP-positive animals, in which both promoters drove GAL4 gene expression. Animals that possessed only the GAL4 gene or UAS-GFP construct did not show GFP fluorescence. In addition, as a further test of the ability of the GAL4/UAS system to drive tissue-specific expression we constructed FiL-GAL4 lines with 3xP3-CFP as the transformation marker. FiL-GAL4 × UAS-GFP crosses showed GFP expression in the posterior silk gland, in which the endogenous FiL gene is normally expressed. These results show that the GAL4/UAS system is applicable to B. mori and emphasize the potential of this system for controlled analyses of B. mori gene function.
Abundant mtDNA Diversity and Ancestral Admixture in Colombian criollo Cattle (Bos taurus)
Authors: Carvajal-Carmona Luis G , Bermudez Nelson , Olivera-Angel Martha , Estrada Luzardo , Ossa Jorge , Bedoya Gabriel , Ruiz-Linares Andrés 
Published: April 2021

Abstract
Various cattle populations in the Americas (known as criollo breeds) have an origin in some of the first livestock introduced to the continent early in the colonial period (16th and 17th centuries). These cattle constitute a potentially important genetic reserve as they are well adapted to local environments and show considerable variation in phenotype. To examine the genetic ancestry and diversity of Colombian criollo we obtained mitochondrial DNA control region sequence information for 110 individuals from seven breeds. Old World haplogroup T3 is the most commonly observed CR lineage in criollo (0.65), in agreement with a mostly European ancestry for these cattle. However, criollo also shows considerable frequencies of haplogroups T2 (0.9) and T1 (0.26), with T1 lineages in criollo being more diverse than those reported for West Africa. The distribution and diversity of Old World lineages suggest some North African ancestry for criollo, probably as a result of the Arab occupation of Iberia prior to the European migration to the New World. The mtDNA diversity of criollo is higher than that reported for European and African cattle and is consistent with a differentiated ancestry for some criollo breeds.
An Analysis of Microsatellite Loci inArabidopsis thaliana: Mutational Dynamics and Application
Authors: Symonds V Vaughan , Lloyd Alan M 
Published: April 2021

AbstractMicrosatellite loci are among the most commonly used molecular markers. These loci typically exhibit variation for allele frequency distribution within a species. However, the factors contributing to this variation are not well understood. To expand on the current knowledge of microsatellite evolution, 20 microsatellite loci were examined for 126 accessions of the flowering plant, Arabidopsis thaliana. Substantial variability in mutation pattern among loci was found, most of which cannot be explained by the assumptions of the traditional stepwise mutation model or infinite alleles model. Here it is shown that the degree of locus diversity is strongly correlated with the number of contiguous repeats, more so than with the total number of repeats. These findings support a strong role for repeat disruptions in stabilizing microsatellite loci by reducing the substrate for polymerase slippage and recombination. Results of cluster analyses are also presented, demonstrating the potential of microsatellite loci for resolving relationships among accessions of A. thaliana.
The Problem of Counting Sites in the Estimation of the Synonymous and Nonsynonymous Substitution Rates: Implications for the Correlation Between the Synonymous Substitution Rate and Codon Usage Bias
Authors: Bierne Nicolas , Eyre-Walker Adam 
Published: April 2021

Abstract
Most methods for estimating the rate of synonymous and nonsynonymous substitution per site define a site as a mutational opportunity: the proportion of sites that are synonymous is equal to the proportion of mutations that would be synonymous under the model of evolution being considered. Here we demonstrate that this definition of a site can give misleading results and that a physical definition of site should be used in some circumstances. We illustrate our point by reexamining the relationship between codon usage bias and the synonymous substitution rate. It has recently been shown that the rate of synonymous substitution, calculated using the Goldman-Yang method, which encapsulates the mutational-opportunity definition of a site at a high level of sophistication, is either positively correlated or uncorrelated to synonymous codon bias in Drosophila. Using other methods, which account for synonymous codon bias but define a site physically, we show that there is a negative correlation between the synonymous substitution rate and codon bias and that the lack of a negative correlation using the Goldman-Yang method is due to the way in which the number of synonymous sites is counted. We also show that there is a positive correlation between the synonymous substitution rate and third position GC content in mammals, but that the relationship is considerably weaker than that obtained using the Goldman-Yang method. We argue that the Goldman-Yang method is misleading in this context and conclude that methods that rely on a mutational-opportunity definition of a site should be used with caution.
Pediatric Burns With Cyanoacrylate Glue: An Inconspicuous Danger
Authors: Carvalho Catarina , Marinho Ana Sofia , Barbosa-Sequeira Joana , Correia Mário Rui , Carvalho Fátima , Banquart-Leitão José , Morgado Hélder 
Published: April 2021

AbstractBurns are a common cause of pediatric injury and represent significant morbidity and mortality in this age group. In children, most burns are thermal, resulting from exposure to a hot surface, liquid, or fire. Cyanoacrylate is a liquid compound commonly found in households, mainly in “superglue” and nail glue. This compound solidifies through an exothermic reaction that is magnified when in contact with certain fibers that act as catalysts, such as cotton. In these circumstances, intense heat is produced in the contact area, potentially causing severe thermal burns. Despite its widespread availability, there is a paucity of safety information about cyanoacrylate and its role as a cause for burns. In the literature, only 18 cases of cyanoacrylate burns are reported in children. We present two cases of pediatric burns with cyanoacrylate and a review of the literature.