bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repair of Damaged and Mismatched DNA by the XPC Homologues Rhp41 and Rhp42 of Fission Yeast
Authors: Marti Thomas M , Kunz Christophe , Fleck Oliver 
Published: April 2021

Abstract
Rhp41 and Rhp42 of Schizosaccharomyces pombe are homologues of human XPC, which is involved in nucleotide excision repair (NER) of damaged DNA. Inactivation of rhp41 caused moderate sensitivity to ultraviolet (UV) radiation. In addition, an increase of mitotic mutation rates was observed in the rhp41 mutant, which was dependent on active translesion polymerase Z. UV sensitivity and mutation rates were not different between rhp42 and wild type, but compared to rhp41 were further increased in rhp41 rhp42 cells. Transcription of the fbp1 gene (induced in vegetative cells) and of the SPBC1289.14 gene (induced during meiosis) was strongly blocked by UV-induced damages in the rhp41 mutant, but not, or only slightly, reduced in rhp42 background. NER-dependent short-patch repair of mismatches formed during meiosis was slightly affected in rhp41, moderately affected in rhp42, and absent in rhp41 rhp42. Epistasis analysis with rhp7 and rhp26 indicates that Rhp41 and Rhp42 are both involved in the global genome and transcription-coupled repair subpathways of NER. Rhp41 plays a major role in damage repair and Rhp42 in mismatch repair.
The G-Protein α-Subunit GasC Plays a Major Role in Germination in the Dimorphic FungusPenicillium marneffei
Authors: Zuber Sophie , Hynes Michael J , Andrianopoulos Alex 
Published: April 2021

AbstractThe opportunistic human pathogen Penicillium marneffei exhibits a temperature-dependent dimorphic switch. At 25°, multinucleate, septate hyphae that can undergo differentiation to produce asexual spores (conidia) are produced. At 37° hyphae undergo arthroconidiation to produce uninucleate yeast cells that divide by fission. This work describes the cloning of the P. marneffei gasC gene encoding a G-protein α-subunit that shows high homology to members of the class III fungal Gα-subunits. Characterization of a ΔgasC mutant and strains carrying a dominant-activating gasCG45R or a dominant-interfering gasCG207R allele show that GasC is a crucial regulator of germination. A ΔgasC mutant is severely delayed in germination, whereas strains carrying a dominant-activating gasCG45R allele show a significantly accelerated germination rate. Additionally, GasC signaling positively affects the production of the red pigment by P. marneffei at 25° and negatively affects the onset of conidiation and the conidial yield, showing that GasC function overlaps with functions of the previously described Gα-subunit GasA. In contrast to the S. cerevisiae ortholog Gpa2, our data indicate that GasC is not involved in carbon or nitrogen source sensing and plays no major role in either hyphal or yeast growth or in the switch between these two forms.
Dynamics of Molecular Markers Linked to the Resistance Loci in a Mosquito-Plasmodium System
Authors: Yan Guiyun , Severson David W 
Published: April 2021

Abstract
Models on the evolution of resistance to parasitism generally assume fitness tradeoffs between the costs of being parasitized and the costs associated with resistance. This study tested this assumption using the yellow fever mosquito Aedes aegypti and malaria parasite Plasmodium gallinaceum system. Experimental mosquito populations were created by mixing susceptible and resistant strains in equal proportions, and then the dynamics of markers linked to loci for Plasmodium resistance and other unlinked neutral markers were determined over 12 generations. We found that when the mixed population was maintained under parasite-free conditions, the frequencies of alleles specific to the susceptible strain at markers closely linked to the loci for resistance (QTL markers) as well as other unlinked markers increased significantly in the first generation and then fluctuated around equilibrium frequencies for all six markers. However, when the mixed population was exposed to an infected blood meal every generation, allele frequencies at the QTL markers for resistance were not significantly changed. Small population size caused significant random fluctuations of allele frequencies at all marker loci. Consistent allele frequency changes in the QTL markers and other unlinked markers suggest that the reduced fitness in the resistant population has a genome-wide effect on the genetic makeup of the mixed population. Continuous exposure to parasites promoted the maintenance of alleles from the resistant Moyo-R strain in the mixed population. The results are discussed in relation to the proposed malaria control strategy through genetic disruption of vector competence.
Cytoplasmic Incompatibility and Sperm Cyst Infection in Different Drosophila-Wolbachia Associations
Authors: Veneti Zoe , Clark Michael E , Zabalou Sofia , Karr Timothy L , Savakis Charalambos , Bourtzis Kostas 
Published: April 2021

AbstractWolbachia are a group of maternally transmitted obligatory intracellular α-proteobacteria that infect a wide range of arthropod and nematode species. Wolbachia infection in Drosophila in most cases is associated with the induction of cytoplasmic incompatibility (CI), manifested as embryonic lethality of offspring in a cross between infected males and uninfected females. While the molecular basis of CI is still unknown, it has been suggested that two bacterial functions are involved: mod (for modification) modifies the sperm during spermatogenesis and resc (for rescue) acts in the female germline and/or in early embryos, neutralizing the modification. There is considerable variation in the level of incompatibility in different Wolbachia/host interactions. We examine the relationship between the levels of CI in a number of naturally infected and transinfected Drosophila hosts and the percentage of Wolbachia-infected sperm cysts. Our results indicate the presence of two main groups of Drosophila-Wolbachia associations: group I, which exhibits a positive correlation between CI levels and the percentage of infected sperm cysts (mod+ phenotype), and group II, which does not express CI (mod– phenotype) irrespective of the infection status of the sperm cysts. Group II can be further divided into two subgroups: The first one contains associations with high numbers of heavily Wolbachia-infected sperm cysts while in the second one, Wolbachia is rarely detected in sperm cysts, being mostly present in somatic cells. We conclude that there are three requirements for the expression of CI in a host-Wolbachia association: (a) Wolbachia has to be able to modify sperm (mod+ genotype), (b) Wolbachia has to infect sperm cysts, and (c) Wolbachia has to be harbored by a permissive host.
Distinct Phospholipase C-γ-Dependent Signaling Pathways in the Drosophila Eye and Wing Are Revealed by a New small wing Allele
Authors: Mankidy Rishikesh , Hastings Jeremy , Thackeray Justin R 
Published: April 2021

Abstract
The Drosophila genome contains a single phospholipase C-γ (PLC-γ) homolog, encoded by small wing (sl), that acts as an inhibitor of receptor tyrosine kinase (RTK) signaling during photoreceptor R7 development. Although the existing sl alleles behave genetically as nulls, they may still produce truncated Sl products that could in theory still provide limited PLC-γ function. Both to identify a true null allele and to probe structure-function relationships in Sl, we carried out an F1 screen for new sl mutations and identified seven new alleles. Flies homozygous for any of these alleles are viable, with the same short-wing phenotype described previously; however, two of the alleles differ from any of those previously isolated in the severity of the eye phenotype: sl9 homozygotes have a slightly more extreme extra-R7 phenotype, whereas sl7 homozygotes have an almost wild-type eye. We determined the mutant defect in all seven alleles, revealing that sl9 is a molecular null due to a very early stop codon, while sl7 has a missense mutation in the highly conserved Y catalytic domain. Together with in vitro mutagenesis of the residue affected by the sl7 mutation, these results confirm the role of Sl in RTK signaling and provide evidence for two genetically separable PLC-γ-dependent pathways affecting the development of the eye and the wing.
Maximum-Likelihood Estimation of Admixture Proportions From Genetic Data
Authors: Wang Jinliang 
Published: April 2021

AbstractFor an admixed population, an important question is how much genetic contribution comes from each parental population. Several methods have been developed to estimate such admixture proportions, using data on genetic markers sampled from parental and admixed populations. In this study, I propose a likelihood method to estimate jointly the admixture proportions, the genetic drift that occurred to the admixed population and each parental population during the period between the hybridization and sampling events, and the genetic drift in each ancestral population within the interval between their split and hybridization. The results from extensive simulations using various combinations of relevant parameter values show that in general much more accurate and precise estimates of admixture proportions are obtained from the likelihood method than from previous methods. The likelihood method also yields reasonable estimates of genetic drift that occurred to each population, which translate into relative effective sizes (Ne) or absolute average Ne's if the times when the relevant events (such as population split, admixture, and sampling) occurred are known. The proposed likelihood method also has features such as relatively low computational requirement compared with previous ones, flexibility for admixture models, and marker types. In particular, it allows for missing data from a contributing parental population. The method is applied to a human data set and a wolflike canids data set, and the results obtained are discussed in comparison with those from other estimators and from previous studies.
Likelihood-Based Estimation of Microsatellite Mutation Rates
Authors: Whittaker John C , Harbord Roger M , Boxall Nicola , Mackay Ian , Dawson Gary , Sibly Richard M 
Published: April 2021

Abstract
Microsatellites are widely used in genetic analyses, many of which require reliable estimates of microsatellite mutation rates, yet the factors determining mutation rates are uncertain. The most straightforward and conclusive method by which to study mutation is direct observation of allele transmissions in parent-child pairs, and studies of this type suggest a positive, possibly exponential, relationship between mutation rate and allele size, together with a bias toward length increase. Except for microsatellites on the Y chromosome, however, previous analyses have not made full use of available data and may have introduced bias: mutations have been identified only where child genotypes could not be generated by transmission from parents' genotypes, so that the probability that a mutation is detected depends on the distribution of allele lengths and varies with allele length. We introduce a likelihood-based approach that has two key advantages over existing methods. First, we can make formal comparisons between competing models of microsatellite evolution; second, we obtain asymptotically unbiased and efficient parameter estimates. Application to data composed of 118,866 parent-offspring transmissions of AC microsatellites supports the hypothesis that mutation rate increases exponentially with microsatellite length, with a suggestion that contractions become more likely than expansions as length increases. This would lead to a stationary distribution for allele length maintained by mutational balance. There is no evidence that contractions and expansions differ in their step size distributions.
The Effects of Host Age, Host Nuclear Background and Temperature on Phenotypic Effects of the Virulent Wolbachia Strain popcorn in Drosophila melanogaster
Authors: Reynolds K Tracy , Thomson Linda J , Hoffmann Ary A 
Published: April 2021

Abstract
Because of their obligate endosymbiotic nature, Wolbachia strains by necessity are defined by their phenotypic effects upon their host. Nevertheless, studies on the influence of host background and environmental conditions upon the manifestation of Wolbachia effects are relatively uncommon. Here we examine the behavior of the overreplicating Wolbachia strain popcorn in four different Drosophila melanogaster backgrounds at two temperatures. Unlike other strains of Wolbachia in Drosophila, popcorn has a major fitness impact upon its hosts. The rapid proliferation of popcorn causes cells to rupture, resulting in the premature death of adult hosts. Apart from this effect, we found that popcorn delayed development time, and host background influenced both this trait and the rate of mortality associated with infection. Temperature influenced the impact of popcorn upon host mortality, with no reduction in life span occurring in flies reared at 19°. No effect upon fecundity was found. Contrary to earlier reports, popcorn induced high levels of incompatibility when young males were used in tests, and CI levels declined rapidly with male age. The population dynamics of popcorn-type infections will therefore depend on environmental temperature, host background, and the age structure of the population.
Deleterious Mutations and the Genetic Variance of Male Fitness Components in Mimulus guttatus
Authors: Kelly John K 
Published: April 2021

Abstract
Deleterious mutations are relevant to a broad range of questions in genetics and evolutionary biology. I present an application of the “biometric method” for estimating mutational parameters for male fitness characters of the yellow monkeyflower, Mimulus guttatus. The biometric method rests on two critical assumptions. The first is that experimental inbreeding changes genotype frequencies without changing allele frequencies; i.e., there is no genetic purging during the experiment. I satisfy this condition by employing a breeding design in which the parents are randomly extracted, fully homozygous inbred lines. The second is that all genetic variation is attributable to deleterious mutations maintained in mutation-selection balance. I explicitly test this hypothesis using likelihood ratios. Of the three deleterious mutation models tested, the first two are rejected for all characters. The failure of these models is due to an excess of additive genetic variation relative to the expectation under mutation-selection balance. The third model is not rejected for either of two log-transformed male fitness traits. However, this model imposes only “weak conditions” and is not sufficiently detailed to provide estimates for mutational parameters. The implication is that, if biometric methods are going to yield useful parameter estimates, they will need to consider mutational models more complicated than those typically employed in experimental studies.
Nonparametric Disequilibrium Mapping of Functional Sites Using Haplotypes of Multiple Tightly Linked Single-Nucleotide Polymorphism Markers
Authors: Cheng Rong , Ma Jennie Z , Wright Fred A , Lin Shili , Gao Xin , Wang Daolong , Elston Robert C , Li Ming D 
Published: April 2021

AbstractAs the speed and efficiency of genotyping single-nucleotide polymorphisms (SNPs) increase, using the SNP map, it becomes possible to evaluate the extent to which a common haplotype contributes to the risk of disease. In this study we propose a new procedure for mapping functional sites or regions of a candidate gene of interest using multiple linked SNPs. Based on a case-parent trio family design, we use expectation-maximization (EM) algorithm-derived haplotype frequency estimates of multiple tightly linked SNPs from both unambiguous and ambiguous families to construct a contingency statistic S for linkage disequilibrium (LD) analysis. In the procedure, a moving-window scan for functional SNP sites or regions can cover an unlimited number of loci except for the limitation of computer storage. Within a window, all possible widths of haplotypes are utilized to find the maximum statistic S* for each site (or locus). Furthermore, this method can be applied to regional or genome-wide scanning for determining linkage disequilibrium using SNPs. The sensitivity of the proposed procedure was examined on the simulated data set from the Genetic Analysis Workshop (GAW) 12. Compared with the conventional and generalized TDT methods, our procedure is more flexible and powerful.
On the Genomic Location of theexuperantia1Gene inDrosophila miranda: The Limits ofin SituHybridization Experiments
Authors: Bachtrog Doris , Charlesworth Brian 
Published: April 2021

AbstractIn situ hybridization to Drosophila polytene chromosomes is a powerful tool for determining the chromosomal location of genes. Using in situ hybridization experiments, Yi and Charlesworth recently reported the transposition of the exuperantia1 gene (exu1) from a neo-sex chromosome to the ancestral X chromosome of Drosophila miranda, close to exuperantia2 (exu2). By characterizing sequences flanking exu1, however, we found the position of exu1 to be conserved on the neo-sex chromosome. Further, the exu2 gene was found to be tandemly duplicated on the X chromosome of D. miranda. The misleading hybridization signal of exu1 may be caused by multiple copies of exu2, which interfere with the hybridization of the exu1 probe to its genomic position on the neo-X chromosome. This suggests that flanking DNA should be used to confirm the positions of members of gene families.
Using Evolutionary Rates to Investigate Protein Functional Divergence and Conservation: A Case Study of the Carbonic Anhydrases
Authors: Knudsen Bjarne , Miyamoto Michael M , Laipis Philip J , Silverman David N 
Published: April 2021

AbstractFunctional constraints on proteins limit their evolutionary rates at specific sites. These constraints allow for the interpretation of conserved residues and sites with a rate change as those most likely underlying the functional similarities and differences among protein subfamilies, respectively. This study describes new likelihood-ratio tests (LRTs) that complement existing ones for the identification of both conserved and rate change sites. These identifications are validated by the recovery of residues that are known from existing biochemical and structural information to be critical for the functional similarities and differences among carbonic anhydrases (CAs). In combination with this other information, these LRTs also support a unique antioxidant defense role for the puzzling CA III. As illustrated by the CAs, these LRTs, in combination with other biological evidence, offer a powerful and cost-effective approach for testing hypotheses, making predictions, and designing experiments in protein functional studies.
Translational Selection and Yeast Proteome Evolution
Authors: Akashi Hiroshi 
Published: April 2021

Abstract
The primary structures of peptides may be adapted for efficient synthesis as well as proper function. Here, the Saccharomyces cerevisiae genome sequence, DNA microarray expression data, tRNA gene numbers, and functional categorizations of proteins are employed to determine whether the amino acid composition of peptides reflects natural selection to optimize the speed and accuracy of translation. Strong relationships between synonymous codon usage bias and estimates of transcript abundance suggest that DNA array data serve as adequate predictors of translation rates. Amino acid usage also shows striking relationships with expression levels. Stronger correlations between tRNA concentrations and amino acid abundances among highly expressed proteins than among less abundant proteins support adaptation of both tRNA abundances and amino acid usage to enhance the speed and accuracy of protein synthesis. Natural selection for efficient synthesis appears to also favor shorter proteins as a function of their expression levels. Comparisons restricted to proteins within functional classes are employed to control for differences in amino acid composition and protein size that reflect differences in the functional requirements of proteins expressed at different levels.
Depletion of H2A-H2B Dimers in Saccharomyces cerevisiae Triggers Meiotic Arrest by Reducing IME1 Expression and Activating the BUB2-Dependen Branch of the Spindle Checkpoint
Authors: Hanlon Sean E , Norris David N , Vershon Andrew K 
Published: April 2021

Abstract
In the yeast Saccharomyces cerevisiae, diploid strains carrying homozygous hta1-htb1Δ mutations express histone H2A-H2B dimers at a lower level than do wild-type cells. Although this mutation has only minor effects on mitotic growth, it causes an arrest in sporulation prior to the first meiotic division. In this report, we show that the hta1-htb1Δ mutant exhibits reduced expression of early and middle-sporulation-specific genes and that the meiotic arrest of the hta1-htb1Δ mutant can be partially bypassed by overexpression of IME1. Additionally, deletions of BUB2 or BFA1, components of one branch of the spindle checkpoint pathway, bypass the meiotic arrest. Mutations in the other branch of the pathway or in the pachytene checkpoint are unable to suppress the meiotic block. These observations indicate that depletion of the H2A-H2B dimer blocks sporulation by at least two mechanisms: disruption of the expression of meiotic regulatory genes and activation of the spindle checkpoint. Our results show that the failure to progress through the meiotic pathway is not the result of global chromosomal alterations but that specific aspects of meiosis are sensitive to depletion of the H2A-H2B dimer.
Inferences on the Evolutionary History of theDrosophila americanaPolymorphicX/4Fusion From Patterns of Polymorphism at theX-LinkedparalyticandelavGenes
Authors: Vieira Cristina P , Coelho Paula A , Vieira Jorge 
Published: April 2021

AbstractIn Drosophila there is limited evidence on the nature of evolutionary forces affecting chromosomal arrangements other than inversions. The study of the X/4 fusion polymorphism of Drosophila americana is thus of interest. Polymorphism patterns at the paralytic (para) gene, located at the base of the X chromosome, suggest that there is suppressed crossing over in this region between fusion and nonfusion chromosomes but not within fusion and nonfusion chromosomes. These data are thus compatible with previous claims that within fusion chromosomes the amino acid clines found at fused1 (also located at the base of the X chromosome) are likely maintained by local selection. The para data set also suggests a young age of the X/4 fusion. Polymorphism data on para and elav (located at the middle region of the X chromosome) suggest that there is no population structure other than that caused by the X/4 fusion itself. These findings are therefore compatible with previous claims that selection maintains the strong association observed between the methionine/threonine variants at fused1 and the status of the X chromosome as fused or unfused to the fourth chromosome.