bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of Conditional Mutations in the Saccharomyces cerevisiae MLH1 Gene in Mismatch Repair and in Meiotic Crossing Over
Authors: Argueso Juan Lucas , Smith Daniel , Yi James , Waase Marc , Sarin Sumeet , Alani Eric 
Published: April 2021

Abstract
In mismatch repair (MMR), members of the MLH gene family have been proposed to act as key molecular matchmakers to coordinate mismatch recognition with downstream repair functions that result in mispair excision. Two members of this gene family, MLH1 and MLH3, have also been implicated in meiotic crossing over. These diverse roles suggest that a mutational analysis of MLH genes could provide reagents required to identify interactions between gene products and to test whether the different roles ascribed to a subset of these genes can be separated. In this report we show that in Saccharomyces cerevisiae the mlh1Δ mutation confers inviability in pol3-01 strain backgrounds that are defective in the Polδ proofreading exonuclease activity. This phenotype was exploited to identify four mlh1 alleles that each confer a temperature-sensitive phenotype for viability in pol3-01 strains. In three different mutator assays, strains bearing conditional mlh1 alleles displayed wild-type or nearly wild-type mutation rates at 26°. At 35°, these strains exhibited mutation rates that approached those observed in mlh1Δ mutants. The mutator phenotype exhibited in mlh1-I296S strains was partially suppressed at 35° by EXO1 overexpression. The mlh1-F228S and -I296S mutations conferred a separation-of-function phenotype in meiosis; both mlh1-F228S and -I296S strains displayed strong defects in meiotic mismatch repair but showed nearly wild-type levels of crossing over, suggesting that the conditional mutations differentially affected MLH1 functions. These genetic studies suggest that the conditional mlh1 mutations can be used to separate the MMR and meiotic crossing-over functions of MLH1 and to identify interactions between MLH1 and downstream repair components.
Selection and Maintenance of Androdioecy in Caenorhabditis elegans
Authors: Stewart Andrew D , Phillips Patrick C 
Published: April 2021

Abstract
Caenorhabditis elegans is an androdioecious nematode composed of selfing hermaphrodites and rare males. A model of male maintenance demonstrates that selfing rates in hermaphrodites cannot be too high or else the frequency of males will be driven down to the rate of spontaneous nondisjunction of the X chromosome. After their outcrossing ability is assessed, males are found to skirt the frequency range in which they would be maintained. When male maintenance is directly assessed by elevating male frequency and observing the frequency change through time, males are gradually eliminated from the population. Males, therefore, appear to reproduce at a rate just below that necessary for them to be maintained. Populations polymorphic for a mutation (fog-2) that effectively changes hermaphrodites into females demonstrate that there is strong selection against dioecy. Factors such as variation in male mating ability and inbreeding depression could potentially lead to the long-term maintenance of males.
Why Are There Males in the Hermaphroditic Species Caenorhabditis elegans?
Authors: Chasnov J R , Chow King L 
Published: April 2021

Abstract
The free-living nematode worm Caenorhabditis elegans reproduces primarily as a self-fertilizing hermaphrodite, yet males are maintained in wild-type populations at low frequency. To determine the role of males in C. elegans, we develop a mathematical model for the genetic system of hermaphrodites that can either self-fertilize or be fertilized by males and we perform laboratory observations and experiments on both C. elegans and a related dioecious species C. remanei. We show that the mating efficiency of C. elegans is poor compared to a dioecious species and that C. elegans males are more attracted to C. remanei females than they are to their conspecific hermaphrodites. We postulate that a genetic mutation occurred during the evolution of C. elegans hermaphrodites, resulting in the loss of an attracting sex pheromone present in the ancestor of both C. elegans and C. remanei. Our findings suggest that males are maintained in C. elegans because of the particular genetic system inherited from its dioecious ancestor and because of nonadaptive spontaneous nondisjunction of sex chromosomes, which occurs during meiosis in the hermaphrodite. A theoretical argument shows that the low frequency of male mating observed in C. elegans can support male-specific genes against mutational degeneration. This results in the continuing presence of functional males in a 99.9% hermaphroditic species in which outcrossing is disadvantageous to hermaphrodites.
Dependence of Epistasis on Environment and Mutation Severity as Revealed by in Silico Mutagenesis of Phage T7
Authors: You Lingchong , Yin John 
Published: April 2021

Abstract
Understanding how interactions among deleterious mutations affect fitness may shed light on a variety of fundamental biological phenomena, including the evolution of sex, the buffering of genetic variations, and the topography of fitness landscapes. It remains an open question under what conditions and to what extent such interactions may be synergistic or antagonistic. To address this question, we employed a computer model for the intracellular growth of bacteriophage T7. We created in silico 90,000 mutants of phage T7, each carrying from 1 to 30 mutations, and evaluated the fitness of each by simulating its growth cycle. The simulations sought to account for the severity of single deleterious mutations on T7 growth, as well as the effect of the resource environment on our fitness measures. We found that mildly deleterious mutations interacted synergistically in poor-resource environments but antagonistically in rich-resource environments. However, severely deleterious mutations always interacted antagonistically, irrespective of environment. These results suggest that synergistic epistasis may be difficult to experimentally distinguish from nonepistasis because its effects appear to be most pronounced when the effects of mutations on fitness are most challenging to measure. Our approach demonstrates how computer simulations of developmental processes can be used to quantitatively study genetic interactions at the population level.
Estimation of Effective Population Size of HIV-1 Within a Host: A Pseudomaximum-Likelihood Approach
Authors: Seo Tae-Kun , Thorne Jeffrey L , Hasegawa Masami , Kishino Hirohisa 
Published: April 2021

Abstract
Using pseudomaximum-likelihood approaches to phylogenetic inference and coalescent theory, we develop a computationally tractable method of estimating effective population size from serially sampled viral data. We show that the variance of the maximum-likelihood estimator of effective population size depends on the serial sampling design only because internal node times on a coalescent genealogy can be better estimated with some designs than with others. Given the internal node times and the number of sequences sampled, the variance of the maximum-likelihood estimator is independent of the serial sampling design. We then estimate the effective size of the HIV-1 population within nine hosts. If we assume that the mutation rate is 2.5 × 10−5 substitutions/generation and is the same in all patients, estimated generation lengths vary from 0.73 to 2.43 days/generation and the mean (1.47) is similar to the generation lengths estimated by other researchers. If we assume that generation length is 1.47 days and is the same in all patients, mutation rate estimates vary from 1.52 × 10−5 to 5.02 × 10−5. Our results indicate that effective viral population size and evolutionary rate per year are negatively correlated among HIV-1 patients.
Differential Regulation of Saccharomyces cerevisiae Phospholipase D in Sporulation and Sec14-Independent Secretion
Authors: Rudge Simon A , Zhou Chun , Engebrecht JoAnne 
Published: April 2021

Abstract
Saccharomyces cerevisiae Spo14, a phosphatidylcholine-specific, phosphatidylinositol (4,5) bisphosphate-activated phospholipase D (PLD), is essential for meiosis and spore formation. Spo14 is also required for secretion in the absence of the phosphatidylinositol/phosphatidylcholine transfer protein Sec14 (i.e., Sec14-independent secretion). In sporulating cells Spo14 is phosphorylated and relocalized within the cell. In contrast, Spo14 does not relocalize and is not phosphorylated in Sec14-independent secretion. Analysis of a partially phosphatidylinositol (4,5) bisphosphate-activated Spo14 mutant, spo14R894G, revealed that Spo14 function in Sec14-independent secretion, unlike the situation in meiosis, requires fully stimulated PLD activity. Consistent with the differential regulation of Spo14 function during sporulation and secretion, we isolated a mutant allele, spo14-S251P, the product of which is improperly phosphorylated and fails to relocalize and rescue the sporulation phenotype of homozygous spo14 diploids, but supports Sec14-independent secretion. Furthermore, we show that the N-terminal domain of Spo14 is both phosphorylated and sufficient for prospore membrane localization during sporulation. These data indicate that Spo14 phosphorylation and relocalization are essential for the process of sporulation, but dispensable for Sec14-independent secretion. Finally, we demonstrate that Spo14 phosphorylation and relocalization are initiated by nitrogen and glucose limitation and occur independently of the process of meiosis.
Domains of Gene Silencing Near the Left End of Chromosome III in Saccharomyces cerevisiae
Authors: Bi Xin 
Published: April 2021

Abstract
In Saccharomyces cerevisiae the HM loci and regions adjacent to the telomeres are transcriptionally silent. HML is situated 11 kb from the left telomere of chromosome III. I have systematically examined gene silencing along this 11-kb chromosomal region. I found that silencing extends at least 1.1 kb beyond HML, indicating that the HML E silencer acts on both sides. Moreover, I obtained evidence indicating that a 0.71-kb sequence near the E silencer acts as a barrier to the spread of silencing and coincides with the left boundary of the silent HML domain. I also showed that silencing at the telomere is limited to an ~2-kb domain. On the other hand, an ~7-kb region between HML and the telomere is not silenced by HML or the telomere. These results provide a clear example of organization of the eukaryotic genome into interspersed domains with distinct potentials for gene expression.
Evidence for Interaction of Schizophyllum commune Y Mating-Type Proteins in Vivo
Authors: Robertson C Ian , Kende Alexander McMahon , Toenjes Kurt , Novotny Charles P , Ullrich Robert C 
Published: April 2021

Abstract
The Aα mating-type locus of Schizophyllum commune regulates sexual development and contains the code for two proteins, Y and Z, which are thought to form a complex and function as a transcription factor. Import of these proteins into the nucleus may be an essential step in Aα-regulated sexual development. The Y proteins contain a bipartite basic sequence, which is an excellent candidate for a nuclear localization sequence (NLS), while Z proteins contain no such sequence. Here we describe experiments in which deletions were made in the putative NLS sequence of Y4. We show that this putative NLS is essential to the function of the Y protein and capable of mislocalizing green fluorescent protein (GFP) to the nucleus in Saccharomyces cerevisiae. Further, we describe genetic experiments that demonstrate the first Y-Y protein interactions in vivo. These results are consistent with our previously postulated hypothesis that the Y-Z complex is likely to be of a higher order than dimer.
Trans-splicing as a Novel Mechanism to Explain Interallelic Complementation in Drosophila
Authors: Mongelard Fabien , Labrador Mariano , Baxter Ellen M , Gerasimova Tatiana I , Corces Victor G 
Published: April 2021

Abstract
Two mutant alleles of the same gene, each located in one of the two homologous chromosomes, may in some instances restore the wild-type function of the gene. This is the case with certain combinations of mutant alleles in the mod(mdg4) gene. This gene encodes several different proteins, including Mod(mdg4)2.2, a component of the gypsy insulator. This protein is encoded by two separate transcription units that can be combined in a trans-splicing reaction to form the mature Mod(mdg4)2.2-encoding RNA. Molecular characterization of complementing alleles shows that they affect the two different transcription units. Flies homozygous for each allele are missing the Mod(mdg4)2.2 protein, whereas wild-type trans-heterozygotes are able to synthesize almost normal levels of the Mod(mdg4)2.2 product. This protein is functional as judged by its ability to form a functional insulator complex. The results suggest that the interallelic complementation in the mod(mdg4) gene is a consequence of trans-splicing between two different mutant transcripts. A conclusion from this observation is that the trans-splicing reaction that takes place between transcripts produced on two different mutant chromosomes ensures wild-type levels of functional protein.
Mutations in the midway Gene Disrupt a Drosophila Acyl Coenzyme A: Diacylglycerol Acyltransferase
Authors: Buszczak Michael , Lu Xiaohui , Segraves William A , Chang Ta Yuan , Cooley Lynn 
Published: April 2021

Abstract
During Drosophila oogenesis, defective or unwanted egg chambers are eliminated during mid-oogenesis by programmed cell death. In addition, final cytoplasm transport from nurse cells to the oocyte depends upon apoptosis of the nurse cells. To study the regulation of germline apoptosis, we analyzed the midway mutant, in which egg chambers undergo premature nurse cell death and degeneration. The midway gene encodes a protein similar to mammalian acyl coenzyme A: diacylglycerol acyltransferase (DGAT), which converts diacylglycerol (DAG) into triacylglycerol (TAG). midway mutant egg chambers contain severely reduced levels of neutral lipids in the germline. Expression of midway in insect cells results in high levels of DGAT activity in vitro. These results show that midway encodes a functional DGAT and that changes in acylglycerol lipid metabolism disrupt normal egg chamber development in Drosophila.
A Complex Array of DNA-Binding Proteins Required for Pairing-Sensitive Silencing by a Polycomb Group Response Element From the Drosophila engrailed Gene
Authors: Americo Jeffrey , Whiteley Mary , Brown J Lesley , Fujioka Miki , Jaynes James B , Kassis Judith A 
Published: April 2021

Abstract
Regulatory DNA from the Drosophila gene engrailed causes silencing of a linked reporter gene (mini-white) in transgenic Drosophila. This silencing is strengthened in flies homozygous for the transgene and has been called “pairing-sensitive silencing.” The pairing-sensitive silencing activities of a large fragment (2.6 kb) and a small subfragment (181 bp) were explored. Since pairing-sensitive silencing is often associated with Polycomb group response elements (PREs), we tested the activities of each of these engrailed fragments in a construct designed to detect PRE activity in embryos. Both fragments were found to behave as PREs in a bxd-Ubx-lacZ reporter construct, while the larger fragment showed additional silencing capabilities. Using the mini-white reporter gene, a 139-bp minimal pairing-sensitive element (PSE) was defined. DNA mobility-shift assays using Drosophila nuclear extracts suggested that there are eight protein-binding sites within this 139-bp element. Mutational analysis showed that at least five of these sites are important for pairing-sensitive silencing. One of the required sites is for the Polycomb group protein Pleiohomeotic and another is GAGAG, a sequence bound by the proteins GAGA factor and Pipsqueak. The identity of the other proteins is unknown. These data suggest a surprising degree of complexity in the DNA-binding proteins required for PSE function.
Analysis of Quantitative Trait Locus Effects on the Size and Shape of Mandibular Molars in Mice
Authors: Workman Michael Scott , Leamy Larry J , Routman Eric J , Cheverud James M 
Published: April 2021

AbstractWhile &gt;50 genes have been found to influence the development of teeth in mice, we still know very little about the genetic basis for the adaptive characteristics of teeth, such as size and shape. We applied interval mapping procedures to Procrustes size and shape data obtained from 10 morphological landmarks on the mandibular molar row of the F2 progeny from a cross between the LG/J and SM/J strains of mice. This revealed many more QTL for molar shape (18) than for molar centroid size (3), although levels of dominance effects were comparable among QTL for size and shape. Comparisons of patterns of Procrustes additive and dominance shape effects and ordination of QTL effects by principal components analysis suggested that the effects of the shape QTL were dispersed among the three molars and thus that none of these molars represents a genetically distinct developmental structure. The results of an analysis of co-occurrence of QTL for molar shape, mandible shape, and cranial dimensions in these mice suggested that many of the QTL for molar shape may be the same as those affecting these other sets of characters, although in some cases this could be due to effects of closely linked genes.
A Phenotype-Sensitizing Apoe-Deficient Genetic Background Reveals Novel Atherosclerosis Predisposition Loci in the Mouse
Authors: Dansky Hayes M , Shu Pei , Donavan M , Montagno Jill , Nagle Deborah L , Smutko John S , Roy Natalie , Whiteing S , Barrios Judith , McBride T J , Smith Jonathan D , Duyk Geoffrey , Breslow Jan L , Moore Karen J 
Published: April 2021

Abstract
Therapeutic intervention for atherosclerosis has predominantly concentrated on regulating cholesterol levels; however, these therapeutics are not efficacious for all patients, suggesting that other factors are involved. This study was initiated to identify mechanisms that regulate atherosclerosis predisposition in mice other than cholesterol level regulation. To do so we performed quantitative trait locus analysis using two inbred strains that each carry the atherosclerosis phenotype-sensitizing Apoe deficiency and that have been shown to have widely disparate predilection to atherosclerotic lesion formation. One highly significant locus on chromosome 10 (LOD = 7.8) accounted for 19% of the variance in lesion area independent of cholesterol. Two additional suggestive loci were identified on chromosomes 14 (LOD = 3.2) and 19 (LOD = 3.2), each accounting for 7–8% of the lesion variance. In all, five statistically significant and suggestive loci affecting lesion size but not lipoprotein levels were identified. Many of these were recapitulated in an independent confirmatory cross. In summary, two independently performed crosses between C57BL/6 and FVB/N Apoe-deficient mice have revealed several previously unreported atherosclerosis susceptibility loci that are distinct from loci linked to lipoprotein levels.
Simultaneous Detection and Fine Mapping of Quantitative Trait Loci in Mice Using Heterogeneous Stocks
Authors: Mott Richard , Flint Jonathan 
Published: April 2021

Abstract
We describe a method to simultaneously detect and fine map quantitative trait loci (QTL) that is especially suited to the mapping of modifier loci in mouse mutant models. The method exploits the high level of historical recombination present in a heterogeneous stock (HS), an outbred population of mice derived from known founder strains. The experimental design is an F2 cross between the HS and a genetically distinct line, such as one carrying a knockout or transgene. QTL detection is performed by a standard genome scan with ~100 markers and fine mapping by typing the same animals using densely spaced markers over those candidate regions detected by the scan. The analysis uses an extension of the dynamic-programming technique employed previously to fine map QTL in HS mice. We show by simulation that a QTL accounting for 5% of the total variance can be detected and fine mapped with &gt;50% probability to within 3 cM by genotyping ~1500 animals.
Isolation and Characterization of Broad-Spectrum Disease-Resistant Arabidopsis Mutants
Authors: Maleck Klaus , Neuenschwander Urs , Cade Rebecca M , Dietrich Robert A , Dangl Jeffery L , Ryals John A 
Published: April 2021

Abstract
To identify Arabidopsis mutants that constitutively express systemic acquired resistance (SAR), we constructed reporter lines expressing the firefly luciferase gene under the control of the SAR-inducible PR-1 promoter (PR-1/luc). After EMS mutagenesis of a well-characterized transgenic line, we screened 250,000 M2 plants for constitutive expression of the reporter gene in vivo. From a mutant collection containing several hundred putative mutants, we concentrated on 16 mutants lacking spontaneous hypersensitive response (HR) cell death. We mapped 4 of these constitutive immunity (cim) mutants to chromosome arms. Constitutive expression of disease resistance was established by analyzing responses to virulent Peronospora parasitica and Pseudomonas syringae strains, by RNA blot analysis for endogenous marker genes, and by determination of salicylic acid levels in the mutants. The variety of the cim phenotypes allowed us to define distinct steps in both the canonical SAR signaling pathway and a separate pathway for resistance to Erysiphe cichoracearum, active in only a subset of the mutants.
Homozygosity and Linkage Disequilibrium
Authors: Sabatti Chiara , Risch Neil 
Published: April 2021

AbstractWe illustrate how homozygosity of haplotypes can be used to measure the level of disequilibrium between two or more markers. An excess of either homozygosity or heterozygosity signals a departure from the gametic phase equilibrium: We describe the specific form of dependence that is associated with high (low) homozygosity and derive various linkage disequilibrium measures. They feature a clear biological interpretation, can be used to construct tests, and are standardized to allow comparison across loci and populations. They are particularly advantageous to measure linkage disequilibrium between highly polymorphic markers.
Overlapping Roles of the Spindle Assembly and DNA Damage Checkpoints in the Cell-Cycle Response to Altered Chromosomes in Saccharomyces cerevisiae
Authors: Garber Peter M , Rine Jasper 
Published: April 2021

Abstract
The MAD2-dependent spindle checkpoint blocks anaphase until all chromosomes have achieved successful bipolar attachment to the mitotic spindle. The DNA damage and DNA replication checkpoints block anaphase in response to DNA lesions that may include single-stranded DNA and stalled replication forks. Many of the same conditions that activate the DNA damage and DNA replication checkpoints also activated the spindle checkpoint. The mad2Δ mutation partially relieved the arrest responses of cells to mutations affecting the replication proteins Mcm3p and Pol1p. Thus a previously unrecognized aspect of spindle checkpoint function may be to protect cells from defects in DNA replication. Furthermore, in cells lacking either the DNA damage or the DNA replication checkpoints, the spindle checkpoint contributed to the arrest responses of cells to the DNA-damaging agent methyl methanesulfonate, the replication inhibitor hydroxyurea, and mutations affecting Mcm2p and Orc2p. Thus the spindle checkpoint was sensitive to a wider range of chromosomal perturbations than previously recognized. Finally, the DNA replication checkpoint did not contribute to the arrests of cells in response to mutations affecting ORC, Mcm proteins, or DNA polymerase δ. Thus the specificity of this checkpoint may be more limited than previously recognized.