bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Generic Estimation of Population Subdivision Using Distances Between Alleles With Special Reference for Microsatellite Loci
Authors: Michalakis Yannis , Excoffier Laurent 
Published: January 2021

Abstract
Several estimators of population differentiation have been proposed in the recent past to deal with various types of genetic markers (i.e., allozymes, nucleotide sequences, restriction fragment length polymorphisms, or microsatellites). We discuss the relationships among these estimators and show how a single analysis of variance framework can accomodate these qualitatively different data types.
C-Terminal Deletions Can Suppress Temperature-Sensitive Mutations and Change Dominance in the Phage Mu Repressor
Authors: Vogel Jodi L , Geuskens Vincent , Desmet Lucie , Higgins N Patrick , Toussaint Ariane 
Published: January 2021

Abstract
Mutations in an N-terminal 70-amino acid domain of bacteriophage Mu's repressor cause temperature-sensitive DNA-binding activity. Surprisingly, amber mutations can conditionally correct the heat-sensitive defect in three mutant forms of the repressor gene, cts25 (D43-G), cts62 (R47-Q and cts71 (M28-I), and in the appropriate bacterial host produce a heat-stable Sts phenotype (for survival of temperature shifts). Sts repressor mutants are heat sensitive when in supE or supF hosts and heat resistant when in Sup° hosts. Mutants with an Sts phenotype have amber mutations at one of three codons, Q179, Q187, or Q190. The Sts phenotype relates to the repressor size: in Sup° hosts sts repressors are shorter by seven, 10, or 18 amino acids compared to repressors in supE or supF hosts. The truncated form of the sts62-1 repressor, which lacks 18 residues (Q179–V196), binds Mu operator DNA more stably at 42° in vitro compared to its full-length counterpart (cts62 repressor). In addition to influencing temperature sensitivity, the C-terminus appears to control the susceptibility to in vivo Clp proteolysis by influencing the multimeric structure of repressor.
The Yeast HRS1 Gene Encodes a Polyglutamine-Rich Nuclear Protein Required for Spontaneous and hpr1-Induced Deletions Between Direct Repeats
Authors: Santos-Rosa Helena , Clever Beate , Heyer Wolf-Dietrich , Aguilera Andrés 
Published: January 2021

Abstract
The hrs1-1 mutation was isolated as an extragenic suppressor of the hyperrecombination phenotype of hpr1Δ cells. We have cloned, sequenced and deleted from the genome the HRS1 gene. The DNA sequence of the HRS1 gene reveals that it is identical to PGD1, a gene with no reported function, and that the Hrs1p protein contains polyglutamine stretches typically found in transcription factors. We have purified a His(6) tagged version of Hrs1p protein from E. coli and have obtained specific anti-Hrs1p polyclonal antibodies. We show that Hrs1p is a 49-kD nuclear protein, as determined by indirect immunofluorescence microscopy and Western blot analysis. The hrs1Δ null mutation reduces the frequency of deletions in wild-type and hpr1Δ backgrounds sevenfold below wild-type and rad52 levels. Furthermore, hrs1Δ cells show reduced induction of the GAL1,10 promoter relative to wild-type cells. Our results suggest that Hrs1p is required for the formation of deletions between direct repeats and that it may function in gene expression. This suggests a connection between gene expression and direct repeat recombination. In this context, we discuss the possible roles of Hrs1p and Hpr1p in initiation of direct-repeat recombination.
3′ → 5′ Exonucleases of DNA Polymerases ϵ and δ Correct Base Analog Induced DNA Replication Errors on Opposite DNA Strands in Saccharomyces cerevisiae
Authors: Shcherbakova Polina V , Pavlov Youri I 
Published: January 2021

Abstract
The base analog 6-N-hydroxylaminopurine (HAP) induces bidirectional GC → AT and AT → GC transitions that are enhanced in DNA polymerase ϵ and δ 3′ → 5′ exonuclease-deficient yeast mutants, pol2-4 and pol3-01, respectively. We have constructed a set of isogenic strains to determine whether the DNA polymerases δ and ϵ contribute equally to proofreading of replication errors provoked by HAP during leading and lagging strand DNA synthesis. Site-specific GC → AT and AT → GC transitions in a Pol→, pol2-4 or pol3-01 genetic background were scored as reversions of ura3 missense alleles. At each site, reversion was increased in only one proofreading-deficient mutant, either pol2-4 or pol3-01, depending on the DNA strand in which HAP incorporation presumably occurred. Measurement of the HAP-induced reversion frequency of the ura3 alleles placed into chromosome III near to the defined active replication origin ARS306 in two orientations indicated that DNA polymerases ϵ and δ correct HAP-induced DNA replication errors on opposite DNA strands.
A Search for a General Phenomenon of Adaptive Mutability
Authors: Galitski Timothy , Roth John R 
Published: January 2021

Abstract
The most prominent systems for the study of adaptive mutability depend on the specialized activities of genetic elements like bacteriophage Mu and the F plasmid. Searching for general adaptive mutability, we have investigated the behavior of Salmonella typhimurium strains with chromosomal lacZ mutations. We have studied 30 revertible nonsense, missense, frameshift, and insertion alleles. One-third of the mutants produced ≥10 late revertant colonies (appearing three to seven days after plating on selective medium). For the prolific mutants, the number of late revertants showed rank correlation with the residual β-galactosidase activity; for the same mutants, revertant number showed no correlation with the nonselective reversion rate (from fluctuation tests). Leaky mutants, which grew slowly on selective medium, produced late revertants whereas tight nongrowing mutants generally did not produce late revertants. However, the number of late revertants was not proportional to residual growth. Using total residual growth and the nonselective reversion rate, the expected number of late revertants was calculated. For several leaky mutants, the observed revertant number exceeded the expected number. We suggest that excess late revertants from these mutants arise from general adaptive mutability available to any chromosomal gene.
The Drosophila ash1 Gene Product, Which Is Localized at Specific Sites on Polytene Chromosomes, Contains a SET Domain and a PHD Finger
Authors: Tripoulas Nicholas , LaJeunesse Dennis , Gildea John , Shearn Allen 
Published: January 2021

Abstract
The determined state of Drosophila imaginal discs depends on stable patterns of homeotic gene expression. The stability of these patterns requires the function of the ash1 gene, a member of the trithorax group. The primary translation product of the 7.5-kb ash1 transcript is predicted to be a basic protein of 2144 amino acids. The ASHl protein contains a SET domain and a PHD finger. Both of these motifs are found in the products of some trithorax group and Polycomb group genes. We have determined the nucleotide sequence alterations in 10 ash1 mutant alleles and have examined their mutant phenotype. The best candidate for a null allele is ashl 22. The truncated protein product of this mutant allele is predicted to contain only 47 amino acids. The ASHl protein is localized on polytene chromosomes of larval salivary glands at &gt;100 sites. The chromosomal localization of ASHl implies that it functions at the transcriptional level to maintain the expression pattern of homeotic selector genes.
Recombination-Dependent Growth in Exonuclease-Depleted recBC sbcBC Strains of Escherichia coli K-12
Authors: Ryder Lizanne , Sharples Gary J , Lloyd Robert G 
Published: January 2021

Abstract
Analysis of the aroLM-sbcCD interval of the Escherichia coli K-12 chromosome revealed a new gene (rdgC) encoding a function required for growth in recombination-deficient recBC sbcBC strains. Deletion of rdgC does not reduce viability, conjugational recombination, or DNA repair in ret +, recA, recB, reCF or recJ mutants. However, it makes the growth of recBC sbcBC strains reliant on the RecA, RecF, and RuvC proteins and, to a large extent, on RuvAB. The recBC sbcBC ΔrdgC ruvAB construct forms colonies, but cell viability is reduced to &lt;5%. A recBC sbcBC ΔrdgC derivative carrying the temperature-sensitive recA200 allele grows at 32° but not 42°. Multicopy rdgC + plasmids reduce the growth rate of recBC sbcBC strains, while multicopy sbcC plasmids that reactivate SbcCD nuclease cannot be maintained without RdgC protein. The data presented are interpreted to suggest that exonuclease-depleted recBC sbcBC strains have difficulty removing the displaced arm of a collapsed replication fork and that this problem is compounded in the absence of RdgC. Recombination then becomes necessary to repair the fork and allow chromosome duplication to be completed. The possibility that RdgC is an exonuclease is discussed.
Genome Duplication in Soybean (Glycine subgenus soja)
Authors: Shoemaker R C , Polzin K , Labate J , Specht J , Brummer E C , Olson T , Young N , Concibido V , Wilcox J , Tamulonis JP , Kochert G , Boerma H R 
Published: January 2021

Abstract
Restriction fragment length polymorphism mapping data from nine populations (Glycine max × G. soja and G. max × G. max) of the Glycine subgenus soja genome led to the identification of many duplicated segments of the genome. Linkage groups contained up to 33 markers that were duplicated on other linkage groups. The size of homoeologous regions ranged from 1.5 to 106.4 cM, with an average size of 45.3 cM. We observed segments in the soybean genome that were present in as many as six copies with an average of 2.55 duplications per segment. The presence of nested duplications suggests that at least one of the original genomes may have undergone an additional round of tetraploidization. Tetraploidization, along with large internal duplications, accounts for the highly duplicated nature of the genome of the subgenus. Quantitative trait loci for seed protein and oil showed correspondence across homoeologous regions, suggesting that the genes or gene families contributing to seed composition have retained similar functions throughout the evolution of the chromosomes.
The Rate of Compensatory Evolution
Authors: Stephan Wolfgang 
Published: January 2021

Abstract
A two-locus model is presented to analyze the evolution of compensatory mutations occurring in stems of RNA secondary structures. Single mutations are assumed to be deleterious but harmless (neutral) in appropriate combinations. In proceeding under mutation pressure, natural selection and genetic drift from one fitness peak to another one, a population must therefore pass through a valley of intermediate deleterious states of individual fitness. The expected time for this transition is calculated using diffusion theory. The rate of compensatory evolution, kc, is then defined as the inverse of the expected transition time. When selection against deleterious single mutations is strong, kc, depends on the recombination fraction r between the two loci. Recombination generally reduces the rate of compensatory evolution because it breaks up favorable combinations of double mutants. For complete linkage, kc, is given by the rate at which favorable combinations of double mutantS are produced by compensatory mutation. For r &gt; 0, kc, decreases exponentially with r. In contrast, kc, becomes independent of r for weak selection. We discuss the dynamics of evolutionary substitutions of compensatory mutants in relation to Wright'S shifting balance theory of evolution and use our results to analyze the substitution process in helices of mRNA secondary structures.
SEC3 Mutations Are Synthetically Lethal With Profilin Mutations and Cause Defects in Diploid-Specific Bud-Site Selection
Authors: Haarer B K , Corbett A , Kweon Y , Petzold A S , Silver P , Brown S S 
Published: January 2021

Abstract
Replacement of the wild-type yeast profilin gene (PFY1) with a mutated form (pfy1-111) that has codon 72 changed to encode glutamate rather than arginine results in defects similar to, but less severe than, those that result from complete deletion of the profilin gene. We have used a colony color-sectoring assay to identify mutations that cause pfy1-111, but not wild-type, cells to be inviable. These profilin synthetic lethal (psl) mutations result in various degrees of abnormal growth, morphology, and temperature sensitivity in PFY1 cells. We have examined psl1 strains in the most detail. Interestingly, these strains display a diploid-specific defect in bud-site selection; haploid strains bud normally, while homozygous diploid strains show a dramatic increase in random budding. We discovered that PSL1 is the late secretory gene, SEC3, and have found that mutations in several other late secretory genes are also synthetically lethal with pfy1-111. Our results are likely to reflect an interdependence between the actin cytoskeleton and secretory processes in directing cell polarity and growth. Moreover, they indicate that the secretory pathway is especially crucial for maintaining budding polarity in diploids.
Targeted Mutagenesis of a Candidate t Complex Responder Gene in Mouse t Haplotypes Does Not Eliminate Transmission Ratio Distortion
Authors: Ewulonu U Kevin , Schimenti Kerry , Kuemerle Barbara , Magnuson Terry , Schimenti John 
Published: January 2021

Abstract
Transmission ratio distortion (TRD) associated with mouse t haplotypes causes +/t males to transmit the t-bearing chromosome to nearly all their offspring. Of the several genes involved in this phenomenon, the t complex responder (Tcrt) locus is absolutely essential for TRD to occur. A candidate Tcrt gene called Tcpl0bt was previously cloned from the genetically defined Tcrt region. Its location, restricted expression in testis, and a unique postmeiotic alternative splicing pattern supported the idea that Tcp10bt was Tcrt. To test this hypothesis in a functional assay, ES cells were derived from a viable partial t haplotype, and the Tcp10bt gene was mutated by homologous recombination. Mutant mice were mated to appropriate partial t haplotypes to determine whether the targeted chromosome exhibited transmission ratios characteristic of the responder. The results demonstrated that the targeted chromosome retained full responder activity. Hence, Tcp10bt does not appear to be Tcrt. These and other observations necessitate a reevaluation of genetic mapping data and the actual nature of the responder.
Synteny Conservation and Chromosome Rearrangements During Mammalian Evolution
Authors: Ehrlich Jason , Sankoff David , Nadeau Joseph H 
Published: January 2021

Abstract
An important problem in comparative genome analysis has been defining reliable measures of synteny conservation. The published analytical measures of synteny conservation have limitations. Nonindependence of comparisons, conserved and disrupted syntenies that are as yet unidentified, and redundant rearrangements lead to systematic errors that tend to overestimate the degree of conservation. We recently derived methods to estimate the total number of conserved syntenies within the genome, counting both those that have already been described and those that remain to be discovered. With this method, we show that ~65% of the conserved syntenies have already been identified for humans and mice, that rates of synteny disruption vary ~25-fold among mammalian lineages, and that despite strong selection against reciprocal translocations, inter-chromosome rearrangements occurred approximately fourfold more often than inversions and other intra-chromosome rearrangements, at least for lineages leading to humans and mice.
The Yeast HRS1 Gene Is Involved in Positive and Negative Regulation of Transcription and Shows Genetic Characteristics Similar to SIN4 and GAL11
Authors: Piruat José I , Chávez Sebastián , Aguilera Andrés 
Published: January 2021

Abstract
We provide genetic evidence that HRS1/PGD1, a yeast gene previously identified as a suppressor of the hyper-recombination phenotype of hpr1, has positive and negative roles in transcriptional regulation. We have analyzed three differently regulated promoters, GAL1, PHO5 and HSP26, by β-galactosidase assays of lacZ-fused promoters and by Northern analysis of the endogenous genes. Transcription of these promoters was derepressed in hrs1Δ mutants under conditions in which it is normally repressed in wild type, Under induced conditions it was either strongly reduced or significantly enhanced depending on the promoter system analyzed. Constitutive transcription was not affected, as determined in ADH1 and TEF2. In addition, Hrs1p was required for mating-factor expression, telomere-linked DNA silencing and DNA supercoiling of plasmids. Furthermore, hrs1Δ suppressed Ty-insertion mutations and conferred a Gal−-phenotype. Many of these phenotypes also result from mutations in GAL11, SIN4 or RGR1, which encode proteins of the RNA polII mediator. We also show that gal11Δ and sin4Δ partially suppress the hyper-rec phenotype of hpr1 mutants, although to a lesser extent than hrs1Δ. Our results provide new evidence for the connection between hrs1Δ-induced deletions and transcription. We discuss the possibility that Hrs1p might be a component of the RNA polII transcription machinery.
The Accumulation of P-Element-Induced Recombinants in the Germline of Male Drosophila melanogaster
Authors: Tanaka Mark M , Liang Xu-Mei , Gray Yasmine H M , Sved John A 
Published: January 2021

Abstract
P-element-induced recombination in Drosophila melanogaster occurs premeiotically. Recombinants are therefore expected to accumulate in the stem cells of the germline of Pelement-carrying males. We show that both the recombination frequency and the incidence of “clustering” increase with the age of males carrying various P-element derivatives. The combination of end-deleted elements can lead to average recombination frequencies &gt;50% with individual instances of 100% recombination. These elements also lowered the fertility of the carriers. We investigated these features by constructing an analytical and a computer simulation model of the course of events in the germline, incorporating the recently proposed hybrid element insertion (HEI) model of Pelement activity. The model is able to predict extreme recombination levels, segregation ratio biases and lowered fertility through cell death in a single analysis.
Geographic Structure of Mitochondrial and Nuclear Gene Polymorphisms in Australian Green Turtle Populations and Male-Biased Gene Flow
Authors: FitzSimmons Nancy N , Moritz Craig , Limpus Colin J , Pope Lisa , Prince Robert 
Published: January 2021

Abstract
The genetic structure of green turtle (Chelonia mydas) rookeries located around the Australian coast was assessed by (1) comparing the structure found within and among geographic regions, (2) comparing microsatellite loci vs. restriction fragment length polymorphism analyses of anonymous single copy nuclear DNA (ascnDNA) loci, and (3) comparing the structure found at nuclear DNA markers to that of previously analyzed mitochondrial (mtDNA) control region sequences. Significant genetic structure was observed over all regions at both sets of nuclear markers, though the microsatellite data provided greater resolution in identifying significant genetic differences in pairwise tests between regions. Inferences about population structure and migration rates from the microsatellite data varied depending on whether statistics were based on the stepwise mutation or infinite allele model, with the latter being more congruent with geography. Estimated rates of gene flow were generally higher than expected for nuclear DNA (nDNA) in comparison to mtDNA, and this difference was most pronounced in comparisons between the northern and southern Great Barrier Reef (GBR). The genetic data combined with results from physical tagging studies indicate that the lack of nuclear gene divergence through the GBR is likely due to the migration of sGBR turtles through the courtship area of the nGBR population, rather than male-biased dispersal. This example highlights the value of combining comparative studies of molecular variation with ecological data to infer population processes.
THE ISLAND MODEL OF POPULATION DIFFERENTIATION: A GENERAL SOLUTION
Authors: Latter B D H 
Published: January 2021

ABSTRACT
The island model deals with a species which is subdivided into a number of discrete finite populations, races or subspecies, between which some migration occurs. If the number of populations is small, an assumption of equal rates of migration between each pair of populations may be reasonable approximation. Mutation at a constant rate to novel alleles may also be assumed.—A general solution is given for the process of population divergence under this model following subdivision of a single parental population, expressed in terms of the observed average frequency of heterozygotes within and between subpopulations at a randomly chosen set of independently segregating loci. No restriction is imposed on the magnitude of the migration or mutation rates involved, nor on the number of populations exchanging migrants.—The properties of two fundamental measures of genetic divergence are deduced from the theory. One is a parameter related to φ, the coefficient of kinship, and the other, γ, measures the rate of mutational divergence between the sub-populations.
THE GENETIC CONSTITUTION OF TANDEM DUPLICATIONS OF THE rII OF BACTERIOPHAGE T4D
Authors: Parma David H , Snyder Marlene 
Published: January 2021

ABSTRACT
Methods for genetically mapping the end points of tandem duplicatictions of the rII region of bacteriophage T4D are presented. Analysis of ten duplications indicates (1) that the position of duplication end points and therefore the length of the duplicated segment differ in strains of independent origin; (2) that there is a direct relationship between segregation frequency and length; (3) that segregation is more frequent than expected on the basis of standard genetic mapping; and (4) that while duplications frequently include non-rII genetic material, frequently they do not include the entire rII region. The duplications studied range from less than two to about five cistrons in length.
THE PHYLOGENETIC RELATIONSHIPS OF THE MEMBERS OF THE DROSOPHILA ROBUSTA GROUP
Authors: Narayanan Yamuna 
Published: January 2021

ABSTRACT
The phylogenetic relationships among the species of the D. robusta group were investigated by the analysis of chromosomal differences. Six of the ten known members of the D. robusta group were available for the study: D. colorata and D. robusta from the United States, and D. sordidula, D. pseudosordidula, D. lacertosa, and D, moriwakii from Japan. Analysis of the metaphase chromosomes from larval ganglion cells suggests that D. moriwakii and D. colorata, with rod-shaped X-chromosomes, are the more ancestral species, while D. sordidula, D. pseudosordidula, D. robusta, and D. lacertosa, with Vshaped X-chromosomes, are derived. The ancestral position of D. colorata and D. moriwakii is further strengthened by the fact that these are the two species in the D. robusta group that are cytologically closest to D. nigromelanica of the related D. melanica group. Of the four derived species, D. sordidula was found to be the closest to the ancestral species. The phylogeny based on the analysis of the gene sequences in the homologous chromosomes agreed with that indicated by the metaphase chromosomes. Since all attempts to obtain hybrids were unsuccessful except for the cross involving D. moriwakii females and D. colorata males, photographic maps of the salivary chromosomes were used to determine homology between the chromosomes of the different species. Evidence is presented to indicate that the D. robusta group originated in Asia (Japan), and that there were two migrations to the New World, the first leading to D. robusta, and the second to D. colorata. It is suggested that the route of migrations was across the Bering Land Bridge, and further, that the migrations occurred during the period from late Oligocene to middle Miocene, 20-25 million years ago.