bluuebunny/crossref_metadata_2025_split huggingface dataset:
Studies on the Recombination Genes of Bacteriophage T4: Suppression of uvsX and uvsY Mutations by uvsW Mutations
Authors: Yonesaki Tetsuro , Minagawa Teiichi 
Published: January 2021

ABSTRACT
Genes uvsW, uvsX and uvsY are dispensable for T4 growth but are implicated in recombination and in the repair of damaged DNA. We found that large-plaque mutants arose efficiently from small-plaque uvsX and uvsY mutants at 42° and were pseudorevertants containing a new mutation in uvsW. Using reconstructed double mutants, we confirmed that a mutation in uvsW partially increases the burst size and UV resistance of uvsX and uvsY mutants. At 41° the uvsW mutation completely restores the arrest in DNA synthesis caused by mutations in genes uvsX, uvsY and 46, but at 30° it only partially restores DNA synthesis in a gene 46 mutant and does not restore DNA synthesis in uvsX and uvsY mutants. Restored DNA synthesis at 41° was paralleled by the overproduction of single-stranded DNA and gene 32 protein. Based on these findings, we propose that the uvsW gene regulates the production of single-stranded DNA and we discuss the phenotype of uvsW mutants and their suppression of some uvsX and uvsY phenotypes. Infection of restrictive cells with am uvsW mutants revealed a defect in the synthesis of a protein of molecular weight 53,000 daltons, suggesting that this protein is the uvsW gene product.
The Regulation of Aldehyde Oxidase in Imaginal Wing Discs of Drosophila Hybrids: Evidence for cis- and trans-Acting Control Elements
Authors: Sprey Th E , Kuhn David T 
Published: January 2021

ABSTRACT
The aldehyde oxidase (Aldox) distribution pattern was determined for wing discs of partial hybrids between D. melanogaster and D. simulans. In these animals the regulation of Aldox activity is not uniform over the disc epithelium as both cis-dominant and trans -acting control were evident in different regions of the disc. The Aldox expression was shown to be regulated by loci on the X chromosome, 2L and 3R of D. melanogaster and 2R and 3R of D. simulans.
Covariance of Inbred Relatives with Special Reference to Selfing
Authors: Wright A J 
Published: January 2021

ABSTRACT
The covariance of inbred relatives from a population in linkage and identity equilibrium in the presence of dominance and epistasis is formulated using a similar procedure to that which B. S. Weir and C. C. Cockerham used to derive a general expression for the genotypic variance. An alternative model based on the description of a genotype in terms of the homozygotes of its constituent alleles is defined which leads to an equivalent set of 21 quadratic components, but when the relatives are descended from a common ancestor by selfing some confounding occurs and only 12 are necessary. This covariance can be subdivided into components arising among families at different levels of the hierarchy generated by a selfing series, and the component among descendants of distinct members of the base population has a different form from those arising at lower levels of the hierarchy. The 12 quadratic components together with an error variance can be estimated using the 20 statistics provided by analyses of variance and covariance of families generated by four generations of selfing.
Persistence of Tandem Arrays: Implications for Satellite and Simple-Sequence DNAs
Authors: Walsh James Bruce 
Published: January 2021

ABSTRACT
Recombination processes acting on tandem arrays are suggested here to have probable intrinsic biases, producing an expected net decrease in array size following each event, in contrast to previous models which assume no net change in array size. We examine the implications of this by modeling copy number dynamics in a tandem array under the joint interactions of sister-strand unequal crossing over (rate γ per generation per copy) and intrastrand recombination resulting in deletion (rate ∊ per generation per copy). Assuming no gene amplification or selection, the expected mean persistence time of an array starting with z excess copies (i.e., array size z + 1) is z(1 + γ/∊) recombinational events. Nontrivial equilibrium distributions of array sizes exist when gene amplification or certain forms of selection are considered. We characterize the equilibrium distribution for both a simple model of gene amplification and under the assumption that selection imposes a minimal array size, n. For the latter case, n + 1/03B1 is an upper bound for mean array size under fairly general conditions, where α(=2∊/γ) is the scaled deletion rate. Further, the distribution of excess copies over n is bounded above by a geometric distribution with parameter α/(1 + α). Tandem arrays are unlikely to be greatly expanded by unequal crossing over unless α &lt;&lt; 1, implying that other mechanisms, such as gene amplification, are likely important in the evolution of large arrays. Thus unequal crossing over, by itself, is likely insufficient to account for satellite DNA.
Mutations that Improve the pRE Promoter of Coliphage Lambda
Authors: Mahoney Michael E , Wulff Daniel L 
Published: January 2021

ABSTRACT
The dya5 mutation, a C→T change at position -43 of the λ pRE promoter, results in a twofold increase in pRE activity in vivo. Smaller increases in pRE activity are found for the dya2 mutation, a T→C change at position -1 of pRE, and the dya3 mutation, an A→G change at +5 of pRE· The mutant pRE promoters retain complete dependence on cII protein for activity. These observations argue, at least for pRE-like promoters, that promoter activities are influenced by nucleotide sequences at least eight nucleotides to the 5′-side of the conventional -35 region consensus sequence, and by nucleotide sequences near the start-site of transcription. Although Hawley and McClure (1983) found A·T pairs more frequently than G·TC pairs in the region of -40 to -45 of prokaryotic promoters, other mutations that change a G·TC pair to an A·T pair at positions -41, -44 and -45 of pRE do not result in increased promoter activity. We also found that a T→C change at position -42 results in a mild decrease in promoter activity. These observations argue that Ts at positions -42 and -43 of pRE are required for maximum promoter activity, but do not support the hypothesis that As and Ts in the -40 to -45 region generally lead to higher promoter activities.
Molecular Evolution and Nucleotide Sequences of the Maize Plastid Genes for the α Subunit of CF1 (atpA) and the Proteolipid Subunit of CF0 (atpH)
Authors: Rodermel Steven R , Bogorad Lawrence 
Published: January 2021

ABSTRACT
The nucleotide sequences of the maize plastid genes for the α subunit of CF1 (atpA) and the proteolipid subunit of CF 0 (atpH) are presented. The evolution of these genes among higher plants is characterized by a transition mutation bias of about 2:1 and by rates of synonymous and nonsynonymous substitution which are much lower than similar rates for genes from other sources. This is consistent with the notion that the plastid genome is evolving conservatively in primary sequence. Yet, the mode and tempo of sequence evolution of these and other plastid-encoded coupling factor genes are not the same. In particular, higher rates of nonsynonymous substitution in atpE (the gene for the ∊ subunit of CF1) and higher rates of synonymous substitution in atpH in the dicot vs. monocot lineages of higher plants indicate that these sequences are likely subject to different evolutionary constraints in these two lineages. The 5′- and 3′ transcribed flanking regions of atpA and atpH from maize, wheat and tobacco are conserved in size, but contain few putative regulatory elements which are conserved either in their spatial arrangement or sequence complexity. However, these regions likely contain variable numbers of "species-specific" regulatory elements. The present studies thus suggest that the plastid genome is not a passive participant in an evolutionary process governed by a more rapidly changing, readily adaptive, nuclear compartment, but that novel strategies for the coordinate expression of genes in the plastid genome may arise through rapid evolution of the flanking sequences of these genes.
Variation in Male Fertilities and Pairwise Mating Probabilities in Picea glauca
Authors: Schoen D J , Stewart S C 
Published: January 2021

ABSTRACT
Frequencies of multilocus male gametes in seeds collected from clones in several blocks of a white spruce seed orchard were analyzed as part of a 2-yr study of mating system variation in this species. Observed frequencies of male gamete types departed significantly from those expected assuming equal male fertilities among clones. Male gamete frequencies in seed crops were significantly heterogeneous among clones within blocks, and among blocks within clones. Clonal male fertilities were estimated from male gamete frequency data. These estimates were highly skewed, with a small proportion of the clones contributing male gametes to the majority of the seed. The estimates were significantly heterogeneous among clones within blocks, and among blocks within clones. Between-year variation in clonal male fertilities was also pronounced, with male fertilities of some clones changing by as much as three orders of magnitude. Clonal male fertility was significantly correlated with clonal male cone production in both years. These results are important with regard to assumptions made for the estimation of general combining ability, average genetic correlation among progeny from single parents, and expected response to selection in open-pollinated plant populations.
X-Y Exchange and the Coevolution of the X and Y rDNA Arrays in Drosophila melanogaster
Authors: Gillings M R , Frankham R , Speirs J , Whalley M 
Published: January 2021

ABSTRACT
The nucleolus organizers on the X and Y chromosomes of Drosophila melanogaster are the sites of 200-250 tandemly repeated genes for ribosomal RNA. As there is no meiotic crossing over in male Drosophila, the X and Y chromosomal rDNA arrays should be evolutionarily independent, and therefore divergent. The rRNAs produced by X and Y are, however, very similar, if not identical. Molecular, genetic and cytological analyses of a series of X chromosome rDNA deletions (bb alleles) showed that they arose by unequal exchange through the nucleolus organizers of the X and Y chromosomes. Three separate exchange events generated compound X·YL chromosomes carrying mainly Y-specific rDNA. This led to the hypothesis that X-Y exchange is responsible for the coevolution of X and Y chromosomal rDNA. We have tested and confirmed several of the predictions of this hypothesis: First, X·YL chromosomes must be found in wild populations. We have found such a chromosome. Second, the X·YL chromosome must lose the YL arm, and/or be at a selective disadvantage to normal X+ chromosomes, to retain the normal morphology of the X chromosome. Six of seventeen sublines founded from homozygous X·YLbb stocks have become fixed for chromosomes with spontaneous loss of part or all of the appended YL. Third, rDNA variants on the X chromosome are expected to be clustered within the X+ nucleolus organizer, recently donated ("Y") forms being proximal, and X-specific forms distal. We present evidence for clustering of rRNA genes containing Type 1 insertions. Consequently, X-Y exchange is probably responsible for the coevolution of X and Y rDNA arrays.
Homoeosis in Drosophila: The Lethal Syndrome of the Regulator of bithorax (or trithorax) Locus and Its Interaction With Other Homoeotic Loci
Authors: Sato Takashi , Denell Robin E 
Published: January 2021

ABSTRACT
Regulator of bithorax (Rg-bx)- [or trithorax (trx)-] lethal zygotes show anterior transformations of various cuticular features of the larval thorax and abdomen. The Rg-bx - lethal syndrome depends on the dosage of the bithorax gene complex (BX-C), and lack of Rg-bx+ function is antagonistic to posterior transformations displayed by Polycomb (Pc)- embryos. Significantly, when the BX-C is deleted, the Rg-bx - embryos disclose homoeosis of mesothoracic to prothoracic cuticular structures. This homoeotic transformation is due to a reduction in Antennapedia (Antp)+ gene activity and is consequently dependent on the dosage of the Antennapedia gene complex (ANT-C), suggesting that the Rg-bx + activity is necessary for proper expression of the Antp + gene. However, the functional relationship between the Rg-bx and Sex combs reduced (Scr) loci in embryogenesis is still to be established.
Linkage of the Steroid Sulfatase Gene to the Sex-Reversed Mutation in the Mouse
Authors: Keitges Elisabeth A , Schorderet Daniel F , Gartler Stanley M 
Published: January 2021

ABSTRACT
Dosage studies and the inheritance pattern of the gene for steroid sulfatase (Sts) in the mouse have previously provided indirect evidence for a functional Y-linked allele which recombines obligatorily with its X-linked allele in male meiosis. In this study, we have investigated the linkage relationship of Sts and the sex-reversed mutation (Sxr), a gene which is known to reside in the pairing region of the Y chromosome. The results clearly demonstrate that Sxr and Sts are linked in a region of obligatory recombination and Sts maps proximal to Sxr with most recombinants occurring proximal to the two genes.
Characterization and in Vivo Cloning of prlC, a Suppressor of Signal Sequence Mutations in Escherichia coli K12
Authors: Trun Nancy J , Silhavy Thomas J 
Published: January 2021

ABSTRACT
The prlC gene of E. coli was originally identified as an allele, prlC1, which suppresses certain signal sequence mutations in the genes for several exported proteins. We have isolated six new alleles of prlC that also confer this phenotype. These mutations can be placed into three classes based on the degree to which they suppress the lamBsignal sequence deletion, lamBs78. Genetic mapping reveals that the physical location of the mutations in prlC correlates with the strength of the suppression, suggesting that different regions of the gene can be altered to yield a suppressor phenotype. We also describe an in vivo cloning procedure using λplacMu9H. The procedure relies on transposition and illegitimate recombination to generate a specialized transducing phage that carries prlC1. This method should be applicable to any gene for which there is a mutant phenotype.
The Cloning and Mapping of ADR6, a Gene Required for Sporulation and for Expression of the Alcohol Dehydrogenase II Isozyme From Saccharomyces cerevisiae
Authors: Taguchi Aileen K W , Young Elton T 
Published: January 2021

ABSTRACT
The alcohol dehydrogenase II (ADH2) gene of the yeast, Saccharomyces cerevisiae, is not transcribed during growth on fermentable carbon sources such as glucose. Growth of yeast cells in a medium containing only nonfermentable carbon sources leads to a marked increase or derepression of ADH2 expression. The recessive mutation, adr6-1, leads to an inability to fully derepress ADH2 expression and to an inability to sporulate. The ADR6 gene product appears to act directly or indirectly on ADH2 sequences 3' to or including the presumptive TATAA box. The upstream activating sequence (UAS) located 5' to the TATAA box is not required for the Adr6- phenotype. Here, we describe the isolation of a recombinant plasmid containing the wild-type ADR6 gene. ADR6 codes for a 4.4-kb RNA which is present during growth both on glucose and on nonfermentable carbon sources. Disruption of the ADR6 transcription unit led to viable cells with decreased ADHII activity and an inability to sporulate. This indicates that both phenotypes result from mutations within a single gene and that the adr6-1 allele was representative of mutations at this locus. The ADR6 gene mapped to the left arm of chromosome XVI at a site 18 centimorgans from the centromere.
Genomic Organization and Developmental Fate of Adjacent Repeated Sequences in a Foldback DNA Clone of Tetrahymena thermophila
Authors: Tschunko Almuth H , Loechel Robert H , McLaren Ning C , Allen Sally Lyman 
Published: January 2021

ABSTRACT
DNA sequence elimination and rearrangement occurs during the development of somatic cell lineages of eukaryotes and was first discovered over a century ago. However, the significance and mechanism of chromatin elimination are not understood. DNA elimination also occurs during the development of the somatic macronucleus from the germinal micronucleus in unicellular ciliated protozoa such as Tetrahymena thermophila. In this study foldback DNA from the micronucleus was used as a probe to isolate ten clones. All of those tested (4/4) contained sequences that were repetitive in the micronucleus and rearranged in the macronucleus. The presence of inverted repeated sequences was clearly demonstrated in one of them by electron microscopy. DNA sequence analysis showed that the left portion of this clone contains three tandem, directly repeated copies of a 340-bp sequence, a 120-bp portion of which appears in inverted orientation at a 1.6-kb distance. This clone, pTtFB1, was subjected to a detailed analysis of its developmental fate. Subregions were subcloned and used as probes against Southern blots of micronuclear and macronuclear DNA. We found that all subregions defined repeated sequence families in the micronuclear genome. A minimum of four different families was defined, two of which are retained in the macronucleus and two of which are completely eliminated. The inverted repeat family is retained with little rearrangement. Two of the families, defined by subregions that do not contain parts of the inverted repeat, one in the "loop" and one in the "right flanking region," are totally eliminated during macronuclear development–and contain open reading frames. A fourth family occurs in the "loop" region and is rearranged extensively during development. The two gene families that are eliminated are stable in the micronuclear genome but are not clustered together as evidenced by experiments in which DNAs from nullisomic strains are used to map family members to specific micronuclear chromosomes. The inverted repeat family is also stable in the micronuclear genome and is dispersed among several chromosomes. The significance of retained inverted repeats to the process of elimination is discussed.
Assessment of X Chromosome Dosage Compensation in Caenorhabditis elegans by Phenotypic Analysis of lin-14
Authors: DeLong Leslie , Casson Lawrence P , Meyer Barbara J 
Published: January 2021

ABSTRACT
Caenorhabditis elegans compensates for the difference in X chromosome gene dose between males (XO) and hermaphrodites (XX) through a mechanism that equalizes the levels of X-specific mRNA transcripts between the two sexes. We have devised a sensitive and quantitative genetic assay to measure perturbations in X chromosome gene expression caused by mutations that affect this process of dosage compensation. The assay is based on quantitating the precocious alae phenotype caused by a mutation that reduces but does not eliminate the function of the X-linked gene lin-14. We demonstrate that in diploid animals the lin-14 gene is dosage compensated between XO and XX animals. In XXX diploid animals, however, lin-14 expression is not compensated, implying that the normal dosage compensation mechanism in C. elegans lacks the capacity to compensate completely for the additional X chromosome in triplex animals. Using the lin-14 assay we compare the effects of mutations in the genes dpy-21, dpy-26, dpy-27, dpy-28, and dpy-22 on X-linked gene expression. Additionally, in the case of dpy-21 we correlate the change in phenotypic expression of lin-14 with a corresponding change in the lin-14 mRNA transcript level.
A Comprehensive Study of Genic Variation in Natural Populations of Drosophila melanogaster. III. Variations in Genetic Structure and Their Causes Between Drosophila melanogaster and Its Sibling Species Drosophila simulans
Authors: Choudhary M , Singh Rama S 
Published: January 2021

ABSTRACT
The natural populations of Drosophila melanogaster and Drosophila simulans were compared for their genetic structure. A total of 114 gene-protein loci were studied in four mainland (from Europe and Africa) and an island (Seychelle) populations of D. simulans and the results were compared with those obtained on the same set of homologous loci in fifteen worldwide populations of D. melanogaster. The main results are as follows: (1) D. melanogaster shows a significantly higher proportion of loci polymorphic than D. simulans (52% vs. 39%, P &lt; 0.05), (2) both species have similar mean heterozygosity and mean number of alleles per locus, (3) the two species share some highly polymorphic loci but they do not share loci that show high geographic differentiation, and (4) D. simulans shows significantly less geographic differentiation than D. melanogaster. The differences in genetic differentiation between the two species are limited to loci located on the X and second chromosomes only; loci on the third chromosome show similar level of geographic differentiation in both species. These two species have previously been shown to differ in their pattern of variation for chromosomal polymorphisms, quantitative and physiological characters, two-dimensional electrophoretic (2DE) proteins, middle repetitive DNA and mitochondrial DNA. Variation in niche-widths and/or genetic "strategies" of adaptation appear to be the main causes of differences in the genetic structure of these two species.
Definition and Estimation of Higher-Order Gene Fixation Indices
Authors: Ritland Kermit 
Published: January 2021

ABSTRACT
Fixation indices summarize the associations between genes that arise from the joint effects of inbreeding and selection. In this paper, fixation indices are derived for pairs, triplets and quadruplets of genes at a single multiallelic locus. The fixation indices are obtained by dividing cumulants by constants; the cumulants describe the statistical distribution of alleles and the constants are functions of gene frequency. The use of cumulants instead of moments is necessary only for four-gene indices, when the fourth cumulant is used. A second type of four-gene index is also required, and this index is based upon the covariation of second-order cumulants. At multiallelic loci, a large number of indices is possible. If alleles are selectively neutral, the number of indices is reduced and the relationship between gene identity and gene cumulants is shown.—Two-gene indices can always be estimated from genotypic frequency data at a single polymorphic locus. Three-gene indices are also estimable except when allele frequency equals one-half. Four-gene indices are not estimable unless selection is assumed to have an equal effect upon each allele (such as under selective neutrality) and the locus contains at least three alleles of unequal frequency. For diallelic or selected loci, an alternative four- gene fixation index is proposed. This index incorporates both types of four-gene associations but cannot be related to gene identity.