bluuebunny/crossref_metadata_2025_split huggingface dataset:
THE EVOLUTION OF RESTRICTED RECOMBINATION AND THE ACCUMULATION OF REPEATED DNA SEQUENCES
Authors: Charlesworth Brian , Langley Charles H , Stephan Wolfgang 
Published: January 2021

ABSTRACT
We suggest hypotheses to account for two major features of chromosomal organization in higher eukaryotes. The first of these is the general restriction of crossing over in the neighborhood of centromeres and telomeres. We propose that this is a consequence of selection for reduced rates of unequal exchange between repeated DNA sequences for which the copy number is subject to stabilizing selection: microtubule binding sites, in the case of centromeres, and the short repeated sequences needed for terminal replication of a linear DNA molecule, in the case of telomeres. An association between proximal crossing over and nondisjunction would also favor the restriction of crossing over near the centromere. The second feature is the association between highly repeated DNA sequences of no obvious functional significance and regions of restricted crossing over. We show that highly repeated sequences are likely to persist longest (over evolutionary time) when crossing over is infrequent. This is because unequal exchange among repeated sequences generates single copy sequences, and a population that becomes fixed for a single copy sequence by drift remains in this state indefinitely (in the absence of gene amplification processes). Increased rates of exchange thus speed up the process of stochastic loss of repeated sequences.
DNA SYNTHESIS AT THE SITE OF A Red-MEDIATED EXCHANGE IN PHAGE Λ
Authors: Stahl Franklin W , Stahl Mary M 
Published: January 2021

ABSTRACT
In phage λ, progeny particles bearing unreplicated chromosomes are recombinant by action of λ's Red system only near the right end of the chromosome. These recombinants are frequently heterozygous (heteroduplex) for markers located there. In replication-blocked crosses involving two heavy-labeled parents we find that particles in the solitary peak, containing progeny with fully conserved DNA, vary in density. Those on the heavy side of this peak are more apt to be heterozygous than are those on the light side. The data fit a model in which a double chain cut at cos, λ's packaging origin, is followed by partial exonucleolytic degradation of λ's r chain from the right end leftward. The exposed l chain, which thereby constitutes a 3′ overhang, invades an intact, circular homologue afrter itself suffering some degradation. Completion of the recombinant chromosome sometimes involves DNA synthesis primed by the invading chain.
HYPER-RECOMBINING RECIPIENT STRAINS IN BACTERIAL CONJUGATION
Authors: Feinstein Sheldon I , Low K Brooks 
Published: January 2021

ABSTRACT
Using a direct enrichment and screening procedure, mutants of Escherichia coli have been isolated in which recombination frequencies for several intragenic Hfr × F- crosses are significantly higher (twofold to sixfold) than in the parental strains. These hyper-recombination mutations comprised five new mutS - and one new mutL - allele. Together with other known mut - alleles, they were analyzed for effects on intragenic recombination using several types of crosses. Hyper-recombination was found for mutS -, mutL -, mutH (=mutR)- and mutU (=uvrD)-, with the largest effects seen for certain alleles of uvrD; these resulted in over 20-fold excesses in recombinant production for Hfr × F- crosses and F'-chromosome homogenotization. Spontaneous mutator ability was not always correlated with degree of hyper-recombination.
ENHANCEMENT AND SUPPRESSION OF A EUCHROMATIC POSITION EFFECT AT NOTCH IN DROSOPHILA
Authors: Welshons W J , Welshons H J 
Published: January 2021

ABSTRACT
The recessive visible rough-eye mutant facet-strawberry, faswb, is caused by the deletion of 0.8 kb of base sequences from the 5' end of the Notch locus. Visible deficiencies adjacent to faswb suppress this mutant effect of the Notch locus, and in the same region (between salivary bands 3C1 and 3C7), we have demonstrated the presence of at least one partial suppressor and one enhancer of the faswb position effect at Notch.—The enhancer seems to be a small inversion approximately equal to the salivary-band doublet 3C2, 3, and the partial suppressor lies between the inversion in 3C2, 3 and the small deletion in faswb immediately distal to 3C7. Neither the enhancer, e(faswb), nor the partial suppressor, su(faswb), can be detected except when linked in cis to faswb. The e(faswb) and the su(faswb), in unison, act antagonistically on the faswb position effect.—The faswb mutant is interpreted to be a nonvariegating position effect at the Notch locus resulting from a novel euchromatic—euchromatic association of base sequences caused by the small deletion.
TWO ALLELES OF MAIZE ALCOHOL DEHYDROGENASE 1 HAVE 3' STRUCTURAL AND POLY(A) ADDITION POLYMORPHISMS
Authors: Sachs M M , Dennis E S , Gerlach W L , Peacock W J 
Published: January 2021

ABSTRACT
Two standard electrophoretic alleles of the maize alcohol dehydrogenase 1 locus (Adh1-1S and Adh1-1F) have been isolated and characterized. Restriction endonuclease mapping shows that a region of less than 5 kb is conserved in both alleles and is flanked both 5' and 3' by regions highly polymorphic for restriction sites. Nucleotide sequence comparison of these two alleles reveals that polymorphism in the 3' flanking region is due to rearrangements including tandem duplications, a transposable element-like insertion and a deletion. S1 nuclease analysis shows that both the Adh1-1S and the Adh1-1F alleles contain multiple poly(A) addition sites; four sites are observed for the Adh1-1S alleles and seven sites for the Adh1-1F allele. Only two of these poly(A) addition sites appear to be identical in the two alleles. No consensus signal for poly(A) addition is observed near any of these sites.
GENETIC VARIATION IN THE SHAPE OF THE MOUSE MANDIBLE AND ITS RELATIONSHIP TO GLUCOCORTICOID-INDUCED CLEFT PALATE ANALYZED BY USING RECOMBINANT INBRED LINES
Authors: Lovell D P , Erickson R P 
Published: January 2021

ABSTRACT
Variation in mandible shape has been investigated in a set of recombinant inbred (RI) lines of mice, the C57BL/6J × A/J (BXA;AXB) RI lines. Considerable genetic variation was detected between the RI lines, but most lines were intermediate in shape when compared with the parent lines. Variation in mandible shape could not be explained by any single gene differences known between the parent lines including the H-2 locus. Some RI lines had mandible shapes unlike either parent, and one in particular, line BXA1, had an unusual shape with a pronounced condyloid process. It was concluded that mandible shape has a complex inheritance involving a number of genes, each with small effects. In some cases, recombination of the genes can produce bone shapes quite different from those of the original parent line.—There was no evidence that the variability in steroid-induced palate incidence in the BXA;AXB RI lines is related to the variation in adult mandible shape as detected in this study.
ON THE DIVERGENCE OF ALLELES IN NESTED SUBSAMPLES FROM FINITE POPULATIONS
Authors: Hudson Richard R , Kaplan Norman L 
Published: January 2021

ABSTRACT
Within-population variation at the DNA level will rarely be studied by sequencing of loci of randomly chosen individuals. Instead, individuals will usually be chosen for sequencing based on some knowledge of their genotype. Data collected in this way require new sampling theory. Motivated by these observations, we have examined the sampling properties of a finite population model with two mutation processes and with no selection or recombination. One mutation process generates new alleles according to an infinite-alleles model, and the other generates polymorphisms at sites according to an infinite-sites model. A sample of n genes is considered. The stationary distribution of the number of segregating sites in a subsample from one of the allelic classes in the sample conditional on the allelic configuration of the sample is studied. A recursive scheme is developed to compute the moments of this distribution, and it is shown that the distribution is functionally independent of the number of additional alleles in the sample and their respective frequencies in the sample. For the case in which the sample contains only two alleles, the distribution of the number of segregating sites in a subsample containing both alleles conditional on the sample frequencies of the alleles is studied. The results are applied to the analysis of DNA sequences of two alleles found at the Adh locus of Drosophila melanogaster. No significant departure from the neutral model is detected.
GLUCOSE REPRESSION OF AMYLASE GENE EXPRESSION IN DROSOPHILA MELANOGASTER
Authors: Benkel Bernhard F , Hickey Donal A 
Published: January 2021

ABSTRACT
We have previously shown that dietary glucose can reduce amylase activity in both adults and larvae of Drosophila; this reduction in enzyme activity reflects a reduction in the quantity of amylase protein, rather than an inhibition of enzyme activity. Here, we report that we have now defined conditions in which the repressive effect of glucose can be greater than 100-fold. Moreover, this repression is partially counteracted by the addition of exogenous cyclic AMP. We also show that there is a direct correlation between changes in amylase activity and changes in the amount of translatable mRNA as assayed in microinjected Xenopus oocytes. This means that the glucose repression is occurring at a pretranslational stage.
GENETIC ANALYSIS OF LIVER NEURAMINIDASE ISOZYMES IN RATTUS NORVEGICUS: INDEPENDENT CONTROL OF NEU-1 AND NEU-2 PHENOTYPES
Authors: Samollow Paul B , Vandeberg John L , Ford Allen L , Kunz Heinz W , Gill Thomas J 
Published: January 2021

ABSTRACT
Two recently identified isozymes of neuraminidase in rat liver were examined for transmission patterns and linkage relationships, and for variation among inbred strains. The isozymes, designated neuraminidase-1 (NEU-1) and neuraminidase-2 (NEU-2), exhibited no electrophoretic mobility variants among the 22 inbred strains examined, but did possess striking interstrain variation in activity phenotypes on electrophoretic gels. The results of a backcross analysis involving the KGH and ACP strains revealed that NEU-1 and NEU-2 phenotypes are independently controlled, each by a single autosomal locus with additively acting alleles. The two loci are unlinked to one another, but the gene controlling NEU-1 is tightly linked to RT1, the rat major histocompatibility complex. This gene is almost certainly identical to Neu-1, a gene identified previously through its effect on "total" activity levels of liver neuraminidase as determined by fluorometric assay of tissue homogenates. NEU-2 and the gene controlling its phenotype were not detected by the fluorometric technique. We designate the genes controlling the NEU-1 and NEU-2 phenotypes as Neu-1 and Neu-2, respectively. Data from this and other studies place Neu-1 between Glo-1 and dw-3. The location of Neu-2 is unknown.
CHROMOSOMAL TRANSLOCATIONS GENERATED BY HIGH-FREQUENCY MEIOTIC RECOMBINATION BETWEEN REPEATED YEAST GENES
Authors: Jinks-Robertson Sue , Petes Thomas D 
Published: January 2021

ABSTRACT
We have examined meiotic and mitotic recombination between repeated genes on nonhomologous chromosomes in the yeast Saccharomyces cerevisiae . The results of these experiments can be summarized in three statements. First, gene conversion events between repeats on nonhomologous chromosomes occur frequently in meiosis. The frequency of such conversion events is only 17-fold less than the analogous frequency of conversion between genes at allelic positions on homologous chromosomes. Second, meiotic and mitotic conversion events between repeated genes on nonhomologous chromosomes are associated with reciprocal recombination to the same extent as conversion between allelic sequences. The reciprocal exchanges between the repeated genes result in chromosomal translocations. Finally, recombination between repeated genes on nonhomologous chromosomes occurs much more frequently in meiosis than in mitosis.
STUDIES OF NORMAL AND POSITION-AFFECTED EXPRESSION OF ROSY REGION GENES IN DROSOPHILA MELANOGASTER
Authors: Clark Stephen H , Chovnick Arthur 
Published: January 2021

ABSTRACT
Transformant complementation, intragenic deletions and Northern blot analyses provide unambiguous localization of the l (3) S12 gene immediately proximal to the 5' end of the rosy locus. We have characterized an array of transformants with respect to l (3) S12 and rosy expression. The l (3) S12 gene is exceedingly sensitive to euchromatic site-specific position effects. Unlike the rosy locus, l (3)S12 is insensitive to heterochromatic position effect in rearrangements, as well as in a transformant located in heterochromatin. Cotransformants for both l(3)S12 and rosy elicit no apparent pattern of concordance with respect to euchromatic site-specific position effects. Heterochromatic-euchromatic rearrangements are examined with respect to position effects on expression of the rosy region genes l(3)12, rosy, snake and piccolo, as well as suppressor effects. Clear distinction is seen between euchromatic and heterochromatic effects.
COINCIDENT GENE CONVERSION EVENTS IN YEAST THAT INVOLVE A LARGE INSERTION
Authors: Golin John E , Falco S Carl , Margolskee Jeanne P 
Published: January 2021

ABSTRACT
In yeast, spontaneous gene conversion events involving sites that are far apart (16 cM) occur 1000 times more frequently in mitotic cells than is expected for two independent acts of recombination. It has been proposed that a major portion of these could be due to a long, continuous heteroduplex intermediate. We have examined this possibility in further detail by introducing, via transformation, a large plasmid insertion between the LEU1 and TRP5 loci and studying its behavior among coincident convertants involving the flanking sites. Among such convertants, there is frequent loss of the plasmid when it is present in hemizygous or homozygous configuration. Our results could support the long heteroduplex model for coincident recombination events, but only if novel assumptions regarding the formation and fate of mismatched DNA are made. Therefore, an alternative model that proposes multiple, concerted recombination events is discussed.
Genetic Functions Promoting Homologous Recombination in Escherichia coli: A Study of Inversions in Phage Λ
Authors: Ennis Don G , Amundsen Susan K , Smith Gerald R 
Published: January 2021

ABSTRACT
We have studied homologous recombination in a derivative of phage λ containing two 1.4-kb repeats in inverted orientation. Inversion of the intervening 2.5-kb segment occurred efficiently by the Escherichia coli RecBC pathway but markedly less efficiently by the λ Red pathway or the E. coli RecE or RecF pathways. Inversion by the RecBCD pathway was stimulated by Chi sites located to the right of the invertible segment; this stimulation decreased exponentially by a factor of about 2 for each 2.2 kb between the invertible segment and the Chi site. In addition to RecA protein and RecBCD enzyme, inversion by the RecBC pathway required single-stranded DNA binding protein, DNA gyrase, DNA polymerase I and DNA ligase. Inversion appeared to occur either intra- or intermolecularly. These results are discussed in the framework of a current molecular model for the RecBC pathway of homologous recombination.
On Recombination Among In(2L)t, α-Gpdh and Adh in Drosophila melanogaster
Authors: Malpica J-M , Vassallo J M , Frías A , Fuentes-Bol F 
Published: January 2021

ABSTRACT
The occurrence and patterns of linkage disequilibrium between an inversion and allozymic loci within it or nearby have been used in attempts to discriminate among different hypotheses for the maintenance of variability. The interpretation of the data on the best-documented case, that of the nonrandom association between In(2L)t and ?-Gpdh or Adh in the second chromosome of Drosophila melanogaster, has been done on the basis that recombination between ?-Gpdh and Adh is almost entirely due to the recombination between In(2L)t and the locus within it (?-Gpdh), the recombination between the inversion and the nearby locus (Adh) being negligible. In this paper, we show that the pattern of recombination is just the opposite.
Distribution and Abundance of Insertion Sequences Among Natural Isolates of Escherichia coli
Authors: Sawyer Stanley A , Dykhuizen Daniel E , DuBose Robert F , Green Louis , Mutangadura-Mhlanga T , Wolczyk David F , Hartl Daniel L 
Published: January 2021

ABSTRACT
A reference collection of 71 natural isolates of Escherichia coli (the ECOR collection) has been studied with respect to the distribution and abundance of transposable insertion sequences using DNA hybridization. The data include 1173 occurrences of six unrelated insertion sequences (IS 1, IS2, IS3, IS4, IS5 and IS 30). The number of insertion elements per strain, and the sizes of DNA restriction fragments containing them, is highly variable and can be used to discriminate even among closely related strains. The occurrence and abundance of pairs of unrelated insertion sequences are apparently statistically independent, but significant correlations result from stratifications in the reference collection. However, there is a highly significant positive association among the insertion sequences considered in the aggregate. Nine branching process models, which differ in assumptions regarding the regulation of transposition and the effect of copy number on fitness, have been evaluated with regard to their fit of the observed distributions. No single model fits all copy number distributions. The best models incorporate no regulation of transposition and a moderate to strong decrease in fitness with increasing copy number for IS1 and IS5, strong regulation of transposition and a negligible to weak decrease in fitness with increasing copy number for IS3, and less than strong regulation of transposition for IS2, IS 4 and IS30.
Meiotic Gene Conversion and Crossing Over Between Dispersed Homologous Sequences Occurs Frequently in Saccharomyces cerevisiae
Authors: Lichten Michael , Borts Rhona H , Haber James E 
Published: January 2021

ABSTRACT
We have examined meiotic recombination between two defined leu2 heteroalleles present at the normal LEU2 locus and in leu2-containing plasmids inserted at four other genomic locations. In diploids where the two leu2 markers were present at allelic locations on parental homologs, the frequency of Leu2+ spores varied 38-fold, in a location-dependent manner. These results indicate that recombination in a genetic interval can be modulated by sequences at least 2.7 kb outside that interval. Leu2+ meiotic segregants were also recovered from diploids where LEU2 was marked with one heteroallele, and the other leu2 heteroallele was inserted at another genomic location. These products of ectopic interactions, between dispersed copies of leu2 sharing only 2.2 kb of homology, were recovered at a frequency comparable to that observed in corresponding allelic crosses. This high frequency of ectopic meiotic recombination was observed in crosses where both recombining partners could potentially pair with sequences at an allelic position. In addition, a significant fraction (22-50%) of these ectopic recombinants were associated with crossing over of flanking sequences.
Use of the Multinomial Dirichlet Model for Analysis of Subdivided Genetic Populations
Authors: Jiang C J , Cockerham C Clark 
Published: January 2021

ABSTRACT
The distribution found by compounding the multinomial distribution with the Dirichlet distribution has been suggested as a basis for the estimation of parameters in subdivided populations, in particular of the "correlation between genotypes" within subpopulations. It is shown that the estimators deriving from these procedures perform poorly when the data are generated by the classical Wright drift model of subdivided populations. This conclusion suggests that the compound distribution estimation approach does not provide a good estimation procedure for real populations which are reasonably described by the Wright model.
Mutations that Affect the Efficiency of Translation of mRNA for the cII Gene of Coliphage Lambda
Authors: Dul Ed , Mahoney Michael E , Wulff Daniel L 
Published: January 2021

ABSTRACT
Starting with the λ p RE -strain λctr1 cy3008, which forms clear plaques, we have isolated two mutant strains, λdya2 ctr1 cy3008 and λdya3 ctr1 cy3008, that form plaques with very slightly turbid centers. The dya2 and dya3 mutations lie in the region of overlap between the PRE promoter and the ribosome recognition region of the cII gene, and have nucleotide alterations at positions -1 and +5 of pRE, and alterations of cII mRNA at -16 and -21 nucleotides before the initial AUG codon of the gene. Both mutations destabilize a stem structure that may be formed by cII mRNA, and dya2 also changes the sequence on cII mRNA that is complementary to the 3′-end of 16 S rRNA from 5′-UAAGGA-3′ to 5′-UGAGGA-3′.—The dya2 and dya3 mutations, along with the ctr1 mutation, which destabilizes either of two alternate stem structures which may be formed by cII mRNA (these being more stable stem structures than the one affected by dya2 and dya3), were tested for their ability to reverse two cII - mutations that are characterized by inefficient translation of cII mRNA. These are cII3088, an A → G mutation four bases before the initial AUG codon, and cII3059, a GUU → GAU (Val2 → Asp) second codon mutation. It was found that ctr1 completely reverses the translation defects of these two mutations, while dya2 partially reverses these translation defects. The dya3 mutation has no effect on translation efficiency under any condition tested. However neither the ctr1 mutation nor the dya2 mutation has much effect on translation efficiency in an otherwise cII + background, indicating that other factors must limit the rate of translation of cII mRNA under these conditions.
Cross-Specificities Between cII-like Proteins and pRE-like Promoters of Lambdoid Bacteriophages
Authors: Wulff Daniel L , Mahoney Michael E 
Published: January 2021

ABSTRACT
We have investigated the activation of transcription from the pRE promoters of phages λ, 21 and P22 by the λ and 21 cII proteins and the P22 c1 (cII-like) protein, using an in vivo system in which cII protein from a derepressed prophage activates transcription from a pRE DNA fragment on a multicopy plasmid. We find that each protein is highly specific for its own cognate pRE promoter, although measureable cross-reactions are observed. The primary recognition sequence for cII protein on λ pRE is a pair of TTGC repeat sequences in the sequence 5′-TTGCN6TTGC-3′ at the -35 region of the promoter. This same sequence is found in 21 pRE, while P22 pRE has the sequence 5′-TTGCN6TTGT-3′, which is the same as that of λctr1, a pRE + variant of λ. λctr1 pRE is half as active as λ+ pRE when assayed with either the λ cII or the P22 c1 proteins. Therefore, the single base change in the P22 repeat sequence cannot explain why the P22 c1 protein is much more active with P22 pRE than λ pRE. The dya5 mutation, a G→A change at position -43 of pRE, makes pRE a stronger promoter when assayed with either the λ or 21 cII proteins or the P22 c1 protein. We conclude that efficient activation of a cII-dependent promoter by a cII protein requires sequence information in addition to the TTGC repeat sequences. We do not know the characteristics of the proteins which are responsible for the specificity of each protein for its own cognate promoter. However, λdya8, which has a Glu27→Lys alteration in the λ cII protein and a cII + phenotype, results in a mutant cII protein that is much more highly specific than wild-type cII protein for its own cognate λ pRE promoter. This is especially remarkable because the dya8 amino acid alteration makes the helix-2 region (the region of the protein predicted to make contact with the phosphodiester backbone of the DNA) of λ cII protein conform exactly with the helix-2 region of the P22 c1 protein in both charge and charge distribution.