bluuebunny/crossref_metadata_2025_split huggingface dataset:
ON THE FREQUENCY OF UNDETECTABLE RECOMBINATION EVENTS
Authors: Stephens J Claiborne 
Published: January 2021

ABSTRACT
Simple analytical results show that many recombination events occur in such a way as to have no effect on the resultant DNA sequence. The proportion of these undetectable events depends on the population size, mutation rate and recombination rate and is quite large for reasonable values of these quantities. Efforts to estimate recombination rates and frequencies directly from DNA sequence data must, therefore, take this undetectable fraction into account.
DIRECTION OF TRAVEL OF RecBC RECOMBINASE THROUGH BACTERIOPHAGE LAMBDA DNA
Authors: Stahl Franklin W , Kobayashi Ichizo , Thaler David , Stahl Mary M 
Published: January 2021

ABSTRACT
We examined linkage relationships for RecBC-mediated recombination in lytic cycle crosses of λ phages bearing two cohesive end sites (cos) oriented in the same direction. The relationships obtained imply that a given recombinant tends to be packaged from the cos site that is the nearer one to the right of the exchange. In view of the previously established coupling of entry of a recombinase at a cos cut and initiation of DNA packaging by that cos cut, these results imply that the recombinase (presumably the RecBC gene product) enters λ's chromosome at the right end.
NICHE EXPANSION IN BACTERIA: CAN INFECTIOUS GENE EXCHANGE AFFECT THE RATE OF EVOLUTION?
Authors: Evans Ralph 
Published: January 2021

ABSTRACT
Recombination occurs by infectious gene transfer in bacteria, at rates much lower than recombination by sexual reproduction in other organisms. Thus, recombination may accelerate evolution in bacteria only under restricted conditions, such as occur when mutations at several loci are required for the evolution of an expanded ecological niche. Mathematical ("chemostat") models of several such cases—evolution of independence from three limiting essential or "interactive-essential" resources; evolution of the ability to use three new substitutable resources; and evolution of resistance to three growth inhibitors—were analyzed by computer simulation. All combinations of three mutation rates (U) and four values for the "infectious gene transfer rate parameter" (χ) were considered. Recombination accelerated evolution most when U was low and χ was high, but was unlikely to have large effects when χ was low enough to be realistic for natural populations of Escherichia coli. Recombination had the largest effects when resources were substitutable, and in that case could have substantially reduced the chance of random loss of the favored "triple mutant" while it was still rare. The simulations also revealed some interesting features of selection for an expanded niche. Evolution of independence from essential resources occurred more rapidly when the resources were weakly complementary than when they did not interact. Selection for the ability to use all substitutable resources was weak after all intermediate types that used only one or two of the resources had arisen.
VARIABILITY OF EVOLUTIONARY RATES OF DNA
Authors: Gillespie John H 
Published: January 2021

ABSTRACT
A statistical analysis of DNA sequences from four nuclear loci and five mitochondrial loci from different orders of mammals is described. A major aim of the study is to describe the variation in the rate of molecular evolution of proteins and DNA. A measure of rate variability is the statistic R, the ratio of the variance in the number of substitutions to the mean number. For proteins, R is found to be in the range 0.16 &lt; R &lt; 35.55, thus extending in both directions the values seen in previous studies. An analysis of codons shows that there is a highly significant excess of double substitutions in the first and second positions, but not in the second and third or first and third positions. The analysis of the dynamics of nucleotide evolution showed that the ergodic Markov chain models that are the basis of most published formulas for correcting for multiple substitutions are incompatible with the data. A bootstrap procedure was used to show that the evolution of the individual nucleotides, even the third positions, show the same variation in rates as seen in the proteins. It is argued that protein and silent DNA evolution are uncoupled, with the evolution at both levels showing patterns that are better explained by the action of natural selection than by neutrality. This conclusion is based primarily on a comparison of the nuclear and mitochondrial results.
HYBRID DYSGENESIS-INDUCED REVERTANTS OF INSERTIONS AT THE 5' END OF THE RUDIMENTARY GENE IN DROSOPHILA MELANOGASTER: TRANSPOSON-INDUCED CONTROL MUTATIONS
Authors: Tsubota Stuart , Schedl Paul 
Published: January 2021

ABSTRACT
Mutations in the 5' control region of the rudimentary (r) gene of Drosophila melanogaster were generated by using hybrid dysgenesis to mobilize P elements that were already inserted within this region. Eighteen new mutations out of 7793 chromosomes were isolated. Among the mutations were small insertions, deletions and inversions. All five of the deletions deleted into the 5' coding region of the r gene resulting in a severe mutant phenotype. The inversions and small insertions left the coding region intact, but altered the 5' control region. Northern analyses of the message levels in adult females indicated that these mutations alter the amount of the wild-type rudimentary message. These data also indicated that there is a region about 800 bp upstream of the start of transcription which is necessary for normal r expression. This region is not involved with the temporal and spatial regulation of r gene expression, but with the quantitative expression. An analysis of the DNA changes associated with each of the mutations demonstrates that P elements usually mobilize in an imprecise manner. Of the 22 mutations that have been isolated to date, only three are precise excisions. This means that P elements are potent mutators of the genome.
THE INFLUENCE OF GENETIC BACKGROUND AND THE HOMOLOGOUS CHROMOSOME 17 ON t-HAPLOTYPE TRANSMISSION RATIO DISTORTION IN MICE
Authors: Gummere Gregory R , McCormick Paulette J , Bennett Dorothea 
Published: January 2021

ABSTRACT
Transmission ratio distortion is a characteristic of complete t-haplotypes, such that heterozygous males preferentially transmit the t-haplotype bearing chromosome 17 to the majority of their progeny. At least two genes contained within the t-haplotype have been identified as being required for such high transmission ratios. In this study we examine the effects of the genetic background and the chromosome homologous to the t-haplotype on transmission ratio distortion. We use two different congenic lines: (1) BTBRTF/Nev.Ttf/t12, in which the t12 haplotype has a transmission ratio of 52%, and (2) C3H/DiSn.Ttf/t12, in which the t12 haplotype has a transmission ratio of 99%. By intercrossing these two strains to produce reciprocal F1 and F2 generations, we have isolated the effects of the homologous chromosome 17 from the effects of the genetic background. We demonstrate that both the homologous chromosome and the genetic background have profound effects on t-haplotype transmission ratio distortion. Furthermore, it is evident that the t-haplotype transmission ratio behaves as a quantitative character rather than an intrinsic property of t-haplotypes.
THE MOLECULAR EVOLUTION OF ACTIN
Authors: Hightower Robin C , Meagher Richard B 
Published: January 2021

ABSTRACT
We have investigated the molecular evolution of plant and nonplant actin genes comparing nucleotide and amino acid sequences of 20 actin genes. Nucleotide changes resulting in amino acid substitutions (replacement substitutions) ranged from 3-7% for all pairwise comparisons of animal actin genes with the following exceptions. Comparisons between higher animal muscle actin gene sequences and comparisons between higher animal cytoplasmic actin gene sequences indicated &lt;3% divergence. Comparisons between plant and nonplant actin genes revealed, with two exceptions, 11-15% replacement substitution. In the analysis of plant actins, replacement substitution between soybean actin genes SAc1, SAc3, SAc4 and maize actin gene MAc1 ranged from 8-10%, whereas these members within the soybean actin gene family ranged from 6-9% replacement substitution. The rate of sequence divergence of plant actin sequences appears to be similar to that observed for animal actins. Furthermore, these and other data suggest that the plant actin gene family is ancient and that the families of soybean and maize actin genes have diverged from a single common ancestral plant actin gene that originated long before the divergence of monocots and dicots. The soybean actin multigene family encodes at least three classes of actin. These classes each contain a pair of actin genes that have been designated kappa (SAc1, SAc6), lambda (SAc2, SAc4) and mu (SAc3, SAc7). The three classes of soybean actin are more divergent in nucleotide sequence from one another than higher animal cytoplasmic actin is divergent from muscle actin. The location and distribution of amino acid changes were compared between actin proteins from all sources. A comparison of the hydropathy of all actin sequences, except from Oxytricha, indicated a strong similarity in hydropathic character between all plant and nonplant actins despite the greater number of replacement substitutions in plant actins. These protein sequence comparisons are discussed with respect to the demonstrated and implicated roles of actin in plants and animals, as well as the tissue-specific expression of actin.
DEVELOPMENTALLY REGULATED RNA TRANSCRIPTS CODING FOR ALCOHOL DEHYDROGENASE IN DROSOPHILA AFFINIDISJUNCTA
Authors: Rowan Robert G , Brennan Mark D , Dickinson W J 
Published: January 2021

ABSTRACT
The organization of the gene coding for alcohol dehydrogenase (Adh) in Drosophila affinidisjuncta has been determined by physically mapping Adh RNA transcripts to cloned genomic DNA. Two distinct transcript types accumulate with developmental specificity. Because only a single genomic Adh locus is detected in D. affinidisjuncta, and since all Adh transcripts appear to be identical except at their termini, the two Adh RNA types are products of the same gene. One type of transcript, abundant in adults, contains a small 5' terminal exon that is completely lacking in the other type of transcript, which accumulates in larvae. This 5' end difference suggests that the D. affinidisjuncta Adh gene, like the homologous gene from the distantly related species D. melanogaster, is expressed from two promoters. According to the transcription map, these D. affinidisjuncta promoters are separated by approximately 560 base pairs of genomic DNA sequence. D. affinidisjuncta Adh transcripts also resemble D. melanogaster Adh transcripts in both their overall organization and their developmental distribution. Multiple 3' ends are responsible for the size heterogeneity of both types of D. affinidisjuncta Adh RNA, and some of these also appear with stage specificity.
A QUANTITATIVE MODEL FOR NONRANDOM GENERALIZED TRANSDUCTION, APPLIED TO THE PHAGE P22–SALMONELLA TYPHIMURIUM SYSTEM
Authors: Mandecki W , Krajewska-Grynkiewicz K , Klopotowski T 
Published: January 2021

ABSTRACT
A mathematical model for nonrandom generalized transduction is proposed and analyzed. The model takes into account the finite number of transducing particle classes for any given marker. The equations for estimation of the distance between markers from cotransduction frequency data are derived and standard errors of the estimates are given. The obtained relationships depend significantly on the number of classes of transducing fragments. The model was applied to estimate the number of transducing fragment classes for a given marker in transduction with phage P22 of Salmonella typhimurium. It was found that the literature data on frequencies of cotransduction in crosses with mutual substitution of selective and nonselective markers can be rationalized most accurately by assuming that the mean number of classes is equal to 2. An improved method for analysis of cotransduction data is proposed on the basis of our model and the results of calculation. The method relies on solving a set of algebraic equations for cotransduction frequencies of markers located within one phage length. The method allows a relatively precise determination of distances between markers, positions of transducing particle ends and deletion or insertion lengths. The approach is applied to the trp-cysB-pyrF and aroC-hisT-purF-dhuA regions of the Salmonella typhimurium chromosome.
STABLE NON-MUTATOR STOCKS OF MAIZE HAVE SEQUENCES HOMOLOGOUS TO THE Mu1 TRANSPOSABLE ELEMENT
Authors: Chandler Vicki , Rivin Carol , Walbot Virginia 
Published: January 2021

ABSTRACT
Mutator stocks of maize produce mutants at many loci at rates 20- to 50-fold above spontaneous levels. Current evidence suggests that this high mutation rate is mediated by an active transposable element system, Mu. Members of this transposable element family are found in ~10-60 copies in Mutator stocks. We report here an initial characterization of previously undetected sequences homologous to Mu elements in eight non-Mutator inbred lines and varieties of maize that have a normal low mutation rate. All stocks have ~40 copies of sequences homologous only to the terminal repeat and show weak homology to an internal probe. In addition, several of the stocks contain an intact Mu element. One intact Mu element and two terminal-specific clones have been isolated from one non-Mutator line, B37. The cloned sequences have been used to demonstrate that in genomic DNA the intact element, termed Mu1.4B37, is modified, such that restriction sites in its termini are not accessible to cleavage by the HinfI restriction enzyme. This modification is similar to that observed in Mutator lines that have lost activity. We hypothesize that the DNA modification of the Mu-like element may contribute to the lack of Mutator activity in B37.
BACTERIOPHAGE T4 ENDONUCLEASES II AND IV, OPPOSITELY AFFECTED BY dCMP HYDROXYMETHYLASE ACTIVITY, HAVE DIFFERENT ROLES IN THE DEGRADATION AND IN THE RNA POLYMERASE-DEPENDENT REPLICATION OF T4 CYTOSINE-CONTAINING DNA
Authors: Carlson Karin , Ȗvervatin Aud 
Published: January 2021

ABSTRACT
Bacteriophage T4 mutants defective in gene 56 (dCTPase) synthesize DNA where cytosine (Cyt) partially or completely replaces hydroxymethylcytosine (HmCyt). This Cyt-DNA is degraded in vivo by T4 endonucleases II and IV, and by the exonuclease coded or controlled by genes 46 and 47.—Our results demonstrate that T4 endonuclease II is the principal enzyme initiating degradation of T4 Cyt-DNA. The activity of endonuclease IV, but not that of endonuclease II, was stimulated in the presence of a wild-type dCMP hydroxymethylase, also when no HmCyt was incorporated into phage DNA, suggesting the possibility of direct endonuclease IV-dCMP hydroxymethylase interactions. Endonuclease II activity, on the other hand, was almost completely inhibited in the presence of very small amounts of HmCyt (3-9% of total Cyt + HmCyt) in the DNA. Possible mechanisms for this inhibition are discussed.—The E. coli RNA polymerase modified by the products of T4 genes 33 and 55 was capable of initiating DNA synthesis on a Cyt-DNA template, although it probably cannot do so on an HmCyt template. In the presence of an active endonuclease IV, Cyt-DNA synthesis was arrested 10-30 min after infection, probably due to damage to the template. Cyt-DNA synthesis dependent on the unmodified (33 - 55 -) RNA polymerase was less sensitive to endonuclease IV action.
GENERAL NONCHEMOTACTIC MUTANTS OF CAULOBACTER CRESCENTUS
Authors: Ely Bert , Gerardot Connie J , Fleming Donna L , Gomes Suely L , Frederikse Peter , Shapiro Lucille 
Published: January 2021

ABSTRACT
We have examined 35 mutants that have defects in general chemotaxis. Genetic analysis of these mutants resulted in the identification of at least eight che genes located at six different positions on the Caulobacter crescentus chromosome. The cheR, cheB and cheT genes appeared to be located in a three-gene cluster. Mutations in these three genes resulted in the inability of the flagellum to reverse the direction of rotation. Defects in the cheR gene resulted in a loss of the ability to methylate the methyl-accepting chemotaxis proteins. In vitro experiments showed that the lack of in vivo methylation in cheR mutants was due to the absence of methyltransferase activity. Defects in the cheB gene resulted in greatly reduced chemotaxis-associated methylation in vivo and a loss of methylesterase activity in vitro. The specific defects responsible for the lack of a chemotactic response have not been determined for the other identified che genes.
THE SELECTION LIMIT DUE TO THE CONFLICT BETWEEN TRUNCATION AND STABILIZING SELECTION WITH MUTATION
Authors: Zeng Zhao-Bang , Hill William G 
Published: January 2021

ABSTRACT
Long-term selection response could slow down from a decline in genetic variance or in selection differential or both. A model of conflict between truncation and stabilizing selection in infinite population size is analysed in terms of the reduction in selection differential. Under the assumption of a normal phenotypic distribution, the limit to selection is found to be a function of κ, the intensity of truncation selection, ω 2, a measure of the intensity of stabilizing selection, and σ 2, the phenotypic variance of the character. The maintenance of genetic variation at this limit is also analyzed in terms of mutation-selection balance by the use of the "House-of-cards" approximation. It is found that truncation selection can substantially reduce the equilibrium genetic variance below that when only stabilizing selection is acting, and the proportional reduction in variance is greatest when the selection is very weak. When truncation selection is strong, any further increase in the strength of selection has little further influence on the variance. It appears that this mutation-selection balance is insufficient to account for the high levels of genetic variation observed in many long-term selection experiments.
Synthesis of a trans-Acting Inhibitor of DNA Maturation by Prohead Mutants of Phage Λ
Authors: Murialdo Helios , Fife Wendy L 
Published: January 2021

ABSTRACT
Bacteriophage λ with mutations in genes that control prohead assembly and other head precursors cannot mature their DNA. In this paper we present evidence that the failure of these phage mutants to mature DNA is a reflection of a mechanism that modulates terminase nicking activity during normal phage development. We have constructed plasmids that contain the λ-cohesive end site (cos) and the genes that code for DNA terminase, the enzyme that matures DNA by cutting at cos. The DNA terminase genes are under control of a thermosensitive cI repressor. These plasmids lack most of the genes involved in prohead morphogenesis and other head precursors. However, when repression is lifted by destruction of the thermosensitive repressor, the terminase synthesized is able to cut almost 100% of the plasmids. Therefore, these plasmids can mature in the absence of proheads and other head gene products. The plasmids are also able to complement mutants of λ deficient in terminase and DNA maturation. However, in these complementation experiments, if the phage carry mutations in prohead genes E or B, not only is phage DNA maturation blocked, but the plasmid also fails to mature. These experiments show that, in the absence of proheads, phage λ produces a trans-acting inhibitor of maturation. The genetic determinant of this inhibitor maps in a region extending from the middle of gene B to the end of gene C. A model is proposed in which the nicking activity of DNA-bound terminase is inhibited by the trans-acting inhibitor. Prohead (and other factors) binding to this complex would release the block to allow DNA cleavage and packaging.
Protease B of Saccharomyces cerevisiae: Isolation and Regulation of the PRB1 Structural Gene
Authors: Moehle Charles M , Aynardi Martha W , Kolodny Michael R , Park Frances J , Jones Elizabeth W 
Published: January 2021

ABSTRACT
We have isolated the structural gene, PRB1, for the vacuolar protease B of Saccharomyces cerevisiae from a genomic library by complementation of the prb1-1122 mutation. Deletion analysis localized the complementing activity to a 3.2-kilobase pair XhoI-HindIII restriction enzyme fragment. The fragment was used to identify a 2.3-kilobase mRNA. S1 endonuclease mapping indicated that the mRNA and the gene were colinear. No introns were detected. The mRNA is of sufficient size to encode a protein of about 69,000 molecular weight, a number much larger than either the mature enzyme (≃30,000 protein molecular weight) or the sole reported precursor (≃39,000 protein molecular weight). These results suggest that proteolytic processing steps beyond that thought to be catalyzed by protease A may be required to convert the initial glycosylated translation product into mature protease B. The PRB1 mRNA is made in substantial amounts only when the cells have exhausted the glucose supply and enter the diauxic plateau. There is an extended time lag between PRB1 transcription and expression of protease B activity. A deletion that removes about 83% of the coding region was constructed as a diploid heterozygote. Spores bearing the deletion germinate, grow at normal rates into colonies, and have no obvious phenotype beyond protease B deficiency.
First Evidence for Diploidy and Genetic Recombination in Free-Living Amoebae of the Genus Naegleria on the Basis of Electrophoretic Variation
Authors: Cariou Marie Louise , Pernin Pierre 
Published: January 2021

ABSTRACT
Electrophoretic variation for 15 enzyme-coding genes was studied in various Naegleria (Rhizopoda, Vahlkampfiidae) species. The occurrence of complex banding patterns provided the first evidence of a diploid structure of the genome of these amoebae. The putative loci identified were found not to be linked and the genotypic distribution suggested chromosomal recombination for one species (Naegleria lovaniensis).
Evolution under Fertility and Viability Selection
Authors: Nagylaki Thomas 
Published: January 2021

ABSTRACT
Evolution at a single multiallelic locus under arbitrary weak selection on both fertility and viability is investigated. Discrete, nonoverlapping generations are posited for autosomal and X-linked loci in dioecious populations, but monoecious populations are studied in both discrete and continuous time. Mating is random. The results hold after several generations have elapsed. With an error of order s [i.e., O(s)], where s represents the selection intensity, the population evolves in Hardy-Weinberg proportions. Provided the change per generation of the fertilities and viabilities due to their explicit time dependence (if any) is O(s 2), the rate of change of the deviation from Hardy-Weinberg proportions is O(s 2). If the change per generation of the viabilities and genotypic fertilities is smaller than second order [i.e., o(s 2)], then to O(s 2) the rate of change of the mean fitness is equal to the genic variance. The mean fitness is the product of the mean fertility and the mean viability; in dioecious populations, the latter is the unweighted geometric mean of the mean viabilities of the two sexes. Hence, as long as there is significant gene frequency change, the mean fitness increases. If it is the fertilities of matings that change slowly [at rate o(s 2)], the above conclusions apply to a modified mean fitness, defined as the product of the mean viability and the square root of the mean fertility.