bluuebunny/crossref_metadata_2025_split huggingface dataset:
Restriction-stimulated homologous recombination of plasmids by the RecE pathway of Escherichia coli.
Authors: Nussbaum A , Shalit M , Cohen A 
Published: January 2021

Abstract
To test the double-strand break (DSB) repair model in recombination by the RecE pathway of Escherichia coli, we constructed chimeric phages that allow restriction-mediated release of linear plasmid substrates of the bioluminescence recombination assay in infected EcoRI+ cells. Kinetics of DSB repair and expression of recombination products were followed by Southern hybridization and by the bioluminescence recombination assay, respectively. Plasmid recombinants were analyzed with restriction endonucleases. Our results indicate that a DSB can induce more than one type of RecE-mediated recombination. A DSB within the homology induced intermolecular recombination that followed the rules of the DSB repair model: (1) Recombination was enhanced by in vivo restriction. (2) Repair of the break depended on homologous sequences on the resident plasmid. (3) Break-repair was frequently associated with conversion of alleles that were cis to the break. (4) Conversion frequency decreased as the distance from the break increased. (5) Some clones contained a mixture of plasmid recombinants as expected by replication of a heteroduplex in the primary recombinant. The rules of the DSB repair model were not followed when recombination was induced by a DSB outside the homology. Both the cut and the uncut substrates were recipients in conversion events. Recombination events were associated with deletions that spanned the break site, but these deletions did not reach the homology. We propose that a break outside the homology may stimulate a RecE-mediated recombination pathway that does not involve direct participation of DNA ends in the homologous pairing reaction.
Analysis of URSG-mediated glucose repression of the GAL1 promoter of Saccharomyces cerevisiae.
Authors: Flick J S , Johnston M 
Published: January 2021

Abstract
Repression of GAL1 expression during growth on glucose is mediated in part by cis-acting promoter elements designated URSG. We show that oligonucleotides containing sequences from two regions of URSG confer glucose repression upon a heterologous promoter. Repression caused by URSG is dependent on trans-acting factors of the glucose repression pathway and is independent of orientation or location within a promoter, suggesting that URSG contains binding sites for a glucose-activated repressor protein(s). Genetic analysis identified three apparently novel genes (URR1, URR3 and URR4) that are specifically required for URSG-mediated repression and may encode such repressor proteins. Mutations in the URR genes suppress the defect in URSG derepression caused by a snf1 mutation.
Molecular genetic analysis of the mldr mouse: a spontaneous revertant at the mld locus containing a recombinant myelin basic protein gene.
Authors: Ainger K , Barbarese E , Berman L , Carson J H 
Published: January 2021

Abstract
The mld mutation is a complex genetic lesion affecting the myelin basic protein (MBP) locus in the mouse. The mutation consists of a variety of DNA rearrangements including: tandem duplication of the MBP structural gene, partial inversion of the 3' end of the upstream gene copy, duplication of a region flanking the rearrangement junction in the upstream copy and insertion between the two gene copies of a segment of extraneous DNA not associated with the wild-type MBP locus. The net result of the mutation is a dysfunctional MBP locus. Homozygous mld/mld mice produce very little MBP and consequently very little myelin. They exhibit a clinical phenotype characteristic of hypomyelination (shaking, convulsions). We have discovered a revertant mld mouse which does not exhibit clinical symptoms of hypomyelination. Genetic analysis indicates that the reversion is allelic to mld. We have designated the revertant locus mldr. Restriction analysis of mldr genomic DNA indicates that there is a single intact MBP gene. Analysis of various junction regions using the polymerase chain reaction indicates that the single MBP gene in mldr is derived by recombination from the 5' end of the upstream gene and the 3' end of the downstream gene. Studies on MBP expression in mldr mice indicate that the developmental regulation, level of expression and pattern of post-transcriptional processing of MBP gene products in mldr are similar to wild type. These results indicate that the recombinant MBP gene in mldr is fully functional. From this we infer that the MBP-deficient phenotype of the original mld mutant is attributable to the complex rearrangements in the upstream gene copy which render the locus dysfunctional.(ABSTRACT TRUNCATED AT 250 WORDS)
Sources of variation in leaf shape among two populations of Achillea lanulosa.
Authors: Gurevitch J 
Published: January 2021

Abstract
Achillea lanulosa has complex, highly dissected leaves that vary in shape and size along an altitudinal gradient. Plants from a high and an intermediate altitude population were clonally replicated and grown in a controlled environment at warm and cool conditions under bright light. There were genetic differences among populations and among individuals within populations in leaf size and shape. Heritabilities for leaf size and shape characters were moderate. Leaves of the lower altitude population were larger and differed from the higher altitude plants in both coarse and fine shape. Plastic response to temperature of the growth environment paralleled the genetic differentiation between low and high altitude populations. There was no apparent trade-off between genetic control over morphology and the capacity for directional plastic response to the environment. Differences in leaf dissection and size at contrasting altitudes in this species are the result of both genetic divergence among populations and of acclimative responses to local environments.
Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui.
Authors: Mylvaganam S , Dennis P P 
Published: January 2021

Abstract
The halophilic archaebacterium, Haloarcula marismortui, contains two nonadjacent ribosomal RNA operons, designated rrnA and rrnB, in its genome. The 16S rRNA genes within these operons are 1472 nucleotides in length and differ by nucleotide substitutions at 74 positions. The substitutions are not uniformly distributed but rather are localized within three domains of 16S rRNA; more than two-thirds of the differences occur within the domain bounded by nucleotides 508 and 823. This domain is known to be important for P site binding of aminoacylated tRNA and for 30-50S subunit association. Using S1 nuclease protection, it has been shown that the 16S rRNAs transcribed from both operons are equally represented in the functional 70S ribosome population. Comparison of these two H. marismortui sequences to the 16S gene sequences from related halophilic genera suggests that (i) in diverging genera, mutational differences in 16S gene sequences are not clustered but rather are more generally distributed throughout the length of the 16S sequence, and (ii) the rrnB sequence, particularly within the 508-823 domain, is more different from the out group sequences than is the rrnA sequence. Several possible explanations for the evolutionary origin and maintenance of this sequence heterogeneity within 16S rRNA of H. marismortui are discussed.
The genetic analysis of snf: a Drosophila sex determination gene required for activation of Sex-lethal in both the germline and the soma.
Authors: Salz H K 
Published: January 2021

Abstract
Our analysis demonstrates that snf is a positive regulator of Sex-lethal in both the germline and the soma. In the germline, unregulated expression of Sex-lethal can bypass the requirement for snf+ gene function, implying that snf is required for Sex-lethal activity in the germline. This conclusion is supported by the finding that the Sex-lethal transcription pattern is abnormal in a snf mutant background. In the soma, activation of Sex-lethal appears to be sensitive to snf gene dosage only when the probability of Sex-lethal activation has been otherwise reduced. We also show that the activity of one of the constitutive Sex-lethal alleles (SxlM1) is sensitive to snf gene dosage, demonstrating that, in spite of its constitutive behavior in some assays, SxlM1 is still subject to some regulation. In spite of snf's role in the somatic activation of Sex-lethal, no lethal alleles of snf were isolated in a screen of approximately 25,000 chromosomes. The observation that the existing snf mutations present a lethal phenotype only in certain genetic backgrounds suggests that snf is required, but is not essential, for the activation of Sex-lethal in the soma. In contrast, snf does appear to be essential for activation of Sex-lethal in the germline, as evidenced by its female-sterile phenotype.
Intraspecific and interspecific variation at the y-ac-sc region of Drosophila simulans and Drosophila melanogaster.
Authors: Martín-Campos J M , Comerón J M , Miyashita N , Aguadé M 
Published: January 2021

Abstract
A 2.2-kb region including the ac gene of Drosophila simulans has been sequenced. Interspecific divergence between Drosophila melanogaster and D. simulans was estimated as 0.0695 and 0.0558 for silent and for all sites, respectively. Estimated silent site divergence for the ac region is comparable to that estimated for other regions of the genome between these species, indicating that silent sites of the ac region are not under significantly stronger functional constraint. Intraspecific variation in both species was also investigated. Restriction-site and length polymorphism in the ac region of D. simulans has been investigated for 103 X chromosome lines sampled from three natural populations in Spain using eight four-cutter restriction enzymes. Neither restriction-site nor length variation was detected in the three populations surveyed. In D. melanogaster restriction-site and length polymorphism in all major transcription units of the y-ac-sc region (23.1-kb region) has been studied using four four-cutter restriction enzymes for 245 X chromosome lines sampled from 10 natural populations (seven from Europe, two from North America and one from Japan). Fourteen restriction-site and 28 length polymorphisms were detected. There was some indication of population subdivision for North American vs. European samples of D. melanogaster. The frequency spectrum of restriction-site polymorphisms in European populations was skewed toward rarer frequencies than predicted by the neutral theory. Comparison of silent site variation at this telomeric region with that in the Adh 5'-flanking region showed a reduced level of heterozygosity in the y-ac-sc region. Since interspecific silent divergence is not reduced in the y-ac-sc region as compared to other regions, the reduction in standing levels of variation at this telomeric locus in both D. simulans and D. melanogaster is most easily explained by a hitchhiking effect of linked selected substitutions.
Genetic study of the loss and restoration of Mutator transposon activity in maize: evidence against dominant-negative regulator associated with loss of activity.
Authors: Brown J , Sundaresan V 
Published: January 2021

Abstract
The Mutator system of transposable elements is characterized by a family of transposons called Mu transposons that share common termini and are actively transposing in Robertson's Mutator (Mu) lines of maize. Mu lines lose transposition activity during propagation by either outcrossing or inbreeding. This loss of transposition activity, which can occur at non-Mendelian frequencies, is in the form of loss of forward transposition activity resulting in a decrease in the generation of new mutations, as well as the loss of mutability of Mu transposon induced mutations, and it has been correlated with hypermethylation of the Mu elements. Previous studies have concluded that restoration of Mutator transposon activity by crossing inactive lines back to active lines is incomplete or transient, and depends upon the sex of the inactive parent. Further, it has been proposed that the inactive system is dominant to the active system, with the dominance possibly mediated through a negative regulatory factor that is preferentially transmitted through the female. In this study, we have examined the frequencies of loss and restoration of Mu transposon activity using a Mu line carrying an insertion in the bronze 1 locus. We find that transmission of Mu transposon activity to non-Mu plants can occur at high rates through males and females, but individual cases of decreased transmission through the male were observed. We also find that in crosses between inactive-Mu and active-Mu plants, reactivation was efficient as well as heritable, regardless of the sex of the inactive parent. Similar results were obtained whether the inactivation occurred in an outcross or a self. In all cases examined, loss of Mu transposon activity was correlated with hypermethylation of Mu elements, and reactivation was correlated with their demethylation. Our results indicate that an inactive Mu system does not exhibit dominance over an active Mu system. We conclude that contrary to current models, inactivation and its maintenance is not obligatorily associated with a dominant negative regulatory factor whether nuclear or cytoplasmic, and we propose a revised model to account for these and other observations.
Interspecific comparison of the transformer gene of Drosophila reveals an unusually high degree of evolutionary divergence.
Authors: O'Neil M T , Belote J M 
Published: January 2021

Abstract
The transformer (tra) gene of Drosophila melanogaster occupies an intermediate position in the regulatory pathway controlling all aspects of somatic sexual differentiation. The female-specific expression of this gene's function is regulated by the Sex lethal (Sxl) gene, through a mechanism involving sex-specific alternative splicing of tra pre-mRNA. The tra gene encodes a protein that is thought to act in conjunction with the transformer-2 (tra-2) gene product to control the sex-specific processing of doublesex (dsx) pre-mRNA. The bifunctional dsx gene carries out opposite functions in the two sexes, repressing female differentiation in males and repressing male differentiation in females. Here we report the results from an evolutionary approach to investigate tra regulation and function, by isolating the tra-homologous genes from selected Drosophila species, and then using the interspecific DNA sequence comparisons to help identify regions of functional significance. The tra-homologous genes from two Sophophoran subgenus species, Drosophila simulans and Drosophila erecta, and two Drosophila subgenus species, Drosophila hydei and Drosophila virilis, were cloned, sequenced and compared to the D. melanogaster tra gene. This comparison reveals an unusually high degree of evolutionary divergence among the tra coding sequences. These studies also highlight a highly conserved sequence within intron one that probably defines a cis-acting regulator of the sex-specific alternative splicing event.
Delineation of cis-acting sequences required for expression of Drosophila mojavensis Adh-1.
Authors: Bayer C A , Curtiss S W , Weaver J A , Sullivan D T 
Published: January 2021

Abstract
The control of expression of the Adh-1 gene of Drosophila mojavensis has been analyzed by transforming ADH null Drosophila melanogaster hosts with P element constructs which contain D. mojavensis Adh-1 having deletions of different extent in the 5' and 3' ends. Adh-1 expression in the D. melanogaster hosts is qualitatively similar to expression in D. mojavensis, although expression is quantitatively lower in transformants. Deletions of the 5' end indicate that information required for normal temporal and tissue expression in larvae is contained within 70 bp of the transcription start site. However, deletion constructs to -70 are deficient in ovarian nurse cell expression, whereas the additional upstream sequences present in constructs containing deletions to -257 do support expression in the ovary. Comparison of the nucleotide sequence in the -257 to -70 region of Adh-1 of four species: D. mojavensis and Drosophila arizona, which express Adh-1 in the ovary, and Drosophila mulleri and Drosophila navojoa, which do not, has led to the identification of regions of sequence similarity that correlate with ovary expression. One of these bears a striking similarity to a conserved sequence located upstream of the three heat shock genes that have constitutive ovarian expression and may be an ovarian control element. We have identified an aberrant aspect of Adh-1 expression. In transformants which carry an Adh-1 gene without a functional upstream Adh-2 gene Adh-1 expression continues into the adult stage instead of ceasing at the onset of metamorphosis. In transformants with a functional Adh-2 gene, Adh-1 expression ceases in the third larval instar stage and aberrant expression in the adult stage does not occur.
New molecular markers for the distal end of the t-complex and their relationships to mutations affecting mouse development.
Authors: Ebersole T , Lai F , Artzt K 
Published: January 2021

Abstract
Many mutations affecting mouse development have been mapped to the t-complex of mouse chromosome 17. We have obtained 17 cosmid clones as molecular markers for this region by screening a hamster-mouse chromosome 17 and 18 cell hybrid cosmid library with mouse-specific repetitive elements and mapping positive clones via t-haplotype vs. C3H restriction fragment length polymorphism (RFLP) analysis. Twelve of the clones mapping distal to Leh66B in t-haplotypes are described here. Using standard RFLP analysis or simple sequence length polymorphism between t-haplotypes, exceptional partial t-haplotypes and nested sets of inter-t-haplotype recombinants, five cosmids have been mapped in or around In(17)3 and seven in the most distal inversion In17(4). More precise mapping of four of the cosmids from In(17)4 shows that they will be useful in the molecular identification of some of the recessive lethals mapped to the t-complex: two cosmids map between H-2K and Crya-1, setting a distal limit in t-haplotypes for the position of the tw5 lethal, one is inseparable from the tw12 lethal, and one maps distal to tf near the t0(t6) lethal and cld.
Insertional mutagenesis of the maize P gene by intragenic transposition of Ac.
Authors: Athma P , Grotewold E , Peterson T 
Published: January 2021

Abstract
The P-rr allele of the maize P gene regulates the synthesis of pigments derived from flavan-4-ol in the pericarp, cob glumes and other floral organs. We characterized 21 P alleles derived by intragenic transposition of Ac from three known positions. Ac transpositions can occur in either direction in the P gene, and with no apparent minimum distance: in one case Ac transposed just 6 bp from its original insertion site. However, the distribution of transposed Ac elements was markedly nonrandom: of 19 transposed Ac elements derived from a single Ac donor, 15 were inserted in a 1.1-kb region at the 5' end of P, while none had inserted in an adjacent 3.2-kb intronic region. All of the Ac insertions affect both pericarp and cob glume pigmentation, providing further evidence that the P-rr allele contains a single gene required for both pericarp and cob glume pigmentation. The distribution of the inserted Ac elements and the phenotype conditioned by each allele suggests a structure of P-rr which is similar to that previously determined molecularly. Possible explanations for the nonrandom distribution of transposed Ac elements are discussed.
The competitive ability and fitness components of the Methoprene-tolerant (Met) Drosophila mutant resistant to juvenile hormone analog insecticides.
Authors: Minkoff C , Wilson T G 
Published: January 2021

Abstract
The Methoprene-tolerant (Met) mutation of Drosophila melanogaster results in a high (100-fold) level of resistance to the insecticide methoprene, a chemical analog of juvenile hormone. Pest species that are under control with methoprene may therefore have the potential to evolve resistance via a mutation homologous to Met. To evaluate the potential of such mutants to persist in wild populations, we must understand the fitness of flies carrying Met. In the absence of methoprene, Met flies were outcompeted by a wild-type strain both in a multigeneration population cage and in single-generation competition experiments. To determine which fitness component(s) is responsible for the competitive disadvantage, the survival, time of development, and fecundity of flies homozygous for each of five Met alleles were compared with wild type. Small but significant differences were found between the pooled Met alleles and wild type for pupal development time, pupal mortality, and early adult fecundity. These differences result in a large competitive disadvantage. Although Met flies were found to have reduced fitness by these measures, the phenotype is not as severe as might be expected from a knowledge of the disruption of juvenile hormone regulation seen in Met flies. It is concluded that (1) although Met flies have a large advantage under methoprene selection, they will quickly become outcompeted upon relaxation of methoprene usage, (2) even a seemingly severe disruption of juvenile hormone regulation has no drastic effect on the vital functions of the insect and (3) small differences in fitness components can translate into a large competitive disadvantage.
Plasmid recombination in a rad52 mutant of Saccharomyces cerevisiae.
Authors: Dornfeld K J , Livingston D M 
Published: January 2021

Abstract
Using plasmids capable of undergoing intramolecular recombination, we have compared the rates and the molecular outcomes of recombination events in a wild-type and a rad52 strain of Saccharomyces cerevisiae. The plasmids contain his3 heteroalleles oriented in either an inverted or a direct repeat. Inverted repeat plasmids recombine approximately 20-fold less frequently in the mutant than in the wild-type strain. Most events from both cell types have continuous coconversion tracts extending along one of the homologous segments. Reciprocal exchange occurs in fewer than 30% of events. Direct repeat plasmids recombine at rates comparable to those of inverted repeat plasmids in wild-type cells. Direct repeat conversion tracts are similar to inverted repeat conversion tracts in their continuity and length. Inverted and direct repeat plasmid recombination differ in two respects. First, rad52 does not affect the rate of direct repeat recombination as drastically as the rate of inverted repeat recombination. Second, direct repeat plasmids undergo crossing over more frequently than inverted repeat plasmids. In addition, crossovers constitute a larger fraction of mutant than wild-type direct repeat events. Many crossover events from both cell types are unusual in that the crossover HIS3 allele is within a plasmid containing the parental his3 heteroalleles.