bluuebunny/crossref_metadata_2025_split huggingface dataset:
P-lacW insertional mutagenesis on the second chromosome of Drosophila melanogaster: isolation of lethals with different overgrowth phenotypes.
Authors: Török T , Tick G , Alvarado M , Kiss I 
Published: January 2021

Abstract
A single P-element insertional mutagenesis experiment was carried out for the second chromosome of Drosophila melanogaster using the P-lacW transposon. Out of 15,475 insertions on the second chromosome, 2,308 lethal and 403 semilethal mutants (altogether 2,711) were recovered. After eliminating clusters, 72% of the mutants represent independent insertions. Some of the mutants with larval, prepupal or pupal lethal phases have a prolonged larval period and show gradual overgrowth of the imaginal discs, brain and/or the hematopoietic organs (lymph glands). In this paper, 16 overgrowth mutants are described. As revealed by in situ hybridization, none of the mutations corresponds to any of the previously known overgrowth mutations on the second chromosome.
A rare tRNA-Arg(CCU) that regulates Ty1 element ribosomal frameshifting is essential for Ty1 retrotransposition in Saccharomyces cerevisiae.
Authors: Kawakami K , Pande S , Faiola B , Moore D P , Boeke J D , Farabaugh P J , Strathern J N , Nakamura Y , Garfinkel D J 
Published: January 2021

Abstract
Translation of the yeast retrotransposon Ty1 TYA1(gag)-TYB1(pol) gene occurs by a +1 ribosomal frameshifting event at the sequence CUU AGG C. Because overexpression of a low abundance tRNA-Arg(CCU) encoded by the HSX1 gene resulted in a reduction in Ty1 frameshifting, it was suggested that a translational pause at the AGG-Arg codon is required for optimum frameshifting. The present work shows that the absence of tRNA-Arg(CCU) affects Ty1 transposition, translational frameshifting, and accumulation of mature TYB1 proteins. Transposition of genetically tagged Ty1 elements decreases at least 50-fold and translational frameshifting increases 3-17-fold in cells lacking tRNA-Arg(CCU). Accumulation of Ty1-integrase and Ty1-reverse transcriptase/ribonuclease H is defective in an hsx1 mutant. The defect in Ty1 transposition is complemented by the wild-type HSX1 gene or a mutant tRNA-Arg(UCU) gene containing a C for T substitution in the first position of the anticodon. Overexpression of TYA1 stimulates Ty1 transposition 50-fold above wild-type levels when the level of transposition is compared in isogenic hsx1 and HSX1 strains. Thus, the HSX1 gene determines the ratio of the TYA1 to TYA1-TYB1 precursors required for protein processing or stability, and keeps expression of TYB1 a rate-limiting step in the retrotransposition cycle.
Deletions and amplifications of tandemly arranged ribosomal 5S genes internal to a P element occur at a high rate in a dysgenic context.
Authors: Pâques F , Wegnez M 
Published: January 2021

Abstract
We observed unusual kinds of rearrangements within tandemly clustered 5S genes internal to a P element in dysgenic context. Rearranged P transposons, initially containing eight 5S genes, were found to display discrete numbers of 5S genes, from 4 up to 17 units. Precise deletions and amplifications occurred at a high rate (40%), at both original and new insertion sites. These events can be explained by a "cut and paste" transposition model. Possible links between rearrangements due to dysgenic-like processes and concerted evolution are discussed.
Cytoplasmic incompatibility and bacterial density in Nasonia vitripennis.
Authors: Breeuwer J A , Werren J H 
Published: January 2021

Abstract
Cytoplasmically (maternally) inherited bacteria that cause reproductive incompatibility between strains are widespread among insects. In the parasitoid wasp Nasonia, incompatibility results in improper condensation and fragmentation of the paternal chromosomes in fertilized eggs. Some form of genome imprinting may be involved. Because of haplodiploidy, incompatibility results in conversion of (diploid) female eggs into (haploid) males. Experiments show that bacterial density is correlated with compatibility differences between male and female Nasonia. Males from strains with high bacterial numbers are incompatible with females from strains with lower numbers. Temporal changes in compatibility of females after tetracycline treatment are generally correlated with decreases in bacterial levels in eggs. However, complete loss of bacteria in mature eggs precedes conversion of eggs to the "asymbiont" compatibility type by 3-4 days. This result is consistent with a critical "imprinting" period during egg maturation, when cytoplasmic bacteria determine compatibility. Consequent inheritance of reduced bacterial numbers in F1 progeny has different effects on compatibility type of subsequent male vs. female progeny. In some cases, partial incompatibility occurs which results in reduced offspring numbers, apparently due to incomplete paternal chromosome elimination resulting in aneuploidy.
Mutations that suppress the deletion of an upstream activating sequence in yeast: involvement of a protein kinase and histone H3 in repressing transcription in vivo.
Authors: Prelich G , Winston F 
Published: January 2021

Abstract
Regulated transcription of most protein-encoding genes in Saccharomyces cerevisiae requires an upstream activating sequence (UAS); in the absence of UAS elements, little or no transcription occurs. In certain mutant strains, however, promoters that have been deleted for their UAS can direct significant levels of transcription, indicating that the remaining promoter elements (the basal promoter) are capable of directing higher levels of transcription, but they are normally represented in wild-type strains. To analyze this repression, we have selected for mutations that cause increased transcription of the SUC2 gene in the absence of its UAS. In addition to some previously studied genes, this selection has identified five genes that we have designated BUR1, BUR2, BUR3, BUR5 and BUR6 (for Bypass UAS Requirement). The bur mutations cause pleiotropic phenotypes, indicating that they affect transcription of many genes. Furthermore, some bur mutations suppress the requirement for the SNF5 trans-activator at both SUC2 and Ty. Additional analysis has demonstrated that BUR1 is identical to SGV1, which encodes a CDC28-related protein kinase. This result indicates that protein phosphorylation is important for repression of the SUC2 basal promoter as well as other aspects of transcription in vivo. Finally, BUR5 is identical to HHT1, encoding histone H3, further implicating chromatin structure as important for expression of SUC2.
Deletion of a single-copy tRNA affects microtubule function in Saccharomyces cerevisiae.
Authors: Reijo R A , Cho D S , Huffaker T C 
Published: January 2021

Abstract
rts1-1 was identified as an extragenic suppressor of tub2-104, a cold-sensitive allele of the sole gene encoding beta-tubulin in the yeast, Saccharomyces cerevisiae. In addition, rts1-1 cells are heat sensitive and resistant to the microtubule-destabilizing drug, benomyl. The rts1-1 mutation is a deletion of approximately 5 kb of genomic DNA on chromosome X that includes one open reading frame and three tRNA genes. Dissection of this region shows that heat sensitivity is due to deletion of the open reading frame (HIT1). Suppression and benomyl resistance are caused by deletion of the gene encoding a tRNA(Arg)AGG (HSX1). Northern analysis of rts1-1 cells indicates that HSX1 is the only gene encoding this tRNA. Deletion of HSX1 does not suppress the tub2-104 mutation by misreading at the AGG codons in TUB2. It also does not suppress by interfering with the protein arginylation that targets certain proteins for degradation. These results leave open the prospect that this tRNA(Arg)AGG plays a novel role in the cell.
A phylogenetic estimator of effective population size or mutation rate.
Authors: Fu Y X 
Published: January 2021

Abstract
A new estimator of the essential parameter theta = 4Ne mu from DNA polymorphism data is developed under the neutral Wright-Fisher model without recombination and population subdivision, where Ne is the effective population size and mu is the mutation rate per locus per generation. The new estimator has a variance only slightly larger than the minimum variance of all possible unbiased estimators of the parameter and is substantially smaller than that of any existing estimator. The high efficiency of the new estimator is achieved by making full use of phylogenetic information in a sample of DNA sequences from a population. An example of estimating theta by the new method is presented using the mitochondrial sequences from an American Indian population.
Luria-Delbrück fluctuation experiments: design and analysis.
Authors: Jones M E , Thomas S M , Rogers A 
Published: January 2021

Abstract
Luria and Delbrück, in a seminal paper, introduced fluctuation analysis primarily as a means to elucidate the timing of mutation in relation to the imposition of selective conditions. Their work, and subsequently that of LEA and COULSON, established also a basis for measuring the frequency of mutational events. The several estimators proposed by these authors differ both in complexity and in efficiency, and the published literature relies mainly on the less efficient but computationally trivial estimators. The estimators as originally proposed assume that all mutants occurring in culture will be counted in the subsequent assay, but a relaxation of this assumption suggests an alternative experimental design and alternative estimators which offer advantages over those currently in common use.
Insertion sequence-related genetic variation in resting Escherichia coli K-12.
Authors: Naas T , Blot M , Fitch W M , Arber W 
Published: January 2021

Abstract
Bacterial subclones recovered from an old stab culture of Escherichia coli K-12 revealed a high degree of genetic diversity, which occurred in spite of a very reduced rate of propagation during storage. This conclusion is based on a pronounced restriction fragment length polymorphism (RFLP) detected upon hybridization with internal fragments of eight resident insertion sequences (IS). Genetic diversity was dependent on the IS considered and, in many cases, a clear consequence of IS transposition. IS5 was particularly active in the generation of variation. All subclones in which IS30 had been active testify to a burst of IS30 transposition. This was correlated with a loss of prototrophy and a reduced growth on rich media. A pedigree of the entire clone could be drawn from the RFLP patterns of the subclones. Out of 118 subclones analyzed, 68 different patterns were found but the putative ancestral population had disappeared. A few patterns were each represented by several subclones displaying improved fitness. These results offer insights into the role of IS elements in the plasticity of the E. coli genome, and they further document that enzyme-mediated DNA rearrangements do occur in resting bacterial cultures.
Efficient targeted integration at leu1-32 and ura4-294 in Schizosaccharomyces pombe.
Authors: Keeney J B , Boeke J D 
Published: January 2021

Abstract
Homologous integration into the fission yeast Schizosaccharomyces pombe has not been well characterized. In this study, we have examined integration of plasmids carrying the leu1+ and ura4+ genes into their chromosomal loci. Genomic DNA blot analysis demonstrated that the majority of transformants have one or more copies of the plasmid vector integrated via homologous recombination with a much smaller fraction of gene conversion to leu1+ or ura4+. Non-homologous recombination events were not observed for either gene. We describe the construction of generally useful leu1+ and ura4+ plasmids for targeted integration at the leu1-32 and ura4-294 loci of S. pombe.
Identification of DNA segments capable of rescuing a non-mendelian mutant in paramecium.
Authors: Kim C S , Preer J R , Polisky B 
Published: January 2021

Abstract
The non-Mendelian mutant d48 of Paramecium tetraurelia contains micronuclear wild type A genes, but at autogamy and conjugation proper processing fails and new macronuclei lack A genes. When cloned A genes are injected into the macronucleus of d48, proper processing is restored at the next autogamy; d48 is rescued, becoming permanently wild type. In the present study we have injected portions of the A gene into d48. We find that the ability to rescue extends over a large portion of the gene, with highest activity near a series of 221-bp repeat units in the middle of the gene. Regions outside the A gene are inactive.
A screen for genetic loci required for body-wall muscle development during embryogenesis in Caenorhabditis elegans.
Authors: Ahnn J , Fire A 
Published: January 2021

Abstract
We have used available chromosomal deficiencies to screen for genetic loci whose zygotic expression is required for formation of body-wall muscle cells during embryogenesis in Caenorhabditis elegans. To test for muscle cell differentiation we have assayed for both contractile function and the expression of muscle-specific structural proteins. Monoclonal antibodies directed against two myosin heavy chain isoforms, the products of the unc-54 and myo-3 genes, were used to detect body-wall muscle differentiation. We have screened 77 deficiencies, covering approximately 72% of the genome. Deficiency homozygotes in most cases stain with antibodies to the body-wall muscle myosins and in many cases muscle contractile function is observed. We have identified two regions showing distinct defects in myosin heavy chain gene expression. Embryos homozygous for deficiencies removing the left tip of chromosome V fail to accumulate the myo-3 and unc-54 products, but express antigens characteristic of hypodermal, pharyngeal and neural development. Embryos lacking a large region on chromosome III accumulate the unc-54 product but not the myo-3 product. We conclude that there exist only a small number of loci whose zygotic expression is uniquely required for adoption of a muscle cell fate.
A Drosophila third chromosome Minute locus encodes a ribosomal protein.
Authors: Andersson S , Saebøe-Larssen S , Lambertsson A , Merriam J , Jacobs-Lorena M 
Published: January 2021

Abstract
Minutes (M) are a group of over 50 phenotypically similar Drosophila mutations widely believed to affect ribosomal protein genes. This report describes the characterization of the P element-induced M(3)95A(Plac92) mutation [allelic to M(3)95A]. This mutation can be reversed by the mobilization of the P element, demonstrating that the mutation is caused by insertion of this transposable element. The gene interrupted by insertion of the P element was cloned by use of inverse polymerase chain reaction. Nucleotide sequence analysis revealed a 70-75% identity to the human and rat ribosomal protein S3 genes, and to the Xenopus ribosomal protein S1a gene. At the amino acid level, the overall identity is approximately 78% for all three species. This is only the second time that a Minute has been demonstrated to encode a ribosomal protein.
Local transposition of P elements in Drosophila melanogaster and recombination between duplicated elements using a site-specific recombinase.
Authors: Golic K G 
Published: January 2021

Abstract
The transposase source delta 2-3(99B) was used to mobilize a P element located at sites on chromosomes X, 2 and 3. The transposition event most frequently recovered was a chromosome with two copies of the P element at or near the original site of insertion. These were easily recognized because the P element carried a hypomorphic white gene with a dosage dependent phenotype; flies with two copies of the gene have darker eyes than flies with one copy. The P element also carried direct repeats of the recombination target (FRT) for the FLP site-specific recombinase. The synthesis of FLP in these flies caused excision of the FRT-flanked white gene. Because the two white copies excised independently, patches of eye tissue with different levels of pigmentation were produced. Thus, the presence of two copies of the FRT-flanked white gene could be verified. When the P elements lay in the same orientation, FLP-mediated recombination between the FRTs on separated elements produced deficiencies and duplications of the flanked region. When P elements were inverted, the predominant consequence of FLP-catalyzed recombination between the inverted elements was the formation of dicentric chromosomes and acentric fragments as a result of unequal sister chromatid exchange.
Isolation and characterization of paramecium mutants defective in their response to magnesium.
Authors: Preston R R , Kung C 
Published: January 2021

Abstract
Four mutant strains of Paramecium tetraurelia with a reduced ability to respond behaviorally to Mg2+ have been isolated. Voltage-clamp analyses showed that their Mg2+ insensitivity is associated with a reduced Ca(2+)-dependent Mg2+ current. The four mutants, which have been doubled "eccentric," result from recessive mutations in two unlinked loci, xntA and xntB. Further analysis of xntA1 showed it to be unlinked to any of the behavioral mutants of P. tetraurelia described previously, but it is allelic to d4-521, a "K(+)-resistant" strain, and d4-596, a "Ba(2+)-shy" mutant. The varied pleiotropic effects of xntA1, which include increased resistance to Ni2+ and Zn2+ poisoning, suggest that the locus encodes a central regulator of cell function in Paramecium.
string of pearls encodes Drosophila ribosomal protein S2, has Minute-like characteristics, and is required during oogenesis.
Authors: Cramton S E , Laski F A 
Published: January 2021

Abstract
The first allele of string of pearls (sop) was isolated as a recessive female sterile mutant in a P element enhancer trap screen. Oogenesis in homozygous sop females arrests at approximately stage 5. In addition, homozygous flies of both sexes have Minute-like characteristics that include reduced bristles, delayed development and larval lethality. sop maps to 30D/E on chromosome 2L and encodes the Drosophila homolog of eukaryotic ribosomal protein S2. The gene is present in a single copy in the Drosophila genome and the level of mRNA present in mutant animals is reduced. The identification of a mutant allele that blocks development at a mid-stage of oogenesis may indicate that sop has a specific developmental role during oogenesis in addition to its general role in protein synthesis as a component of the small ribosomal subunit.
Saccharomyces cerevisiae RAD52 alleles temperature-sensitive for the repair of DNA double-strand breaks.
Authors: Kaytor M D , Livingston D M 
Published: January 2021

Abstract
We have screened for mutations of the Saccharomyces cerevisiae RAD52 gene which confer a temperature-sensitive (ts) phenotype with respect to either the repair of DNA lesions caused by methyl methanesulfonate (MMS) or the recombination of an intrachromosomal recombination reporter. We were readily able to isolate alleles ts for the repair of lesions caused by MMS but were unable to find alleles with a severe ts deficiency in intrachromosomal recombination. We extensively characterized four strains conferring ts growth on MMS agar. These strains also exhibit ts survival when exposed to gamma-radiation or when the HO endonuclease is constitutively expressed. Although none of the four alleles confers a severe ts defect in intrachromosomal recombination, two confer significant defects in tests of mitotic, interchromosomal recombination carried out in diploid strains. The mutant diploids sporulate, but the two strains with defects in interchromosomal recombination have reduced spore viability. Meiotic recombination is not depressed in the two diploids with reduced spore viability. Thus, in the two strains with reduced spore viability, defects in mitotic and meiotic recombination do not correlate. Sequence analysis revealed that in three of the four ts alleles the causative mutations are in the first one-third of the open reading frame while the fourth is in the C-terminal third.
Presence of different O antigen forms in three isolates of one clone of Escherichia coli.
Authors: Liu D , Reeves P R 
Published: January 2021

Abstract
Escherichia coli strains ECOR2, ECOR3 and K-12 are very closely related in genotype as indicated by multilocus enzyme electrophoresis. We show that they have very different rfb regions indicating that recombination has occurred in this region, and we suggest that it may be associated with niche adaptation.
Chromosome damage and early developmental arrest caused by the Rex element of Drosophila melanogaster.
Authors: Robbins L G , Pimpinelli S 
Published: January 2021

Abstract
Rex (Ribosomal exchange) is a genetically identified repeated element within the ribosomal DNA (rDNA) of Drosophila melanogaster. Rex has a semidominant maternal effect that promotes exchange between and within rDNA arrays in the first few embryonic mitoses. Several of Rex's genetic properties suggest that its primary effect is rDNA-specific chromosome breakage that is resolved by recombination. We report here that rDNA crossovers are only a small, surviving minority of Rex-induced events. Cytology of embryos produced by Rex-homozygous females reveals obvious chromosome damage in at least a quarter of the embryos within the first three mitotic divisions. More than half of the embryos produced by Rex females die, and the developmental arrest is among the earliest reported for any maternal-effect lethal. The striking lethal phenotype suggests that embryos with early chromosome damage could be particularly fruitful subjects for analysis of the cell biology of early embryos.
Genetic analysis of systematic mitochondrial heteroplasmy in rabbits.
Authors: Casane D , Dennebouy N , de Rochambeau H , Mounolou J C , Monnerot M 
Published: January 2021

Abstract
One unusual property of rabbit mitochondrial DNA (mtDNA) is the existence of repeated 153-bp motifs in the vicinity of the replication origin of its H strand. Furthermore, every individual is heteroplasmic: it carries mtDNA molecules with a variable number of repeats. A systematic study of 8 females and their progeny has been devised to analyze mtDNA transmission through generations. The results suggest that three mechanisms are acting simultaneously. (1) Genetic drift in the germ line is revealed by the evolution of heteroplasmy when two major molecular forms are present in a female. (2) A high mutation rate (around 10(-2) per animal generation) generating molecular diversity, by deletion and addition of repeated units, is required to explain the observation of heteroplasmy in every individual. Moreover, the rates of mutation from the most frequent type to the other types are unequal. The deletion of one unit is more frequent than a deletion of two units, which is in turn more frequent than a deletion of three. (3) Selection for shorter molecules in somatic cells is probable. The frequency distribution of mtDNA types depends on the organ analyzed (kidney-spleen and liver vs. gonads).