bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mismatch correction acts as a barrier to homeologous recombination in Saccharomyces cerevisiae.
Authors: Selva E M , New L , Crouse G F , Lahue R S 
Published: January 2021

Abstract
A homeologous mitotic recombination assay was used to test the role of Saccharomyces cerevisiae mismatch repair genes PMS1, MSH2 and MSH3 on recombination fidelity. A homeologous gene pair consisting of S. cerevisiae SPT15 and its S. pombe homolog were present as a direct repeat on chromosome V, with the exogenous S. pombe sequences inserted either upstream or downstream of the endogenous S. cerevisiae gene. Each gene carried a different inactivating mutation, rendering the starting strain Spt15-. Recombinants that regenerated SPT15 function were scored after nonselective growth of the cells. In strains wild type for mismatch repair, homeologous recombination was depressed 150- to 180-fold relative to homologous controls, indicating that recombination between diverged sequences is inhibited. In one orientation of the homeologous gene pair, msh2 or msh3 mutations resulted in 17- and 9.6-fold elevations in recombination and the msh2 msh3 double mutant exhibited an 43-fold increase, implying that each MSH gene can function independently in trans to prevent homeologous recombination. Homologous recombination was not significantly affected by the msh mutations. In the other orientation, only msh2 strains were elevated (12-fold) for homeologous recombination. A mutation in MSH3 did not affect the rate of recombination in this orientation. Surprisingly, a pms1 deletion mutant did not exhibit elevated homeologous recombination.
Meiotic chromosome pairing in triploid and tetraploid Saccharomyces cerevisiae.
Authors: Loidl J 
Published: January 2021

Abstract
Meiotic chromosome pairing in isogenic triploid and tetraploid strains of yeast and the consequences of polyploidy on meiotic chromosome segregation are studied. Synaptonemal complex formation at pachytene was found to be different in the triploid and in the tetraploid. In the triploid, triple-synapsis, that is, the connection of three homologues at a given site, is common. It can even extend all the way along the chromosomes. In the tetraploid, homologous chromosomes mostly come in pairs of synapsed bivalents. Multiple synapsis, that is, synapsis of more than two homologues in one and the same region, was virtually absent in the tetraploid. About five quadrivalents per cell occurred due to the switching of pairing partners. From the frequency of pairing partner switches it can be deduced that in most chromosomes synapsis is initiated primarily at one end, occasionally at both ends and rarely at an additional intercalary position. In contrast to a considerably reduced spore viability (approximately 40%) in the triploid, spore viability is only mildly affected in the tetraploid. The good spore viability is presumably due to the low frequency of quadrivalents and to the highly regular 2:2 segregation of the few quadrivalents that do occur. Occasionally, however, quadrivalents appear to be subject to 3:1 nondisjunction that leads to spore death in the second generation.
Further characterization of the Odysseus locus of hybrid sterility in Drosophila: one gene is not enough.
Authors: Perez D E , Wu C I 
Published: January 2021

Abstract
Previously we mapped by genetical and molecular means a gene that contributes to hybrid-male sterility between Drosophila mauritiana and D. simulans to the cytological interval of 16D. In this report, we refine the mapping of this gene, Odysseus (Ods) and show that it can be delineated to a region the size of an average gene. We further demonstrate that, while Ods appears to be a discrete element, it requires other nearby gene(s) to be cointrogressed to confer full hybrid sterility effect. This observation is in agreement with the view that reproductive isolation between closely related species of Drosophila is usually caused by several genes of weak effect from the same species that interact strongly among themselves as well as with the foreign genetic background.
A transgenic mouse assay for agouti protein activity.
Authors: Perry W L , Hustad C M , Swing D A , Jenkins N A , Copeland N G 
Published: January 2021

Abstract
The mouse agouti gene encodes an 131 amino acid paracrine signaling molecule that instructs hair follicle melanocytes to switch from making black to yellow pigment. Expression of agouti during the middle part of the hair growth cycle in wild-type mice produces a yellow band on an otherwise black hair. The ubiquitous unregulated expression of agouti in mice carrying dominant yellow alleles is associated with pleiotropic effects including increased yellow pigment in the coat, obesity, diabetes and increased tumor susceptibility. Agouti shows no significant homology to known genes, and the molecular analysis of agouti alleles has shed little new light on the important functional elements of the agouti protein. In this paper, we show that agouti expression driven by the human beta-ACTIN promoter produces obese yellow transgenic mice and that this can be used as an assay for agouti activity. We used this assay to evaluate a point mutation associated with the a16H allele within the region encoding agouti's putative signal sequence and our results suggest that this mutation is sufficient to cause the a16H phenotype. Thus, in vitro mutagenesis followed by the generation of transgenic mice should allow us to identify important functional elements of the agouti protein.
Factors that affect the location and frequency of meiosis-induced double-strand breaks in Saccharomyces cerevisiae.
Authors: Wu T C , Lichten M 
Published: January 2021

Abstract
Double-strand DNA breaks (DSBs) initiate meiotic recombination in Saccharomyces cerevisiae. DSBs occur at sites that are hypersensitive in nuclease digests of chromatin, suggesting a role for chromatin structure in determining DSB location. We show here that the frequency of DSBs at a site is not determined simply by DNA sequence or by features of chromatin structure. An arg4-containing plasmid was inserted at several different locations in the yeast genome. Meiosis-induced DSBs occurred at similar sites in pBR322-derived portions of the construct at all insert loci, and the frequency of these breaks varied in a manner that mirrored the frequency of meiotic recombination in the arg4 portion of the insert. However, DSBs did not occur in the insert-borne arg4 gene at a site that is frequently broken at the normal ARG4 locus, even though the insert-borne arg4 gene and the normal ARG4 locus displayed similar DNase I hypersensitivity patterns. Deletions that removed active DSB sites from an insert at HIS4 restored breaks to the insert-borne arg4 gene and to a DSB site in flanking chromosomal sequences. We conclude that the frequency of DSB at a site can be affected by sequences several thousand nucleotides away and suggest that this is because of competition between DSB sites for locally limited factors.
Microsatellite variation in honey bee (Apis mellifera L.) populations: hierarchical genetic structure and test of the infinite allele and stepwise mutation models.
Authors: Estoup A , Garnery L , Solignac M , Cornuet J M 
Published: January 2021

Abstract
Samples from nine populations belonging to three African (intermissa, scutellata and capensis) and four European (mellifera, ligustica, carnica and cecropia) Apis mellifera subspecies were scored for seven microsatellite loci. A large amount of genetic variation (between seven and 30 alleles per locus) was detected. Average heterozygosity and average number of alleles were significantly higher in African than in European subspecies, in agreement with larger effective population sizes in Africa. Microsatellite analyses confirmed that A. mellifera evolved in three distinct and deeply differentiated lineages previously detected by morphological and mitochondrial DNA studies. Dendrogram analysis of workers from a given population indicated that super-sisters cluster together when using a sufficient number of microsatellite data whereas half-sisters do not. An index of classification was derived to summarize the clustering of different taxonomic levels in large phylogenetic trees based on individual genotypes. Finally, individual population x loci data were used to test the adequacy of the two alternative mutation models, the infinite allele model (IAM) and the stepwise mutation models. The better fit overall of the IAM probably results from the majority of the microsatellites used including repeats of two or three different length motifs (compound microsatellites).
A second superoxide dismutase gene in the medfly, Ceratitis capitata.
Authors: Banks G K , Robinson A S , Kwiatowski J , Ayala F J , Scott M J , Kriticou D 
Published: January 2021

Abstract
We report the first case of two Cu/Zn Sod genes (ccSod1 and ccSod2) that have been cloned and sequenced from an insect, the medfly, Ceratitis capitata. Biochemical evidence suggested the presence of two Sod genes in the medfly. The two genes are isolated using different molecular strategies: ccSod1 via cross-hybridization to a genomic library using a heterologous probe and ccSod2 from cDNA using a homologous probe generated by PCR. Sequence analysis shows that ccSod1 and ccSod2 are different genes. The inferred amino sequences show that all essential residues of the active site are strictly conserved, which suggests both genes encode functional Cu/Zn superoxide dismutase (SOD). Phylogenetic analysis by the maximum parsimony method with bootstrap resampling of previously known Cu/Zn SOD reveals two monophyletic groups, vertebrates and insects. The position of ccSOD2 in this phylogeny is undefined with respect to dipteran ccSOD1, vertebrate, plant, fungal, and extracellular Cu/Zn SOD, which suggests that the duplication detected in Ceratitis is ancient, perhaps as old as the origins of the arthropod phylum in the Cambrian more than 500 million years ago. In situ hybridization to polytene chromosomes places the genes on different chromosomes, which is consistent with an ancient gene duplication.
An autosomal genetic linkage map of the sheep genome.
Authors: Crawford A M , Dodds K G , Ede A J , Pierson C A , Montgomery G W , Garmonsway H G , Beattie A E , Davies K , Maddox J F , Kappes S W 
Published: January 2021

Abstract
We report the first extensive ovine genetic linkage map covering 2070 cM of the sheep genome. The map was generated from the linkage analysis of 246 polymorphic markers, in nine three-generation full-sib pedigrees, which make up the AgResearch International Mapping Flock. We have exploited many markers from cattle so that valuable comparisons between these two ruminant linkage maps can be made. The markers, used in the segregation analyses, comprised 86 anonymous microsatellite markers derived from the sheep genome, 126 anonymous microsatellites from cattle, one from deer, and 33 polymorphic markers of various types associated with known genes. The maximum number of informative meioses within the mapping flock was 222. The average number of informative meioses per marker was 140 (range 18-209). Linkage groups have been assigned to all 26 sheep autosomes.
Heritability and selection on body size in a natural population of Drosophila buzzatii.
Authors: Leibowitz A , Santos M , Fontdevila A 
Published: January 2021

Abstract
An attempt was made to assess whether the phenotypic differences in body size (as measured by wing length) between wild-caught mating and single Drosophila buzzatii males could be attributed to genetic differences between the samples. Mating males were found to be larger and less variable than a random sample of the population. The progeny of the mating males (produced by crossing to a random female from a stock derived from the same population) were on average larger than those of the single males, but not significantly so (P = 0.063), and less phenotypically variable. This difference in variance between the samples suggests that there are indeed genetic differences between the paternal samples but tests for significant differences in the additive genetic component of variance proved inconclusive. For both samples it was found that while the ratio of additive genetic variation in the laboratory to phenotypic variation in the field yielded estimates of ĥs2(N) congruent to 10% the regression of offspring reared in the laboratory on parents from the wild was not significantly different from zero. In addition, it was found that the average development time of the progeny of the mating males is shorter than that of the random sample.
Conserved alternative splicing patterns and splicing signals in the Drosophila sodium channel gene para.
Authors: Thackeray J R , Ganetzky B 
Published: January 2021

Abstract
We cloned genomic DNA corresponding to the Drosophila virilis homologue of para, a gene encoding a sodium channel alpha-subunit, and obtained many partial cDNA clones from embryos and adults. Para protein has been well conserved, and the optional elements at six different sites of alternative splicing in D. melanogaster are present in D. virilis, in addition to one new optional exon. Among 31 different splice-types observed in D. virilis, the stage-specific pattern of alternative splicing seen in D. melanogaster is also conserved. Comparison of genomic DNA sequence revealed three aspects that vary between alternatively and constitutively used exon sequences. Sixteen short blocks (10-75 bp), the only recognizably conserved intron sequence, were disproportionately associated with alternatively used splice sites. Silent site substitutions were found much less frequently in alternative than constitutive exon elements, and the degree of match to the Drosophila splice site consensus tended to be lower at less frequently selected alternative splice junctions. This study shows that the developmentally regulated variability of para products is highly conserved and therefore likely to be of functional significance and suggests that a variety of different sequence-dependent mechanisms may regulate this pattern of alternative splicing.
The Fundamental Theorem of Natural Selection in Ewens' sense (case of fertility selection).
Authors: Lessard S , Castilloux A M 
Published: January 2021

Abstract
We show that the Fundamental Theorem of Natural Selection in Ewens' sense is valid in the case of fertility selection: the additive genetic variance in fertility divided by the mean fertility is exactly equal to the partial change in the mean fertility from the current generation to the next. This partial change is the increase in the mean additive value caused by frequency changes from on generation to the next. This partial change is the increase in the mean additive value caused by frequency changes from one generation to the next but keeping unchanged the additive values. The only hypothesis on mating is that it does not affect the allelic frequencies in the sense that these are the same before and after mating in the parental generation, which occurs for a wide range of mating patterns going from random mating to several regular systems of inbreeding and cases of assortative mating. The fertility of couples is determined by the genes at an arbitrary number of loci, and the additive (average) allelic allelic effects are defined by a linear system of equations, which is used to extend Ewens' optimality principle to the case of fertility selection.
Regulation of gene expression is linked to life span in adult Drosophila.
Authors: Rogina B , Helfand S L 
Published: January 2021

Abstract
Examination of gene expression and aging in adult Drosophila reveals that the expression of some genes is regulated by age-dependent mechanisms. Genetic mutations, Hyperkinetic and Shaker, which are known to shorten life span through an acceleration of the aging process, were used to study the expression of an enhancer trap marked gene. The temporal pattern of expression for such a marked gene shows scaling with respect to life span; it is altered in direct proportion to the life expectancy of the adult animal. This demonstrates that expression of this gene is controlled through mechanisms coupled to physiologic as opposed to chronologic age. Results provide direct evidence for linkage between the regulation of gene expression and life span and establish a model system for the genetic analysis of aging.
Alkylating agents induce UVM, a recA-independent inducible mutagenic phenomenon in Escherichia coli.
Authors: Wang G , Palejwala V A , Dunman P M , Aviv D H , Murphy H S , Rahman M S , Humayun M Z 
Published: January 2021

Abstract
Noninstructive DNA damage in Escherichia coli induces SOS functions hypothesized to be required for mutagenesis and translesion DNA synthesis at noncoding DNA lesions. We have recently demonstrated that in E. coli cells incapable of SOS induction, prior UV-irradiation nevertheless strongly enhances mutagenesis at a noninstructive lesion borne on M13 DNA. Here, we address the question whether this effect, named UVM for UV modulation of mutagenesis, can be induced by other DNA damaging agents. Exponentially growing delta recA cells were pretreated with alkylating agents before transfection with M13 single-stranded DNA bearing a site-specific ethenocytosine residue. Effect of cell pretreatment on survival of the transfected DNA was determined as transfection efficiency. Mutagenesis at the ethenocytosine site in pretreated or untreated cells was analyzed by multiplex DNA sequencing, a phenotype-independent technology. Our data show that 1-methyl-3-nitro-1-nitrosoguanidine, N-nitroso-N-methylurea and dimethylsulfate, but not methyl iodide, are potent inducers of UVM. Because alkylating agents induce the adaptive response to defend against DNA alkylation, we asked if the genes constituting the adaptive response are required for UVM. Our data show that MNNG induction of UVM is independent of ada, alkA and alkB genes and define UVM as an inducible mutagenic phenomenon distinct from the E. coli adaptive and SOS responses.
An alpha tubulin mutation suppresses nuclear migration mutations in Aspergillus nidulans.
Authors: Willins D A , Xiang X , Morris N R 
Published: January 2021

Abstract
Microtubules and cytoplasmic dynein, a microtubule-dependent motor, are required for nuclei to move along the hyphae of filamentous fungi. Nuclear migration in Aspergillus nidulans is blocked by heat-sensitive (hs-) mutations in the nudA gene, which encodes dynein heavy chain, and the nudF gene, which encodes a G protein beta-subunit-like protein. Hs- mutations in the nudC and nudG genes also prevent nuclear migration. We have isolated extragenic suppressor mutations that reverse the hs- phenotypes caused by these mutations. Here we show that one nudF suppressor also suppresses hs- mutations in nudA, nudC, and nudG and deletions in nudA and nudF. This suppressor mutation is in the tubA alpha tubulin gene, and its characteristics suggest that it destabilizes microtubules. The mutation alters microtubule staining and confers sensitivity to cold and benomyl, two treatments that destabilize microtubules. Treatment with low concentrations of benomyl also suppresses the hs- nudA, nudC, nudF, and nudG mutations and the nudA and nudF deletions. Suppression of the hs- nudA mutation and the nudA deletion is especially interesting because these strains lack active dynein heavy chain. Together, these results suggest that microtubule destabilization allows nuclei to migrate even in the absence of cytoplasmic dynein motor function.
Multiple Non-LTR Retrotransposons in the Genome of Arabidopsis thaliana
Authors: Wright David A , Ke Ning , Smalle Jan , Hauge Brian M , Goodman Howard M , Voytas Daniel F 
Published: January 2021

Abstract
DNA sequence analysis near the Arabidopsis thaliana AB13 gene revealed the presence of a non-LTR retrotransposon insertion that we have designated Ta11-1. This insertion is 6.2 kb in length and encodes two overlapping reading frames with similarity to non-LTR retrotransposon proteins, including reverse transcriptase. A polymerase chain reaction assay was developed based on conserved amino acid sequences shared between the Ta11-1 reverse transcriptase and those of non-LTR retrotransposons from other species. Seventeen additional A. thaliana reverse transcriptases were identified that range in nucleotide similarity from 48–88% (Ta12-Ta28). Phylogenetic analyses indicated that the A. thaliana sequences are more closely related to each other than to elements from other organisms, consistent with the vertical evolution of these sequences over most of their evolutionary history. One sequence, Ta17, is located in the mitochondrial genome. The remaining are nuclear and of low copy number among 17 diverse A. thaliana ecotypes tested, suggesting that they are not highly active in transposition. The paucity of retrotransposons and the small genome size of A. thaliana support the hypothesis that most repetitive sequences have been lost from the genome and that mechanisms may exist to prevent amplification of extant element families.
DNA Sequence Analyses Support the Role of Interrupted Gap Repair in the Origin of Internal Deletions of the Maize Transposon, MuDR
Authors: Hsia An-Ping , Schnable Patrick S 
Published: January 2021

Abstract
Previous research has demonstrated that the autonomous Cy transposon can activate the excision of Mu transposons. To determine the relationship between Cy and the more recently described autonomous Mu transposon, MuDR, a Cy transposon inserted at the mutable a1 allele, a1-m5216, was isolated and cloned. DNA sequence analyses established that this Cy insertion is identical to MuDR (Mu9, GenBank accession No.: m76978.gb_pl). Therefore, Cy will henceforth be termed MuDR:Cy. Defective derivatives of MuDR:Cy were isolated that had lost their capacity to activate their own excision or the excision of a Mu7 transposon. Most of these derivatives are nonautonomous transposons because they can excise, but only in the presence of unlinked MuDR:Cy transposons. Physical mapping and DNA sequence analyses have established that six of these defective derivatives carry internal deletions. It has been proposed previously that such deletions arise via interrupted gap repair. The DNA sequences of the break points associated with all four sequenced deletions are consistent with this model. The finding that three of the excision-defective derivatives carry deletions that disrupt the coding region of the mudrA (but not the mudrB) transcript supports the view that mudrA plays a role in the excision of Mu transposons.
Site-Specific Codon Bias in Bacteria
Authors: Smith J Maynard , Smith N H 
Published: January 2021

Abstract
Sequences of the gapA and ompA genes from 10 genera of enterobacteria have been analyzed. There is strong bias in codon usage, but different synonymous codons are preferred at different sites in the same gene. Site-specific preference for unfavored codons is not confined to the first 100 codons and is usually manifest between two codons utilizing the same tRNA. Statistical analyses, based on conclusions reached in an accompanying paper, show that the use of an unfavored codon at a given site in different genera is not due to common descent and must therefore be caused either by sequence-specific mutation or sequence-specific selection. Reasons are given for thinking that sequence-specific mutation cannot be responsible. We are unable to explain the preference between synonymous codons ending in C or T, but synonymous choice between A and G at third sites is largely explained by avoidance of AGG (where the hyphen indicates the boundary between codons). We also observed that the preferred codon for proline in Enterobacter cloacea has changed from CCG to CCA.