bluuebunny/crossref_metadata_2025_split huggingface dataset:
Homology requirements for unequal crossing over in humans.
Authors: Metzenberg A B , Wurzer G , Huisman T H , Smithies O 
Published: January 2021

Abstract
To gain insight into mechanisms of unequal homologous recombination in vivo, genes generated by homologous unequal crossovers in the human beta-globin gene cluster were examined by nucleotide sequencing and hybridization experiments. The naturally occurring genes studied included one delta-beta Lepore-Baltimore fusion gene, one delta-beta Lepore-Hollandia fusion gene, 12 delta-beta Lepore-Boston genes, one A gamma-beta fusion Kenya gene, one A gamma-G gamma fusion (the central gene of a triplication) and one G gamma-A gamma fusion. A comparison of the nucleotide sequences of three Lepore-Boston genes indicates that they were derived from at least two independent homologous but unequal crossover events, although the crossovers occurred within the same 58-bp region. Nine additional Lepore-Boston genes from individuals of various ethnic origins were shown, by hybridization to specific oligonucleotide probes, to have been generated by a crossover in the same region as the sequenced genes. Evidence for gene conversion accompanying a homologous unequal crossover event was found in only one case (although some of the single nucleotide differences observed in other genes in this study may be related to the crossover events in ways that we do not presently understand). Thus, as judged by this limited sample, concurrent gene conversions are not commonly associated with homologous but unequal exchange in humans in vivo. Classification of the recombinant chromosomes by their polymorphic restriction sites in the beta-globin gene cluster indicated that the Lepore-Boston genes are found in at least six different haplotype backgrounds. Therefore the total number of independent examples in this study is at least 6, and at most 12. We have shown that in at least six cases of genes that have arisen by homologous but unequal crossing over in vivo, each event occurred in a relatively extensive region of uninterrupted identity between the parental genes. This preference cannot be explained by a mechanism whereby crossovers occur at random within misaligned related but not identical genes. In general, crossovers occur in regions that are among the largest available stretches of identity for a particular pair of mismatched genes. Our data are in agreement with those of other types of studies of homologous recombination, and support the idea that sequence identity, rather than general homology, is a critical factor in homologous recombination.
A tester system for detecting each of the six base-pair substitutions in Saccharomyces cerevisiae by selecting for an essential cysteine in iso-1-cytochrome c.
Authors: Hampsey M 
Published: January 2021

Abstract
A collection of isogenic yeast strains that is specifically diagnostic for the six possible base-pair substitutions is described. Each strain contains a single, unique base-pair substitution at the Cys-22 codon of the CYC1 gene, which codes for iso-1-cytochrome c. These mutations encode replacements of the functionally critical Cys-22 and render each strain unable to grow on media containing nonfermentable carbon sources (Cyc-). Specific base-pair substitutions, which restore the Cys-22 codon, can be monitored simply by scoring for reversion to the Cyc+ phenotype. These strains revert spontaneously at very low frequencies and exhibit specific patterns of reversion in response to different mutagens. Only true (CYC1+) revertants were recovered after 7 days on selection medium. The following mutagen specificities were observed: ethyl methanesulfonate and N-methyl-N'-nitro-N-nitrosoguanidine, G.C----A.T; 4-nitroquinoline-1-oxide, G.C----T.A and G.C----A.T; diepoxybutane, A.T----T.A, A.T----G.C and G.C----T.A; 5-azacytidine, G.C----C.G. Methyl methanesulfonate induced all six mutations, albeit at relatively low frequencies, with preference for A.T----T.A and A.T----G.C. Ultraviolet light was the most inefficient mutagen used in this study, consistent with its preference for transition mutations at dipyrimidine sequences reported in other systems. This tester system is valuable as a simple and reliable assay for specific mutations without DNA sequence analysis.
DNA repair and the evolution of transformation in Bacillus subtilis. III. Sex with damaged DNA.
Authors: Hoelzer M A , Michod R E 
Published: January 2021

Abstract
Natural genetic transformation in the bacterium Bacillus subtilis provides an experimental system for studying the evolutionary function of sexual recombination. The repair hypothesis proposes that during transformation the exogenous DNA taken up by cells is used as template for recombinational repair of damages in the recipient cell's genome. Earlier results demonstrated that the population density of transformed cells (i.e., sexual cells) increases, relative to nontransformed cells (primarily asexual cells), with increasing dosage of ultraviolet irradiation, provided that the cells are transformed with undamaged homologous DNA after they have become damaged. In nature, however, donor DNA for transformation is likely to come from cells that are as damaged as the recipient cells. In order to better simulate the effects of transformation in natural populations we conducted similar experiments as those just described using damaged donor DNA. We document in this report that transformants continue to increase in relative density even if they are transformed with damaged donor DNA. These results suggest that sites of transformation are often damaged sites in the recipient cell's genome.
The independent distorting ability of the Enhancer of Segregation Distortion, E(SD), in Drosophila melanogaster.
Authors: Temin R G 
Published: January 2021

Abstract
Segregation distortion is a meiotic drive system, discovered in wild populations, in which males heterozygous for an SD chromosome and a sensitive SD+ homolog transmit the SD chromosome almost exclusively. SD represents a complex of three closely linked loci in the centromeric region of chromosome 2: Sd, the Segregation distorter gene; E(SD), the Enhancer of Segregation Distortion, required for full expression of drive; and Rsp, the target for the action of Sd, existing in a continuum of states classifiable into sensitive (Rsps) and insensitive (Rspi). In an SD/SD+ male which is Sd E(SD) Rspi/Sd+ E(SD)+ Rsps, the Sd and E(SD) elements act jointly to induce the dysfunction of those spermatids receiving the Rsps chromosome. By manipulating the number of copies and the position of the Enhancer region, I demonstrated that: (1) E(SD), whether in its normal position or translocated to the Y chromosome, is able to enhance the degree of Sd-caused distortion in a dosage-dependent manner; (2) even in the absence of Sd, the E(SD) allele in two doses can cause significant distortion, in Sd+ or Df(Sd)-bearing genotypes; (3) quantitative differences among Enhancers of different sources suggest allelic variation at E(SD), which could account at least in part for differences among wild SD chromosomes in strength of distortion; (4) E(SD)/E(SD)-mediated distortion, like that of Sd, is directed at the Rsp target, whether Rsp is on the second or the Y chromosome; (5) E(SD), like Sd, is suppressed by an unlinked dominant suppressor of SD action. These results show that E(SD) is independently capable of acting on Rsp and is not a simple modifier of the action of Sd. E(SD) provides an example of a trans-acting gene embedded in heterochromatin that can interact with another heterochromatic gene, Rsp, as well as parallel the effect of a euchromatic gene, Sd.
The molecular structure of TE146 and its derivatives in Drosophila melanogaster.
Authors: Lovering R , Harden N , Ashburner M 
Published: January 2021

Abstract
TE146 is a giant transposon of Drosophila melanogaster. It carries two copies of the white and roughest genes, normally found on the X chromosome. The structure of this transposon has been studied at the molecular level. TE146 may transpose to new chromosome positions, excise and be lost from the genome or undergo internal rearrangements. The termini of TE146 are foldback DNA elements (FB); the transposon also carries two internal FB elements. Loss or internal rearrangement of TE146 involves recombination between different FB elements. These events have been mapped molecularly, by taking advantage of the fact that the FB sequences are composed largely of a regular 155-bp repeat sequence that is cut by the restriction enzyme TaqI, and are shown to be nonrandom. We suggest that these FB-FB exchange events occur by mitotic sister-chromatid exchange in the premeiotic germ line.
Putative origin and function of the intergenic region between COI and COII of Apis mellifera L. mitochondrial DNA.
Authors: Cornuet J M , Garnery L , Solignac M 
Published: January 2021

Abstract
The mitochondrial genome of honeybees is characterized by the presence of a long intergenic sequence located between the COI and COII genes. In addition, the length of this sequence varies between and within subspecies. Four length categories (200, 250, 450 and 650 bp) have been found in 63 sampled colonies. Analysis of the sequence of the largest type reveals the existence of two units: P (54 bp, 100% A + T) and Q (196 bp, 93.4% A + T). The lengths encountered in the sample are explained by the following combinations: Q, PQ, PQQ and PQQQ. According to similarities in primary and secondary structures, the sequence Q has been divided into three parts: Q1 (similar to the 3' end of the COI gene), Q2 (similar to the neighboring tRNA(leu) gene) and Q3 (highly similar to the P sequence). These relationships led us to hypothesize that these sequences, which do not have any counterpart in Drosophila yakuba mitochondrial DNA (mtDNA), arose by tandem duplication. The usual location of length variation in mtDNA control regions prompted us to examine the hypothesis that this COI-COII intergenic region might contain an origin of replication. High A + T content, stability profile, hairpin and cloverleaf putative secondary structures are all in favor of this hypothesis.
A deletion common to two independently derived waxy mutations of maize.
Authors: Okagaki R J , Neuffer M G , Wessler S R 
Published: January 2021

Abstract
A mutation at the maize waxy locus, wx1240, was isolated following treatment of pollen with EMS and self-pollinating ears on M1 plants. This allele was cloned and found to contain a 30-bp deletion within the gene and additional lesions upstream of the transcription start site. Using fine structure genetic mapping, we determined that the deletion is responsible for the mutant phenotype. In addition, the position of wx1240 on the genetic map coincided with the previously determined positions of two other waxy mutations, the spontaneous wx-C, which is reference allele, and the putative ethyl methanesulfonate (EMS)-induced wx-BL2. Molecular analysis of these alleles revealed that both contain the same deletion as wx1240, and that the wx-BL2 allele is similar to wx-C and possibly resulted from wx-C contamination. The deleted sequence responsible for these mutations is flanked by a short, 4-bp, direct repeat. Similar structures are favored sites for spontaneous deletions in other organisms. The data suggests that EMS is capable of inducing structural alterations in plant genes in addition to the point mutations normally ascribed to EMS-induced mutations.
Isolation by distance in a quantitative trait.
Authors: Lande R 
Published: January 2021

Abstract
Random genetic drift in a quantitative character is modeled for a population with a continuous spatial distribution in an infinite habitat of one or two dimensions. The analysis extends Wright's concept of neighborhood size to spatially autocorrelated sampling variation in the expected phenotype at different locations. Weak stabilizing selection is assumed to operate toward the same optimum phenotype in every locality, and the distribution of dispersal distances from parent to offspring is a (radially) symmetric function. The equilibrium pattern of geographic variation in the expected local phenotype depends on the neighborhood size, the genetic variance within neighborhoods, and the strength of selection, but is nearly independent of the form of the dispersal function. With all else equal, geographic variance is smaller in a two-dimensional habitat than in one dimension, and the covariance between expected local phenotypes decreases more rapidly with the distance separating them in two dimensions than in one. The equilibrium geographic variance is less than the phenotypic variance within localities, unless the neighborhood size is small and selection is extremely weak, especially in two dimensions. Nevertheless, dispersal of geographic variance created by random genetic drift is an important mechanism maintaining genetic variance within local populations. For a Gaussian dispersal function it is shown that, even with a small neighborhood size, a population in a two-dimensional habitat can maintain within neighborhoods most of the genetic variance that would occur in an infinite panmictic population.
Isolation and characterization of Schizosaccharomyces pombe mutants affected in mitotic recombination.
Authors: Gysler-Junker A , Bodi Z , Kohli J 
Published: January 2021

Abstract
A haploid Schizosaccharomyces pombe strain carrying a heteroallelic duplication of the ade6 gene was used to isolate mitotic recombination-deficient mutants. Recombination between the different copies of the ade6 gene can lead to Ade+ segregants. These are observed as growing papillae when colonies of a suitable size are replicated onto selective medium. We isolated mutants which show an altered papillation phenotype. With two exceptions, they exhibit a decrease in the frequency of mitotic recombination between the heteroalleles of the duplication. The two other mutants display a hyper-recombination phenotype. The 12 mutations were allocated to at least nine distinct loci by recombination tests. Of the eight rec mutants analyzed further, six were also affected in mitotic intergenic recombination in the intervals cen2-mat or cen3-arg 1. No effect on mitotic intragenic recombination was observed. These data suggest that mitotic gene conversion and crossing over can be separated mutationally. Meiotic recombination occurs at the wild-type frequency in all mutants investigated.
Interspecific backcross mice show sex-specific differences in allelic inheritance.
Authors: Siracusa L D , Alvord W G , Bickmore W A , Jenkins N A , Copeland N G 
Published: January 2021

Abstract
Transmission distortion is identified as a difference in transmission frequency of two alleles from the normal 1:1 Mendelian segregation in diploid organisms. Transmission distortion can extend over part or all of a chromosome. The recent development of interspecific mouse backcrosses has provided a powerful method for multilocus mapping of entire chromosomes in a single cross, and consequently for identifying distortions in allelic inheritance. We used an interspecific backcross of [(C57BL/6J x Mus spretus)F1 x C57BL/6J] mice to map molecular loci to mouse chromosome 2 and had previously found that the distal region of the chromosome showed distortions in allelic inheritance. We now report the mapping of five loci (Actc-1, D2Hgu1, His-1, Hox-4.1 and Neb) to chromosome 2, which, in addition to the Abl, Ada, B2m, Bmp-2a, Hc, Emv-15, Fshb, Hck-1, Pax-1, Pck-1, Spna-2 and Vim loci previously mapped in our interspecific backcross, serve as markers to measure allelic inheritance along approximately 75% of mouse chromosome 2. Statistical analyses are used to identify and delimit chromosomal regions showing transmission distortion and to determine whether there are sex-specific differences in allelic inheritance. These studies provide evidence for sex-specific differences in allelic inheritance for chromosome 2 and suggest biological explanations for this form of transmission distortion.
The structure of genealogies and the distribution of fixed differences between DNA sequence samples from natural populations.
Authors: Hey J 
Published: January 2021

Abstract
When two samples of DNA sequences are compared, one way in which they may differ is in the presence of fixed differences, which are defined as sites at which all of the sequences in one sample are different from all of the sequences in a second sample. The probability distribution of the number of fixed differences is developed. The theory employs Wright-Fisher genealogies and the infinite sites mutation model. For the case when both samples are drawn randomly from the same population it is found that genealogies permitting fixed differences are very unlikely. Thus the mere presence of fixed differences between samples is statistically significant, even for small samples. The theory is extended to samples from populations that have been separated for some time. The relationship between a simple Poisson distribution of mutations and the distribution of fixed differences is described as a function of the time since populations have been isolated. It is shown how these results may contribute to improved tests of recent balancing or directional selection.
Rex and a suppressor of Rex are repeated neomorphic loci in the Drosophila melanogaster ribosomal DNA.
Authors: Rasooly R S , Robbins L G 
Published: January 2021

Abstract
The Rex locus of Drosophila melanogaster induces a high frequency of mitotic exchange between two separated ribosomal DNA arrays on a single chromosome. The exchanges take place in the progeny of Rex mothers and occur very early, before the third mitotic division. A number of common laboratory stocks have also been found to carry dominant suppressors of Rex (Su(Rex)). Rex was mapped to the X centric heterochromatin, proximal to su(f), by genetic and molecular analysis of two spontaneous recombinants. Using deficiencies and duplications of the heterochromatin, both Rex and one Su(Rex) were shown to behave as neomorphs. Rex-induced exchange in a target chromosome bearing both Rex and Su(Rex) was then used to map these functions to the bb locus itself. Molecular analysis of the recombinants, using length variants of the ribosomal DNA intergenic spacer as genetic markers, mapped Su(Rex) and Rex within the bb locus and demonstrated that both are repeated elements.
Repeated use of GAL1 for gene disruption in Candida albicans.
Authors: Gorman J A , Chan W , Gorman J W 
Published: January 2021

Abstract
A technique which has the potential to allow repeated use of the same selectable marker to create gene disruptions in Candida albicans has been developed. In this approach, originally described for Saccharomyces cerevisiae, the selectable marker is flanked by direct repeats. Mitotic recombination between these repeats leads to elimination of the selectable marker. A module in which the GALq1 gene is flanked by direct repeats of the bacterial CAT gene was constructed and used to disrupt one copy of the URA3 gene in a gal1 mutant. Gal- revertants were selected by plating on 2-deoxy-D-galactose (2DOG). The frequency of 2DOG-resistant colonies recovered was 20 times higher than that obtained with a similar construct not flanked by direct repeats. Of these, 20% had lost the GAL1 gene by recombination between the direct repeats. The GAL1 gene was used again to disrupt the remaining wild-type copy of the URA3 gene of one of these gal1 isolates, resulting in a stable ura3 mutant. This technique should be generally applicable to derive homozygous gene disruptions in this diploid organism.
Interallelic complementation among DER/flb alleles: implications for the mechanism of signal transduction by receptor-tyrosine kinases.
Authors: Raz E , Schejter E D , Shilo B Z 
Published: January 2021

Abstract
The large number of available embryonic lethal alleles in the Drosophila EGF receptor homolog (DER)/faint little ball locus allowed us to test the possibility of positive or negative interactions among different DER alleles. These interactions were monitored by examining the embryonic cuticular phenotypes of different heteroallelic combinations. Several positive interactions were identified, while negative interactions were restricted to a single allele. This is the first example of positive interactions within the same cell type among alleles of a receptor tyrosine kinase gene. The basis for these interactions is likely to arise from the mechanism of signal transduction by receptor tyrosine kinases, which involves receptor aggregation. A combination of two different DER mutant proteins defective in temporally distinct stages of the signal transduction process, may thus form a functional heterodimer. The mutation sites in four alleles showing positive interactions were localized. They identify regions within the protein which are likely to be important for these temporally distinct signal transduction processes.
Replacement of bovine mitochondrial DNA by a sequence variant within one generation.
Authors: Koehler C M , Lindberg G L , Brown D R , Beitz D C , Freeman A E , Mayfield J E , Myers A M 
Published: January 2021

Abstract
Inheritance of mitochondrial DNA (mtDNA) in Holstein cattle was characterized by pedigree analysis of nucleotide sequence variation. mtDNA was purified from leukocytes of 174 individuals representing 35 independent maternal lineages, and analyzed for nucleotide sequence variation by characterization of restriction fragment length polymorphism and direct sequence determination. These data revealed 11 maternal lineages in which leukocytes from some individuals seemingly were homoplasmic for the reference mtDNA sequence at nucleotide 364, whereas those from other individuals were homoplasmic for a sequence variant at this position. Both alternative alleles were detected in all branches of these 11 lineages, suggesting that mutation at nucleotide 364 and fixation of the variant sequence occurred frequently in independent events. Thirteen instances were detected of mother-daughter pairs in which leukocytes of each of the two animals seemingly were homoplasmic for a different allele at nucleotide 364, demonstrating the bovine mitochondrial genome can be replaced completely by a nucleotide sequence variant within a single generation. The two alternative sequences seemingly arose de novo at similar frequency, ruling out replicative advantage or other selective bias as the explanation for rapid fixation of mutations at nucleotide 364. Another instance of intralineage sequence variation was detected at nucleotide 5602. This variation was detected in only one of the lineages examined, and evidently arose within three generations.