bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of TRP-1 mRNA levels in dominant and recessive mutations at the mouse brown (b) locus.
Authors: Jackson I J , Chambers D , Rinchik E M , Bennett D C 
Published: April 2021

Abstract
The mouse brown locus encodes a putative membrane-bound metalloenzyme, tyrosinase-related protein-1 (TRP-1). We have examined the effect on mRNA expression of the locus of a number of mutant alleles. The common null mutant allele, brown, produces wild-type levels of TRP-1 mRNA, which is nonfunctional. Another recessive allele, cordovan-Harwell, has an intermediate, dark-brown phenotype and produces only very low levels of presumably normal TRP-1 mRNA. Two dominant alleles appear to act by killing the melanocyte in which they are expressed. One of them, Light, has normal size and amounts of TRP-1 mRNA. The other, White-based brown, produces no detectable TRP-1 mRNA. It has a gross DNA rearrangement at the 5' end, and we speculate that this results in activation of transcription of sequences not usually seen in melanocytes, and that this is toxic to the cell. The relationship between phenotype and molecular structure at the locus is discussed, and we draw some general principles applicable to other developmental genes.
Molecular variation at the vermilion locus in geographically diverse populations of Drosophila melanogaster and D. simulans.
Authors: Begun D J , Aquadro C F 
Published: April 2021

Abstract
We surveyed nucleotide variation at vermilion in population samples of Drosophila melanogaster from Africa, Asia and the Americas to test the hypothesis that the vermilion gene was a target of balancing selection and to improve our understanding of geographic differentiation. Patterns of polymorphism and divergence showed no evidence for non-neutral evolution. However, the frequency spectrum of polymorphic sites in some non-African samples departed from the neutral equilibrium expectation. Furthermore, there were high levels of linkage disequilibrium in non-African samples, despite apparently high rates of crossing over in the vermilion region. In the absence of comparable data from other loci in these same population samples, we cannot determine whether the unusual patterns of variation at vermilion reflect demographic as opposed to locus-specific events. We found surprisingly high levels of differentiation at vermilion between U.S. and Congo samples of D. simulans. In light of previously published allozyme and mtDNA data that provided no evidence for significant differentiation between African and non-African D. simulans populations, the vermilion data raise the possibility that both mtDNA and allozymes have been influenced by selection.
Characterization of the major transcripts encoded by the regulatory MuDR transposable element of maize.
Authors: Hershberger R J , Benito M I , Hardeman K J , Warren C , Chandler V L , Walbot V 
Published: April 2021

Abstract
The MuDR element controls the transposition of the Mutator transposable element family in maize. Previous studies reported the presence of two major MuDR-homologous transcripts that correlate with Mutator activity. In this study, we describe the structure and processing of these two major transcripts. The transcripts are convergent, initiating from opposite ends of the element within the 220-bp terminal inverted repeats. The convergent transcripts do not overlap, and only 200 bp of internal MuDR sequences are not transcribed. Cloning and sequencing of multiple MuDR cDNAs revealed unusual intron/exon junctions, differential splicing, and multiple polyadenylation sites. RNase protection experiments indicated that some splicing failure occurs in young seedlings, and that a low level of antisense RNA exists for both transcripts. On a whole plant level, the presence of the major MuDR transcripts strictly correlates with Mutator activity in that no MuDR transcripts are observed in non-Mutator or inactive Mutator stocks. Examination of various tissues from active Mutator stocks indicates that the two transcripts are present in all organs and tissues tested, including those with no apparent transposition activity. This suggests that Mutator activity is not simply controlled by the level of the major MuDR transcripts.
Multiple trait analysis of genetic mapping for quantitative trait loci.
Authors: Jiang C , Zeng Z B 
Published: April 2021

Abstract
We present in this paper models and statistical methods for performing multiple trait analysis on mapping quantitative trait loci (QTL) based on the composite interval mapping method. By taking into account the correlated structure of multiple traits, this joint analysis has several advantages, compared with separate analyses, for mapping QTL, including the expected improvement on the statistical power of the test for QTL and on the precision of parameter estimation. Also this joint analysis provides formal procedures to test a number of biologically interesting hypotheses concerning the nature of genetic correlations between different traits. Among the testing procedures considered are those for joint mapping, pleiotropy, QTL by environment interaction, and pleiotropy vs. close linkage. The test of pleiotropy (one pleiotropic QTL at a genome position) vs. close linkage (multiple nearby nonpleiotropic QTL) can have important implications for our understanding of the nature of genetic correlations between different traits in certain regions of a genome and also for practical applications in animal and plant breeding because one of the major goals in breeding is to break unfavorable linkage. Results of extensive simulation studies are presented to illustrate various properties of the analyses.
The log-linear relationship between sexual isolation and sequence divergence in Bacillus transformation is robust.
Authors: Zawadzki P , Roberts M S , Cohan F M 
Published: April 2021

Abstract
The relationship between sexual isolation and sequence divergence in Bacillus transformation was previously shown to be log linear. In the present study, we have shown that this relationship is robust with respect to naturally occurring genetic variation among recipient strains of Bacillus subtilis and B. mojavensis. Naturally occurring restriction endonuclease activity was shown not to affect this relationship. Also, seven out of eight recombination mutants tested for their sensitivity to sequence divergence have shown the same relationship between sequence divergence and sexual isolation; a mutant for recH was more sensitive to sequence divergence, suggesting that the product of this gene may be involved in resolution of mismatches in heterogamic transformation. We have also shown that the relationship between sexual isolation and sequence divergence is robust with respect to variation in the conditions of transformation, including variation in the length of donor DNA, the concentration of donor DNA, and intracellular competition between donor-derived and recipient-derived DNA. The robustness of the relationship between sexual isolation and sequence divergence among naturally occurring strains and across transformation conditions allows us to predict the eventual outcome of sequence divergence among B. subtilis and its closest relatives.
Homologous recombination as the main mechanism for DNA integration and cause of rearrangements in the filamentous ascomycete Ashbya gossypii.
Authors: Steiner S , Wendland J , Wright M C , Philippsen P 
Published: April 2021

Abstract
A slow and a fast growth phenotype were observed after transformation of the phytopathogenic fungus Ashbya gossypii using a plasmid carrying homologous DNA and as selectable marker the Tn903 aminoglycoside resistance gene expressed from a strong A. gossypii promoter. Transformations with circular plasmids yielded slowly and irregularly growing geneticin-resistant mycelia in which 1% of nuclei contained plasmid sequences. Occasionally, fast growing sectors appeared which were shown to be initiated by homologous integration of the transforming DNA. Transformants obtained with plasmids linearized within the homology region immediately exhibited fast radial growth. In all 28 transformants analyzed plasmid DNA was integrated homologously. Such apparent lack of nonhomologous recombination has so far not been observed in filamentous ascomycetes. In 14 transformants two to four tandemly integrated plasmid copies were found. They underwent several types of genetic changes, mainly in the older mycelium: excision of whole plasmid copies and rearrangements within the integrated DNA (inversions and deletions). These internal rearrangements involved 360-bp inverted repeats, remnants of IS-elements flanking the resistance gene, and 156-bp direct repeats, originating from the strong A. gossypii promoter. Improved vectors lacking sequence repetitions were constructed and used for stable one-step gene replacement in A. gossypii.
DNA structures generated during recombination initiated by mismatch repair of UV-irradiated nonreplicating phage DNA in Escherichia coli: requirements for helicase, exonucleases, and RecF and RecBCD functions.
Authors: Feng W Y , Hays J B 
Published: April 2021

Abstract
During infection of homoimmune Escherichia coli lysogens ("repressed infections"), undamaged nonreplicating lambda phage DNA circles undergo very little recombination. Prior UV irradiation of phages dramatically elevates recombinant frequencies, even in bacteria deficient in UvrABC-mediated excision repair. We previously reported that 80-90% of this UvrABC-independent recombination required MutHLS function and unmethylated d(GATC) sites, two hallmarks of methyl-directed mismatch repair. We now find that deficiencies in other mismatch-repair activities--UvrD helicase, exonuclease I, exonuclease VII, RecJ exonuclease--drastically reduce recombination. These effects of exonuclease deficiencies on recombination are greater than previously observed effects on mispair-provoked excision in vitro. This suggests that the exonucleases also play other roles in generation and processing of recombinagenic DNA structures. Even though dsDNA breaks are thought to be highly recombinagenic, 60% of intracellular UV-irradiated phage DNA extracted from bacteria in which recombination is low--UvrD-, ExoI-, ExoVII-, or Rec(J-)--displays (near-)blunt-ended dsDNA ends (RecBCD-sensitive when deproteinized). In contrast, only bacteria showing high recombination (Mut+ UvrD+ Exo+) generate single-stranded regions in nonreplicating UV-irradiated DNA. Both recF and recB recC mutations strikingly reduce recombination (almost as much as a recF recB recC triple mutation), suggesting critical requirements for both RecF and RecBCD activity. The mismatch repair system may thus process UV-irradiated DNA so as to initiate more than one recombination pathway.
The role of DNA repair genes in recombination between repeated sequences in yeast.
Authors: Liefshitz B , Parket A , Maya R , Kupiec M 
Published: April 2021

Abstract
The presence of repeated sequences in the genome represents a potential source of karyotypic instability. Genetic control of recombination is thus important to preserve the integrity of the genome. To investigate the genetic control of recombination between repeated sequences, we have created a series of isogenic strains in which we could assess the role of genes involved in DNA repair in two types of recombination: direct repeat recombination and ectopic gene conversion. Naturally occurring (Ty elements) and artificially constructed repeats could be compared in the same cell population. We have found that direct repeat recombination and gene conversion have different genetic requirements. The role of the RAD51, RAD52, RAD54, RAD55, and RAD57 genes, which are involved in recombinational repair, was investigated. Based on the phenotypes of single and double mutants, these genes can be divided into three functional subgroups: one composed of RAD52, a second one composed of RAD51 and RAD54, and a third one that includes the RAD55 and RAD57 genes. Among seven genes involved in excision repair tested, only RAD1 and RAD10 played a role in the types of recombination studied. We did not detect a differential effect of any rad mutation on Ty elements as compared to artificially constructed repeats.
Non-locus-specific polygenes giving responses to selection for gene conversion frequencies in Ascobolus immersus.
Authors: Zwolinski S A , Lamb B C 
Published: April 2021

Abstract
Selection for higher and lower meiotic conversion frequencies was investigated in the fungus Ascobolus immersus. Strains carrying the same known gene conversion control factors, which have major effects on conversion frequencies at their specific target locus, sometimes gave significant differences in conversion frequency. Selection for high or low conversion frequencies at the w1-78 site was practiced for five generations, giving significant responses in both directions. These responses were due to polygenes, or genes of minor effect, not to new conversion control factors of major effect. Crosses of selected strains to strains with other mutations showed that the genes' effects were not specific to w1-78, but could affect conversion frequencies of another mutation, w1-3C1, at that locus and of two other loci, w-BHj and w9, which are unlinked to w1 or to each other. The proportional changes in gene conversion frequency due to selection varied according to the locus and site involved and according to the conversion control factor alleles present. There were differences of &gt; or = 277% in conversion frequency between "high" and "low" strains. Selection for conversion frequency had little effect on other features of conversion, such as the frequency of postmeiotic segregation or the relative frequencies of conversion to mutant or wild type.
Environmental programming of heritable epigenetic changes in paramutant r-gene expression using temperature and light at a specific stage of early development in maize seedlings.
Authors: Mikula B C 
Published: April 2021

Abstract
Different heritable expression-states were programmed into R alleles from R/R-1st heterozygotes under different temperature conditions applied during a developmental period in which flowering is induced. At maturity, R-allele expressions in test crosses of male gametes derived from R/R-1st seedlings raised 15 days in 32 degrees and continuous light conditions differed significantly from those of sib seedlings raised for 15 days in 22 degrees and continuous light conditions and shifted to six 12-hr light-dark cycles, day 16-21. This experiment provides the first evidence in higher organisms that environmental conditions, applied at a specific stage of development cause a heritable change in a specific allele expression. My earlier evidence required a statistical analysis for demonstrating heritable change; I present photographic evidence of this environmental effect on four R alleles.
HYBRID DYSGENESIS IN DROSOPHILA MELANOGASTER: A SYNDROME OF ABERRANT TRAITS INCLUDING MUTATION, STERILITY AND MALE RECOMBINATION
Authors: Kidwell Margaret G , Kidwell James F , Sved John A 
Published: April 2021

ABSTRACT
A syndrome of associated aberrant traits is described in Drosophila melanogaster. Six of these traits, mutation, sterility, male recombination, transmission ratio distortion, chromosomal aberrations and local increases in female recombination, have previously been reported. A seventh trait, nondisjunction, is described for the first time. All of the traits we have examined are found nonreciprocally in F1 hybrids. We present evidence that at least four of the traits are not found in nonhybrids. Therefore we have proposed the name hybrid dysgenesis to describe this syndrome.—A partition of tested strains into two types, designated P and M, was made according to the paternal or maternal contribution required to produce hybrid dysgenesis. This classification seems to hold for crosses of strains from within the United States and Australia, as well as for crosses between strains from the two countries. Strains collected recently from natural populations are typically of the P type and those having a long laboratory history are generally of the M type. However, a group of six strains collected from the wild in the 1960's are unambiguously divided equally between the P and M types. The dichotomy of this latter group raises interesting questions concerning possible implications for speciation.—Temperature often has a critical effect on the manifestation of hybrid dysgenesis. High F1 developmental temperatures tend to increase the expression of sterility, sometimes to extreme levels. Conversely, low developmental temperatures tend to inhibit the expression of some dysgenic traits.—There are potentially important practical implications of hybrid dysgenesis for laboratory experimentation. The results suggest that care should be exercised in planning experiments involving strain crosses.
PERSISTENCE OF COMMON ALLELES IN TWO RELATED POPULATIONS OR SPECIES
Authors: Li Wen-Hsiung , Nei Masatoshi 
Published: April 2021

ABSTRACT
Mathematical studies are conducted on three problems that arise in molecular population genetics. (1) The time required for a particular allele to become extinct in a population under the effects of mutation, selection, and random genetic drift is studied. In the absence of selection, the mean extinction time of an allele with an initial frequency close to 1 is of the order of the reciprocal of the mutation rate when 4Nv &lt;&lt; 1, where N is the effective population size and v is the mutation rate per generation. Advantageous mutations reduce the extinction time considerably, whereas deleterious mutations increase it tremendously even if the effect on fitness is very slight. (2) Mathematical formulae are derived for the distribution and the moments of extinction time of a particular allele from one or both of two related populations or species under the assumption of no selection. When 4Nv &lt;&lt; 1, the mean extinction time is about half that for a single population, if the two populations are descended from a common original stock. (3) The expected number as well as the proportion of common neutral alleles shared by two related species at the tth generation after their separation are studied. It is shown that if 4Nv is small, the two species are expected to share a high proportion of common alleles even 4N generations after separation. In addition to the above mathematical studies, the implications of our results for the common alleles at protein loci in related Drosophila species and for the degeneration of unused characters in cave animals are discussed.
INVERSION CLINES IN POPULATIONS OF DROSOPHILA MELANOGASTER
Authors: Mettler L E , Voelker R A , Mukai Terumi 
Published: April 2021

ABSTRACT
Twenty different natural populations of Drosophila melanogaster were sampled to determine the frequencies of inversions. Based on their frequencies and geographical distributions, the inversions could be classified as follows: (1) Common cosmopolitan inversions that are present in many populations in frequencies exceeding five percent and that may exhibit frequency clines over large geographical regions; (2) Rare cosmopolitan inversions that occur throughout the species range but usually at frequencies below five percent and that may be absent in many populations; (3) Recurrent endemic inversions that are found in several adjacent populations in frequencies usually not exceeding one or two percent; and (4) Unique endemic inversions that are found only among the progeny of a single individual and that may represent one aspect of the syndrome termed "hybrid dysgenesis". Four common cosmopolitan inversions that exhibit highly significant clines in populations in the eastern United States are In(2L)t, In(2R)NS, In(3L)P and In(3R)P.
ADAPTATION AT SPECIFIC LOCI. I. NATURAL SELECTION ON PHOSPHOGLUCOSE ISOMERASE OF COLIAS BUTTERFLIES: BIOCHEMICAL AND POPULATION ASPECTS
Authors: Watt Ward B 
Published: April 2021

ABSTRACT
Electrophoretic variants of phosphoglucose isomerase (PGI) in Colias butterflies have been studied from field and laboratory viewpoints. The transmission pattern is that of a dimeric enzyme controlled by one structural gene locus. Populations usually harbor four to six allelic mobility classes. These mobility classes are shared among species complexes, though their frequencies differ widely. Preliminary Ferguson plot analysis of the variants has been carried out. Purified preparations of Colias PGI alleles are more effective in standardizing Ferguson plots than heterologous proteins, such as ferritin. Variation of Ferguson plot parameters is not an infallible guide to electrophoretically "cryptic alleles," as one putative case proved to be due to nonallele-specific effects. S, M, and F mobility classes in two Colias semispecies show the same retardation coefficients in Ferguson plots. Adults early in the flight periods of their nonoverlapping generations show genotype frequencies in Hardy-Weinberg equilibrium, but heterozygote excess develops as the insects age. Simple directional selection and large-scale population mixing are unlikely to be causes of this, although several other selection modes remain possible. Identical-by-descent lines of the four frequent-to-common alleles in C. eurytheme have been set up in culture, and enzyme has been purified from these for study of functional properties. Major differenecs in heat stability and in various kinetic parameters are found among the ten possible genotypes. In some cases, heterosis for kinetic parameters is seen; in other cases, opposing trends in kinetic function and heat stability create potential for net heterosis in function. Possible interpretations of these results in an adaptive metabolic context are discussed, and directions for further work are stated.
THE TIMING OF UV MUTAGENESIS IN YEAST: A PEDIGREE ANALYSIS OF INDUCED RECESSIVE MUTATION
Authors: James A P , Kilbey B J 
Published: April 2021

ABSTRACT
The mechanism of UV-induced mutation in eukaryotes was studied in individual yeast cells by a procedure that combined pedigree analysis and tetrad analysis. The technique involved the induction of recessive lethals and semilethals in G1 diploid cells. Induced frequencies were 25 and 61 percent at survival levels of 90 and 77 percent, respectively. No evidence of gross chromosome aberrations was detected. Recessive mutations that affect only one strand or that affect both strands of the DNA molecule are induced much at random among a population of cells, and both types can occur within the same cell. However, the data confirm that two-strand mutations are in the majority after a low level of irradiation. The simplest explanation involves a mechanism whereby most mutations are fixed in both strands prior to the first round of post-irradiation DNA replication. The recessive mutational consequences of irradiation are exhausted at the conclusion of the first post-irradiation cell division, although dominant-lethal sectoring continues at a high level through the second post-irradiation division. It is concluded that pyrimidine dimers that persist to the second round of DNA replication are rare or ineffective.