bluuebunny/crossref_metadata_2025_split huggingface dataset:
Among-environment heteroscedasticity and genetic autocorrelation: implications for the study of phenotypic plasticity.
Authors: Dutilleul P , Potvin C 
Published: January 2021

Abstract
The impact of among-environment heteroscedasticity and genetic autocorrelation on the analysis of phenotypic plasticity is examined. Among-environment heteroscedasticity occurs when genotypic variances differ among environments. Genetic autocorrelation arises whenever the responses of a genotype to different environments are more or less similar than expected for observations randomly associated. In a multivariate analysis-of-variance model, three transformations of genotypic profiles (reaction norms), which apply to the residuals of the model while preserving the mean responses within environments, are derived. The transformations remove either among-environment heteroscedasticity, genetic autocorrelation or both. When both nuisances are not removed, statistical tests are corrected in a modified univariate approach using the sample covariance matrix of the genotypic profiles. Methods are illustrated on a Chlamydomonas reinhardtii data set. When heteroscedasticity was removed, the variance component associated with the genotype-by-environment interaction increased proportionally to the genotype variance component. As a result, the genetic correlation rg was altered. Genetic autocorrelation was responsible for statistical significance of the genotype-by-environment interaction and genotype main effects on raw data. When autocorrelation was removed, the ranking of genotypes according to their stability index dramatically changed. Evolutionary implications of our methods and results are discussed.
Genetic characterization of ms (3) K81, a paternal effect gene of Drosophila melanogaster.
Authors: Yasuda G K , Schubiger G , Wakimoto B T 
Published: January 2021

Abstract
The vast majority of known male sterile mutants of Drosophila melanogaster fail to produce mature sperm or mate properly. The ms(3) K81(1) mutation is one of a rare class of male sterile mutations in which sterility is caused by developmental arrest after sperm entry into the egg. Previous studies showed that males homozygous for the K81(1) mutation produce progeny that arrest at either of two developmental stages. Most embryos arrest during early nuclear cycles, whereas the remainder are haploid embryos that arrest at a later stage. This description of the mutant phenotype was based on the analysis of a single allele isolated from a natural population. It was therefore unclear whether this unique paternal effect phenotype reflected the normal function of the gene. The genetic analysis and initial molecular characterization of five new K81 mutations are described here. Hemizygous conditions and heteroallelic combinations of the alleles were associated with male sterility caused by defects in embryogenesis. No other mutant phenotypes were observed. Thus, the K81 gene acted as a strict paternal effect gene. Moreover, the biphasic pattern of developmental arrest was common to all the alleles. These findings strongly suggested that the unusual embryonic phenotype caused by all five new alleles was due to loss of function of the K81+ gene. The K81 gene is therefore the first clear example of a strict paternal effect gene in Drosophila. Based on the embryonic lethal phenotypes, we suggest that the K81+ gene encodes a sperm-specific product that is essential for the male pronucleus to participate in the first few embryonic nuclear divisions.
5-Fluoroindole resistance identifies tryptophan synthase beta subunit mutants in Arabidopsis thaliana.
Authors: Barczak A J , Zhao J , Pruitt K D , Last R L 
Published: January 2021

Abstract
A study of the biochemical genetics of the Arabidopsis thaliana tryptophan synthase beta subunit was initiated by characterization of mutants resistant to the inhibitor 5-fluoroindole. Thirteen recessive mutations were recovered that are allelic to trp2-1, a mutation in the more highly expressed of duplicate tryptophan synthase beta subunit genes (TSB1). Ten of these mutations (trp2-2 through trp2-11) cause a tryptophan requirement (auxotrophs), whereas three (trp2-100 through trp2-102) remain tryptophan prototrophs. The mutations cause a variety of changes in tryptophan synthase beta expression. For example, two mutations (trp2-5 and trp2-8) cause dramatically reduced accumulation of TSB mRNA and immunologically detectable protein, whereas trp2-10 is associated with increased mRNA and protein. A correlation exists between the quantity of mutant beta and wild-type alpha subunit levels in the trp2 mutant plants, suggesting that the synthesis of these proteins is coordinated or that the quantity or structure of the beta subunit influences the stability of the alpha protein. The level of immunologically detectable anthranilate synthase alpha subunit protein is increased in the trp2 mutants, suggesting the possibility of regulation of anthranilate synthase levels in response to tryptophan limitation.
Genetic analysis of the fimbrin-actin binding interaction in Saccharomyces cerevisiae.
Authors: Brower S M , Honts J E , Adams A E 
Published: January 2021

Abstract
Yeast fimbrin is encoded by the SAC6 gene, mutations of which suppress temperature-sensitive mutations in the actin gene (ACT1). To examine the mechanism of suppression, we have sequenced 17 sac6 suppressor alleles, and found that they change nine different residues, all of which cluster in three regions of one of the two actin-binding domains of Sac6p. Two of these clusters occur in highly conserved regions (ABS1 and ABS3) that have been strongly implicated in the binding of related proteins to actin. The third cluster changes residues not previously implicated in the interaction with actin. As changes in any of nine different residues can suppress several different act1 alleles, it is likely that the suppressors restore the overall affinity, rather than specific lost interactions, between Sac6p and actin. Using mutagenesis, we have identified two mutations of the second actin-binding domain that can also suppress the act1 mutations of interest. This result suggests the two actin-binding domains of Sac6p interact with the same region of the actin molecule. However, differences in strength of suppression of temperature-sensitivity and sporulation indicate that the two actin-binding domains are distinct, and explain why second-domain mutations were not identified previously.
A genetic analysis of the Drosophila closely linked interacting genes bulge, argos and soba.
Authors: Wemmer T , Klämbt C 
Published: January 2021

Abstract
The Drosophila gene argos encodes a diffusible protein that acts as a negative regulator of cell fate decisions. To define interacting gene products, we performed a genetic analysis of argos, which suggests the presence of several partially redundant gene functions in its immediate vicinity at the chromosomal position 73A. Dose titration experiments have identified two of these loci. One of them corresponds to the gene bulge. Loss of function bulge alleles suppress the rough eye phenotype associated with overexpression of argos; conversely, amorphic argos mutations suppress the eye phenotype seen in flies bearing a single dominant bulge allele. Recombination mapping localized bulge 0.15 cM distal to argos. A second gene, suppressor of bulge and argos (soba), corresponds to the recently described lethal complementation group 73Aj. soba alleles suppress the eye phenotypes seen in flies expressing either the dominant bulge allele or the hs-argos construct. soba resides 120 kb proximal to argos. In addition, we have identified one allele of a new gene, clown, which like soba suppresses the eye phenotypes associated with hs-argos and bulgeDominant. clown maps on chromosome 3 at the cytological position 68CD.
Intermolecular transposition of IS10 causes coupled homologous recombination at the transposition site.
Authors: Eichenbaum Z , Livneh Z 
Published: January 2021

Abstract
Interplasmid and chromosome to plasmid transposition of IS10 were studied by assaying inactivation of the phage 434 cI gene, carried on a low copy number plasmid. This was detected by the activity of the tet gene expressed from the phage 434 PR promoter. Each interplasmid transposition resulted in the fusion of the donor and acceptor plasmids into cointegrate structure, with a 9-bp duplication of the target DNA at the insertion site. Cointegrate formation was abolished in delta recA strains, although simple insertions of IS10 were observed. This suggests a two-stage mechanism involving IS10 conservative transposition, followed by homologous recombination between the donor and the acceptor. Two plasmids carrying inactive IS10 sequences were fused to cointegrates at a 100-fold lower frequency, suggesting that homologous recombination is coupled to and stimulated by the transposition event. Each IS10 transposition from the chromosome to the acceptor plasmid involved replicon fusion, providing a mechanism for IS10-mediated integration of extrachromosomal elements into the chromosome. This was accompanied by the formation of an additional copy of IS10 in the chromosome. Thus, like replicative transposition, conservative transposition of IS10 is accompanied by cointegrate formation and results in duplication of the IS10.
Evolutionary relationships and sequence variation of alpha-amylase variants encoded by duplicated genes in the Amy locus of Drosophila melanogaster.
Authors: Inomata N , Shibata H , Okuyama E , Yamazaki T 
Published: January 2021

Abstract
To infer the genealogical relationships of alpha-amylase electromorphs of Drosophila melanogaster, we determined the nucleotide sequences of a collection of electromorphs sampled throughout the world. On average there were 1.0 amino acid substitutions between identical electromorphs and 3.9 between different electromorphs, respectively. We found that the evolution of AMY1 through AMY6 electromorphs occurred by sequential accumulation of single amino acid substitutions each causing one charge difference. The nucleotide diversities at synonymous sites within Amy1,Amy2,Amy3,Amy4 and Amy6 were 0.0321, 0.0000, 0.0355, 0.0059 and 0.0030, respectively. We also obtained evidence of genetic exchanges, such as intrachromosomal recombination, interchromosomal recombination or gene conversion, between the two duplicated Amy genes as well as among the alleles.
Molecular basis of polymorphism at the esterase-5B locus in Drosophila pseudoobscura.
Authors: Veuille M , King L M 
Published: January 2021

Abstract
Sequence variation was studied in a 2.2-kb region encompassing the esterase-5B locus in Drosophila pseudoobscura from two California populations. In these populations, two common electrophoretic classes and many less frequent variants occur, and it was formerly shown by KEITH (1983) that allele frequencies differed from random distribution under an infinite allele model. Nucleotide polymorphisms were determined in 16 sequences representing 14 electrophoretic classes. There was no significant sequence differentiation between populations, and both synonymous and nonsynonymous polymorphisms are distributed homogeneously along the sequence. The data show that the two major electrophoretic classes are heterogeneous at the amino acid level with no diagnostic amino acid(s) distinguishing them. At the nucleotide level, members of one major class are more similar to members of other electrophoretic classes than they are to each other. It appears that random combinations of the neutral amino acid polymorphisms and other undefined physical properties of the proteins generate the different electrophoretic classes and maintain considerable variation at Est-5B.
Chaser (Csr), a new gene affecting larval foraging behavior in Drosophila melanogaster.
Authors: Pereira H S , MacDonald D E , Hilliker A J , Sokolowski M B 
Published: January 2021

Abstract
Chaser (Csr) was uncovered in a gamma mutagenesis screen to identify genes that modify the larval foraging behavior of sitters to rovers. Rover larvae have significantly longer path lengths than sitters while foraging on a yeast and water paste. This difference is influenced by one major gene, foraging (for), which has two naturally occurring alleles, forR (rover) and fors (sitter). In a mutagenesis screen for modifiers of for, we identified three lines with viable mutations on chromosome 3 that alter foraging behavior. Each of these mutations increased larval path lengths in fors/fors larvae in a dominant fashion, and were not separable by recombination. These mutations are therefore probably allelic and define a new gene that we have called Csr. Csr was genetically localized using the lethal-tagging technique. This technique resulted in seven lines with a significant decrease in larval path-length and recessive lethal mutations on chromosome 3. We refer to these as reverted Csr (Csrrv) lines. Deficiencies that uncovered cytologically visible chromosome rearrangements in three of the seven reverted lines were used in a complementation analysis. In this way we mapped the lethal mutations in the Csrrv lines to cytological region 95F7-96A1 on the right arm of chromosome 3.
Islands of complex DNA are widespread in Drosophila centric heterochromatin.
Authors: Le M H , Duricka D , Karpen G H 
Published: January 2021

Abstract
Heterochromatin is a ubiquitous yet poorly understood component of multicellular eukaryotic genomes. Major gaps exist in our knowledge of the nature and overall organization of DNA sequences present in heterochromatin. We have investigated the molecular structure of the 1 Mb of centric heterochromatin in the Drosophila minichromosome Dp1187. A genetic screen of irradiated minichromosomes yielded rearranged derivatives of Dp1187 whose structures were determined by pulsed-field Southern analysis and PCR. Three Dp1187 deletion derivatives and an inversion had one breakpoint in the euchromatin and one in the heterochromatin, providing direct molecular access to previously inaccessible parts of the heterochromatin. End-probed pulsed-field restriction mapping revealed the presence of at least three "islands" of complex DNA, Tahiti, Moorea, and Bora Bora, constituting approximately one half of the Dp1187 heterochromatin. Pulsed-field Southern analysis demonstrated that Drosophila heterochromatin in general is composed of alternating blocks of complex DNA and simple satellite DNA. Cloning and sequencing of a small part of one island, Tahiti, demonstrated the presence of a retroposon. The implications of these findings to heterochromatin structure and function are discussed.
Mutations in the myp1 gene of Ustilago maydis attenuate mycelial growth and virulence.
Authors: Giasson L , Kronstad J W 
Published: January 2021

Abstract
Mating between haploid, budding cells of the dimorphic fungus Ustilago maydis results in the formation of a dikaryotic, filamentous cell type. Mating compatibility is governed by two mating-type loci called a and b; transformation of genes from these loci (e.g. a1 and b1) into a haploid strain of different mating type (e.g. a2 b2) allows filamentous growth and establishes a pathogenic cell type. Several mutants with a nonmycelial colony morphology were isolated after insertional mutagenesis of a filamentous, pathogenic haploid strain. The mutagenized region in one such mutant was recovered by plasmid rescue and employed to isolate a gene involved in conditioning the mycelial phenotype (myp1). An 1150 amino acid open reading frame is present at the myp1 locus; the predicted polypeptide is rich in serine residues and contains short regions with similarity to SH3 domain ligands. Construction of myp1 disruption and deletion mutants in haploid strains confirmed that this gene plays a role in mycelial growth and virulence.
Isolation of dominant XO-feminizing mutations in Caenorhabditis elegans: new regulatory tra alleles and an X chromosome duplication with implications for primary sex determination.
Authors: Hodgkin J , Albertson D G 
Published: January 2021

Abstract
A strain of Caenorhabditis elegans was constructed that permits selection of dominant or sex-linked mutations that transform XO animals (normally male) into fertile females, using a feminizing mutation, tra-2(e2046gf), which by itself does not sexually transform XO males. Twenty-three mutations were isolated after chemical mutagenesis and found to fall into both expected classes (four dominant tra-1 mutations and eight recessive xol-1 mutations) and novel classes. The novel mutations include 10 second-site mutations of tra-2, which are called eg mutations, for enhanced gain-of-function. The tra-2(gf, eg) alleles lead to complete dominant transformation of XO animals from fertile male into fertile female. Also isolated was a duplication of the left end of the X chromosome, eDp26, which has dominant XO lethal and feminizing properties, unlike all previously isolated duplications of the X chromosome. The properties of eDp26 indicate that it carries copies of one or more numerator elements, which act as part of the primary sex-determination signal, the X:A ratio. The eDp26 duplication is attached to the left tip of the X chromosome in inverted orientation and consequently can be used to generate unstable attached-X chromosomes.
Individual variation in inbreeding depression: the roles of inbreeding history and mutation.
Authors: Schultz S T , Willis J H 
Published: January 2021

Abstract
We use mutation-selection recursion models to evaluate the relative contributions of mutation and inbreeding history to variation among individuals in inbreeding depression and the ability of experiments to detect associations between individual inbreeding depression and mating system genotypes within populations. Poisson mutation to deleterious additive or recessive alleles generally produces far more variation among individuals in inbreeding depression than variation in history of inbreeding, regardless of selfing rate. Moreover, variation in inbreeding depression can be higher in a completely outcrossing or selfing population than in a mixed-mating population. In an initially random mating population, the spread of a dominant selfing modifier with no pleiotropic effects on male outcross success causes a measurable increase in inbreeding depression variation if its selfing rate is large and inbreeding depression is caused by recessive lethals. This increase is observable during a short period as the modifier spreads rapidly to fixation. If the modifier alters selfing rate only slightly, it fails to spread or causes no measurable increase in inbreeding depression variance. These results suggest that genetic associations between mating loci and inbreeding depression loci could be difficult to demonstrate within populations and observable only transiently during rapid evolution to a substantially new selfing rate.
Chromosome rearrangements that involve the nucleolus organizer region in Neurospora.
Authors: Perkins D D , Raju N B , Barry E G , Butler D K 
Published: January 2021

Abstract
In approximately 3% of Neurospora crassa rearrangements, part of a chromosome arm becomes attached to the nucleolus organizer region (NOR) at one end of chromosome 2 (linkage group V). Investigations with one inversion and nine translocations of this type are reported here. They appear genetically to be nonreciprocal and terminal. When a rearrangement is heterozygous, about one-third of viable progeny are segmental aneuploids with the translocated segment present in two copies, one in normal position and one associated with the NOR. Duplications from many of the rearrangements are highly unstable, breaking down by loss of the NOR-attached segment to restore normal chromosome sequence. When most of the rearrangements are homozygous, attenuated strands can be seen extending through the unstained nucleolus at pachytene, joining the translocated distal segment to the remainder of chromosome 2. Although the rearrangements appear genetically to be nonreciprocal, molecular evidence shows that at least several of them are physically reciprocal, with a block of rDNA repeats translocated away from the NOR. Evidence that NOR-associated breakpoints are nonterminal is also provided by intercrosses between pairs of translocations that transfer different-length segments of the same donor-chromosome arm to the NOR.
Identification and cloning of unc-119, a gene expressed in the Caenorhabditis elegans nervous system.
Authors: Maduro M , Pilgrim D 
Published: January 2021

Abstract
A spontaneous mutation affecting locomotion of the nematode Caenorhabditis elegans has been mapped to a new gene, unc-119. Phenotypic characterization of the mutants suggests the defect does not lie in the musculature and that the animals also have defects in feeding behavior and chemosensation. unc-119 has been physically mapped relative to a previously identified chromosomal break in linkage group III, and DNA clones covering the region can rescue the mutant phenotype in transgenic animals. Three more alleles at the locus, with identical phenotypes, have been induced and characterized, all of which are putative null alleles. The predicted UNC-119 protein has no significant similarity to other known proteins. Expression of an unc-119/lacZ fusion in transgenic animals is seen in many neurons, suggesting that the unc-119 mutant phenotype is due to a defect in the nervous system.
Mutational analyses of fs(1)Ya, an essential, developmentally regulated, nuclear envelope protein in Drosophila.
Authors: Liu J , Song K , Wolfner M F 
Published: January 2021

Abstract
The fs(1)Ya protein (YA) is an essential, maternally encoded, nuclear lamina protein that is under both developmental and cell cycle control. A strong Ya mutation results in early arrest of embryos. To define the function of YA in the nuclear envelope during early embryonic development, we characterized the phenotypes of four Ya mutants alleles and determined their molecular lesions. Ya mutant embryos arrest with abnormal nuclear envelopes prior to the first mitotic division; a proportion of embryos from two leaky Ya mutants proceed beyond this but arrest after several abnormal divisions. Ya unfertilized eggs contain nuclei of different sizes and condensation states, apparently due to abnormal fusion of the meiotic products immediately after meiosis. Lamin is localized at the periphery of the uncondensed nuclei in these eggs. These results suggest that YA function is required during and after egg maturation to facilitate proper chromatin condensation, rather than to allow a lamin-containing nuclear envelope to form. Two leaky Ya alleles that partially complement have lesions at opposite ends of the YA protein, suggesting that the N- and C-termini are important for YA function and that YA might interact with itself either directly or indirectly.
Haplotype test reveals departure from neutrality in a segment of the white gene of Drosophila melanogaster.
Authors: Kirby D A , Stephan W 
Published: January 2021

Abstract
Restriction map studies previously revealed extensive linkage disequilibria in the transcriptional unit of the white locus in natural Drosophila melanogaster populations. To understand the causes of these disequilibria, we sequenced a 4722-bp region of the white gene from 15 lines of D. melanogaster and 1 line of Drosophila simulans. Statistical tests applied to the entire 4722-bp region do not reject neutrality. In contrast, a test for high-frequency haplotypes ("Haplotype test") revealed an 834-bp segment, encompassing the 3' end of intron 1 to the 3' end of intron 2, in which the structure of variation deviates significantly from the predictions of a neutral equilibrium model. The variants in this 834-bp segment segregate as single haplotype blocks. We proposed that these unusually large haplotype blocks are due to positive selection on polymorphisms within the white gene, including a replacement polymorphism, Arg--&gt;Leu, within this segment.