bluuebunny/crossref_metadata_2025 huggingface dataset:
Isolation of Degradation-Deficient Mutants Defective in the Targeting of Fructose-1,6-bisphosphatase into the Vacuole for Degradation in Saccharomyces cerevisiae
Authors: Hoffman Mark , Chiang Hui-Ling
Published: January 2021

The key regulatory enzyme in the gluconeogenesis pathway, fructose-1,6-bisphosphatase (FBPase), is induced when Saccharomyces cerevisiae are grown in medium containing a poor carbon source. FBPase is targeted to the yeast vacuole for degradation when glucose-starved cells are replenished with fresh glucose. To identify genes involved in the FBPase degradation pathway, mutants that failed to degrade FBPase in response to glucose were isolated using a colony-blotting procedure. These vacuolar import and degradation-deficient (vid) mutants were placed into 20 complementation groups. They are distinct from the known sec, ups or pep mutants affecting protein secretion, vacuolar sorting and vacuolar proteolysis in that they sort CpY correctly and regulate osmotic pressure normally. Despite the presence of FBPase antigen in these mutants, FBPase is completely inactivated in all uid mutants, indicating that the c-AMP-dependent signal transduction pathway and inactivation must function properly in vid mutants. vid mutants block FBPase dzgradation by accumulating FBPase in the cytosol and also in small vesicles in the cytoplasm. FBPase may be targeted to small vesicles before uptake by the vacuole.
The Product of the het-C Heterokaryon Incompatibility Gene of Neurospora crassa Has Characteristics of a Glycine-Rich Cell Wall Protein
Authors: Saupe Sven J , Kuldau Gretchen A , Smith Myron L , Glass N Louise
Published: January 2021

Filamentous fungi are capable of hyphal fusion, but heterokaryon formation between different isolates is controlled by specific loci termed het loci. Heterokaryotic cells formed between strains of different het genotype are rapidly destroyed or strongly inhibited in their growth. In Neurospora crassa, at least 11 loci, including the mating type locus, affect the capacity to form a heterokaryon between different isolates. In this report, we describe the molecular characterization of the vegetative incompatibility locus, het-C. The het-COR allele was cloned by genetically identifying the het-C locus in a chromosome walk, and the activity of clones containing the het-COR allele was tested in a functional transformation assay. The het-COR allele encodes a 966amino acid polypeptide with a putative signal peptide, a coiled-coil motif and a Gterminal glycine-rich domain, similar to glycine-rich domains detected in various extracellular and structural cell envelope proteins. Both the coiled-coil and one-third of the glycine-rich carboxyl terminal domains were required for full het-COR activity. Mutants of het-COR were obtained by repeat-induced point mutation (RIP) ; these mutants were indistinguishable from wild type during vegetative growth and sexual reproduction hut displayed dual compatibility with both of two mutually incompatible het-COR and het-cPA strains.
The Regulatory Properties of Autonomous Subtelomeric P Elements Are Sensitive to a Suppressor of variegation in Drosophila melanogaster
Authors: Ronsseray Stéphane , Lehmann Monique , Nouaud Danielle , Anxolabéhère Dominique
Published: January 2021

Genetic recombination was used in Drosophila melanogaster to isolate P elements, inserted at the telomeres of X chromosomes (cytological site 1A) from natural populations, in a genetic background devoid of other P elements. We show that complete maternally inherited P repression in the germline (P cytotype) can be elicited by only two autonomous P elements at 1A and that a single element at this site has partial regulatory properties. The analysis of the surrounding chromosomal regions of the P elements at 1A shows that in all cases these elements are flanked by Telomeric Associated Sequences, tandemly repetitive noncoding sequences that have properties of heterochromatin. In addition, we show that the regulatory properties of P elements at 1A can be inhibited by some of the mutant alleles of the Su(var)205 gene and by a deficiency of this gene. However, the regulatory properties of reference P strains (Harwich and Texas 007) are not impaired by Su(var)205 mutations. Su(var)205 encodes Heterochromatin Protein 1 (HP1). These results suggest that the HP1 dosage effect on the P element properties is sitedependent and could involve the structure of the chromatin.
Rapid Evolution of a Coadapted Gene Complex: Evidence From the Segregation Distorter (SD) System of Meiotic Drive in Drosophila melanogaster
Authors: Palopoli Michael F , Wu Chung-I
Published: January 2021

Segregation Distorter (SD) is a system of meiotic drive found in natural populations of Drosophila melanogaster. Males heterozygous for an SD second chromosome and a normal homologue (SD  +) produce predominantly SD-bearing sperm. The coadapted gene complex responsible for this transmission advantage spans the second chromosome centromere, consisting of three major and several minor interacting loci. To investigate the evolutionary history of this system, we surveyed levels of polymorphism and divergence at six genes that together encompass this pericentromeric region and span seven map units. Interestingly, there was no discernible divergence between SD and SD  + chromosomes for any of these molecular markers. Furthermore, SD chromosomes harbored much less polymorphism than did SD  + chromosomes. The results suggest that the SD system evolved recently, swept to appreciable frequencies worldwide, and carried with it the entire second chromosome centromeric region (roughly 10% of the genome). Despite its well-documented genetic complexity, this coadapted system appears to have evolved on a time scale that is much shorter than can be gauged using nucleotide substitution data. Finally, the large genomic region hitchhiking with SD indicates that a multilocus, epistatically selected system could affect the levels of DNA polymorphism observed in regions of reduced recombination.
Intragenic Recombination in the Adh Locws of the Wild Plant Arabidopsis thaliana
Authors: Innan Hideki , Tajima Fumio , Terauchi Ryohei , Miyashita Naohiko T
Published: January 2021

Nucleotide variation in the Adh region of the wild plant Arabidopsis thaliana was analyzed in 17 ecotypes sampled worldwide to investigate DNA polymorphism in natural plant populations. The investigated 2.4kb Adh region was divided into four blocks by intragenic recombinations between two parental sequence types that diverged 6.3 million years (Myr) ago, if the nucleotide mutation rate μ = 10−9 is assumed. Within each block, dimorphism of segregating variations was observed with intermediate frequencies, which caused a substantial amount of nucleotide variation in A. thaliana at the species level. The first recombination introduced the divergent variation that resulted in dimorphism in this plant species ~3.3 Myr ago, and three subsequent intragenic recombinations have occurred sporadically in ~1.1-Myr intervals. It was shown that there was only a limited number (six) of sequence types in this species and that no clear association was observed between sequence type and geographic origin. Taken together, these results suggest that A. thaliana has spread over the world only recently. It can be concluded that recombination played an important role in the evolutionary history of A. thaliana, especially through the generation of DNA polymorphism in the natural populations of this plant species.
Maximum Likelihood Analysis of Rare Binary Traits Under Different Modes of Inheritance
Authors: Thaller G , Dempfle L , Hoeschele I
Published: January 2021

Maximum likelihood methodology was applied to determine the mode of inheritance of rare binary traits with data structures typical for swine populations. The genetic models considered included a monogenic, a digenic, a polygenic, and three mixed polygenic and major gene models. The main emphasis was on the detection of major genes acting on a polygenic background. Deterministic algorithms were employed to integrate and maximize likelihoods. A simulation study was conducted to evaluate model selection and parameter estimation. Three designs were simulated that differed in the number of sires/number of dams within sires (10/10, 30/30, 100/30). Major gene effects of at least one SD of the liability were detected with satisfactory power under the mixed model of inheritance, except for the smallest design. Parameter estimates were empirically unbiased with acceptable standard errors, except for the smallest design, and allowed to distinguish clearly between the genetic models. Distributions of the likelihood ratio statistic were evaluated empirically, because asymptotic theory did not hold. For each simulation model, the Average Information Criterion was computed for all models of analysis. The model with the smallest value was chosen as the best model and was equal to the true model in almost every case studied.
Selfish Operons: Horizontal Transfer May Drive the Evolution of Gene Clusters
Authors: Lawrence Jeffrey G , Roth John R
Published: January 2021

A model is presented whereby the formation of gene clusters in bacteria is mediated by transfer of DNA within and among taxa. Bacterial operons are typically composed of genes whose products contribute to a single function. If this function is subject to weak selection or to long periods with no selection, the contributing genes may accumulate mutations and be lost by genetic drift. From a cell's perspective, once several genes are lost, the function can be restored only if all missing genes were acquired simultaneously by lateral transfer. The probability of transfer of multiple genes increases when genes are physically proximate. From a gene's perspective, horizontal transfer provides a way to escape evolutionary loss by allowing colonization of organisms lacking the encoded functions. Since organisms bearing clustered genes are more likely to act as successful donors, clustered genes would spread among bacterial genomes. The physical proximity of genes may be considered a selfish property of the operon since it affects the probability of successful horizontal transfer but may provide no physiological benefit to the host. This process predicts a mosaic structure of modern genomes in which ancestral chromosomal material is interspersed with novel, horizontally transferred operons providing peripheral metabolic functions.
rdgE: A Novel Retinal Degeneration Mutation in Drosophila melanogaster
Authors: Zars Troy , Hyde David R
Published: January 2021

We report isolating the Drosophila retinal degeneration E (rdgE) mutation. The hypomorphic rdgE  1 allele causes rapid photoreceptor degeneration in light and a slower rate of degeneration when the flies are raised in constant darkness. The rdgE  1 flies exhibited an electrophysiological light response that decreased with age, coinciding with the degeneration. This suggests that degeneration caused the loss of the light response. We determined that the ninaE (rhodopsin) mutation, but not norpA [phospholipase C (PLC)], slowed the rdgE-dependent degeneration. This was consistent with the light-enhanced degeneration, but revealed that the degeneration is independent of the PLC-mediated phototransduction cascade. Transmission electron microscopy revealed that rdgE  1 photoreceptors exhibited a number of vesicular transport defects including unpacking/vesiculation of rhabdomeres, endocytosis of novel vesicles by photoreceptors, a buildup of very large multivesicular bodies, and an increased amount of rough endoplasmic reticulum. We determined that the rdgE null phenotype is a late embryonic lethality. Therefore, rdgE  + is required in cells outside of the retina, quite possibly in a large number of neurons. Thus, rdgE may define a mutational class that exhibits both light-enhanced retinal degeneration and a recessive null lethality by perturbing neuronal membrane biosynthesis and/or recycling.
Differentiation of Muller's Chromosomal Elements D and E in the Obscura Group of Drosophila
Authors: Segarra Carmen , Ribó Griselda , Aguadé Montserrat
Published: January 2021

Twenty-two markers located on Muller's elements D or E have been mapped by in situ hybridization in six species of the obscura group of Drosophila and in D. melanogaster. The obscura species can be grouped into a Palearctic cluster (D. subobscura, D. madeirensis and D. guanche) and a Nearctic one (D. pseudoobscura, D. persimilis and D. miranda). Eleven of the probes contain known genes: E74, Acp70A, Est-5, hsp28/23, hsp83, emc, hsp70, Xdh, Acph-I, Cec and rp49. The remaining probes are recombinant phages isolated from a D. subobscura genomic library. All these markers hybridize to the putative homologous chromosome or chromosomal arm of elements D and E. Thus, these elements have conserved their genic content during species divergence. Chromosomal homologies proposed previously for each element among the species of the same cluster have been compared with the present results. The distribution of markers within each element has changed considerably as inferred from pairwise comparisons of obscura species included in the two different clusters. Only chromosomal segments defined by closely linked markers have been conserved: one such segment has been detected in element D and three in element E between D. subobscura and D. pseudoobscura.
The Drosophila Eip78C Gene Is Not Vital But Has a Role in Regulating Chromosome Puffs
Authors: Russell Steven R H , Heimbeck Gertrud , Goddard Catherine M , Carpenter Adelaide T C , Ashburner Michael
Published: January 2021

We have generated a number of chromosomal aberrations that disrupt the early-late ecdysone-induced 78C puff gene (Eip78C, ecdysone-induced protein, FlyBase name for the E78 gene of Stone and Thummel 1993), which encodes the two members of the nuclear hormone receptor superfamily Eip78C-A and Eip78C-B. The aberrations include deletions of the ligand-binding/dimeriization domain of both, inversions that split Eip78C-A but retain residual Eip78C-B expression, and a small deletion specific for Eip78C-B. We find that wild-type Eip78C functions are completely dispensable for normal development under laboratory conditions. However, we show that Eip78C-B is required for the maximal puffing activity of a subset of late puffs (63E and 82F) since these puffs are reduced in size in Eip78C-B mutant backgrounds. Paradoxically the same late puffs are reduced, as well as at least one other, when the Eip78C-B cDNA is overexpressed from a heat shock promoter. These data indicate either that Eip78C function is redundant or that it plays a subtle modulating role in the regulation of chromosome puffing.
Large Genetic Change at Small Fatness Cost in Large Populations of Drosophila melanogaster Selected for Wind Tunnel Flight: Rethinking Fitness Surfaces
Authors: Weber K E
Published: January 2021

The fitness effects of extreme genetic change by selection were studied in large populations subjected to prolonged, intense selection. Two replicate populations of Drosophila melanogaster, with estimated effective sizes 500 ≥ Ne ≥ 1000, were selected for increased performance in a wind tunnel, selecting on average the fastest 4.5% of flies. The mean apparent flying speed of both lines increased from ~2 to 170 cm/sec and continued to respond at diminishing rates, without reaching a plateau, for 100 generations. Competitive fitness tests in generations 50 and 85 showed minimal or no fitness loss in selected lines compared to controls. Sublines relaxed in generations 65 and 85 showed minimal or no regression in apparent flying speed. Hybrid lines, from a cross of selected × control lines in generation 75, responded to reselection saltationally, showing that the chromosomes of the selected lines had been assembled from alleles at many loci, from many different chromosomes in the base population. Thus, major genetic change was achieved, but without the costs usually associated with strong directional selection. Large population size has been interpreted, in opposing models, as either a brake or an accelerator in its effects on long-term change by selection. These results favor the second model, and challenge the concept of rugged fitness surfaces underlying the first model.
Coupled Site-Directed Mutagenesis/Transgenesis Identifies Important Functional Domains of the Mouse Agouti Protein
Authors: Perry William L , Nakamura Takuro , Swing Deborah A , Secrest Lisa , Eagleson Bryn , Hustad Carolyn M , Copeland Neal G , Jenkins Nancy A
Published: January 2021

The agouti locus encodes a novel paracrine signaling molecule containing a signal sequence, an N-linked glycosylation site, a central lysine-rich basic domain, and a C-terminal tail containing 10 cysteine (Cys) residues capable of forming five disulfide bonds. When overexpressed, agouti causes a number of pleiotropic effects including yellow coat and adult-onset obesity. Numerous studies suggest that agouti causes yellow coat color by antagonizing the binding of a-melanocyte-stimulating hormone (α-MSH) to the a-MSH-(melanocortin-1) receptor. With the goal of identifying functional domains of agouti important for its diverse biological activities, we have generated 14 agouti mutations by in vitro sitedirected mutagenesis and analyzed these mutations in transgenic mice for their effects on coat color and obesity. These studies demonstrate that the signal sequence, the N-linked glycosylation site, and the C-terminal Cys residues are important for full biological activity, while at least a portion of the lysine-rich basic domain is dispensable for normal function. They also show that the same functional domains of agouti important in coat color determination are important for inducing obesity, consistent with the hypothesis that agouti induces obesity by antagonizing melanocortin binding to other melanocortin receptors.
Marker-Based Inferences About Epistasis for Genes Influencing Inbreeding Depression
Authors: Ful Yong-Bi , Ritland Kermit
Published: January 2021

We describe a multilocus, marker-based regression method for inferring interactions between genes controlling inbreeding depression in self-fertile organisms. It is based upon selfing a parent heterozygous for several unlinked codominant markers, then analyzing the fitness of progeny marker genotypes. If loci causing inbreeding depression are linked to marker loci, then viability selection is manifested by distorted segregation of markers, and fecundity selection by dependence of the fecundity character upon the marker genotype. To characterize this selection, fitness is regressed on the proportion of loci homozygous for markers linked to deleterious alleles, and epistasis is detected by nonlinearity of the regression. Alternatively, fitness can be regressed on the proportion of heterozygous loci. Other modes of selection can be incorporated with a bivariate regression involving both homozygote and heterozygote marker genotypes. The advantage of this marker-based approach is that “purging” is minimized and specific chromosomal segments are identified; its disadvantage lies in low statistical power when linkage is not strong and/ or the linkage phase between marker and selected loci is uncertain. Using this method, in the wildflower Mimulus guttatus, we found predominant multiplicative gene interaction determining fecundity and some negative synergistic (nonmultiplicative) interaction for viability.
Heterozygosity, Heteromorphy, and Phylogenetic Trees in Asexual Eukaryotes
Authors: Birky C William
Published: January 2021

Little attention has been paid to the consequences of long-term asexual reproduction for sequence evolution in diploid or polyploid eukaryotic organisms. Some elementary theory shows that the amount of neutral sequence divergence between two alleles of a protein-coding gene in an asexual individual will be greater than that in a sexual species by a factor of 2tu, where t is the number of generations since sexual reproduction was lost and u is the mutation rate per generation in the asexual lineage. Phylogenetic trees based on only one allele from each of two or more species will show incorrect divergence times and, more often than not, incorrect topologies. This allele sequence divergence can be stopped temporarily by mitotic gene conversion, mitotic crossing-over, or ploidy reduction. If these convergence events are rare, ancient asexual lineages can be recognized by their high allele sequence divergence. At intermediate frequencies of convergence events, it will be impossible to reconstruct the correct phylogeny of an asexual clade from the sequences of protein coding genes. Convergence may be limited by allele sequence divergence and heterozygous chromosomal rearrangements which reduce the homology needed for recombination and result in aneuploidy after crossing-over or ploidy cycles.
Mutants of Saccharomyces cerevisiae with Defects in Acetate Metabolism: Isolation and Characterization of Acn− Mutants
Authors: McCammon Mark T
Published: January 2021

The two carbon compounds, ethanol and acetate, can be oxidatively metabolized as well as assimilated into carbohydrate in the yeast Saccharomyces cerevisiae. The distribution of acetate metabolic enzymes among several cellular compartments, mitochondria, peroxisomes, and cytoplasm makes it an intriguing system to study complex metabolic interactions. To investigate the complex process of carbon catabolism and assimilation, mutants unable to grow on acetate were isolated. One hundred five Acn− (“Acetate Nonutilizing”) mutants were sorted into 21 complementation groups with an additional 20 single mutants. Five of the groups have defects in TCA cycle enzymes: MDH1, CIT1, ACO1, IDH1, and IDH2. A defect in RTG2, involved in the retrograde communication between the mitochondrion and the nucleus, was also identified. Four genes encode enzymes of the glyoxylate cycle and gluconeogenesis: ICL1, MLS1, MBH2, and PCK1. Five other genes appear to be defective in regulating metabolic activity since elevated levels of enzymes in several metabolic pathways, including the glyoxylate cycle, gluconeogenesis, and acetyl-coA metabolism, were detected in these mutants: ACN8, ACN9, ACNl7, ACN18, and ACN42. In summary, this analysis has identified at least 22 and as many as 41 different genes involved in acetate metabolism.
Molecular Genetic Analysis of Drosophila ash2, a Member of the Trithorax Group Required for Imaginal Disc Pattern Formation
Authors: Adamson Amy L , Shearn Allen
Published: January 2021

The ash2 gene is a member of the trithorax group of genes whose products function to maintain active transcription of homeotic selector genes. Mutations in ash2 cause the homeotic transformations expected for a gene in this group but, in addition, cause a variety of pattern formation defects that are not necessarily expected. The ash2 gene is located in cytogenetic region 96A17–19 flanked by slowpoke and tolloid and is included in a cosmid that contains part of slowpoke. The ash2 transcript is 2.0 kb and is present throughout development. The ASH2 protein predicted from the nucleotide sequence of the open reading frame has a putative double zinc-finger domain, called a PHD finger, that is present not only in the products of other trithorax group genes such as TRX and MH1, but also in the product of a Polycomb group gene, PCL. Polyclonal antibodies directed against ASH2 detect the protein in imaginal discs and in the nuclei of salivary gland and fat body cells. On immunoblots these affinity-purified antibodies detect a 70-kDa protein in larvae and a 53-kDa protein in pupae.
Stock Structure and Homing Fidelity in Gulf of Mexico Sturgeon (Acipenser oxyrinchus desotoi) Based on Restriction Fragment Length Polymorphism and Sequence Analyses of Mitochondrial DNA
Authors: Stabile Joseph , Waldman John R , Parauka Frank , Wirgin Isaac
Published: January 2021

Efforts have been proposed worldwide to restore sturgeon populations through the use of hatcheries to supplement natural reproduction and to reintroduce sturgeon where they have become extinct. We examined the population structure and inferred the extent of homing in the anadromous Gulf of Mexico (Gulf) sturgeon (Acipenser oxyrinchus desotoi). Restriction fragment length polymorphism and control region sequence analyses of mitochondrial DNA (mtDNA) were used to identify haplotypes of Gulf sturgeon specimens obtained from eight drainages spanning the subspecies' entire distribution from Louisiana to Florida. Significant differences in haplotype frequencies indicated substantial geographic structuring of populations. A minimum of four regional or river-specific populations were identified (from west to east): (1) Pearl River, LA and Pascagoula River, MS, (2) Escambia and Yellow rivers, FL, (3) Choctawhatchee River, FL, and (4) Apalachicola, Ochlockonee, and Suwannee rivers, FL. Estimates of maternally mediated gene flow between any pair of the four regional or river-specific stocks ranged between 0.15 to 1.2. Tandem repeats in the mtDNA control region of Gulf sturgeon were not perfectly conserved. This result, together with an absence of heteroplasmy and length variation in Gulf sturgeon mtDNA, indicates that the molecular mechanisms of mtDNA control region sequence evolution differ among acipenserids.
Genepool Variation in Genus Glycine Subgenus Soja Revealed by Polymorphic Nuclear and Chloroplast Microsatellites
Authors: Powell W , Morgante M , Doyle J J , McNicol J W , Tingey S V , Rafalski A J
Published: January 2021

A combination of nuclear and chloroplast simple sequence repeats (SSRs) have been used to investigate the levels and pattern of variability detected in Glycine max and G. soja genotypes. Based on the analysis of 700 soybean genotypes with 115 restriction fragment length polymorphism (RFLP) probes, 12 accessions were identified that represent 92% of the allelic variability detected in this genepool. These 12 core genotypes together with a sample of G. max and G. soja accessions were evaluated with 11 nuclear SSRs that detected 129 alleles. Compared with the other G. max and G. soja genotypes sampled, the core genotypes represent 40% of the allelic variability detected with SSRs. Despite the multi-allelic nature of soybean SSRs, dendrograms representing phenetic relationships between accessions clustered according to their subspecies origin. In addition to biparentally inherited nuclear SSRs, two uniparentally (maternally) transmitted chloroplast SSRs were also studied. A total of seven haplotypes were identified, and diversity indices of 0.405 ± 0.088 and 0.159 ± 0.071 were obtained for the two chloroplast SSRs. The availability of polymorphic SSR loci in the chloroplast genome provides new opportunities to investigate cytonuclear interactions in plants.
Kinesin Mutations Cause Motor Neuron Disease Phenotypes by Disrupting Fast Axonal Transport in Drosophila
Authors: Hurd Daryl D , Saxton William M
Published: January 2021

Previous work has shown that mutation of the gene that encodes the microtubule motor subunit kinesin heavy chain (Khc) in Drosophila inhibits neuronal sodium channel activity, action potentials and neurotransmitter secretion. These physiological defects cause progressive distal paralysis in larvae. To identify the cellular defects that cause these phenotypes, larval nerves were studied by light and electron microscopy. The axons of Khc mutants develop dramatic focal swellings along their lengths. The swellings are packed with fast axonal transport cargoes including vesicles, synaptic membrane proteins, mitochondria and prelysosomal organelles, but not with slow axonal transport cargoes such as cytoskeletal elements. Khc mutations also impair the development of larval motor axon terminals, causing dystrophic morphology and marked reductions in synaptic bouton numbers. These observations suggest that as the concentration of maternally provided wild-type KHC decreases, axonal organelles transported by kinesin periodically stall. This causes organelle jams that disrupt retrograde as well as anterograde fast axonal transport, leading to defective action potentials, dystrophic terminals, reduced transmitter secretion and progressive distal paralysis. These phenotypes parallel the pathologies of some vertebrate motor neuron diseases, including some forms of amyotrophic lateral sclerosis (ALS), and suggest that impaired fast axonal transport is a key element in those diseases.
Subunit Interactions in the mariner Transposase
Authors: Lohe Allan R , Sullivan David T , Hartl Daniel L
Published: January 2021

We have studied the Mos1 transposase encoded by the transposable element mariner. This transposase is a member of the “D,D(35)E” superfamily of proteins exhibiting the motif D,D(34)D. It is not known whether this transposase, or other eukaryote transposases manifesting the D,D(35)E domain, functions in a multimeric form. Evidence for oligomerization was found in the negative complementation of Mos1 by an EMS-induced transposase mutation in the catalytic domain. The transposase produced by this mutation has a glycine-to-arginine replacement at position 292. The G292R mutation strongly interferes with the ability of wild-type transposase to catalyze excision of a target element. Negative complementation was also observed for two other EMS mutations, although the effect was weaker than observed with G292R. Results from the yeast two-hybrid system also imply that Mos1 subunits interact, suggesting the possibility of subunit oligomerization in the transposition reaction. Overproduction of Mos1 subunits through an hsp70 promoter also inhibits excision of the target element, possibly through autoregulatory feedback on transcription or through formation of inactive or less active oligomers. The effects of both negative complementation and overproduction may contribute to the regulation of mariner transposition.
Genes Regulating the Remote Wing Margin Enhancer in the Drosophila cut Locus
Authors: Morcillo Patrick , Rosen Christina , Dorsett Dale
Published: January 2021

The mechanisms that allow enhancers to activate promoters from thousands of base pairs away are disrupted by the suppressor of Hairy-wing protein (SUHW) of Drosophila. SUHW binds a DNA sequence in the gypsy retrotransposon and prevents enhancers promoter-distal to a gypsy insertion in a gene from activating without affecting promoter-proximal enhancers. Several observations indicate that SUHW does not affect enhancer-binding activators. Instead, SUHW may interfere with factors that structurally facilitate interactions between an enhancer and promoter. To identify putative enhancer facilitators, a screen for mutations that reduce activity of the remote wing margin enhancer in the cut gene was performed. Mutations in scalloped, mastermind, and a previously unknown gene, Chip, were isolated. A TEA DNA-binding domain in the Scalloped protein binds the wing margin enhancer. Interactions between scalloped, mastermind and Chip mutations indicate that mastermind and Chip act synergistically with scalloped to regulate the wing margin enhancer. Chip is essential and also affects expression of a gypsy insertion in Ultrabithorax. Relative to mutations in scalloped or mastermind, a Chip mutation hypersensitizes the wing margin enhancer in cut to gypsy insertions. Therefore, Chip might encode a target of SUHW enhancer-blocking activity.
The Essence of Single Ascertainment
Authors: Hodge Susan E , Vieland Veronica J
Published: January 2021

We propose a fundamental new definition of single ascertainment, namely, that single ascertainment is any ascertainment scheme in whichP[pedigree is ascertained∣true structure of pedigree]∝p(θ)where p(θ) is some function of genetic parameters θ but is not a function of pedigree structure. Stated in words: Under single ascertainment, all pedigrees have equal (or proportional with respect to genetic parameters) probabilities of being ascertained, independent of pedigree size or structure. This new definition of single ascertainment allows us to show several results: (1 ) The correct likelihood consists of the probability of the data conditioned on the observed pedigree, divided by the function p(θ), whether sampling is “proband-independent” or “proband-dependent.” ( 2 ) More-familiar definitions of single ascertainment all represent special cases of our definition. ( 3 ) When p(θ) represents the prevalence of the trait being studied, our definition corresponds to “classical” single ascertainment, i.e., ascertainment through a single “proband.” However, the concept of p(θ) can also be generalized to represent the population frequency of configurations of affected relatives (such as affected sib pairs); we call this “generalized single ascertainment.”
Effective Sizes and Dynamics of Uniparentally and Diparentally Inherited Genes
Authors: Chesser Ronald K , Baker Robert J
Published: January 2021

Models to determine the temporal dynamics and spatial heterogeneity for maternally and paternally inherited genes were derived for populations that may or may not exhibit spatial subdivision. Results were compared to those for diparentally inherited genes. The models permit definition of parameters for mean and variance of litter sizes, breeding group (subpopulation) sizes, and numbers of female mates per male, dispersal rates, and multiple paternity. Exact solutions for asymptotic effective size and spatial divergence (F  Ls) for maternal and paternal genes are derived. It is shown that solutions for effective size and F  Ls are transformations of the same quadratic equation. When compared to values for diparentally inherited genes, it is shown that effective sizes for maternal genes may be considerably higher when female dispersal is low as in many mammalian taxa. Likewise, effective sizes for paternal genes may be higher than for diparentally inherited traits when male dispersal is relatively low, as in many species of birds. The traditional assumption that the effective size for maternal genes is approximately equal to the number of females is seldom realized. Spatial heterogeneity and temporal dynamics of genes are inextricably linked as is shown by the interdependency of effective size and spatial heterogeneity.
Measwring and Testing Genetic Differentiation With Ordered Versus Unordered Alleles
Authors: Pons O , Petit R J
Published: January 2021

Estimates and variances of diversity and differentiation measures in subdivided populations are proposed that can be applied to haplotypes (ordered alleles such as DNA sequences, which may contain a record of their own histories). Hence, two measures of differentiation can be compared for a single data set: one (GST) that makes use only of the allelic frequencies and the other (NST) for which similarities between the haplotypes are taken into account in addition. Tests are proposed to compare NST and GST with zero and with each other. The difference between NST and GST can be caused by several factors, including sampling artefacts, unequal effect of mutation rates and phylogeographic structure. The method presented is applied to a published data set where a nuclear DNA sequence had been determined from individuals of a grasshopper distributed in 24 regions of Europe. Additional insights into the genetic subdivision of these populations are obtained by progressively combining related haplotypes and reanalyzing the data each time.
Evidence That the Transcriptional Regulators SIN3 and RPD3, and a Novel Gene (SDS3) with Similar Functions, Are Involved in Transcriptional Silencing in S. cerevisiae
Authors: Vannier David , Balderes Dina , Shore David
Published: January 2021

In a screen for extragenic suppressors of a silencing defective rap1s hmrΔA strain, recessive mutations in 21 different genes were found that restored repression to HMR. We describe the characterization of three of these SDS (suppressors of defective silencing) genes. SDS16 and SDS6 are known transcriptional modifiers, SIN3(RPD1/UME4/SDI1/GAM2) and RPD3(SD12), respectively, while the third is a novel gene, SDS3. SDS3 shares the meiotic functions of SIN3 and RPD3 in that it represses IME2 in haploid cells and is necessary for sporulation in diploid cells. However, sds3 mutations differ from sin3 and rpd3 mutations in that they do not derepress TRK2. These sds mutations suppress a variety of cis- and trans-defects, which impair the establishment of silencing at HMR. Any one of the sds mutations slightly increases telomere position effect while a striking synergistic increase in repression is observed in a rap1s background. Epistasis studies suggest that SDS3 works in a different pathway from RPD3 and SIN3 to affect silencing at HMR. Together these results show that defects in certain general transcriptional modifiers can have a pronounced influence on position-effect gene silencing in yeast. Mechanisms for this increase in postion effect are discussed.
Correlation of Genetic and Physical Maps at the A Mating-Type Locus of Coprinus cinereus
Authors: Lukens Lewis , Yicun Huang , May Georgiana
Published: January 2021

The A mating type locus of Coprinus cinereus is remarkable for its extreme diversity, with over 100 different alleles in natural populations. Classical genetic studies have demonstrated that this hypervariability arises in part from recombination between two subloci of A, alpha and beta, although more recent population genetic data have indicated a third segregating sublocus. In this study, we characterized the molecular basis by which recombination generates nonparental A mating types. We mapped the frequency and location of all recombination events in two crosses and correlated the genetic and physical maps of A. We found that all recombination events were located in 6 kb of noncoding DNA between the alpha and beta subloci and that the rate of recombination in this noncoding region matched that generally observed for this genome. No recombination within gene clusters or within coding regions was observed, and the two alpha and beta subloci described in genetic analyses correlated with the previously characterized alpha and beta gene clusters. We propose that pairs of genes constitute both the sex determining and the hereditary unit of A.
Contrasting Histories of Three Gene Regions Associated With In(3L)Payne of Drosophila melanogaster
Authors: Hasson Esteban , Eanes Walter F
Published: January 2021

In the present report, we studied nucleotide variation in three gene regions of Drosophila melanogaster, spanning >5 kb and showing different degrees of association with the cosmopolitan inversion In(3-L)Payne. The analysis of sequence variation in the regions surrounding the breakpoints and the heat shock 83 (Hsp83) gene locus, located close to the distal breakpoint, revealed the absence of shared polymorphisms and the presence of a number of fixed differences between arrangements, indicating absence of genetic exchange. In contrast, for the esterase-6 gene region, located in the center of the inversion, we observed the presence of shared polymorphisms between arrangements suggesting genetic exchange. In the regions close to the breakpoints, the common St arrangement is 10 times more polymorphic than inverted chromosomes. We propose that the lack of recombination between arrangements in these regions coupled with genetic hitchhiking is the best explanation for the low heterozygosity observed in inverted lines. Using the data for the breakpoints, we estimate that this inversion polymorphism is around 0.36 million yr old. Although it is widely accepted that inversions are examples of balanced polymorphisms, none of the current neutrality tests including our Monte Carlo simulations showed significant departure from neutral expectations.
Segregation Distortion in Drosophila melanogaster: Genomic Organization of Responder Sequences
Authors: Moschetti Roberta , Caizzi Ruggiero , Pimpinelli Sergio
Published: January 2021

The heterochromatic Responder (Rsp) locus of Drosophila melanogaster is the target of the two distorter loci Sd and E(SD). Rsp is located in a specific heterochromatic region of the second chromosome and is made up of AT-rich satellite sequences whose abundance is related to its sensitivity to the distorter chromosomes. Here we report that a cluster of Rsp sequences is also located in the third chromosome. The third-chromosome cluster has the same flanking sequences as the clone originally used to identify the Rsp elements, and one of the flanking sequences is a rearranged 412 retrotrsansposon. The presence of a second, unlinked Rsp-sequence cluster makes re-interpretation necessary for some earlier experiments in which segregation of the third chromosome had not been followed and raises interesing possibilities for the origin of the Rsp locus.
Quantitative Trait Loci Analysis for Five Milk Production Traits on Chromosome Six in the Dutch Holstein-Friesian Population
Authors: Spelman Richard J , Coppieters Wouter , Karim Latifa , van Arendonk Johan A M , Bovenhuis Henk
Published: January 2021

Twenty Dutch Holstein-Friesian families, with a total of 715 sires, were evaluated in a granddaughter experiment design for marker-QTL associations. Five traits—milk, fat and protein yield and fat and protein percent—were analyzed. Across-family analysis was undertaken using multimarker regression principles. One and two QTL models were fitted. Critical values for the test statistic were calculated empirically by permuting the data. Individual trait distributions of permuted test statistics differed and, thus distributions, had to be calculated for each trait. Experimentwise critical values, which account for evaluating marker-QTL associations on all 29 autosomal bovine chromosomes and for five traits, were calculated. A QTL for protein percent was identified in one and two QTL models and was significant at the 1 and 2% level, respectively. Extending the multimarker regression approach to an analysis including two QTL was limited by families not being informative at all markers, which resulted in singularity. Below average heterozygosity for the first and last marker lowered information content for the first and last marker bracket. Highly informative markers at the ends of the mapped chromosome would overcome the decrease in information content in the first and last marker bracket and singularity for the two QTL model.
Sequence Variations in the Bovine Growth Hormone Gene Characterized by Single-Strand Conformation Polymorphism (SSCP) Analysis and Their Association with Milk Production Traits in Holsteins
Authors: Yao Jianbo , Aggrey Samuel E , Zadworny David , Hayes J Flan , Kühnlein Urs
Published: January 2021

Sequence variations in the bovine growth hormone (GH) gene were investigated by single strand conformation polymorphism (SSCP) analysis of seven amplified fragments covering almost the entire gene (2.7 kb). SSCPs were detected in four of these fragments and a total of six polymorphisms were found in a sample of 128 Holstein bulls. Two polymorphisms, a T→C transition in the third intron (designated GH4.1) and an A→C transversion in the fifth exon (designated GH6.2), were shown to be associated with milk production traits. GH4.1c/GH4.1c bulls had higher milk yield than GH4.1c/GH4.1t (P ≤ 0.005) and GH4.1t/GH4.1t (P ≤ 0.0022) bulls. GH4.1c/GH4.1c bulls had higher kg fat (P ≤ 0.0076) and protein (P ≤ 0.0018) than GH4.1c/GH4.1t bulls. Similar effects on milk production traits with the GH6.2 polymorphism were observed with the GH6.2a allele being the favorable allele. The average effects of the gene substitution for GH4.1 and GH6.2 are similar, with ±300 kg for milk yield, ±8 kg for fat content and ±7 kg for protein content per lactation. The positive association of GH4.1c and GH6.2a with milk production traits may be useful for improving milk performance in dairy cattle.
Inferring Patterns of Migration From Gene Frequencies Under Equilibrium Conditions
Authors: Tufto Jarle , Engen Steinar , Hindar Kjetil
Published: January 2021

A new maximum likelihood method to simultaneously estimate the parameters of any migration pattern from gene frequencies in stochastic equilibrium is developed, based on a model of multivariate genetic drift in a subdivided population. Motivated by simulations of this process in the simplified case of two subpopulations, problems related to the nuisance parameter q, the equilibrium gene frequency, are eliminated by conditioning on the observed mean gene frequency. The covariance matrix of this conditional distribution is calculated by constructing an abstract process that mimics the behavior of the original process in the subspace of interest. The approximation holds as long as there is limited differentiation between subpopulations. The bias and variance of estimates of long-range and short-range migration in a finite stepping stone model are evaluated by fitting the model to simulated data with known values of the parameters. Possible ecological extensions of the model are discussed.
glp-3 Is Required for Mitosis and Meiosis in the Caenorhabditis elegans Germ Line
Authors: Kadyk Lisa C , Lambie Eric J , Kimble Judith
Published: January 2021

The germ line is the only tissue in Caenorhabditis elegans in which a stem cell population continues to divide mitotically throughout life; hence the cell cycles of the germ line and the soma are regulated differently. Here we report the genetic and phenotypic characterization of the glp-3 gene. In animals homozygous for each of five recessive loss-of-function alleles, germ cells in both hermaphrodites and males fail to progress through mitosis and meiosis, but somatic cells appear to divide normally. Germ cells in animals grown at 15° appear by DAPI staining to be uniformly arrested at the G2/M transition with <20 germ cells per gonad on average, suggesting a checkpoint-mediated arrest. In contrast, germ cells in mutant animals grown at 25° frequently proliferate slowly during adulthood, eventually forming small germ lines with several hundred germ cells. Nevertheless, cells in these small germ lines never undergo meiosis. Double mutant analysis with mutations in other genes affecting germ cell proliferation supports the idea that glp-3 may encode a gene product that is required for the mitotic and meiotic cell cycles in the C. elegans germ line.
Interactions of Drosophila Ultrabithorax Regulatory Regions With Native and Foreign Promoters
Authors: Casares Fernando , Bender Welcome , Merriam John , Sánchez-Herrero Ernesto
Published: January 2021

The Ultrabithorax (Ubx) gene of the Drosophila bithorax complex is required to specify parasegments 5 and 6. Two P-element “enhancer traps” have been recovered within the locus that contain the bacterial lacZ gene under the control of the P-element promoter. The P insertion that is closer to the Ubx promoter expresses lucZ in a pattern similar to that of the normal Ubx gene, but also in parasegment 4 during embryonic development. Two deletions have been recovered that remove the normal Ubx promoter plus several kilobases on either side, but retain the lacZ reporter gene. The lacZ patterns from the deletion derivatives closely match the normal pattern of Ubx expression in late embryos and imaginal discs. The lacZ genes in the deletion derivatives are also negatively regulated by Ubx and activated in trans by Contrabithorax mutations, again like the normal Ubx gene. Thus, the deleted regions, including several kilobases around the Ubx promoter, are not required for long range interactions with Ubx regulatory regions. The deletion derivatives also stimulate transvection, a pairing-dependent interaction with the Ubx promoter on the homologous chromosome.