bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temperature-sensitive mutations that cause stage-specific defects in Zebrafish fin regeneration.
Authors: Johnson S L , Weston J A 
Published: January 2021

Abstract
When amputated, the fins of adult zebrafish rapidly regenerate the missing tissue. Fin regeneration proceeds through several stages, including wound healing, establishment of the wound epithelium, recruitment of the blastema from mesenchymal cells underlying the wound epithelium, and differentiation and outgrowth of the regenerate. We screened for temperature-sensitive mutations that affect the regeneration of the fin. Seven mutations were identified, including five that fail to regenerate their fins, one that causes slow growth during regeneration, and one that causes dysmorphic bumps or tumors to develop in the regenerating fin. reg5 mutants fail to regenerate their caudal fins, whereas reg6 mutants develop dysmorphic bumps in their regenerates at the restrictive temperature. Temperature-shift experiments indicate that reg5 and reg6 affect different stages of regeneration. The critical period for reg5 occurs during the early stages of regeneration before or during establishment of the blastema, resulting in defects in subsequent growth of the blastema and failure to differentiate bone-forming cells. The critical period for reg6 occurs after the onset of bone differentiation and during early stages of regenerative outgrowth. Both reg5 and reg6 also show temperature-sensitive defects in embryonic development or in ontogenetic outgrowth of the juvenile fin.
Genetic Analysis of the Saccharomyces cerevisiae RHO3 Gene, Encoding a Rho-Type Small GTPase, Provides Evidence for a Role in Bud Formation
Authors: Imai Jun , Toh-e Akio , Matsui Yasushi 
Published: January 2021

Abstract
RHO3 encodes a Rho-type small GTPase of the yeast Saccharomyces cereuisiae. We isolated temperature-sensitive alleles and a dominant active allele of RHO3. Ts- rho3 cells lost cell polarity during bud formation and grew more isotropically than wild-type cells at nonpermissive temperatures. In contrast, cells carrying a dominant active mutant RHO3 displayed cold sensitivity, and the cells became elongated and bent, often at the position where actin patches were concentrated. These phenotypes of the rho3 mutants strongly suggest that RHO3 is involved in directing the growing points during bud formation. In addition, we found that SRO6, previously isolated as a multicopy suppressor of rho3, is the same as SEC4. The sec4-2 mutation was synthetic lethal with temperature-sensitive rho3 mutations and suppressed the cold sensitivity caused by a dominant active mutant RHO3. The genetic interactions between RHO3 and SEC4, taken together with the fact that the Rab-type GTPase Sec4p is required to fuse secretory vesicles together with plasma membrane for exocytosis, support a model in which the Rho3p pathway modulates morphogenesis during bud growth via directing organization of the actin cytoskeleton and the position of the secretory machinery for exocytosis.
Length Variation, Heteroplasmy and Sequence Divergence in the Mitochondrial DNA of Four Species of Sturgeon (Acipenser)
Authors: Brown James R , Beckenbach Karen , Beckenbach Andrew T , Smith Michael J 
Published: January 2021

Abstract
The extent of mtDNA length variation and heteroplasmy as well as DNA sequences of the control region and two tRNA genes were determined for four North American sturgeon species: Acipenser transmontanus, A. medirostris, A. fulvescens and A. oxyrhnychus. Across the Continental Divide, a division in the occurrence of length variation and heteroplasmy was observed that was concordant with species biogeography as well as with phylogenies inferred from restriction fragment length polymorphisms (RFLP) of whole mtDNA and pairwise comparisons of unique sequences of the control region. In all species, mtDNA length variation was due to repeated arrays of 78-82-bp sequences each containing a D-loop strand synthesis termination associated sequence (TAS). Individual repeats showed greater sequence conservation within individuals and species rather than between species, which is suggestive of concerted evolution. Differences in the frequencies of multiple copy genomes and heteroplasmy among the four species may be ascribed to differences in the rates of recurrent mutation. A mechanism that may offset the high rate of mutation for increased copy number is suggested on the basis that an increase in the number of functional TAS motifs might reduce the frequency of successfully initiated H-strand replications.
copia-, gypsy- and LINE-Like Retrotransposon Fragments in the Mitochondrial Genome of Arabidopsis thaliana
Authors: Knoop Volker , Unseld Michael , Marienfeld Joachim , Brandt Petra , Sünkel Sabine , Ullrich Henriette , Brennicke Axel 
Published: January 2021

Abstract
Several retrotransposon fragments are integrated in the mitochondrial genome of Arabidopsis thaliana. These insertions are derived from all three classes of nuclear retrotransposons, the Tyl/copia, Ty3/gypsy- and non-LTR/LINE-families. Members of the Ty3/gypsy group of elements have not yet been identified in the nuclear genome of Arabidopsis. The varying degrees of similarity with nuclear elements and the dispersed locations of the sequences in the mitochondrial genome suggest numerous independent transfer-insertion events in the evolutionary history of this plant mitochondrial genome. Overall, we estimate remnants of retrotransposons to cover ≥5% of the mitochondrial genome in Arabidopsis.
Mutations in the RNA Polymerase II Transcription Machinery Suppress the Hyperrecombination Mutant hpr1 Δ of Saccharomyces cerevisiae
Authors: Fan Hua-Ying , Cheng Kenneth K , Klein Hannah L 
Published: January 2021

Abstract
The soh1, soh2 and soh4 mutants were isolated as suppressors of the temperature dependent growth of the hyperrecombination mutant hprl of Saccharomyces cerevisiae. Cloning and sequence analysis of these suppressor genes has unexpectedly shown them to code for components of the RNA polymerase II transcription complex. SOH2 is identical to RPB2, which encodes the second largest subunit of RNA polymerase II, and SOH4 is the same as SUA7, encoding the yeast transcription initiation factor TFIIB. SOH1 encodes a novel 14-kD protein with limited sequence similarity to RNA polymerases. Interestingly, SOH1 not only interacts with factors involved in DNA repair, but transcription as well. Thus, the Soh1 protein may serve to couple these two processes. The Soh1 protein interacts with a DNA repair protein, Rad5p, in a two-hybrid system assay. Soh1p may functionally interact with components of the RNA polymerase II complex as suggested from the synthetic lethality observed in soh1 rpb1Δ104, soh1 soh2-1 (rpb2), and soh1 soh4 (sua7) double mutants. Because mutations in SOH1, RPB2 and SUA7 suppress the hyperrecombination phenotype of hpr1 mutants, this suggests a link between recombination in direct repeats and transcription.
Genetic Interactions Among Sex-Determining Genes in the Fern Ceratopteris richardii
Authors: Eberle James R , Banks Jo Ann 
Published: January 2021

Abstract
Haploid gametophytes of the fern Ceratopteris are either male or hermaphroditic. The determinant of sex type is the pheromone antheridiogen, which is secreted by the hermaphrodite and directs male development of young, sexually undetermined gametophytes. Three phenotypic classes of mutations that affect sex-determination were previously isolated and include the hermaphroditic (her), the transformer (tra) and feminization (fem) mutations. In the present study, linkage analysis and tests of epistasis among the different mutants have been performed to assess the possible interactions among these genes. The results indicate that sex determination in Ceratopteris involves at least seven interacting genes in addition to antheridiogen, the primary sex-determining signal. Two models describing how antheridiogen may influence the activity states of these genes and the sex of the gametophyte are discussed.
RFLP Mapping in Cultivated Sugarcane (Saccharum spp.): Genome Organization in a Highly Polyploid and Aneuploid Interspecific Hybrid
Authors: Grivet Laurent , D'Hont Angelique , Roques Daniele , Feldmann Philippe , Lanaud Claire , Glaszmann Jean Christophe 
Published: January 2021

Abstract
Sugarcane cultivars are polyploid, aneuploid, interspecific hybrids between the domesticated species Saccharum officinarum and the wild relative S. spontaneum. Cultivar chromosome numbers range from 100 to 130 with ~10% contributed by S. spontaneum. We have undertaken a mapping study on the progeny of a selfed cultivar, R570, to analyze this complex genome structure. A set of 128 restriction fragment length polymorphism probes and one isozyme was used. Four hundred and eight markers were placed onto 96 cosegregation groups, based on linkages in coupling only. These groups could tentatively be assembled into 10 basic linkage groups on the basis of common probes. Origin of markers was investigated for 61 probes and the isozyme, leading to the identification of 80 S. officinarum and 66 S. spontaneum derived markers, respectively. Their distribution in cosegregation groups showed better map coverage for the S. spontaneum than for the S. officinnrum genome fraction and occasional recombination between the two genomes. The study of repulsions between markers suggested the prevalence of random pairing between chromosomes, typical of autopolyploids. However, cases of preferential pairing between S. spontaneum chromosomes were also detected. A tentative Saccharum map was constructed by pooling linkage information for each linkage group.
Epigenetic Control of a Transposon-Inactivated Gene in Neurospora is Dependent on DNA Methylation
Authors: Cambareri Edward B , Foss Henriette M , Rowtree Michael R , Selker Eric U , Kinsey John A 
Published: January 2021

Abstract
An unstable allele of the Neurospora am (GDH) gene resulting from integration of the retrotransposon Tad3-2 into 5′ noncoding sequences was found in previous work. We report that reversion to Am+ depends on DNA methylation within and upstream of Tad. Levels of methylation were correlated with the proportion of Am+ conidia, whether the cultures were derived from Am− or Am+ isolates. Reversion to Am+ did not occur when conidia were plated on 5-azacytidine, which reduces DNA methylation. The mutation dim-2, which appears to abolish DNA methylation, also prevented reversion to Am+. The native am allele, in a strain that lacked Tad elements, was replaced with am:: Tad3-2 or with a deletion derivative that prevents transposition of Tad. Transformants of both classes showed instability comparable with that of the original isolates, which contain multiple Tad elements. Deletion of the upstream enhancer-like sequences, URSamα and β, did not prevent the instability of am:: Tad3-2. The results suggest that am expression is dependent on DNA methylation but not on proliferation or transposition of the Tad element and that the instability does not require the upstream sequences of am.
Suppression and Enhancement of the Aspergillus nidulans medusa Mutation by Altered Dosage of the bristle and stunted Genes
Authors: Busby Tina M , Miller Karen Y , Miller Bruce L 
Published: January 2021

Abstract
Asexual reproduction in Aspergillus nidulans is characterized by the orderly differentiation of multicellular reproductive structures (conidiophores) and chains of uninucleate conidia (spores). Mutations in the developmental modifier medusa (medA) result in aberrant conidiophores with branching chains of reiterated reproductive cells (metulae), delayed conidial differentiation and frequent reinitiation of secondary conidiophores. We show that incorrect morphology is in part a consequence of modified bristle (brlA) and abacus (abaA) expression, key regulators of the core genetic pathway directing conidial differentiation. First, correct temporal expression of both brlA transcripts (brlAα and br1Aβ) requires MedAp. Second, MedAp functions as a coactivator required for normal levels of abaA expression. Finally, we show that wild-type morphology results from a finely tuned balance in the expression of brlA, medA and the developmental modifier stunted (stuA). One extra copy of brlA suppresses medA mutations and restores normal abaA mRNA abundance. In contrast, an extra copy of stuA in a medA − strain results in an enhanced medusoid phenotype with extensive metulae proliferation and nearly complete absence of conidia. abaA and brlA± transcription are completely repressed in these strains. In general, low stuA:brlA ratios promoted conidiation while high ratios caused proliferation of unicellular sterigmata and inhibited conidiation.
The REC1 Gene of Ustilago maydis, Which Encodes a 3′ → 5′ Exonuclease, Couples DNA Repair and Completion of DNA Synthesis to a Mitotic Checkpoint
Authors: Onel Kenan , Koff Andrew , Bennett Richard L , Unrau Paul , Holloman William K 
Published: January 2021

Abstract
Mutation in the REC1 gene of Ustilago maydis results in extreme sensitivity to killing by ultraviolet light. The lethality of the rec1-1 mutant was found to be partially suppressed if irradiated cells were held artificially in G2-phase by addition of a microtubule inhibitor. This mutant was also found to be sensitive to killing when DNA synthesis was inhibited by external means through addition of hydroxyurea or by genetic control in a temperature-sensitive mutant strain defective in DNA synthesis. Flow cytometric analysis of exponentially growing cultures indicated that wild-type cells accumulated in G2 after UV irradiation, while rec1-1 cells appeared to exit from G2 and accumulate in G1/S. Analysis of mRNA levels in synchronized cells indicated that the REC1 gene is periodically expressed with the cell cycle and reaches maximal levels at G1/S. The results are interpreted to mean that a G2-M checkpoint is disabled in the rec1-1 mutant. It is proposed that the REC1 gene product functions in a surveillance system operating during S-phase and G2 to find and repair stretches of DNA with compromised integrity and to communicate with the cell cycle apparatus.
Genetic and Molecular Analysis of spe-27, a Gene Required for Spermiogenesis in Caenorhabditis elegans Hermaphrodites
Authors: Minniti Alicia N , Sadler Cathryn , Ward Samuel 
Published: January 2021

Abstract
Hermaphrodites with mutations in the spe-27gene are self-sterile, laying only unfertilized eggs; mutant males are fertile. Hermaphrodites make spermatids that fail to activate to crawling spermatozoa so passing oocytes sweep them out of the spermatheca. These spermatids do activate and produce self-progeny if young mutant hermaphrodites are mated by fertile (or sterile) males. Spermatids isolated from either mutant males or hermaphrodites initiate activation in vitro when treated with proteases, but then arrest with spiky membrane projections that resemble those of a normal intermediate in pseudopod formation. These phenotypes are identical to spe-8 and spe-12 mutants. They can be explained if males and hermaphrodites have distinct pathways for spermatid activation, and these three genes are necessary only for the hermaphrodite pathway. Consistent with this model, when spe-27 mutant male spermatids without seminal fluid are artificially inseminated into hermaphrodites, they fail to activate. The spe-27 gene has been isolated, sequenced and its regulatory regions identified. The sequence predicts a 131 amino acid polypeptide that has no striking structural motifs and no resemblance to known proteins. Two of the mutations in spe-27alter mRNA splicing; a third mutation is a temperature-sensitive missense mutation.
Elimination of Introns at the Drosophila suppressor-of-forked Locus by P-Element-Mediated Gene Conversion Shows That an RNA Lacking a Stop Codon is Dispensable
Authors: Williams Carol J , O'Hare Kevin 
Published: January 2021

Abstract
The suppressor of forked [su(f)] locus affects the phenotype of mutations caused by transposable element insertions at unlinked loci. It encodes a putative 84-kD protein with homology to two proteins involved in mRNA 3′ end processing; the product of the yeast RNA14 gene and the 77-kD subunit of human cleavage stimulation factor. Three su(f) mRNAs are produced by alternative polyadenylation. The 2. 6 and 2.9-kb mRNAs encode the same 84-kD protein while a 1.3-kb RNA, which terminates within the fourth intron, is unusual in having no stop codon. Using P-element-mediated gene replacement we have copied sequences from a transformation construct into the su(f) gene creating a su(f) allele at the normal genomic location that lacks the first five introns. This allele is viable and appears wild type for su(f) function, demonstrating that the 1.3-kb RNA and the sequences contained within the deleted introns are dispensable for su(f) function. Compared with studies on gene replacement at the white locus, chromosomal breaks at su(f) appear to be less efficiently repaired from ectopic sites, perhaps because of the location of su(f) at the euchromatin/heterochromatin boundary on the X chromosome.
Genetics of Differences in Pheromonal Hydrocarbons Between Drosophila melanogaster and D. simulans
Authors: Coyne Jerry A 
Published: January 2021

Abstract
Females of Drosophila melanogaster and its sibling species D. simulans have very different cuticular hydrocarbons, with the former bearing predominantly 7,11-heptacosadiene and the latter 7-tricosene. This difference contributes to reproductive isolation between the species. Genetic analysis shows that this difference maps to only the third chromosome, with the other three chromosomes having no apparent effect. The D. simulans alleles on the left arm of chromosome 3 are largely recessive, allowing us to search for the relevant regions using D. melanogaster deficiencies. At least four nonoverlapping regions of this arm have large effects on the hydrocarbon profile, implying that several genes on this arm are responsible for the species difference. Because the right arm of chromosome 3 also affects the hydrocarbon profile, a minimum of five genes appear to be involved. The large effect of the third chromosome on hydrocarbons has also been reported in the hybridization between D. simulans and its closer relative D. sechellia, implying either an evolutionaly convergence or the retention in D. sechllia of an ancestral sexual dimorphism.
Nucleotide Variation at the Gpdh Locus in the Genus Drosophila
Authors: Wells R Spencer 
Published: January 2021

Abstract
The Gpdh locus was sequenced in a broad range of Drosophila species. In contrast to the extreme evolutionary constraint seen at the amino acid level, the synonymous sites evolve at rates comparable to those of other genes. Gpdh nucleotide sequences were used to infer a phylogenetic tree, and the relationships among the species of the obscura group were examined in detail. A survey of nucleotide polymorphism within D. pseudoobscura revealed no amino acid variation in this species. Applying a modified McDonald-Kreitman test, the amino acid divergence between species in the obscura group does not appear to be excessive, implying that drift is adequate to explain the patterns of amino acid change at this locus. In addition, the level of polymorphism at the Gpdh locus in D. pseudoobscura is comparable to that found at other loci, as determined by a Hudson-Kreitman-Aguadé test. Thus, the pattern of nucleotide variation within and between species at the Gpdh locus is consistent with a neutral model.
Patterns of Nucleotide Substitution in Mitochondrial Protein Coding Genes of Vertebrates
Authors: Kumar Sudhir 
Published: January 2021

Abstract
Maximum likelihood methods were used to study the differences in substitution rates among the four nucleotides and among different nucleotide sites in mitochondrial protein-coding genes of vertebrates. In the lst+2nd codon position data, the frequency of nucleotide G is negatively correlated with evolutionary rates of genes, substitution rates vary substantially among sites, and the transition / transversion rate bias (R) is two to five times larger than that expected at random. Generally, largest transition biases and greatest differences in substitution rates among sites are found in the highly conserved genes. The 3rd positions in placental mammal genes exhibit strong nucleotide composition biases and the transitional rates exceed transversional rates by one to two orders of magnitude. Tamura-Nei and Hasegawa-Kishino-Yano models with gamma distributed variable rates among sites (gamma parameter, α) adequately describe the nucleotide substitution process in 1st+2nd position data. In these data, ignoring differences in substitution rates among sites leads to largest biases while estimating substitution rates. Kimura's two-parameter model with variable-rates among sites performs satisfactorily in likelihood estimation of R, α, and overall amount of evolution for lst+2nd position data. It can also be used to estimate pairwise distances with appropriate values of α for a majority of genes.
New Statistical Tests of Neutrality for DNA Samples From a Population
Authors: Fu Yun-xin 
Published: January 2021

Abstract
The purpose of this paper is to develop statistical tests of the neutral model of evolution against a class of alternative models with the common characteristic of having an excess of mutations that occurred a long time ago or a reduction of recent mutations compared to the neutral model. This class of population genetics models include models for structured populations, models with decreasing effective population size and models of selection and mutation balance. Four statistical tests were proposed in this paper for DNA samples from a population. Two of these tests, one new and another a modification of an existing test, are based on EWENS' sampling formula, and the other two new tests make use of the frequencies of mutations of various classes. Using simulated samples and regression analyses, the critical values of these tests can be computed from regression equations. This approach for computing the critical values of a test was found to be appropriate and quite effective. We examined the powers of these four tests using simulated samples from structured populations, populations with linearly decreasing sizes and models of selection and mutation balance and found that they are more powerful than existing statistical tests of the neutral model of evolution.
Detecting Heterogeneity of Substitution Along DNA and Protein Sequences
Authors: Goss Peter J E , Lewontin R C 
Published: January 2021

Abstract
Regions of differing constraint, mutation rate or recombination along a sequence of DNA or amino acids lead to a nonuniform distribution of polymorphism within species or fixed differences between species. The power of five tests to reject the null hypothesis of a uniform distribution is studied for four classes of alternate hypothesis. The tests explored are the variance of interval lengths; a modified variance test, which includes covariance between neighboring intervals; the length of the longest interval; the length of the shortest third-order interval; and a composite test. Although there is no uniformly most powerful test over the range of alternate hypotheses tested, the variance and modified variance tests usually have the highest power. Therefore, we recommend that one of these two tests be used to test departure from uniformity in all circumstances. Tables of critical values for the variance and modified variance tests are given. The critical values depend both on the number of events and the number of positions in the sequence. A computer program is available on request that calculates both the critical values for a specified number of events and number of positions as well as the significance level of a given data set.