bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of Deleterious Genotypes in Multigenerational Studies. I. Disruptions in Individual Arabidopsis Actin Genes
Authors: Gilliland Laura U , McKinney Elizabeth C , Asmussen Marjorie A , Meagher Richard B 
Published: April 2021

Abstract
Plant actins are involved in numerous cytoskeletal processes effecting plant development, including cell division plane determination, cell elongation, and cell wall deposition. Arabidopsis thaliana has five ancient subclasses of actin with distinct patterns of spatial and temporal expression. To test their functional roles, we identified insertion mutants in three Arabidopsis actin genes, ACT2, ACT4, and ACT7, representing three subclasses. Adult plants homozygous for the act2-1, act4-1, and act7-1 mutant alleles appear to be robust, morphologically normal, and fully fertile. However, when grown as populations descended from a single heterozygous parent, all three mutant alleles were found at extremely low frequencies relative to the wild-type in the F2 generation. Thus, all three mutant alleles appear to be deleterious. The act2-1 mutant allele was found at normal frequencies in the F1, but at significantly lower frequencies than expected in the F2 and F3 generations. These data suggest that the homozygous act2-1/act2-1 mutant adult plants have a reduced fitness in the 2N sporophytic portion of the life cycle, consistent with the vegetative expression of ACT2. These data are interpreted in light of the extreme conservation of plant actin subclasses and genetic redundancy.
The Molecular Basis of Quantitative Genetic Variation in Central and Secondary Metabolism in Arabidopsis
Authors: Mitchell-Olds Thomas , Pedersen Deana 
Published: April 2021

Abstract
To find the genes controlling quantitative variation, we need model systems where functional information on physiology, development, and gene regulation can guide evolutionary inferences. We mapped quantitative trait loci (QTLs) influencing quantitative levels of enzyme activity in primary and secondary metabolism in Arabidopsis. All 10 enzymes showed highly significant quantitative genetic variation. Strong positive genetic correlations were found among activity levels of 5 glycolytic enzymes, PGI, PGM, GPD, FBP, and G6P, suggesting that enzymes with closely related metabolic functions are coregulated. Significant QTLs were found influencing activity of most enzymes. Some enzyme activity QTLs mapped very close to known enzyme-encoding loci (e.g., hexokinase, PGI, and PGM). A hexokinase QTL is attributable to cis-acting regulatory variation at the AtHXK1 locus or a closely linked regulatory locus, rather than polypeptide sequence differences. We also found a QTL on chromosome IV that may be a joint regulator of GPD, PGI, and G6P activity. In addition, a QTL affecting PGM activity maps within 700 kb of the PGM-encoding locus. This QTL is predicted to alter starch biosynthesis by 3.4%, corresponding with theoretical models, suggesting that QTLs reflect pleiotropic effects of mutant alleles.
UV Light Induces IS10 Transposition in Escherichia coli
Authors: Eichenbaum Zehava , Livneh Zvi 
Published: April 2021

Abstract
A new mutagenesis assay system based on the phage 434 cI gene carried on a low-copy number plasmid was used to investigate the effect of UV light on intermolecular transposition of IS10. Inactivation of the target gene by IS10 insertion was detected by the expression of the tet gene from the phage 434 PR promoter, followed by Southern blot analysis of plasmids isolated from TetR colonies. UV irradiation of cells harboring the target plasmid and a donor plasmid carrying an IS10 element led to an increase of up to 28-fold in IS10 transposition. Each UV-induced transposition of IS10 was accompanied by fusion of the donor and acceptor plasmid into a cointegrate structure, due to coupled homologous recombination at the insertion site, similar to the situation in spontaneous IS10 transposition. UV radiation also induced transposition of IS10 from the chromosome to the target plasmid, leading almost exclusively to the integration of the target plasmid into the chromosome. UV induction of IS10 transposition did not depend on the umuC and uvrA gene product, but it was not observed in lexA3 and ΔrecA strains, indicating that the SOS stress response is involved in regulating UV-induced transposition. IS10 transposition, known to increase the fitness of Escherichia coli, may have been recruited under the SOS response to assist in increasing cell survival under hostile environmental conditions. To our knowledge, this is the first report on the induction of transposition by a DNA-damaging agent and the SOS stress response in bacteria.
Distribution of a Limited Sir2 Protein Pool Regulates the Strength of Yeast rDNA Silencing and Is Modulated by Sir4p
Authors: Smith Jeffrey S , Brachmann Carrie Baker , Pillus Lorraine , Boeke Jef D 
Published: April 2021

Abstract
Transcriptional silencing in Saccharomyces cerevisiae occurs at the silent mating-type loci HML and HMR, at telomeres, and at the ribosomal DNA (rDNA) locus RDN1. Silencing in the rDNA occurs by a novel mechanism that depends on a single Silent Information Regulator (SIR) gene, SIR2. SIR4, essential for other silenced loci, paradoxically inhibits rDNA silencing. In this study, we elucidate a regulatory mechanism for rDNA silencing based on the finding that rDNA silencing strength directly correlates with cellular Sir2 protein levels. The endogenous level of Sir2p was shown to be limiting for rDNA silencing. Furthermore, small changes in Sir2p levels altered rDNA silencing strength. In rDNA silencing phenotypes, sir2 mutations were shown to be epistatic to sir4 mutations, indicating that SIR4 inhibition of rDNA silencing is mediated through SIR2. Furthermore, rDNA silencing is insensitive to SIR3 overexpression, but is severely reduced by overexpression of full-length Sir4p or a fragment of Sir4p that interacts with Sir2p. This negative effect of SIR4 overexpression was overridden by co-overexpression of SIR2, suggesting that SIR4 directly inhibits the rDNA silencing function of SIR2. Finally, genetic manipulations of SIR4 previously shown to promote extended life span also resulted in enhanced rDNA silencing. We propose a simple model in which telomeres act as regulators of rDNA silencing by competing for limiting amounts of Sir2 protein.
Female Genotypes Affect Sperm Displacement in Drosophila
Authors: Clark Andrew G , Begun David J 
Published: April 2021

Abstract
Differential success of sperm is likely to be an important component of fitness. Extensive variation among male genotypes in competitive success of sperm in multiply mated females has been documented for Drosophila melanogaster. However, virtually all previous studies considered the female to be a passive vessel. Nevertheless, under certain conditions female fitness could be determined by her role in mediating use of sperm from multiple males. Here we ask whether females differ among genotypes in their tendency to exhibit last-male precedence. Competition of sperm from two tester male genotypes (bwD and B3-09, a third-chromosome isogenic line from Beltsville, MD) was quantified by doubly mating female lines that had been rendered homozygous for X, second, or third chromosomes isolated from natural populations. The composite sperm displacement parameter, P2′, was highly heterogeneous among lines, whether or not viability effects were compensated, implying the presence of polymorphic genes affecting access of sperm to eggs. Genetic variation of this type is completely neutral in the absence of pleiotropy or interaction between variation in the two sexes.
Inference of Population History Using a Likelihood Approach
Authors: Weiss Gunter , von Haeseler Arndt 
Published: April 2021

AbstractWe introduce an approach to revealing the likelihood of different population histories that utilizes an explicit model of sequence evolution for the DNA segment under study. Based on a phylogenetic tree reconstruction method we show that a Tamura-Nei model with heterogeneous mutation rates is a fair description of the evolutionary process of the hypervariable region I of the mitochondrial DNA from humans. Assuming this complex model still allows the estimation of population history parameters, we suggest a likelihood approach to conducting statistical inference within a class of expansion models. More precisely, the likelihood of the data is based on the mean pairwise differences between DNA sequences and the number of variable sites in a sample. The use of likelihood ratios enables comparison of different hypotheses about population history, such as constant population size during the past or an increase or decrease of population size starting at some point back in time. This method was applied to show that the population of the Basques has expanded, whereas that of the Biaka pygmies is most likely decreasing. The Nuu-Chah-Nulth data are consistent with a model of constant population.
A Rank-Based Nonparametric Method for Mapping Quantitative Trait Loci in Outbred Half-Sib Pedigrees: Application to Milk Production in a Granddaughter Design
Authors: Coppieters Wouter , Kvasz Alexandre , Farnir Frédéric , Arranz Juan-Jose , Grisart Bernard , Mackinnon Margaret , Georges Michel 
Published: April 2021

Abstract
We describe the development of a multipoint nonparametric quantitative trait loci mapping method based on the Wilcoxon rank-sum test applicable to outbred half-sib pedigrees. The method has been evaluated on a simulated dataset and its efficiency compared with interval mapping by using regression. It was shown that the rank-based approach is slightly inferior to regression when the residual variance is homoscedastic normal; however, in three out of four other scenarios envisaged, i.e., residual variance heteroscedastic normal, homoscedastic skewed, and homoscedastic positively kurtosed, the latter outperforms the former one. Both methods were applied to a real data set analyzing the effect of bovine chromosome 6 on milk yield and composition by using a 125-cM map comprising 15 microsatellites and a granddaughter design counting 1158 Holstein-Friesian sires.
GIT1, a Gene Encoding a Novel Transporter for Glycerophosphoinositol in Saccharomyces cerevisiae
Authors: Patton-Vogt J L , Henry S A 
Published: April 2021

Abstract
Phosphatidylinositol catabolism in Saccharomyces cerevisiae cells cultured in media containing inositol results in the release of glycerophosphoinositol (GroPIns) into the medium. As the extracellular concentration of inositol decreases with growth, the released GroPIns is transported back into the cell. Exploiting the ability of the inositol auxotroph, ino1, to use exogenous GroPIns as an inositol source, we have isolated mutants (Git−) defective in the uptake and metabolism of GroPIns. One mutant was found to be affected in the gene encoding the transcription factor, SPT7. Mutants of the positive regulatory gene INO2, but not of its partner, INO4, also have the Git− phenotype. Another mutant was complemented by a single open reading frame (ORF) termed GIT1 (glycerophosphoinositol). This ORF consists of 1556 bp predicted to encode a polypeptide of 518 amino acids and 57.3 kD. The predicted Git1p has similarity to a variety of S. cerevisiae transporters, including a phosphate transporter (Pho84p), and both inositol transporters (Itr1p and Itr2p). Furthermore, Git1p contains a sugar transport motif and 12 potential membrane-spanning domains. Transport assays performed on a git1 mutant together with the above evidence indicate that the GIT1 gene encodes a permease involved in the uptake of GroPIns.
The Macromelanophore Locus and the Melanoma Oncogene Xmrk Are Separate Genetic Entities in the Genome of Xiphophorus
Authors: Weis Silke , Schartl Manfred 
Published: April 2021

AbstractFish of the genus Xiphophorus are polymorphic for black pigmentation patterns. Certain intra- or interspecific hybrids exhibit enhanced expression of these patterns, leading in many cases to malignant melanoma. Because no recombination was ever observed between the pattern information and the genetic predisposition to develop melanoma after hybridization, a “tumor gene” (Tu) was postulated that encodes both phenotypes. A dominant oncogene, ONC-Xmrk, was then found to be necessary and sufficient for the transforming function of Tu. Here we present molecular evidence that ONC-Xmrk and the pigment pattern information are encoded by separate, although intimately linked loci. No ONC-Xmrk gene was present in the 15 Xiphophorus strains investigated which exhibit no black pigmentation pattern. Five different patterns from Xiphophorus maculatus, X. evelynae, X. milleri, X. cortezi, and X. montezumae were associated with ONC-Xmrk and were melanomagenic, while fish of X. helleri, X. variatus, X. nezahualcoyotl, and X. montezumae with five other patterns had no ONC-Xmrk and consequently did not produce hybrid melanoma. These data provide evidence that ONC-Xmrk is sufficient for tumorigenesis in Xiphophorus hybrids, and that a separate, pigment pattern-encoding locus is closely linked to it.
Complex Structure of Knob DNA on Maize Chromosome 9: Retrotransposon Invasion into Heterochromatin
Authors: Ananiev E V , Phillips R L , Rines H W 
Published: April 2021

Abstract
The recovery of maize (Zea mays L.) chromosome addition lines of oat (Avena sativa L.) from oat × maize crosses enables us to analyze the structure and composition of specific regions, such as knobs, of individual maize chromosomes. A DNA hybridization blot panel of eight individual maize chromosome addition lines revealed that 180-bp repeats found in knobs are present in each of these maize chromosomes, but the copy number varies from ~100 to 25,000. Cosmid clones with knob DNA segments were isolated from a genomic library of an oat-maize chromosome 9 addition line with the help of the 180-bp knob-associated repeated DNA sequence used as a probe. Cloned knob DNA segments revealed a complex organization in which blocks of tandemly arranged 180-bp repeating units are interrupted by insertions of other repeated DNA sequences, mostly represented by individual full size copies of retrotransposable elements. There is an obvious preference for the integration of retrotransposable elements into certain sites (hot spots) of the 180-bp repeat. Sequence microheterogeneity including point mutations and duplications was found in copies of 180-bp repeats. The 180-bp repeats within an array all had the same polarity. Restriction maps constructed for 23 cloned knob DNA fragments revealed the positions of polymorphic sites and sites of integration of insertion elements. Discovery of the interspersion of retrotransposable elements among blocks of tandem repeats in maize and some other organisms suggests that this pattern may be basic to heterochromatin organization for eukaryotes.
Characterization of an Allele-Nonspecific Intragenic Suppressor in the Yeast Plasma Membrane H+-ATPase Gene (PMA1)
Authors: Maldonado Ana M , de la Fuente Natalia , Portillo Francisco 
Published: April 2021

AbstractWe have analyzed the ability of A165V, V169I/D170N, and P536L mutations to suppress pma1 dominant lethal alleles and found that the P536L mutation is able to suppress the dominant lethality of the pma1-R271T, -D378N, -D378E, and -K474R mutant alleles. Genetic and biochemical analyses of site-directed mutants at Pro-536 suggest that this amino acid may not be essential for function but is important for biogenesis of the ATPase. Proteins encoded by dominant lethal pma1 alleles are retained in the endoplasmic reticulum, thus interfering with transport of wild-type Pma1. Immunofluorescence studies of yeast conditionally expressing revertant alleles show that the mutant enzymes are correctly located at the plasma membrane and do not disturb targeting of the wild-type enzyme. We propose that changes in Pro-536 may influence the folding of the protein encoded by a dominant negative allele so that it is no longer recognized and retained as a misfolded protein by the endoplasmic reticulum.
Genetic and Molecular Characterization of the Caenorhabditis elegans Gene, mel-26, a Postmeiotic Negative Regulator of MEI-1, a Meiotic-Specific Spindle Component
Authors: Dow M Rhys , Mains Paul E 
Published: April 2021

Abstract
We have previously described the gene mei-1, which encodes an essential component of the Caenorhabditis elegans meiotic spindle. When ectopically expressed after the completion of meiosis, mei-1 protein disrupts the function of the mitotic cleavage spindles. In this article, we describe the cloning and the further genetic characterization of mel-26, a postmeiotic negative regulator of mei-1. mel-26 was originally identified by a gain-of-function mutation. We have reverted this mutation to a loss-of-function allele, which has recessive phenotypes identical to the dominant defects of its gain-of-function parent. Both the dominant and recessive mutations of mel-26 result in mei-1 protein ectopically localized in mitotic spindles and centrosomes, leading to small and misoriented cleavage spindles. The loss-of-function mutation was used to clone mel-26 by transformation rescue. As suggested by genetic results indicating that mel-26 is required only maternally, mel-26 mRNA was expressed predominantly in the female germline. The gene encodes a protein that includes the BTB motif, which is thought to play a role in protein-protein interactions.
Increased Transmitter Release and Aberrant Synapse Morphology in a Drosophila Calmodulin Mutant
Authors: Arredondo LaChelle , Nelson Heidi B , Beckingham Kathy , Stern Michael 
Published: April 2021

Abstract
The ubiquitous calcium-binding protein calmodulin (CaM) has been implicated in the development and function of the nervous system in a variety of eukaryotic organisms. We have generated mutations in the single Drosophila Calmodulin (Cam) gene and examined the effects of these mutations on behavior, synaptic transmission at the larval neuromuscular junction, and structure of the larval motor nerve terminal. Flies hemizygous for Cam3c1, a mutation in the first Ca2+-binding site, exhibit behavioral, neurophysiological, and neuroanatomical abnormalities. In particular, adults exhibit defects in locomotion, coordination, and flight. Larvae exhibit increased neurotransmitter release from the motor nerve terminal at low [Ca2+] in the presence of the K+ channel-blocking drug quinidine. In addition, synaptic bouton structure at motor nerve terminals is altered. These effects are distinct from those produced by altering the activity of the CaM target enzymes CaM-activated kinase II (CaMKII) and CaM-activated adenylyl cyclase (CaMAC). Furthermore, previous in vitro studies of mutant Cam3c1 demonstrated that although its Ca2+ affinity is decreased, Cam3c1 protein can activate CaMKII, CaMAC, and CaM-activated phosphatase calcineurin in a manner similar to wild-type CaM. Thus, the Cam3c1 mutation might affect Ca2+ buffering or interfere with the activation or inhibition of a CaM target distinct from CaMKII or CaMAC.
The Complete Nucleotide Sequence of a Snake (Dinodon semicarinatus) Mitochondrial Genome With Two Identical Control Regions
Authors: Kumazawa Yoshinori , Ota Hidetoshi , Nishida Mutsumi , Ozawa Tomowo 
Published: April 2021

AbstractThe 17,191-bp mitochondrial DNA (mtDNA) of a Japanese colubrid snake, akamata (Dinodon semicarinatus), was cloned and sequenced. The snake mtDNA has some peculiar features that were found in our previous study using polymerase chain reaction: duplicate control regions that have completely identical sequences over 1 kbp, translocation of tRNALeu(UUR) gene, shortened TψC arm for most tRNA genes, and a pseudogene for tRNAPro. Phylogenetic analysis of amino acid sequences of protein genes suggested an unusually high rate of molecular evolution in the snake compared to other vertebrates. Southern hybridization experiments using mtDNAs purified from multiple akamata individuals showed that the duplicate state of the control region is not a transient or unstable feature found in a particular individual, but that it stably occurs in mitochondrial genomes of the species. This may, therefore, be regarded as an unprecedented example of stable functional redundancy in animal mtDNA. However, some of the examined individuals contain a rather scanty proportion of heteroplasmic mtDNAs with an organization of genes distinct from that of the major mtDNA. The gene organization of the minor mtDNA is in agreement with one of models that we present to account for the concerted evolution of duplicate control regions.
The Complete Nucleotide Sequence of the Mitochondrial DNA of the Dogfish, Scyliorhinus canicula
Authors: Delarbre Christiane , Spruyt Nathalie , Delmarre Cateline , Gallut Cyril , Barriel Véronique , Janvier Philippe , Laudet Vincent , Gachelin Gabriel 
Published: April 2021

AbstractWe have determined the complete nucleotide sequence of the mitochondrial DNA (mtDNA) of the dogfish, Scyliorhinus canicula. The 16,697-bp-long mtDNA possesses a gene organization identical to that of the Osteichthyes, but different from that of the sea lamprey Petromyzon marinus. The main features of the mtDNA of osteichthyans were thus established in the common ancestor to chondrichthyans and osteichthyans. The phylogenetic analysis confirms that the Chondrichthyes are the sister group of the Osteichthyes.
Genealogical Inference From Microsatellite Data
Authors: Wilson Ian J , Balding David J 
Published: April 2021

AbstractEase and accuracy of typing, together with high levels of polymorphism and widespread distribution in the genome, make microsatellite (or short tandem repeat) loci an attractive potential source of information about both population histories and evolutionary processes. However, microsatellite data are difficult to interpret, in particular because of the frequency of back-mutations. Stochastic models for the underlying genetic processes can be specified, but in the past they have been too complicated for direct analysis. Recent developments in stochastic simulation methodology now allow direct inference about both historical events, such as genealogical coalescence times, and evolutionary parameters, such as mutation rates. A feature of the Markov chain Monte Carlo (MCMC) algorithm that we propose here is that the likelihood computations are simplified by treating the (unknown) ancestral allelic states as auxiliary parameters. We illustrate the algorithm by analyzing microsatellite samples simulated under the model. Our results suggest that a single microsatellite usually does not provide enough information for useful inferences, but that several completely linked microsatellites can be informative about some aspects of genealogical history and evolutionary processes. We also reanalyze data from a previously published human Y chromosome microsatellite study, finding evidence for an effective population size for human Y chromosomes in the low thousands and a recent time since their most recent common ancestor: the 95% interval runs from ~15,000 to 130,000 years, with most likely values around 30,000 years.
Roles of Prenyl Protein Proteases in Maturation of Saccharomyces cerevisiae a-Factor
Authors: Boyartchuk Victor L , Rine Jasper 
Published: April 2021

Abstract
In eukaryotes small secreted peptides are often proteolytically cleaved from larger precursors. In Saccharomyces cerevisiae multiple proteolytic processing steps are required for production of mature 12-amino-acid a-factor from its 36-amino-acid precursor. This study provides additional genetic data supporting a direct role for Afc1p in cleavage of the carboxyl-terminal tripeptide from the CAAX motif of the prenylated a-factor precursor. In addition, Afc1p had a second role in a-factor processing that was independent of, and in addition to, its role in the carboxyl-terminal processing in vivo. Using ubiquitin-a-factor fusions we confirmed that the pro-region of the a-factor precursor was not required for production of the mature pheromone. However, the pro-region of the a-factor precursor contributed quantitatively to a-factor production.