bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Comparison of the Structure and Function of the Highly Homologous Maize Antioxidant Cu/Zn Superoxide Dismutase Genes, sod4 and Sod4A
Authors: Kernodle Sheri P , Scandalios John G 
Published: January 2021

Abstract
Two highly similar cytosolic Cu/Zn Sod (Sod4 and Sod4A) genes have been isolated from maize. Sod4A contains eight exons and seven introns. The Sod4 partial sequence contains five introns. The introns in both genes are located in the same position and have highly homologous sequences in several regions. The largest intron (&gt;1200 bp) interrupts the 5′ leader sequence. The presence of different regulatory motifs in the promoter region of each gene may indicate distinct responses to various conditions. Zymogram and RNA blot analyses show that Sod4 and Sod4A are expressed in all tissues of the maize plant. The developmental profiles of Sod4 and Sod4A mRNA accumulation differ in scutella during sporophytic development. RNA blot analysis of the respective Sod mRNAs indicates a differential, tissue-specific response of each gene to certain stressors. RNA isolated from stem tissue of ethephon-treated seedlings shows an increase in the Sod4 but not the Sod4A transcript while there is no change in transcripts of either gene in leaves or roots. There is differential mRNA accumulation between the two genes in leaf and stem tissue of paraquat-treated seedlings. Other agents that can cause oxidative stress were also tested for differential expression of the genes.
Estimation of Deleterious-Mutation Parameters in Natural Populations
Authors: Deng Hong-Wen , Lynch Michael 
Published: January 2021

Abstract
The rate and average effects of spontaneous deleterious mutations are important determinants of the evolution of breeding systems and of the vulnerability of small populations to extinction. Nevertheless, few attempts have been made to estimate the properties of such mutations, and those studies that have been performed have been extremely labor intensive, relying on long-term, laboratory mutation-accumulation experiments. We present an alternative to the latter approach. For populations in which the genetic variance for fitness is a consequence of selection-mutation balance, the mean fitness and genetic variance of fitness in outbred and inbred generations can be expressed as simple functions of the genomic mutation rate, average homozygous effect and average dominance coefficient of new mutations. Using empirical estimates for the mean and genetic variance of fitness, these expressions can then be solved to obtain joint estimates of the deleterious-mutation parameters. We employ computer simulations to evaluate the degree of bias of the estimators and present some general recommendations on the application of the technique. Our procedures provide some hope for obtaining estimates of the properties of deleterious mutations from a wide phylogenetic range of species as well as a mechanism for testing the validity of alternative models for the maintenance of genetic variance for fitness.
Genetic Distances and Reconstruction of Phylogenetic Trees From Microsatellite DNA
Authors: Takezaki Naoko , Nei Masatoshi 
Published: January 2021

Abstract
Recently many investigators have used microsatellite DNA loci for studying the evolutionary relationships of closely related populations or species, and some authors proposed new genetic distance measures for this purpose. However, the efficiencies of these distance measures in obtaining the correct tree topology remains unclear. We therefore investigated the probability of obtaining the correct topology (PC) for these new distances as well as traditional distance measures by using computer simulation. We used both the infinite-allele model (IAM) and the stepwise mutation model (SMM), which seem to be appropriate for classical markers and microsatellite loci, respectively. The results show that in both the IAM and SMM Cavalli-Sforza and Edwards' chord distance (Dc) and NEI et al.'s DA distance generally show higher PC values than other distance measures, whether the bottleneck effect exists or not. For estimating evolutionary times, however, NEI'S standard distance and Goldstein et al's (δμ) are more appropriate than other distances. Microsatellite DNA seems to be very useful for clarifying the evolutionary relationships of closely related populations.
Polymorphism in Genes That Influence Sperm Displacement
Authors: Prout Timothy , Clark Andrew G 
Published: January 2021

Abstract
Paternity of offspring of multiply inseminated females is in many organisms highly skewed, with an advantage generally going to the male that most recently mated. Variation in sperm competitive ability can result in strong natural selection, and one expects that a gene that offers an advantage in sperm displacement would, all else being equal, be rapidly fixed, leaving low equilibrium levels of variability in sperm competition. However, empirical studies have demonstrated genetic variation in sperm displacement, begging the question of how this variation can be maintained. Here we develop a population genetic model to find conditions that maintain polymorphism in alleles that influence sperm displacement. We consider a one-locus model in which allelic variants have pleiotropic effects on fecundity and mating ability in addition to sperm displacement. This model can admit more than one stable polymorphism, and we find conditions for protected polymorphism. Induced overdominance is not necessary for stable polymorphism. These results have direct bearing on the observed variation in the ability of resident sperm to defend against displacement.
Neutral Genetic Markers and Conservation Genetics: Simulated Germplasm Collections
Authors: Bataillon Thomas M , David Jacques L , Schoen Daniel J 
Published: January 2021

Abstract
This study examines the use of neutral genetic markers to guide sampling from a large germplasm collection with the objective of establishing from it a smaller, but genetically representative sample. We simulated evolutionary change and germplasm sampling in a subdivided population of a diploid hermaphrodite annual plant to create an initially large collection. Several strategies of sampling from this collection were then compared. Our results show that a strategy based on information obtained from marker genes led to retention of the maximum number of neutral and nonneutral alleles in the smaller sample. This occurred when demes were composed of self-fertilizing individuals or when no migration occurred among demes, but not when demes of an outcrossing population were connected by high levels of migration.
Destabilization of Bacteriophage T4 mRNAs by a Mutation of Gene 61.5
Authors: Kai Toshie , Selick Harold E , Yonesaki Tetsuro 
Published: January 2021

Abstract
We identified a novel gene of bacteriophage T4, gene 61.5, which appears to be involved in protein synthesis late in infection. Northern blot analysis revealed that a mutant of 61.5 accumulated truncated transcripts of representative late genes. Using a double mutant of genes 61.5 and 55, which prevents transcription of late genes, we demonstrate that even transcripts of middle genes, while full-length when initially expressed, are similarly truncated at later stages of infection. These results indicate that the abnormality in transcript length occurs late in infection, regardless of whether the transcript derives from a middle or a late gene. Primer-extension analysis revealed that the 5′ ends of the late gene 23 transcripts that accumulated in gene 61.5 mutant-infected cells were located at internal discrete sites as well as at the expected transcription start site. Moreover, the decay rates of full-length transcripts from genes uvsY or 45 were more than twofold faster in the absence of a functional gene 61.5. These results suggest that mutation of gene 61.5 activates endonucleolytic cleavage of middle and late transcripts, probably by RNase M.
A Mutation in a Saccharomyces cerevisiae Gene (RAD3) Required for Nucleotide Excision Repair and Transcription Increases the Efficiency of Mismatch Correction
Authors: Yang Yingying , Johnson Anthony L , Johnston Leland H , Siede Wolfram , Friedberg Errol C , Ramachandran Karthikeyan , Kunz Bernard A 
Published: January 2021

Abstract
RAD3 functions in DNA repair and transcription in Saccharomyces cerevisiae and particular rad3 alleles confer a mutator phenotype, possibly as a consequence of defective mismatch correction. We assessed the potential involvement of the Rad3 protein in mismatch correction by comparing heteroduplex repair in isogenic rad3-1 and wild-type strains. The rad3-1 allele increased the spontaneous mutation rate but did not prevent heteroduplex repair or bias its directionality. Instead, the efficiency of mismatch correction was enhanced in the rad3-1 strain. This surprising result prompted us to examine expression of yeast mismatch repair genes. We determined that MSH2, but not MLH1, is transcriptionally regulated during the cell-cycle like PMSl, and that rad3-1 does not increase the transcript levels for these genes in log phase cells. These observations suggest that the rad3-1 mutation gives rise to an enhanced efficiency of mismatch correction via a process that does not involve transcriptional regulation of mismatch repair. Interestingly, mismatch repair also was more efficient when error-editing by yeast DNA polymerase δ was eliminated. We discuss our results in relation to possible mechanisms that may link the rad3-1 mutation to mismatch correction efficiency.
Cha4p of Saccharomyces cerevisiae Activates Transcription Via Serine/Threonine Response Elements
Authors: Holmberg Steen , Schjerling Peter 
Published: January 2021

Abstract
The CHA1 gene of Saccharomyces cereuisiae encodes the catabolic l-serine (l-threonine) deaminase responsible for the utilization of serine/threonine as nitrogen sources. Previously, we identified two serine/threonine response elements in the CHA1 promoter, UASCHA. We report isolation of a mutation, cha4-1, that impairs serine/threonine induction of CHA1 transcription. The cha4-l allele causes noninducibility of a CHA1p-lacZ translational gene fusion, indicating that Cha4p exerts its action through the CHA1 promoter. Molecular and genetic mapping positioned the cha4 locus 17 cM centromere proximal to put1 on chromosome XII. The coding region of CHA4 predicts a 648-amino acid protein with a DNA-binding motif (residues 43–70) belonging to the Cys6 zinc cluster class. Gel retardation employing a recombinant peptide, Cha4p1-174, demonstrated that the peptide in vitro specifically binds UASCHA. Binding is abolished by a G-C to T-A mutation in the middle bases of the two CEZ-elements in UASCHA. The transcriptional activating ability of UASCHA derivatives in vivo correlates with their ability to bind Cha4p1-174 in vitro. We conclude that Cha4p is a positive regulator of CHA1 transcription and that Cha4p alone, or as part of a complex, is binding UASCHA.
Premature Death in Podospora anserina: Sporadic Accumulation of the Deleted Mitochondrial Genome, Translational Parameters and Innocuity of the Mating Types
Authors: Contamine Véronique , Lecellier Gael , Belcour Leon , Picard Marguerite 
Published: January 2021

Abstract
The Podospora anserina premature death syndrome was described as early growth arrest caused by a site-specific deletion of the mitochondrial genome (mtDNA) and occurring in strains displaying the genotype AS1-4 mat−. The AS1-4 mutation lies in a gene encoding a cytosolic ribosomal protein, while mat− is one of the two forms (mat− and mat+) of the mating-type locus. Here we show that, depending on culture conditions, death due to the accumulation of the deleted mtDNA molecule can occur in the AS1-4 mat+ context and can be delayed in the AS1-4 mat− background. Furthermore, we show that premature death and the classical senescence process are mutually exclusive. Several approaches permit the identification of the mat-linked gene involved in the appearance of premature death. This gene, rmp, exhibits two natural alleles, rmp− linked to mat− and rmp+ linked to mat+. The first is probably functional while the second probably carries a nonsense mutation and is sporadically expressed through natural suppression. A model is proposed that emphasizes the roles played by the AS1-4 mutation, the rmp gene, and environmental conditions in the accumulation of the deleted mitochondrial genome characteristic of this syndrome.
Macrorestriction Analysis of Caenorhabditis elegans Genomic DNA
Authors: Browning Heidi , Berkowitz Laura , Madej Cynthia , Paulsen Janet E , Zolan Miriam E , Strome Susan 
Published: January 2021

Abstract
The usefulness of genomic physical maps is greatly enhanced by linkage of the physical map with the genetic map. We describe a “macrorestriction mapping” procedure for Caenarhabditis elegans that we have applied to this endeavor. High molecular weight, genomic DNA is digested with infrequently cutting restriction enzymes and size-fractionated by pulsed field gel electrophoresis. Southern blots of the gels are probed with clones from the C. elegans physical map. This procedure allows the construction of restriction maps covering several hundred kilobases and the detection of polymorphic restriction fragments using probes that map several hundred kilobases away. We describe several applications of this technique. (1) We determined that the amount of DNA in a previously uncloned region is &lt;220 kb. (2) We mapped the mes-1 gene to a cosmid, by detecting polymorphic restriction fragments associated with a deletion allele of the gene. The 25-kb deletion was initially detected using as a probe sequences located ~400 kb away from the gene. (3) We mapped the molecular endpoint of the deficiency hDf6, and determined that three spontaneously derived duplications in the unc-38-dpy-5 region have very complex molecular structures, containing internal rearrangements and deletions.
Molecular Characterization of hobo-Mediated Inversions in Drosophila melanogaster
Authors: Eggleston William B , Rim Nac R , Lim Johng K 
Published: January 2021

Abstract
The structure of chromosomal inversions mediated by hobo transposable elements in the Uc-1 X chromosome was investigated using cytogenetic and molecular methods. Uc-1 contains a phenotypically silent hobo element inserted in an intron of the Notch locus. Cytological screening identified six independent Notch mutations resulting from chromosomal inversions with one breakpoint at cytological position 3C7, the location of Notch. In situ hybridization to salivary gland polytene chromosomes determined that both ends of each inversion contained hobo and Notch sequences. Southern blot analyses showed that both breakpoints in each inversion had hobo-Notch junction fragments indistinguishable in structure from those present in the Uc-1 X chromosome prior to the rearrangements. Polymerase chain reaction amplification of the 12 hobo-Notch junction fragments in the six inversions, followed by DNA sequence analysis, determined that each was identical to one of the two hobo-Notch junctions present in Uc-1. These results are consistent with a model in which hobo-mediated inversions result from homologous pairing and recombination between a pair of hobo elements in reverse orientation.
Dosage Compensation Regulatory Proteins and the Evolution of Sex Chromosomes in Drosophila
Authors: Bone James R , Kuroda Mitzi I 
Published: January 2021

Abstract
In the fruitfly Drosophila melanogaster, the four male-specific lethal (msl) genes are required to achieve dosage compensation of the male X chromosome. The MSL proteins are thought to interact with cis-acting sites that confer dosage compensation to nearby genes, as they are detected at hundreds of discrete sites along the length of the polytene X chromosome in males but not in females. The histone H4 acetylated isoform, H4Ac16, colocalizes with the MSL proteins at a majority of sites on the D. melanogaster X chromosome. Using polytene chromosome immunostaining of other species from the genus Drosophila, we found that X chromosome association of MSL proteins and H4Ac16 is conserved despite differences in the sex chromosome karyotype between species. Our results support a model in which cis-acting regulatory sites for dosage compensation evolve on a neo-X chromosome arm in response to the degeneration of its former homologue.
Quantitative Genetic Variation of Odor-Guided Behavior in a Natural Population of Drosophila melanogaster
Authors: Mackay Trudy F C , Hackett J Brant , Lyman Richard F , Wayne Marta L , Anholt Robert R H 
Published: January 2021

Abstract
Quantitative genetic variation in behavioral response to the odorant, benzaldehyde, was assessed among a sample of 43 X and 35 third chromosomes extracted from a natural population and substituted into a common inbred background. Significant genetic variation among chromosome lines was detected. Heritability estimates for olfactory response, however, were low, as is typical for traits under natural selection. Furthermore, the loci affecting naturally occurring variation in olfactory response to benzaldehyde were not the same in males and females, since the genetic correlation between the sexes was low and not significantly different from zero for the chromosome 3 lines. Competitive fitness, viability and fertility of the chromosome 3 lines were estimated using the balancer equilibrium technique. Genetic correlations between fitness and odor-guided behavior were not significantly different from zero, suggesting the number of loci causing variation in olfactory response is small relative to the number of loci causing variation in fitness. Since different genes affect variation in olfactory response in males and females, genetic variation for olfactory response could be maintained by genotype × sex environment interaction. This unusual genetic architecture implies that divergent evolutionary trajectories for olfactory behavior may occur in males and females.
Sequence Analysis of Ewkaryotic Developmental Proteins: Ancient and Novel Domains
Authors: Mushegian Arcady R , Koonin Eugene V 
Published: January 2021

Abstract
Most of the genes involved in the development of multicellular eukaryotes encode large, multidomain proteins. To decipher the major trends in the evolution of these proteins and make functional predictions for uncharacterized domains, we applied a strategy of sequence database search that includes construction of specialized data sets and iterative subsequence masking. This computational approach allowed us to detect previously unnoticed but potentially important sequence similarities. Developmental gene products are enriched in predicted nonglobular regions as compared to unbiased sets of eukaryotic and bacterial proteins. Developmental genes that act intracellularly, primarily at the level of transcription regulation, typically code for proteins containing highly conserved DNA-binding domains, most of which appear to have evolved before the radiation of bacteria and eukaryotes. We identified bacterial homologues, namely a protein family that includes the Escherichia coli universal stress protein UspA, for the MADS-box transcription regulators previously described only in eukaryotes. We also show that the FUS6 family of eukaryotic proteins contains a putative DNA-binding domain related to bacterial helix-turn-helix transcription regulators. Developmental proteins that act extracellularly are less conserved and often do not have bacterial homologues. Nevertheless, several provocative similarities between different groups of such proteins were detected.
Genetic and Physical Variability at the Mating Type Locus of the Oomycete, Phytophthora infestans
Authors: Judelson Howard S 
Published: January 2021

Abstract
Mating type in the oomyceteous fungus, Phytophthora infestans, is determined by a single locus. In a previous study of a few isolates, the locus segregated in a manner genetically consistent with its linkage to a system of balanced lethal loci. To determine the prevalence of this phenomenon within P. infestans, genetic analyses were performed using isolates representative of the diversity within the species that had been selected by DNA fingerprinting using probes linked to mating type. Non-Mendelian segregation of the mating type locus was observed in crosses performed with each isolate. An unusual group of isolates was identified in which the mating type determinants had been rearranged within the genome; these strains also produced an aberrantly large number of self-fertile progeny. Curiously, in all isolates, markers linked to the mating type locus appeared prone to duplication, transposition, deletion, or other rearrangement. This was not observed for loci unlinked to mating type. Data from the crosses and analyses of marker variation were used to erect models to explain the bases of mating type determination and of the unusual segregation of the chromosomal region containing the mating type locus.
Cloning and Characterization of the scute (sc) Gene of Drosophila subobscura
Authors: Botella L M , Doñoro C , Sáchez L , Segarra C , Granadino B 
Published: January 2021

Abstract
The scute (sc) gene, a member of the achaete-scute complex of Drosophila melanogaster, has dual functions: sisterless (sis-b) function required for sex determination and dosage compensation and scute function, which is involved in neurogenesis. The sc homologue of D. subobscura was cloned. It lacks introns and encodes a single 1.7-kb transcript slightly larger than that of D. melanogaster (1.6 kb). The Sc protein of D. subobscura is slightly larger than that of D. melanogaster (382 vs. 345 amino acids). Sequence comparisons between both species show the Sc protein to have a highly conserved bHLH domain. Outside this domain, amino acid replacements are not randomly distributed. Two additional conserved domains, of 20 and 36 amino acids, are present near the C-terminal end. They may represent domains confering specificity upon the Sc protein with respect to other proteins of the achaete-scute complex. In its 3′ untranslated region, Sc RNA contains uridine stretches, putative Sxl protein DNA-binding sites. The D. subobscura Sc protein can cooperate with other D. melanogaster bHLH proteins because D. subobscura sc supplies sis-b function when introduced into D. melanogaster transgenic flies mutant for sc.
Mutations in New Cell Cycle Genes That Fail to Complement a Multiply Mutant Third Chromosome of Drosophila
Authors: White-Cooper Helen , Cannena Mar , Gonzalez Cayetano , Glover David M 
Published: January 2021

Abstract
We have simultaneously screened for new alleles and second site mutations that fail to complement five cell cycle mutations of Drosophila carried on a single third chromosome (gnu, polo, mgr, asp, stg). Females that are either transheterozygous for scott of the antartic (scant) and polo, or homozygous for scant produce embryos that show mitotic defects. A maternal effect upon embryonic mitoses is also seen in embryos derived from females transheterozygous with helter skelter (hsk) and either mgr or asp. deopatra (cleo), fails to complement asp but is not uncovered by a deficiency for asp. The mitotic phenotype of larvae heterozygous for cleo and the multiple mutant chromosome is similar to weak alleles of asp, but there are no defects in male meiosis. Mutations that failed to complement stgfell into two complementation groups corresponding to stg and a new gene noose. Three of the new stg alleles are early zygotic lethals, whereas the fourth is a pharate adult lethal allele that affects both mitosis and meiosis. Mutations in noose fully complement a small deficiency that removes stg, but when placed in trans to certain stg alleles, result in late lethality and mitotic abnormalities in larval brains.