bluuebunny/crossref_metadata_2025_split huggingface dataset:
The selection-mutation-drift theory of synonymous codon usage.
Authors: Bulmer M 
Published: January 2021

Abstract
It is argued that the bias in synonymous codon usage observed in unicellular organisms is due to a balance between the forces of selection and mutation in a finite population, with greater bias in highly expressed genes reflecting stronger selection for efficiency of translation. A population genetic model is developed taking into account population size and selective differences between synonymous codons. A biochemical model is then developed to predict the magnitude of selective differences between synonymous codons in unicellular organisms in which growth rate (or possibly growth yield) can be equated with fitness. Selection can arise from differences in either the speed or the accuracy of translation. A model for the effect of speed of translation on fitness is considered in detail, a similar model for accuracy more briefly. The model is successful in predicting a difference in the degree of bias at the beginning than in the rest of the gene under some circumstances, as observed in Escherichia coli, but grossly overestimates the amount of bias expected. Possible reasons for this discrepancy are discussed.
Association between rDNA alleles and quantitative traits in doubled haploid populations of barley.
Authors: Powell W , Thomas W T , Thompson D M , Swanston J S , Waugh R 
Published: January 2021

Abstract
Doubled haploids (DH) were generated from reciprocal F1 hybrids which were heterozygous for alleles at the Nor-H3 locus on chromosome 5H of barley. The r-DNA alleles did not deviate significantly from the expected 1:1 ratio and the DH progenies were classified into two groups based on the allelic constitution of the Nor-H3 locus. The DHs were grown in a randomized, replicated field experiment and a range of agronomic and quality traits were recorded. The Nor-H3 locus was associated with a significant portion of the genetic variation for: yield, thousand corn weight, water sensitivity and milling energy requirement of the grain. However, the magnitude of the differences between groups was dependent on the direction of the cross. The milling energy requirement of the grain was consistently associated with alleles at the Nor-H3 locus. These results are presented in relation to the dynamics of rDNA evolution and variability. The potential of molecular markers in conjunction with doubled haploids to map quantitative traits in barley is also discussed.
The molecular through ecological genetics of abnormal abdomen. IV. Components of genetic variation in a natural population of Drosophila mercatorum.
Authors: Hollocher H , Templeton A R , DeSalle R , Johnston J S 
Published: January 2021

Abstract
Natural populations of Drosophila mercatorum are polymorphic for a phenotypic syndrome known as abnormal abdomen (aa). This syndrome is characterized by a slow-down in egg-to-adult developmental time, retention of juvenile abdominal cuticle in the adult, increased early female fecundity, and decreased adult longevity. Previous studies revealed that the expression of this syndrome in females is controlled by two closely linked X chromosomal elements: the occurrence of an R1 insert in a third or more of the X-linked 28S ribosomal genes (rDNA), and the failure of replicative selection favoring uninserted 28S genes in larval polytene tissues. The expression of this syndrome in males in a laboratory stock was associated with the deletion of the rDNA normally found on the Y chromosome. In this paper we quantify the levels of genetic variation for these three components in a natural population of Drosophila mercatorum found near Kamuela, Hawaii. Extensive variation is found in the natural population for both of the X-linked components. Moreover, there is a significant association between variation in the proportion of R1 inserted 28S genes with allelic variation at the underreplication (ur) locus such that both of the necessary components for aa expression in females tend to cosegregate in the natural population. Accordingly, these two closely linked X chromosomal elements are behaving as a supergene in the natural population. Because of this association, we do not believe the R1 insert to be actively transposing to an appreciable extent. The Y chromosomes extracted from nature are also polymorphic, with 16% of the Ys lacking the Y-specific rDNA marker. The absence of this marker is significantly associated with the expression of aa in males. Hence, all three of the major genetic determinants of the abnormal abdomen syndrome are polymorphic in this natural population.
Molecular analysis of a Salmonella enterica group E1 rfb gene cluster: O antigen and the genetic basis of the major polymorphism.
Authors: Wang L , Romana L K , Reeves P R 
Published: January 2021

Abstract
Salmonella enterica is highly polymorphic for the O antigen, a surface polysaccharide that is subject to intense selection by the host immune system. This polymorphism is used for serotyping Salmonella isolates. The genes encoding O antigen biosynthesis are located in the rfb gene cluster. We report here the cloning and sequence of the 19-kb rfb region from strain M32 (serovar anatum, group E1) and compare it with that of strain LT2 (serovar typhimurium, group B). Genes for biosynthetic pathways common to both strains are conserved and have very similar sequences. In contrast, the five genes for CDP-abequose synthesis, present in strain LT2, are absent in strain M32; three open reading frames (ORFs) of strain LT2, thought to include genes for transferases, are not present in strain M32 but are replaced by three different ORFs with little or low level of similarity. Both rfb gene clusters are low in G + C content, indicating that they were transferred from a common ancestral species with low G + C content to S. enterica relatively recently (in the evolutionary sense). We discuss the recombination and lateral transfer events which may have been involved in the evolution of the polymorphism.
l(1)trol and l(1)devl, loci affecting the development of the adult central nervous system in Drosophila melanogaster.
Authors: Datta S , Kankel D R 
Published: January 2021

Abstract
Adult optic lobes of Drosophila melanogaster are composed of neurons specific to the adult which develop postembryonically. The structure of the optic lobes and aspects of its development have been described, and a number of mutants that affect its development have been identified. The focus of every screen to date has been on disruption of adult structure or function. Although these loci were originally identified on the basis of viable mutants, some have proven capable of giving rise to lethal alleles. It seems reasonable to assume that mutants which strongly affect development of the imaginal-specific central nervous system may evidence abnormalities during the late larval or pupal stages when the adult central nervous system is undergoing final assembly and might show a lethal phase prior to eclosion (as is true for mutations at the previously defined l(1)ogre locus). We have carried out the first screen of autosomal and sex-linked late larval and pupal lethals to identify mutations that affect the development of the optic lobes. Our screen yielded nine mutants that could tentatively be grouped into three classes, depending on the neuroblast population affected and imaginal disc phenotypes. Two of these, including one that is allelic to l(1)zw1, were chosen for further analysis.
Mode of origin and sources of genotypic diversity in triploid gynogenetic fish clones (Poeciliopsis: Poeciliidae).
Authors: Quattro J M , Avise J C , Vrijenhoek R C 
Published: January 2021

Abstract
Most tributaries of the Río Fuerte in northwestern Mexico contain one or more clones of allotriploid fish of the genus Poeciliopsis. We used multilocus allozyme genotypes and mitochondrial DNA (mtDNA) haplotypes to examine several potential modes of origin of these gynogenetic all-female fish. The allozyme studies corroborated earlier morphological work revealing the hybrid constitution of two triploid biotypes, Poeciliopsis 2 monacha-lucida and Poeciliopsis monacha-2 lucida. Each biotype carries one or two whole genomes from the each of the sexual species P. monacha and P. lucida. Restriction site analysis of mtDNA revealed that P. monacha was the maternal ancestor of five electrophoretically distinguishable triploid clones. Four of five clones were marked by closely related, composite, allozyme/mtDNA genotypes, suggesting they had common origins from an allodiploid clone of the P. monacha-lucida biotype. Genotypic analysis revealed that all five clones arose via the "genome addition" pathway. Fertilization of unreduced ova in P. monacha-lucida females by sperm from P. monacha and P. lucida males, respectively, gave rise to both biotypes.
Persistence of repeated sequences that evolve by replication slippage.
Authors: Tachida H , Iizuka M 
Published: January 2021

Abstract
The evolution of short repeated sequences by replication slippage under the assumption of selective neutrality is modeled using a linear birth and death process. The equilibrium distribution, the distribution of the life expectancy of a repeated sequence when the process starts from two repeats, the age distribution of repeats, the probability of obtaining two genes with i and j copies which diverged t generations ago and the conditional variance of copy number given the repeat number is more than one are computed. The distributions of life expectancy and age are shown to have long tails. Also the statistic which estimates the conditional variance is shown to have a large coefficient of variation. Using these theoretical results, we develop an approximate test of our model and analyze persistent repeated sequences found in the primate beta-globin gene region and Oenothera chloroplast DNA which are polymorphic within species. We found one sequence in Oenothera chloroplast DNA which does not fit to our neutral model.
Disruption of a silencer domain by a retrotransposon.
Authors: Mastrangelo M F , Weinstock K G , Shafer B K , Hedge A M , Garfinkel D J , Strathern J N 
Published: January 2021

Abstract
A galactose-inducible Ty element carrying the HIS3 gene has been used as an insertional mutagen to generate alpha-factor resistant mutants. This collection of Ty-induced mutations includes insertions into the gene for the alpha-factor receptor (STE2), several nonspecific STE genes, and mutations that lead to the expression of the normally silent HML alpha locus. The hml alpha "on" mutations fall into two classes, those that disrupt trans-acting regulators involved in silencing HML alpha and a novel class of mutations that activate HML alpha by insertion at that locus. The hml alpha::Ty "on" mutations illustrate the unusual ability of these retrotransposons to activate genes by overcoming gene silencing mechanisms. The hml alpha::Ty "on" mutations include examples of multimeric Ty arrays. Single Ty and solo delta insertion derivatives of these Ty multimers restore the ability of the silencing mechanism to repress HML alpha.
Serine and threonine catabolism in Saccharomyces cerevisiae: the CHA1 polypeptide is homologous with other serine and threonine dehydratases.
Authors: Bornaes C , Petersen J G , Holmberg S 
Published: January 2021

Abstract
The catabolic L-serine (L-threonine) dehydratase of Saccharomyces cerevisiae allows the yeast to grow on media with L-serine or L-threonine as sole nitrogen source. Previously we have cloned the CHA1 gene by complementation of a mutant, cha1, lacking the dehydratase activity. Here we present the DNA sequence of a 1,766-bp fragment of the CHA1 region encompassing an open reading frame of 1080 bp. Comparison of the predicted amino acid sequence of the CHA1 polypeptide with that of other serine/threonine dehydratases revealed several blocks of sequence homology. Thus, the amino acid sequence of rat liver serine dehydratase (SDH2) and the CHA1 polypeptide are 44% homologous allowing for conservative substitutions, while 36% similarity is found between the catabolic threonine dehydratase (tdcB) of Escherichia coli and the CHA1 protein. This strongly suggests that CHA1 is the structural gene for the yeast catabolic serine (threonine) dehydratase. S1-nuclease mapping of the CHA1 mRNA ends showed a major transcription initiation site corresponding to an untranslated leader of about 19 nucleotides, while a major polyadenylation site was located about 86 nucleotides downstream from the open reading frame. Furthermore, we have mapped the chromosomal position of the CHA1 gene to less than 0.5 kb centromere proximal to HML on the left arm of chromosome III.
Sexual development genes of Neurospora crassa.
Authors: Nelson M A , Metzenberg R L 
Published: January 2021

Abstract
The filamentous fungus Neurospora crassa undergoes a complex program of sexual development to form a fruiting body composed of several kinds of specialized tissue. Subtractive hybridization was used to isolate genes that are expressed preferentially during this sexual phase. Many such sexual development (sdv) genes were identified in a cosmid library of Neurospora genomic DNA. Fourteen of the sdv genes were subcloned, and their expression in mutant strains and under crossing and vegetative growth conditions was examined. All of the regulated transcripts were less abundant (and in many cases not detectable) in strains grown under vegetative (high nitrogen) conditions, suggesting that nitrogen starvation is required for their synthesis. The expression of most of the sdv genes also required a functional A mating type product, even under crossing growth conditions, suggesting that this product functions as a master control in sexual development. To determine if the products of the sdv genes play essential roles in the sexual cycle, a reverse-genetic approach (based on RIP (repeat-induced point mutation)-mediated gene disruptions) was used to create mutations in the genes. A mutant strain (asd-1) with a recessive crossing defect (apparently caused by the RIP process) was isolated; in this strain, early development is normal and may asci are formed, but ascospores are never delineated. A second recessive mutant strain (asd-2) was apparently created by ectopic integration of the transforming DNA into a gene required for the sexual process; in this strain the sexual process was blocked at an early stage, and the ascogeneous tissue underwent little development.
A colony color assay for Saccharomyces cerevisiae mutants defective in kinetochore structure and function.
Authors: Périer F , Carbon J 
Published: January 2021

Abstract
We have designed a colony color assay for monitoring centromere DNA-protein interactions in yeast (Saccharomyces cerevisiae). The assay is based on the ability of centromere DNA sequences to block (in cis) transcription initiated from a hybrid CEN-GAL1 promoter. Using a IacZ reporter gene under control of the CEN-GAL1 promoter, we screened colonies derived from mutagenized cells for a blue color phenotype indicative of derepression of the hybrid construct. A limited screen in which a 61-bp CEN11 DNA fragment containing an intact CDEIII subregion plus flanking sequences was used as the "pseudo-operator" led to the identification of mutations (blu) in three complementation groups. The blu1 mutants exhibited a decrease in activity of the major CEN DNA-binding proteins in vitro. The BLU1 gene was shown to be identical to the previously isolated SPT3 gene, known to be involved in the transcriptional regulation of a subset of yeast genes. Our results indicate that the BLU1/SPT3 gene product may also be required to maintain optimal levels of functional centromere DNA-binding proteins.
The relapsing fever agent Borrelia hermsii has multiple copies of its chromosome and linear plasmids.
Authors: Kitten T , Barbour A G 
Published: January 2021

Abstract
Borrelia hermsii, a spirochete which causes relapsing fever in humans and other mammals, eludes the immune response by antigenic variation of the "Vmp" proteins. This occurs by replacement of an expressed vmp gene with a copy of a silent vmp gene. Silent and expressed vmp genes are located on separate linear plasmids. To further characterize vmp recombination, copy numbers were determined for two linear plasmids and for the 1-megabase chromosome by comparing hybridization of probes to native DNA with hybridization to recombinant plasmids containing borrelial DNA. Plasmid copy numbers were also estimated by ethidium bromide fluorescence. Total cellular DNA content was determined by spectrophotometry. For borrelias grown in mice, copy numbers and 95% confidence intervals were 14 (12-17) for an expression plasmid, 8 (7-9) for a silent plasmid, and 16 (13-18) for the chromosome. Borrelias grown in broth medium had one-fourth to one-half this number of plasmids and chromosomes. Staining of cells with 4',6-diamidino-2-phenylindole revealed DNA to be distributed throughout most of the spirochete's length. These findings indicate that borrelias organize their total cellular DNA into several complete genomes and that cells undergoing serotype switches do one or more of the following: (1) coexpress Vmps from switched and unswitched expression plasmids for at least three to five generations, (2) suppress transcription from some expression plasmid copies, or (3) partition expression plasmids nonrandomly. The lower copy number of the silent plasmid indicates that nonreciprocal Vmp gene recombination may result from loss of recombinant silent plasmids by segregation.
Comparative studies of Drosophila Antennapedia genes.
Authors: Hooper J E , Pérez-Alonso M , Bermingham J R , Prout M , Rocklein B A , Wagenbach M , Edstrom J E , de Frutos R , Scott M P 
Published: January 2021

Abstract
The Antennapedia (Antp) homeotic gene of Drosophila melanogaster controls cell fates and pattern formation in the epidermis, nervous system and mesoderm of thoracic segments. Its expression is controlled at the levels of transcription, alternative RNA splicing, polyadenylation and translation. Two nested Antp transcription units extend over 103 kb and produce sixteen different transcripts. We have compared the Antp genes of Drosophila virilis, Drosophila subobscura and D. melanogaster to determine which structural features are conserved and therefore may be important to the gene's function. The overall gene structures are similar. There are many conserved sequence blocks throughout the large introns, at least 15 kb upstream of the first promoter, and at least 3 kb downstream of the last polyadenylation site. Intron and exon sequence conservation around alternative splice sites indicates that alternative protein coding forms may also be conserved. Protein coding potential is perfectly conserved around the C-terminal homeodomain, well conserved in the N-terminal region, and more variable in the middle. The large size of the Antp gene may reflect a large number of control elements necessary for appropriate Antp protein expression. The conservation of transcript complexity suggests functional requirements for the different protein forms.
The use of simulated annealing in chromosome reconstruction experiments based on binary scoring.
Authors: Cuticchia A J , Arnold J , Timberlake W E 
Published: January 2021

Abstract
We present a method of combinatorial optimization, simulated annealing, to order clones in a library with respect to their position along a chromosome. This ordering method relies on scoring each clone for the presence or absence of specific target sequences, thereby assigning a digital signature to each clone. Specifically, we consider the hybridization of oligonucleotide probes to a clone to constitute the signature. In that the degree of clonal overlap is reflected in the similarity of their signatures, it is possible to construct maps based on the minimization of the differences in signatures across a reconstructed chromosome. Our simulations show that with as few as 30 probes and a clonal density of 4.5 genome equivalents, it is possible to assemble a small eukaryotic chromosome into 33 contiguous blocks of clones (contigs). With higher clonal densities and more probes, this number can be reduced to less than 5 contigs per chromosome.
The distribution of spontaneous mutations on quantitative traits and fitness in Drosophila melanogaster.
Authors: Santiago E , Albornoz J , Domínguez A , Toro M A , López-Fanjul C 
Published: January 2021

Abstract
Starting from a completely homozygous population of Drosophila melanogaster, two groups of 100 inbred lines each were established and maintained for 46 generations, by a single brother-sister mating and two double first cousin matings, respectively. Sternopleural bristle number, wing length and wing width were simultaneously scored in all lines every 4-5 generations. The means of four lines in each group departed significantly from the overall mean and, in each case, this was attributed to a single mutation of relatively large effect on at least one trait (0.3-1.4 environmental standard deviations in absolute value). Further analyses revealed widespread pleiotropy, similar gene action of a given mutation for all traits affected, and predominant additive action. No apparent association was found between the magnitudes of mutational effects on the traits and fitness. However, all recessive mutations were deleterious. The distribution of mutant effects was asymmetrical (positive for bristles and negative for wing measurements). Moreover, these distributions had a high variance and may be leptokurtic, due to the presence of major genes. Estimates of the ratio of new mutational variance to environmental variance ranged within (0.7-3.4) x 10(-3), those for wing measurements being generally larger. In agreement with theory, the rate of between-line differentiation was independent of population size.
Gene dosage analysis in Azotobacter vinelandii.
Authors: Maldonado R , Garzón A , Dean D R , Casadesús J 
Published: January 2021

Abstract
For more than a decade, Azotobacter vinelandii has been considered a polyploid bacterium on the basis of physical studies of chromosome size and DNA content per cell. However, as described in the present work, many genetic operations can be performed in A. vinelandii without the constraints expected in a polyploid bacterium: (i) reversion of transposon-induced mutations is usually associated with loss of the transposable element; (ii) revertants retaining the transposon always carry secondary transpositions; (iii) heterozygotic transconjugants and transformants are unstable and segregate homozygotic colonies even in the absence of selection. Physical monitoring of segregation, achieved by colony hybridization, indicates that phenotypic expression of an allele is always correlated with its physical presence, thus ruling out the existence of either threshold dosage requirements or transcriptionally inactive DNA. Chromosomal lac fusions constructed by double crossover with a linearized plasmid show a segregation pattern consistent with the inheritance of one or several chromosomes per daughter cell. Analysis of the delay required for the expression of recessive chromosomal mutations such as rif, nal and str provides further evidence that A. vinelandii is not a polyploid bacterium.