bluuebunny/crossref_metadata_2025 huggingface dataset:
Isolation and Analysis of the arg-13 Gene of Neurospora crassa
Authors: Liu Qiuyun , Dunlap Jay C
Published: January 2021

Mutations in arg-13 result in slow growth in minimal medium and can suppress mutations in carbamyl phosphate synthase-aspartate carbamyl transferase within the pyrimidine pathway; the exact biochemical function of the gene product is unknown. To understand the role of arg-13 in arginine metabolism, cosmids rescuing growth in arg-13 mutants were cloned and mapped to the position of arg-13 on LG IR. Northern analysis showed the arg-13 message to contain ~2100 nt, although a 1.4kb genomic fragment truncated at the 5′ and 3′ ends of the gene encodes a shortened transcript that can rescue arg-13 function. Expression of mRNA arising from the mutant arg-13 gene is induced by arginine starvation, although wild type (arg-13  +) is not derepressed in minimal medium. The sequence of the arg-13 gene shows ARGl3 to be a member of the mitochondrial carrier superfamily with three repeats of a ~100-amino acid domain, six putative membrane spanning regions, and three copies of the mitochondrial carrier consensus pattern. This information plus available and new nutritional data are consistent with the hypothesis that arg-13 encodes a mitochondrial basic amino acid carrier whose existence was predicted based upon previous physiological, nutritional and biochemical data.
Genetic Analysis of the Roles of daf28 and age-1 in Regulating Caenorhabditis elegans Dauer Formation
Authors: Malone Elizabeth A , Inoue Takao , Thomas James H
Published: January 2021

Based on environmental cues, the nervous system of Caenorhabditis ekgans regulates formation of the dauer larva, an alternative larval form specialized for long-term survival under harsh conditions. Mutations that cause constitutive or defective dauer formation (Daf-c or Daf-d) have been identified and the genes ordered in a branched pathway. Most Daf-c mutations also affect recovery from the dauer stage. The semidominant mutation daf-28(sa191) is Daf-c but has no apparent effect on dauer recovery. We use this unique aspect of daf28(sal91) to characterize the effects of several Daf-d and synthetic Daf-c mutations on dauer recovery. We present double mutant analysis that indicates that daf-28(saI91) acts at a novel point downstream in the genetic pathway for dauer formation. We also show that daf-28(sa191) causes a modest increase (12-13%) in life span. The phenotypes and genetic interactions of daf-28(sa191) are most similar to those of daf-2 and daf-23 mutations, which also cause a dramatic increase in life span. We present mapping and complementation data that suggest that daf-23 is the same gene as age-I, identified previously by mutations that extend life span. We find that age-l alleles are also Daf-c at 27°.
Comparing Mutational Variabilities
Authors: Houle David , Morikawa Bob , Lynch Michael
Published: January 2021

We have reviewed the available data on VM, the amount of genetic variation in phenotypic traits produced each generation by mutation. We use these data to make several qualitative tests of the mutation-selection balance hypothesis for the maintenance of genetic variance (MSB). To compare VM values, we use three dimensionless quantities: mutational heritability, the mutational coefficient of variation, CVM; and the ratio of the standing genetic variance to VM, VG/VM. Since genetic coefficients of variation for life history traits are larger than those for morphological traits, we predict that under MSB, life history traits should also have larger CVM. This is confirmed; life history traits have a median CVM value more than six times higher than that for morphological traits. VG/VM approximates the persistence time of mutations under MSB in an infinite population. In order for MSB to hold, VG/VM must be small, substantially less than 1000, and life history traits should have smaller values than morphological traits. VG/VM averages about 50 generations for life history traits and 100 generations for morphological traits. These observations are all consistent with the predictions of a mutation-selection balance model.
The Maternal Nude1 Protein of Drosophila Has Two Distinct Roles Important for Embryogenesis
Authors: Hong Charles C , Hashimoto Carl
Published: January 2021

The nudel gene is maternally required to define dorsoventral polarity of the Drosophila embryo. It encodes an unusual mosaic protein with a protease domain that may trigger the protease cascade required for ventral development. We describe phenotypic and molecular analyses of nudel mutations that provide further insight into nudel protein function. Surprisingly, nudel mutations primarily cause either dorsalized embryos in which dorsal cell fates are expanded over ventral and lateral cell fates or fragile eggs that fail to develop beyond early embryonic stages. The nudel protein is therefore required not only for embryonic dorsoventral polarity but also for structural integrity of the egg. Complementation and antagonistic interactions between nudel alleles suggest that the nudel protein is functionally modular and that protein-protein interactions are important for nudel protein function. Three nudel mutations that produce dorsalized embryos map to the protease domain of nudel, suggesting that this domain is specifically required for defining embryonic dorsoventral polarity. Finally, certain combinations of nudel alleles simultaneously produce completely dorsalized and normal embryos yet very few embryos of intermediate mutant phenotypes. The unusual biphasic distribution of phenotypes may indicate that nudel activity above a threshold is required to generate embryonic dorsoventral polarity.
Quantitative Genetics of Transgenic Mice: Components of Phenotypic Variation in Body Weights and Weight Gains
Authors: Clutter A C , Pomp D , Murray J D
Published: January 2021

Transgenic mice possessing an ovine growth hormone gene were used to study the effects of elevated growth hormone on quantitative genetic variation. Males hemizygous for the transgene were mated to wild-type females to produce half- and full-sib families in which approximately half the progeny were transgenic and half were wild type. Analyses of body weights at 3–10 weeks, and weight gains from 3 to 6, and 6 to 10 weeks produced estimates of the proportion of total variance due to additive genetic effects (h2) and common litter effects (c2), and the genetic correlation between transgenic and wild-type expression of each trait. At 10 weeks, body weight of transgenics exceeded that of wild types by 26 and 49% in males and females, respectively. Estimated genetic variances in the transgenic group were significantly greater than zero for body weights at most ages and for both measurements of gain. Common litter effects accounted for a similar proportion of variation in the wild-type and transgenic groups. Additive genetic correlations between wild-type and transgenic expression of body weights tended to decline with age, indicating that a partially different array of genes may have begun to affect body weight in the transgenic group.
The Use of Multiple Markers in a Bayesian Method for Mapping Quantitative Trait Loci
Authors: Uimari Pekka , Thaller Georg , Hoeschele Ina
Published: January 2021

Information on multiple linked genetic markers was used in a Bayesian method for the statistical mapping of quantitative trait loci (QTL). Bayesian parameter estimation and hypothesis testing were implemented via Markov chain Monte Carlo algorithms. Variables sampled were the augmented data (marker-QTL genotypes, polygenic effects), an indicator variable for linkage or nonlinkage, and the parameters. The parameter vector included allele frequencies at the markers and the QTL, map distances of the markers and the QTL, QTL substitution effect, and polygenic and residual variances. The criterion for QTL detection was the marginal posterior probability of a QTL being located on the chromosome carrying the markers, The method was evaluated empirically by analyzing simulated granddaughter designs consisting of 2000 sons, 20 related sires, and their ancestors.
Comparison of the Structure and Expression of odd-skipped and Two Related Genes That Encode a New Family of Zinc Finger Proteins in Drosophila
Authors: Hart Marilyn C , Wang Lei , Coulter Douglas E
Published: January 2021

The odd-skipped (odd) gene, which was identified on the basis of a pair-rule segmentation phenotype in mutant embryos, is initially expressed in the Drosophila embryo in seven pair-rule stripes, but later exhibits a segment polarity-like pattern for which no phenotypic correlate is apparent. We have molecularly characterized two embryonically expressed odd-cognate genes, sob and bowel (bowl), that encode proteins with highly conserved C2H2 zinc fingers. While the Sob and Bowl proteins each contain five tandem fingers, the Odd protein lacks a fifth (C-terminal) finger and is also less conserved among the four common fingers. Reminiscent of many segmentation gene paralogues, the closely linked odd and sob genes are expressed during embryogenesis in similar striped patterns; in contrast, the less-tightly linked bowlgene is expressed in a distinctly different pattern at the termini of the early embryo. Although our results indicate that odd and sob are more likely than bowl to share overlapping developmental roles, some functional divergence between the Odd and Sob proteins is suggested by the absence of homology outside the zinc fingers, and also by amino acid substitutions in the Odd zinc fingers at positions that appear to be constrained in Sob and Bowl.
Cloning of the Drosophila melanogaster Meiotic Recombination Gene mei-218: A Genetic and Molecular Analysis of Interval 15E
Authors: McKim Kim S , Dahmus Jeffrey B , Hawley R Scott
Published: January 2021

The mei-218 gene product is required for both meiotic crossing over and for the production of recombination nodules, suggesting that these organelles are required for meiotic exchange. In this study the null phenotype of mei-218 was defined through the analysis of three preexisting and five new alleles. Consistent with previous studies, in homozygous mi-218 mutants meiotic crossing over is reduced to <10% of normal levels. A molecular analysis of mei-218 was initiated with the isolation and mapping of lethal mutations and genome rearrangements in the region containing mi-218, polytene interval 15E on the X chromosome. This high resolution genetic map was aligned with a physical map constructed from cosmid and P1 clones by genetically mapping restriction fragment length polymorphisms and localizing rearrangement breakpoints. Within a region of 65 kb, we have identified seven transcription units, including mei-218 and the Minute(l)l5D gene, which encodes ribosomal protein S5. The mei-218 mutant phenotype has been rescued by germline transformation with both a genomic fragment and a cDNA under the control of the hsp83 promoter. The mei-218 gene is predicted to produce an 1186 amino acid protein that has no significant similarities to any known proteins.
The Effects of Natural Hybridization on the Regulation of Doubly Uniparental mtDNA Inheritance in Blue Mussels (Mytilus spp.)
Authors: Ramon Paul D , Secor Carol L , Hilbish Thomas J
Published: January 2021

Blue mussels in the Mythilus edulis species complex have a doubly uniparental mode of mtDNA inheritance with separate maternal and paternal mtDNA lineages. Female mussels inherit their mtDNA solely from their mother, while males inherit mtDNA from both parents. In the male gonad the paternal mtDNA is preferentially replicated so that only paternal mtDNA is transmitted from fathers to sons. Hybridization is common among differentiated blue mussel taxa; whenever it involves M. trossulus, doubly uniparental mtDNA inheritance is disrupted. We have found high frequencies of males without and females with paternal mtDNA among hybrid mussels produced by interspecific matings between M. galloprovincialis and M. trossulus. In contrast, hybridization between M. galloprovincialis and M. edulis does not affect doubly uniparental inheritance, indicating a difference in the divergence of the mechanisms regulating mtDNA inheritance among the three blue mussel taxa. Our data indicate a high frequency of disrupted mtDNA transmission in F1 hybrids and suggest that two separate mechanisms, one regulating the transmission of paternal mtDNA to males and another inhibiting the establishment of paternal mtDNAin females, act to regulate doubly uniparental inheritance. We propose a model for the regulation of doubly uniparental inheritance that is consistent with these observations.
A Test of the Double-Strand Break Repair Model for Meiotic Recombination in Saccharomyces cerevisiae
Authors: Gilbertson Larry A , Stahl Franklin W
Published: January 2021

We tested predictions of the double-strand break repair (DSBR) model for meiotic recombination by examining the segregation patterns of small palindromic insertions, which frequently escape mismatch repair when in heteroduplex DNA. The palindromes flanked a well characterized DSB site at the ARC4 locus. The “canonical” DSBR model, in which only 5′ ends are degraded and resolution of the four-stranded intermediate is by Holliday junction resolvase, predicts that hDNA will frequently occur on both participating chromatids in a single event. Tetrads reflecting this configuration of hDNA were rare. In addition, a class of tetrads not predicted by the canonical DSBR model was identified. This class represented events that produced hDNA in a “trans” configuration, on opposite strands of the same duplex on the two sides of the DSB site. Whereas most classes of convertant tetrads had typical frequencies of associated crossovers, tetrads with trans hDNA were parental for flanking markers. Modified versions of the DSBR model, including one that uses a topoisomerase to resolve the canonical DSBR intermediate, are supported by these data.
A Genetic Linkage Map of the Male Goat Genome
Authors: Vaiman Daniel , Schibler Laurent , Bourgeois Florence , Oustry Anne , Amigues Yves , Cribiu Edmond P
Published: January 2021

This paper presents a first genetic linkage map of the goat genome. Primers derived from the flanking sequences of 612 bovine, ovine and goat microsatellite markers were gathered and tested for amplification with goat DNA under standardized PCR conditions. This screen made it possible to choose a set of 55 polymorphic markers that can be used in the three species and to define a panel of 223 microsatellites suitable for the goat. Twelve half-sib paternal goat families were then used to build a linkage map of the goat genome. The linkage analysis made it possible to construct a meiotic map covering 2300 cM, i.e., >SO% of the total estimated length of the goat genome. Moreover, eight cosmids containing microsatellites were mapped by fluorescence in situ hybridization in goat and sheep. Together with 11 microsatellite-containing cosmids previously mapped in cattle (and supposing conservation of the banding pattern between this species and the goat) and data from the sheep map, these results made the orientation of 15 linkage groups possible. Furthermore, 12 coding sequences were mapped either genetically or physically, providing useful data for comparative mapping.
Both Loss-of-Function and Gain-of-Function Mutations in snf Define a Role for snRNP Proteins in Regulating Sex-lethal Pre-mRNA Splicing in Drosophila Development
Authors: Salz Helen K , Flickinger Thomas W
Published: January 2021

The Drosophila snf gene encodes a protein with functional homology to the mammalian UlA and U2B″ snRNP proteins. Studies, based on the analysis of three viable alleles, have suggested a role for snf in establishing the female-specific splicing pattern of the sex determination switch gene, Sex-lethal. Here, we show that the non-sex-specific lethal null allele is required for female sex determination, arguing against the formal possibility that the viable alleles disrupt a function unrelated to snf's wild-type function. Moreover, we find snf is required for normal cell growth and/or survival, as expected for a protein involved in a cell-vital process such as RNA splicing. We also show that of the three viable alleles only one, snfJA2, is a partial loss-of-function mutation. The other two viable alleles, snf1621 and snfe8H, encode antimorphic proteins. We find the antimorphic proteins are mislocalized and correlate their mislocalization with their molecular lesions and mutant phenotypes. Finally, we provide genetic evidence that the antimorphic alleles interfere with the autoregulatory splicing function of the Sex-lethal protein. Based on these studies we suggest a model in which the snRNP protein, Snf, functions with Sex-lethal to block recognition of the regulated male-specific exon.
In Vivo Analysis Reveals That the Interdomain Region of the Yeast Proliferating Cell Nuclear Antigen Is Important for DNA Replication and DNA Repair
Authors: Amin Neelam S , Holm Connie
Published: January 2021

To identify the regions of the proliferating cell nuclear antigen (PCNA) that are important for function in vivo, we used random mutagenesis to isolate 10 cold-sensitive (Cs−) and 31 methyl methanesulfonate-sensitive (Mmss) mutations of the PCNA gene (POL30) in Saccharomyces cerevisiae. Unlike the Mmss mutations, the CsC mutations are strikingly clustered in the interdomain region of the three-dimensional PCNA monomer structure. At the restrictive temperature, the Cs−  pol30 mutants undergo a RAD9 dependent arrest as large-budded cells with a 2c DNA content. Defects in DNA synthesis are suggested by a significant delay in the progression of synchronized pol30 cells through S phase at the restrictive temperature. DNA repair defects are revealed by the observation that Cs−  pol30 mutants are very sensitive to the alkylating agent MMS and mildly sensitive to ultraviolet radiation, although they are not sensitive to gamma radiation. Finally, analysis of the chromosomal DNA in pol30 cells by velocity sedimentation gradients shows that pol30 cells accumulate single-stranded DNA breaks at the restrictive temperature. Thus, our results show that PCNA plays an essential role in both DNA replication and DNA repair in vivo.
Multicopy FZF1 (SUL1) Suppresses the Sulfite Sensitivity but Not the Glucose Derepression or Aberrant Cell Morphology of a grr1 Mutant of Saccharomyces cerevisiae
Authors: Avram Dorina , Bakalinsky Alan T
Published: January 2021

An ssu2 mutation in Sacccharomyces cermisiae, previously shown to cause sulfite sensitivity, was found to be allelic to GRR1, a gene previously implicated in glucose repression. The suppressor rgt1, which suppresses the growth defects of grr1 strains on glucose, did not fully suppress the sensitivity on glucose or nonglucose carbon sources, indicating that it is not strictly linked to a defect in glucose metabolism. Because the Cln1 protein was previously shown to be elevated in grr1 mutants, the effect of CLN1 overexpression on sulfite sensitivity was investigated. Overexpression in GRR1 cells resulted in sulfite sensitivity, suggesting a connection between CLN1 and sulfite metabolism. Multicopy FZF1, a putative transcription factor, was found to suppress the sulfite sensitive phenotype of grr1 strains, but not the glucose derepression or aberrant cell morphology. Multicopy FZF1 was also found to suppress the sensitivity of a number of other unrelated sulfite-sensitive mutants, but not that of ssu1 or met20, implying that FZF1 may act through Ssulp and Met20p. Disruption of FZF1 resulted in sulfite sensitivity when the construct was introduced in single copy at the FZF1 locus in a GRR1 strain, providing evidence that FZF1 is involved in sulfite metabolism.
Isolation of Two apsA Suppressor Strains in Aspergillus nidulans
Authors: Krüger Miriam , Fischer Reinhard
Published: January 2021

Aspergillus nidulans reproduces asexually with single nucleated conidia. In apsA (anucleate primary sterigmata) strains, nuclear positioning is affected and conidiation is greatly reduced. To get further insights into the cellular functions of apSA, aconidial apsA strains were mutagenized and conidiating suppressor strains were isolated. The suppressors fell into two complementation groups, samA and samB (suppressor of anucleate metulae). samA mapped on linkage group I close to pyrG. The mutant allele was dominant in diploids homozygous for apsA. Viability of conidia of samA suppressor strains (samA  −; apsA  −) was reduced to 50% in comparison to wild-type conidia. Eighty percent of viable spores produced small size colonies that were temperature- and benomyl-sensitive. samB mapped to chromosome VIII and was recessive. Viability of conidia from samB suppressor strains (apSA  −; samB−) was also affected but no small size colonies were observed. Both suppressors produced partial defects in sexual reproduction and both suppressed an apsA deletion mutation. In wild-type background the mutant loci affected hyphal growth rate (samA) or changed the colony morphology (samB) and inhibited sexual spore formation (samA and samB). Only subtle effects on conidiation were found. We conclude that both suppressor genes bypass the apsA function and are involved in microtubule-dependent processes.
Female Fertility and Mating Type Effects on Effective Population Size and Evolution in Filamentous Fungi
Authors: Leslie John F , Klein Keith K
Published: January 2021

The idealized individual in many fungal species is a haploid self-sterile hermaphrodite that may be propagated by asexually produced spores or that may reproduce sexually. In field populations, polymorphism occurs for female-sterile / hermaphrodite status, and female-sterile mutants, which function only as males during sexual reproduction, may comprise >50% of the population. The effective population number may be based on the number of strains of different mating type or the relative frequency of hermaphrodites. The female-sterile mutants are at a selective disadvantage every time sexual reproduction occurs, and must have an advantage during vegetative propagation to persist at a significant frequency. When a high frequency of female-sterile strains is observed in field populations, it indicates that vegetative propagation is a significant component of the fungus' natural history. Depending on the mutation rate to female sterility and the selective advantage of the femalesterile strains during vegetative propagation, the ratio of sexual:asexual generations can range from 1:15 to 1:2300 for species in the Gibberella fujikuroi complex. The relative rarity of sexual reproduction may permit female-sterile strains to accumulate to a level such that local populations could completely lose sexuality and appear as asexual (imperfect) species.
Prediction of Heterosis from DNA Fingerprints in Chickens
Authors: Gavora J S , Fairfull R W , Benkel B F , Cantwell W J , Chambers J R
Published: January 2021

To assess the value of DNA fingerprints for the prediction of heterosis in chickens, retrospective analyses of data from three crossbreeding experiments and DNA fingerprints (DFP) of parental strains were conducted using two minisatellite and one middle-repetitive DNA probes. DFP bands were assessed on pooled DNA samples of 10-15 individuals per parental genetic group. The number of DFP bands evaluated in the experiments ranged from 81 to 139. The probes varied in their predictive value, but predictability of heterosis generally increased with multiple probes. Highly significant correlations (0.68-0.87) between band sharing ratios (SH) and heterosis were found in 25 crosses of White Leghorns in the first egg production cycle for age at sexual maturity, egg production, and mature body weight: traits with heterosis of 10% or more of the means. Regressions on SH explained 78.4% of the variation in heterosis in age at sexual maturity, 60.2% in egg production and 46.4% in mature body weight. For “broiler” traits with heterosis of <1%, none of the correlations, based on 13 crosses, were significant. It was concluded that multilocus probe DFP of pooled DNA samples show promise as predictors of heterosis.
Effects of Differential Selection in the Sexes on Cytonuclear Polymorphism and Disequilibria
Authors: Babcock Christina S , Asmussen Marjorie A
Published: January 2021

We develop a series of models that examine the effects of differential selection between the sexes on cytonuclear polymorphism and disequilibria. A detailed analysis is provided for populations under constant fertility or viability selection censused at life stages without frequency differences in the sexes. We show analytically that cytonuclear disequilibria can be generated de novo if the cytoplasmic and nuclear loci each affect female fitness and there is a nonmultiplicative fitness interaction between them. While computer simulations demonstrate that the majority of disequilibria produced by random selection are transient and small in magnitude, measurable permanent disequilibria can result from selective differences both within and between the two sexes. We derive analytic conditions for a protected cytonuclear polymorphism and use numerical simulations to quantitate the likelihood of obtaining permanent nuclear, cytoplasmic, and cytonuclear variation under various patterns of selection. The numerical analysis identifies special selection regimes more likely to generate disequilibria and maintain cytonuclear polymorphism and reveals a direct correlation to the strength of selection. As a byproduct, our models also provide the first decomposition of the different parental contributions to cytonuclear dynamics and the analytic conditions under which selection can cause cytoplasmic frequency changes or a cytonuclear hitchhiking effect.
Wolbachia Infection and Cytoplasmic Incompatibility in Drosophila Species
Authors: Bourtzis Kostas , Nirgianaki Androniki , Markakis George , Savakis Charalambos
Published: January 2021

Forty-one stocks from 30 Drosophila species were surveyed for Wolbachia infection using PCR technology. D. sechellia and two strains of D. auraria were found to be infected and were tested for the expression of cytoplasmic incompatibility, along with D. ananassae and D. melanogaster strains, which are already known to be infected. D. ananassae and D. melanogaster show levels of incompatibility up to 25%, while D. auraria and D. sechellia exhibit levels of egg mortality ~60%. A dot-blot assay using the dnaA sequence as probe was developed to assess the infection levels in individual males that were used in incompatibility crosses. A positive correlation between bacterial density and cytoplasmic incompatibility was observed. The stocks examined can be clustered into at least two groups, depending on the levels of infection relative to the degree of cytoplasmic incompatibility exhibited. One group, containing D. simuluns Hawaii, D. sechellia, and D. auraria, exhibits high levels of cytoplasmic incompatibility relative to levels of infection; all the other species and D. simulans Riverside exhibit significantly lower levels of cytoplasmic incompatibility relative to levels of infection. These data show that, in addition to bacterial density, bacterial and/or host factors also affect the expression of cytoplasmic incompatibility.
The Evolution of Genomic Imprinting
Authors: Mochizuki Atsushi , Takeda Yasuhiko , Iwasa Yoh
Published: January 2021

In some mammalian genes, the paternally and maternally derived alleles are expressed differently: this phenomenon is called genomic imprinting. Here we study the evolution of imprinting using multivariate quantitative genetic models to examine the feasibility of the genetic conflict hypothesis. This hypothesis explains the observed imprinting patterns as an evolutionary outcome of the conflict between the paternal and maternal alleles. We consider the expression of a zygotic gene, which codes for an embryonic growth factor affecting the amount of maternal resources obtained through the placenta. We assume that the gene produces the growth factor in two different amounts depending on its parental origin. We show that genomic imprinting evolves easily if females have some probability of multiple partners. This is in conflict with the observation that not all genes controlling placental development are imprinted and that imprinting in some genes is not conserved between mice and humans. We show however that deleterious mutations in the coding region of the gene create selection against imprinting.
Maximizing Transcription Efficiency Causes Codon Usage Bias
Authors: Xia Xuhua
Published: January 2021

The rate of protein synthesis depends on both the rate of initiation of translation and the rate of elongation of the peptide chain. The rate of initiation depends on the encountering rate between ribosomes and mRNA; this rate in turn depends on the concentration of ribosomes and mRNA. Thus, patterns of codon usage that increase transcriptional efficiency should increase mRNA concentration, which in turn would increase the initiation rate and the rate of protein synthesis. An optimality model of the transcriptional process is presented with the prediction that the most frequently used ribonuclectide at the third codon sites in mRNA molecules should be the same as the most abundant ribonucleotide in the cellular matrix where mRNA is transcribed. This prediction is supported by four kinds of evidence. First, A-ending codons are the most frequently used synonymous codons in mitochondria, where ATP is much more abundant than that of the three other ribonucleotides. Second, A-ending codons are more frequently used in mitochondrial genes than in nuclear genes. Third, protein genes from organisms with a high metabolic rate use more A-ending codons and have higher A content in their introns than those from organisms with a low metabolic rate.
Two Classes of Tn10 Transposase Mutants That Suppress Mutations in the Tn10 Terminal Inverted Repeat
Authors: Sakai J , Kleckner N
Published: January 2021

Tn10 transposition requires IS10 transposase and essential sequences at the two ends of the element. Mutations in terminal basepairs 6–13 confer particularly strong transposition defects. We describe here the identification of transposase mutations that suppress the transposition defects of such terminus mutations. These mutations are named “SEM” for suppression of ends mutations. All of the SEM mutations suppress more than a single terminus mutation and thus are not simple alterations of transposase/end recognition specificity. The mutations identified fall into two classes on the basis of genetic tests, location within the protein and nature of the amino acid substitution. Class I mutations, which are somewhat allele specific, appear to define a small structural and functional domain of transposase in which hydrophobic interactions are important at an intermediate stage of the transposition reaction, after an effective interaction between the ends but before transposon excision. Class II mutations, which are more general in their effects, occur at a single residue in a small noncritical amino-terminal proteolytic domain of transposase and exert their affects by altering a charge interaction; these mutations may affect act early in the reaction, before or during establishment of an effective interaction between the ends.
A Novel Involvement of the PurG and PurI Proteins in Thiamine Synthesis Via the Alternative Pyrimidine Biosynthetic (APB) Pathway in Salmonella typhimurium
Authors: Zilles Julie L , Downs Diana M
Published: January 2021

Thiamine is thought to be synthesized by two alternative pathways, one involving the first four enzymes of the purine pathway and a second that can function independently of the purine pathway. Insertion mutations in purG and purl prevent thiamine synthesis through the alternative pyrimidine biosynthetic (APB) pathway under aerobic but not anaerobic growth conditions. In contrast, point mutations in purG and purl caused one of three distinct phenotypes: Pur− Apb−, Pur− Apb+, or Pur+ Apb−. Analysis of these three mutant classes demonstrated two genetically separable functions for PurG and PurI in thiamine synthesis. In addition to their known enzymatic role in de novo purine synthesis, we propose that PurG and PurI play a novel, possibly nonenzymatic role in the APB pathway. Suppression analysis of Pur− Apb− mutants identified two new genetic loci involved in the APB pathway, apbB and apbD. We show here that mutations in apbB and apbD cause distinct, allele-specific suppression of the thiamine requirement of purG and purl mutants. Our results suggest that PurG and PurI and one or more components of the APB pathway may function as a complex needed for aerobic function of the APB pathway.
SGS1, a Homologue of the Bloom's and Werner's Syndrome Genes, Is Required for Maintenance of Genome Stability in Saccharomyces cerevisiae
Authors: Watt Paul M , Hickson Ian D , Borts Rhona H , Louis Edward J
Published: January 2021

The Saccharomyces cerevisiae SGS1 gene is homologous to Escherichia coli RecQ and the human BLM and WRN proteins that are defective in the cancer-prone disorder Bloom's syndrome and the premature aging disorder Werner's syndrome, respectively. While recQ mutants are deficient in conjugational recombination and DNA repair, Bloom's syndrome cell lines show hyperrecombination. Bloom's and Werner's syndrome cell lines both exhibit chromosomal instability. sgslΔ strains show mitotic hyperrecombination, as do Bloom's cells. This was manifested as an increase in the frequency of interchromosomal homologous recombination, intrachromosomal excision recombination, and ectopic recombination. Hyperrecombination was partially independent of both RAD52 and RAD1. Meiotic recombination was not increased in sgs1Δ mutants, although meiosis I chromosome missegregation has been shown to be elevated. sgs1Δ suppresses the slow growth of a top3Δ strain lacking topoisomerase 111. Although there was an increase in subtelomeric Y' instability in sgs1Δ strains due to hyperrecombination, no evidence was found for an increase in the instability of terminal telomeric sequences in a top3Δ or a sgs1Δ strain. This contrasts with the telomere maintenance defects of Werner's patients. We conclude that the SGS1 gene product is involved in the maintenance of genome stability in S. cermisiae.
Yeast Mutants That Produce a Novel Type of Ascus Containing Asci Instead of Spores
Authors: Xue Zhixiong , Shan Xiaoyin , Sinelnikov Alex , Melese Teri
Published: January 2021

Tetraploid yeast cells lacking BFR1 or overexpressing an essential gene BBPl produce a novel type of ascus that contains asci instead of spores. We show here that the asci within an ascus likely arise because a/α spores undergo a second round of meiosis. Cells depleted of Bbplp or lacking Bfr1p are defective in a number of processes such as nuclear segregation, bud formation, cytokinesis and nuclear spindle formation. Furthermore, deletion of BFR1 or overexpression of BBP1 leads to an increase in cell ploidy, indicating that Bfr1p and Bbplp play roles in both the mitotic cell cycle and meiosis. Bfr1p and Bbp1p interact with each other in a two hybrid assay, further suggesting that they might form a complex important for cell cycle coordination.
Genotypic and Phenotypic Characterization of the Drosophila melanogaster Olfactory Mutation Indifferent
Authors: Cobb Matthew
Published: January 2021

Two Drosophila melanogaster third chromosomes carrying the EMS-induced mutations IndifferentA (IndfA) and IndifferentB (IndfB), previously isolated from larvae showing an anosmia when stimulated with nonanol, were recombined with a multi-marked chromosome in order to localize the mutant character(s). Recombinant strains were tested for their larval olfactory responses and classed as either mutant or wild type; both Indf characters were found to be located on the right arm of the chromosome, between ebony and claret. Deletion mapping suggests that the Indifferent wild-type character is a haplo-insufficiency and that IndfA and IndfB are located in cytological region 96A2-7. Deficiencies and both mutant strains were tested with 14 closely related odors (alcohols, acetates, acids and methyl esters, between eight and 10 carbons long). When stimulated with methyl octanoate, IndfA and IndfB appeared recessive; noncomplementation was observed for this phenotype in IndfA/IndfB hybrids indicating that the two characters are allelic. The overall responses of IndfA, IndfB and the deficiencies indicate that Indf is involved in processing organic odors of between eight and 10 carbons in length.
Zygotic Lethal Mutations With Maternal Effect Phenotypes in Drosophila melanogaster. II. Loci on the Second and Third Chromosomes Identified by P-Element-Induced Mutations
Authors: Perrimon Norbert , Lanjuin Anne , Arnold Charles , Noll Elizabeth
Published: January 2021

Screens for zygotic lethal mutations that are associated with specific maternal effect lethal phenotypes have only been conducted for the X chromosome. To identify loci on the autosomes, which represent four-fifths of the Drosophila genome, we have used the autosomal “FLP-DFS” technique to screen a collection of 496 P element-induced mutations established by the Berkeley Drosophila Genome Project. We have identified 64 new loci whose gene products are required for proper egg formation or normal embryonic development.
Drosophila syntaxin Is Required for Cell Viability and May Function in Membrane Formation and Stabilization
Authors: Schulze Karen L , Bellen Hugo J
Published: January 2021

The role of the Drosophila homologue of syntaxin-1A (syx) in neurotransmission has been extensively studied. However, developmental Northern analyses and in situ hybridization experiments show that SYX mRNA is expressed during all stages and in many tissues. We have isolated new mutations in syx that reveal roles for syx outside the nervous system. In the ovary, SYX is present in the germarium, but it is predominantly localized to nurse cell membranes. Mitotic recombination experiments in the germ-line show SYX is essential for oogenesis and may participate in membrane biogenesis in the nurse cells. In the early embryo, a large contribution of maternally deposited RNA is present, and the protein is localized at cell membranes during cellularization. After the maternal contribution is depleted, zygotically produced SYX assists secretion events occurring late in embryogenesis, such as cuticle deposition and neurotransmitter release. However, SYX is also required in larval imaginal discs, as certain hypomorphic mutant combinations exhibit rough eyes and wing notch defects indicative of cell death. Furthermore, recombinant clones that lack syx cause cell lethality in the developing eye. We propose that, similar to its roles in cuticle secretion and neurotransmitter release, SYX may mediate membrane assembly events throughout Drosophila development.
Mom1 is a Semi-Dominant Modifier of Intestinal Adenoma Size and Multiplicity in Min/+ Mice
Authors: Gould Karen A , Dietrich William F , Borenstein Natalie , Lander Eric S , Dove William F
Published: January 2021

The intestinal tumor multiplicity in mice heterozygous for ApcMin is strongly modulated by genetic background. On the sensitive C57BL/6J (B6) background, mice develop large numbers of intestinal adenomas. The AKR/J (AKR) strain carries alleles that correlate with a strong reduction in tumor multiplicity. To study the effect of one of these modifiers, Mom1, we have generated a mouse line in which the AKR allele of Mom1 is carried on the sensitive B6 genetic background. This strain was produced by using a marker-assisted selection method to eliminate unlinked AKR alleles more rapidly. The application and efficiency of this method are discussed. We used this strain to determine that Mom1 affects both tumor multiplicity and tumor size in a semi-dominant fashion.
Isolation of Y Chromosome-Specific Sequences From Silene latifolia and Mapping of Male Sex-Determining Genes Using Representational Difference Analysis
Authors: Donnison Iain S , Siroky Jiri , Vyskot Boris , Saedler Heinz , Grant Sarah R
Published: January 2021

The genomic subtraction method representational difference analysis (RDA) was used to identify male-specific restriction fragments in the dioecious plant Silene latifolia. Male-specific restriction fragments are linked to the male sex chromosome (the Y chromosome). Four RDA-derived male-specific restriction fragments were used to identify polymorphisms in a collection of X-ray-generated mutant plants with either hermaphroditic or asexual flowers. Some of the mutants have cytologically detectable deletions in the Y chromosome that were correlated with loss of male-specific restriction fragments. One RDA-derived probe detected a restriction fragment present in all mutants, indicating that each has retained Y chromosomal DNA. The other three probes detected genomic fragments that were linked in a region deleted in some hermaphroditic and some asexual mutants. Based on the mutant phenotypes and the correlation of cytologically visible deletions with loss of male-specific restriction fragments, these markers were assigned to positions on the Y chromosome close to the carpel suppression locus. This RDA mapping also revealed a Y-linked locus, not previously described, which is responsible for early stamen development.
Testing Differentiation in Diploid Populations
Authors: Goudet Jérôme , Raymond Michel , de Meeüs Thierry , Rousset François
Published: January 2021

We examine the power of different exact tests of differentiation for diploid populations. Since there is not necessarily random mating within populations, the appropriate hypothesis to construct exact tests is that of independent sampling of genotypes. There are two categories of tests, FST-estimator tests and goodness of fit tests. In this latter category, we distinguish “allelic statistics”, which account for the nature of alleles within genotypes, from “genotypic statistics” that do not. We show that the power of FST-estimator tests and of allelic goodness of fit tests are similar when sampling is balanced, and higher than the power of genotypic goodness of fit tests. When sampling is unbalanced, the most powerful tests are shown to belong to the allelic goodness of fit group.
Statistical Properties of a DNA Sample Under the Finite-Sites Model
Authors: Yang Ziheng
Published: January 2021

Statistical properties of a DNA sample from a random-mating population of constant size are studied under the finite-sites model. It is assumed that there is no migration and no recombination occurs within the locus. A Markov process model is used for nucleotide substitution, allowing for multiple substitutions at a single site. The evolutionary rates among sites are treated as either constant or variable. The general likelihood calculation using numerical integration involves intensive computation and is feasible for three or four sequences only; it may be used for validating approximate algorithms. Methods are developed to approximate the probability distribution of the number of segregating sites in a random sample of n sequences, with either constant or variable substitution rates across sites. Calculations using parameter estimates obtained for human D-loop mitochondrial DNAs show that among-site rate variation has a major effect on the distribution of the number of segregating sites; the distribution under the finite-sites model with variable rates among sites is quite different from that under the infinite-sites model.
Assessing Dissimilarity of Genes by Comparing Their RNAse A Mismatch Cleavage Patterns
Authors: Rzhetsky Andrey , Dopazo Joaquín , Snyder Eric , Dangler Charles A , Ayala Francisco José
Published: January 2021

We propose a simple algorithm for estimating the number of nucleotide differences between a pair of RNA or DNA sequences through comparison of their RNAse A mismatch cleavage patterns. In the RNAse A mismatch cleavage technique two or more sample sequences are hybridized to the same RNA probe, the hybrids are partially digested with RNAse A, and the digestion products are compared on an electrophoretic gel. Here we provide an algorithm for converting the numbers of unique and matching electrophoretic bands into an estimate of the number of nucleotide differences between the sequences. Computer simulation indicates that the proposed method yields a robust estimate of the genetic distance despite stochastic errors and occasional violation of certain assumptions. Our study suggests that the method performs best when the distance between the sequences is <15 differences. When the sequences under analysis are likely to have larger distances, we advise to substitute one long riboprobe with a set of shorter nonoverlapping probes. The new algorithm is applied to infer the proximity of several strains of pseudorabies virus.
Characterization of Functional Domains of the su(Hw) Protein That Mediate the Silencing Effect of mod(mdg4) Mutations
Authors: Gdula David A , Corces Victor G
Published: January 2021

The suppressor of Hairy-wing [su(Hw)] protein represses enhancer function in a unidirectional fashion: enhancers segregated from the promoter by the su(Hw) binding region are rendered inactive, whereas those in the same domain are unaffected. In the case of the gypsy-induced y2 allele, the repressive effect of su(Hw) is rendered bidirectional in mod(mdg4) mutant flies, and all enhancers of the affected gene become inactive. This silencing of enhancer elements might be due to exposure of specific domains of su(Hw) when the mod(mdg4) protein is absent. Two of three regions of su(Hw) that are located adjacent to the leucine zipper motif and are conserved across Drosophila species are necessary for both the unidirectional and bidirectional repression of transcription by su(Hw). In contrast, two acidic domains that are dispensable for the unidirectional repression of enhancer elements are critical for the bidirectional silencing of enhancer activity observed in mutants lacking functional mod(mdg4) protein.
The Swi5 Transcription Factor of Saccharomyces cerevisiae Has a Role in Exit From Mitosis Through Induction of the cdk-Inhibitor Sic1 in Telophase
Authors: Toyn Jeremy H , Johnson Anthony L , Donovan Joseph D , Toone W Mark , Johnston Leland H
Published: January 2021

Deactivation of the B cyclin kinase (Cdc28/Clb) drives the telophase to G1 cell cycle transition. Here we investigate one of the control pathways that contributes to kinase deactivation, involving the cell cycle-regulated production of the cdk inhibitor Sic1. We show that the cell cycle timing of SIC1 expression depends on the transcription factor Swi5, and that Swi5-dependent SIC1 expression begins during telophase. In contrast to Swi5, the related transcription factor Ace2, which can also induce SIC1 expression, is not active during telophase. The functional consequence of Swi5-regulated SIC1 expression in vivo is that both sic1Δ and swi5Δ strains have identical mitotic exit-related phenotypes. First, both are synthetically lethal with dbf2Δ, resulting in cell cycle arrest in telophase. Second, both are hypersensitive to overexpression of the B cyclin CLB2. Thus, Swi5-dependent activation of the SIC1 gene contributes to the deactivation of the B cyclin kinase, and hence exit from mitosis.