bluuebunny/crossref_metadata_2025 huggingface dataset:
Two genetically and molecularly distinct functions involved in early neurogenesis reside within the Enhancer of split locus of Drosophila melanogaster.
Authors: Delidakis C , Preiss A , Hartley D A , Artavanis-Tsakonas S
Published: January 2021

Molecular correlation of the genetic aspects of the function of the neurogenic gene Enhancer of split [E(spl)] has previously been hampered by the densely transcribed nature of the chromosomal region within which it resides. We present data indicating that two distinct molecular species contribute to E(spl) function. Analysis of new E(spl) alleles has allowed us to define two complementing functions within the locus. Subsequent phenotypic analysis of different E(spl) deficiencies combined with P element-transformed constructs has demonstrated that these two functions correspond to: (1) a family of helix-loop-helix (HLH) protein-encoding genes and (2) the single copy gene E(spl) m9/10, whose product shares homology with G-protein beta subunits. The zygotically active E(spl) HLH genes can, at least partially, substitute for one another's functions and their total copy number determines the activity of the locus. E(spl) m9/10 acts synergistically with the E(spl) HLH genes and other neurogenic genes in the process of neurogenesis. The maternal component of E(spl) m9/10 has the most pronounced effect in neurogenesis, while its zygotic component is predominantly required during postembryonic development. The lethality of trans-heterozygotes of null E(spl) deficiency alleles with a strong Delta point mutation is a result of the concomitant reduction in activity of both E(spl) HLH and m9/10 functions. Immunocytochemical localization of the E(spl) m9/10 protein has revealed that it is a ubiquitously distributed nuclear component in embryonic, larval and imaginal tissues.
swi6, a gene required for mating-type switching, prohibits meiotic recombination in the mat2-mat3 "cold spot" of fission yeast.
Authors: Klar A J , Bonaduce M J
Published: January 2021

Mitotic interconversion of the mating-type locus (mat1) of the fission yeast Schizosaccharomyces pombe is initiated by a double-strand break at mat1. The mat2 and mat3 loci act as nonrandom donors of genetic information for mat1 switching such that switches occur primarily (or only) to the opposite mat1 allele. Location of the mat1 "hot spot" for transposition should be contrasted with the "cold spot" of meiotic recombination located within the adjoining mat2-mat3 interval. That is, meiotic interchromosomal recombination in mat2, mat3 and the intervening 15-kilobase region does not occur at all. swi2 and swi6 switching-deficient mutants possess the normal level of double-strand break at mat1, yet they fail to switch efficiently. By testing for meiotic recombination in the cold spot, we found the usual lack of recombination in a swi2 mutant but a significant level of recombination in a swi6 mutant. Therefore, the swi6 gene function is required to keep the donor loci inert for interchromosomal recombination. This finding, combined with the additional result that switching primarily occurs intrachromosomally, suggests that the donor loci are made accessible for switching by folding them onto mat1, thus causing the cold spot of recombination.
Chromosome rearrangement by ectopic recombination in Drosophila melanogaster: genome structure and evolution.
Authors: Montgomery E A , Huang S M , Langley C H , Judd B H
Published: January 2021

Ectopic recombination between interspersed repeat sequences generates chromosomal rearrangements that have a major impact on genome structure. A survey of ectopic recombination in the region flanking the white locus of Drosophila melanogaster identified 25 transposon-mediated rearrangements from four parallel experiments. Eighteen of the 25 were generated from females carrying X chromosomes heterozygous for interspersed repeat sequences. The cytogenetic and molecular analyses of the rearrangements and the parental chromosomes show: (1) interchromosomal and intrachromosomal recombinants are generated in about equal numbers; (2) ectopic recombination appears to be a meiotic process that is stimulated by the interchromosomal effect to about the same degree as regular crossing over; (3) copies of the retrotransposon roo were involved in all of the interchromosomal exchanges; some copies were involved much more frequently than others in the target region; (4) homozygosis for interspersed repeat sequences and other sequence variations significantly reduced ectopic recombination.
Changes in state of the Wx-m5 allele of maize are due to intragenic transposition of Ds.
Authors: Weil C F , Marillonnet S , Burr B , Wessler S R
Published: January 2021

The molecular basis for the unusual phenotype conditioned by the waxy(Wx)-m5 Ds allele has been elucidated. Unlike most Ds alleles, Wx-m5 is phenotypically wild-type in the absence of Ac. We find that the Wx-m5 gene contains a 2-kb Ds element at -470 relative to the start of Wx transcription, representing the most 5' insertion of any transposable element allele characterized to date in plants. Despite its wild type phenotype, Wx-m5 has reduced levels of Wx enzymatic activity indicating that Ds insertion influences Wx gene expression. In the presence of Ac, Wx-m5 kernels have sectors of null expression on a wild-type background and give rise to stable wx and unstable wx-m germinal derivatives. Seventeen of 20 derivatives examined are wx-m alleles and at least 15 of these appear to result from intragenic transposition of Ds from -470 to new sites within the Wx gene. Three wx-m alleles contain two Ds elements, one at -470 and a second in Wx coding sequences. Surprisingly, only 3 out of 20 derivatives are stable wx mutants and these have sustained gross rearrangements of Wx and flanking sequences. For most other maize transposable element alleles somatic sectors and germinal derivatives usually arise following element excision or deletions of element sequences. In contrast, element insertion following intragenic transposition is apparently responsible for most of the somatic sectors and germinal derivatives of Wx-m5.
Size polymorphisms due to changes in the number of O-glycosylated tandem repeats in the Dictyostelium discoideum glycoprotein PsA.
Authors: Gooley A A , Marshchalek R , Williams K L
Published: January 2021

The molecular weight polymorphism in the Dictyostelium discoideum cell surface glycoprotein PsA is due to incremental copies of an O-glycosylated tandem tetrapeptide repeat. Allelic variation at the pspA locus results in a PsA glycoprotein with three, four or five tandem copies of Pro-Thr-Val-Thr. The simplest explanation for the origin of this polymorphism is an unequal crossing over event in the ancestral gene containing four copies. Each Thr in the tandem repeat is substituted with carbohydrate, which is completely absent from PsA in strains carrying a glycosylation defective modB mutation. Glycosylated tandem repeats appear to be a common feature of cell surface glycoproteins which are characterized by short domains rich in Pro and Thr or Ser. It is probable that the glycosylated repeat domain acts as a "spacer" peptide that projects the globular domain above the glycocalyx.
A genetic mapping system in Caenorhabditis elegans based on polymorphic sequence-tagged sites.
Authors: Williams B D , Schrank B , Huynh C , Shownkeen R , Waterston R H
Published: January 2021

We devised an efficient genetic mapping system in the nematode Caenorhabditis elegans which is based upon the differences in number and location of the transposable element Tc1 between the Bristol and Bergerac strains. Using the nearly completed physical map of the C. elegans genome, we selected 40 widely distributed sites which contain a Tc1 element in the Bergerac strain, but not in the Bristol strain. For each site a polymerase chain reaction assay was designed that can distinguish between the Bergerac Tc1-containing site and the Bristol "empty" site. By combining appropriate assays in a single reaction, one can score multiple sites within single worms. This permits a mutation to be rapidly mapped, first to a linkage group and then to a chromosomal subregion, through analysis of only a small number of progeny from a single interstrain cross.
On the theory of partially inbreeding finite populations. III. Fixation probabilities under partial selfing when heterozygotes are intermediate in viability.
Authors: Pollak E , Sabran M
Published: January 2021

In a previous paper by the senior author, an approximation to the probability of survival was given for a mutant, which is originally present in a single heterozygote, in a population that reproduces partly by selfing and partly by random mating. The population was assumed to be very large, but the result obtained is general with regard to the level of dominance in viability. In this paper two errors which were made in that earlier work are corrected. A general approximate expression is then derived for the probability that an allele A is fixed in a partially self fertilizing population of size N, if its initial frequency is p, selection is weak and heterozygotes with the allele are exactly intermediate in viability compared with genotypes AA and AA. A rigorous proof is given for a special case that is a generalization of the classical binomial sampling model. In this case, but not in general, the approximate fixation probability is independent of the probability of reproduction by selfing. Some implications are discussed.
Characterization of mutant alleles of myospheroid, the gene encoding the beta subunit of the Drosophila PS integrins.
Authors: Bunch T A , Salatino R , Engelsgjerd M C , Mukai L , West R F , Brower D L
Published: January 2021

This paper presents the characterization of nine alleles of myospheroid, which encodes the beta PS subunit of the Drosophila PS integrins. On Southern blots, the mysXB87, mysXN101 and mysXR04 genes yield restriction digest patterns similar to that seen for wild-type chromosomes, however the mys1 and mysXG43 genes contain detectable deletions. mys1, mysXB87 and mysXG43 make little or no stable protein product, and genetically behave as strong lethal alleles. For the mysXN101 mutation, protein product is seen on immunoblots and a reduced amount of beta PS protein is seen at muscle attachment sites of embryos; this mutant protein retains some wild-type function, as revealed by complementation tests with weak alleles. Protein is also seen on immunoblots from mysXR04 embryos, and this allele behaves as an antimorph, being more deleterious in some crosses than the complete deficiency for the locus. mysts2 and mysnj42 are typically lethal in various combinations with other alleles at high temperatures only, but even at high physiological temperatures, neither appears to eliminate gene function completely. The complementation behaviors of mysts1 and mysts3 are quite unusual and suggest that these mutations involve regulatory phenomena. For mysts3, the data are most easily explained by postulating transvection effects at the locus. The results for mysts1 are less straightforward, but point to the possibility of a chromosome pairing-dependent negative interaction.
Estimation of levels of gene flow from DNA sequence data.
Authors: Hudson R R , Slatkin M , Maddison W P
Published: January 2021

We compare the utility of two methods for estimating the average levels of gene flow from DNA sequence data. One method is based on estimating FST from frequencies at polymorphic sites, treating each site as a separate locus. The other method is based on computing the minimum number of migration events consistent with the gene tree inferred from their sequences. We compared the performance of these two methods on data that were generated by a computer simulation program that assumed the infinite sites model of mutation and that assumed an island model of migration. We found that in general when there is no recombination, the cladistic method performed better than FST while the reverse was true for rates of recombination similar to those found in eukaryotic nuclear genes, although FST performed better for all recombination rates for very low levels of migration (Nm = 0.1).
Maximum likelihood mapping of quantitative trait loci using full-sib families.
Authors: Knott S A , Haley C S
Published: January 2021

A maximum likelihood method is presented for the detection of quantitative trait loci (QTL) using flanking markers in full-sib families. This method incorporates a random component for common family effects due to additional QTL or the environment. Simulated data have been used to investigate this method. With a fixed total number of full sibs power of detection decreased substantially with decreasing family size. Increasing the number of alleles at the marker loci (i.e., polymorphism information content) and decreasing the interval size about the QTL increased power. Flanking markers were more powerful than single markers. In testing for a linked QTL the test must be made against a model which allows for between family variation (i.e., including an unlinked QTL or a between family variance component) or the test statistic may be grossly inflated. Mean parameter estimates were close to the simulated values in all situations when fitting the full model (including a linked QTL and common family effect). If the common family component was omitted the QTL effect was overestimated in data in which additional genetic variance was simulated and when compared with an unlinked QTL model there was reduced power. The test statistic curves, reflecting the likelihood of the QTL at each position along the chromosome, have discontinuities at the markers caused by adjacent pairs of markers providing different amounts of information. This must be accounted for when using flanking markers to search for a QTL in an outbred population.
Intraclass and interclass correlations of allele sizes within and between loci in DNA typing data.
Authors: Chakraborty R , Srinivasan M R , de Andrade M
Published: January 2021

Nonparametric measures of correlations of DNA fragment lengths within and between variable number of tandem repeat (VNTR) loci are proposed to test the hypothesis of random association of allele sizes at VNTR loci. Transformations of these nonparametric correlation measures are suggested to detect deviations of their null expectations caused by population subdivision and errors of measurement of VNTR fragment lengths. Analytic and permutation-based computer simulation studies are performed to show that under the hypothesis of independence of allele sizes the transformed correlation measures are normally distributed, irrespective of the VNTR fragment size distribution in the population even when the number of individuals samples is as low as 100. Power calculations are performed to establish that the current population data on six VNTR loci in the US Hispanic sample are in accordance with the hypothesis of random association of allele sizes within and between loci. Implications of these results in the context of forensic use of DNA typing are also discussed.
The Cs sec mutants of Escherichia coli reflect the cold sensitivity of protein export itself.
Authors: Pogliano K J , Beckwith J
Published: January 2021

We have found that temperature can have a striking effect upon protein export in Escherichia coli, suggesting that there is a cold-sensitive step in the protein export pathway. Cs mutations comprise the largest class of mutations affecting the membrane-localized Sec proteins SecD, SecE, SecF and SecY. Although some of these mutations could encode cold-labile proteins, this is unlikely to account for the Cs phenotype of most export mutants, as mutations which simply produce lower amounts of SecE protein have the same phenotype. Certain signal sequence mutations affecting maltose binding protein are also cold sensitive for export. These effects appear to arise by a specific interaction of cold with certain export defects. We believe that the Cs sec mutations are representative of a large class of conditional lethal mutations, whose conditional phenotype reflects an underlying thermal sensitivity of the process in which they are involved.
Genetic evidence that the meiotic recombination hotspot at the HIS4 locus of Saccharomyces cerevisiae does not represent a site for a symmetrically processed double-strand break.
Authors: Porter S E , White M A , Petes T D
Published: January 2021

In the yeast Saccharomyces cerevisiae, the binding of the Rap1 protein to a site located between the 5' end of the HIS4 gene and the 3' end of BIK1 stimulates meiotic recombination at both flanking loci. By using strains that contain mutations located in HIS4 and BIK1, we found that most recombination events stimulated by the binding of Rap1 involve HIS4 or BIK1, rather than bidirectional events including both loci. The patterns of aberrant segregation indicate that most of the Rap1-stimulated recombination events do not represent the symmetric processing of a double-strand DNA break located at the Rap1-binding site.
Inheritance of the morphological differences between maize and teosinte: comparison of results for two F2 populations.
Authors: Doebley J , Stec A
Published: January 2021

Molecular marker loci (MMLs) were employed to map quantitative trait loci (QTLs) in an F2 population derived from a cross of maize (Zea mays ssp. mays) and its probable progenitor, teosinte (Z. mays ssp. parviglumis). A total of 50 significant associations (putative QTLs) between the MMLs and nine key traits that distinguish maize and teosinte were identified. Results from this analysis are compared with our previous analysis of an F2 population derived from a cross of a different variety of maize and another subspecies of teosinte (Z. mays ssp. mexicana). For traits that measure the architectural differences between maize and teosinte, the two F2 populations possessed similar suites of QTLs. For traits that measure components of yield, substantially different suites of QTLs were identified in the two populations. QTLs that control about 20% or more of the phenotypic variance for a trait in one population were detected in the other population 81% of the time, while QTLs that control less than 10% of the variance in one population were detected in the other population only 28% of the time. In our previously published analysis of the maize x ssp. mexicana population, we identified five regions of the genome that control most of the key morphological differences between maize and teosinte. These same five regions also control most of the differences in the maize x ssp. parviglumis population. Results from both populations support the hypothesis that a relatively small number of loci with large effects were involved in the early evolution of the key traits that distinguish maize and teosinte. It is suggested that loci with large effects on morphology may not be a specific feature of crop evolution, but rather a common phenomenon in plant evolution whenever a species invades a new niche with reduced competition.
Pleiotropic models of polygenic variation, stabilizing selection, and epistasis.
Authors: Gavrilets S , de Jong G
Published: January 2021

We show that in polymorphic populations many polygenic traits pleiotropically related to fitness are expected to be under apparent "stabilizing selection" independently of the real selection acting on the population. This occurs, for example, if the genetic system is at a stable polymorphic equilibrium determined by selection and the nonadditive contributions of the loci to the trait value either are absent, or are random and independent of those to fitness. Stabilizing selection is also observed if the polygenic system is at an equilibrium determined by a balance between selection and mutation (or migration) when both additive and nonadditive contributions of the loci to the trait value are random and independent of those to fitness. We also compare different viability models that can maintain genetic variability at many loci with respect to their ability to account for the strong stabilizing selection on an additive trait. Let Vm be the genetic variance supplied by mutation (or migration) each generation, Vg be the genotypic variance maintained in the population, and n be the number of the loci influencing fitness. We demonstrate that in mutation (migration)-selection balance models the strength of apparent stabilizing selection is order Vm/Vg. In the overdominant model and in the symmetric viability model the strength of apparent stabilizing selection is approximately 1/(2n) that of total selection on the whole phenotype. We show that a selection system that involves pairwise additive by additive epistasis in maintaining variability can lead to a lower genetic load and genetic variance in fitness (approximately 1/(2n) times) than an equivalent selection system that involves overdominance. We show that, in the epistatic model, the apparent stabilizing selection on an additive trait can be as strong as the total selection on the whole phenotype.
Isolation of the Chlamydomonas regulatory gene NIT2 by transposon tagging.
Authors: Schnell R A , Lefebvre P A
Published: January 2021

Genetic evidence suggests that the NIT2 gene of Chlamydomonas reinhardtii encodes a positive regulator of the nitrate-assimilation pathway. To learn more about the function of the NIT2 gene product, we isolated the gene using a transposon-tagging strategy. A nit2 mutation caused by the insertion of a transposon was identified by testing spontaneous nit2 mutants for the presence of new copies of Gulliver or TOC1, transposable elements that have been identified in Chlamydomonas. In 2 of the 14 different mutants that were analyzed, a Gulliver element was found to be genetically and phenotypically associated with the nit2 mutation. Using the Gulliver element as a probe, one of the transposon-induced nit2 alleles was isolated, and a sequence adjoining the transposon was used to isolate the corresponding wild-type locus. The NIT2 gene was delimited by mapping DNA rearrangements associated with nit2 mutations and mutant rescue by genetic transformation. The NIT2 gene encodes a 6-kb transcript that was not detected in cells grown in the presence of ammonium. Likewise, NIT2-dependent genes are repressed in ammonium-grown cells. These results suggest that repression of the NIT2 gene may mediate metabolite repression of the nitrate assimilation pathway in Chlamydomonas.
Genetic and cytogenetic analysis of the 43A-E region containing the segment polarity gene costa and the cellular polarity genes prickle and spiny-legs in Drosophila melanogaster.
Authors: Heitzler P , Coulson D , Saenz-Robles M T , Ashburner M , Roote J , Simpson P , Gubb D
Published: January 2021

A cytogenetic analysis of the 43A-E region of chromosome 2 in Drosophila melanogaster is presented. Within this interval 27 complementation groups have been identified by extensive F2 screens and ordered by deletion mapping. The region includes the cellular polarity genes prickle and spiny-legs, the segmentation genes costa and torso, the morphogenetic locus sine oculis and is bounded on its distal side by the eye-color gene cinnabar. In addition 19 novel lethal complementation groups and two semi-lethal complementation groups with morphogenetic escaper phenotypes are described.
The HIR4-1 mutation defines a new class of histone regulatory genes in Saccharomyces cerevisiae.
Authors: Spector M S , Osley M A
Published: January 2021

Both activation and repression have been implicated in the cell cycle-regulated transcription of the histone HTA1-HTB1 locus in Saccharomyces cerevisiae. Transcriptional repressors have been identified through the isolation of recessive mutations in the HIR1, HIR2 and HIR3 genes. These three regulatory genes encode proteins that act at a negative site in the HTA1-HTB1 promoter, and their inactivation results in cell cycle-independent transcription. We report here on the characterization of a fourth HIR mutant. The HIR4-1 mutation is dominant, and the phenotypes that it confers suggest that the mutant gene encodes an altered transcriptional activator. The function of this activator is very specific: it uniquely regulates transcription of the HTA1-HTB1 locus, and it may antagonize repressors that act through the HTA1-HTB1 negative site.
Loss of function of Saccharomyces cerevisiae kinesin-related CIN8 and KIP1 is suppressed by KAR3 motor domain mutations.
Authors: Hoyt M A , He L , Totis L , Saunders W S
Published: January 2021

The kinesin-related products of the CIN8 and KIP1 genes of Saccharomyces cerevisiae redundantly perform an essential function in mitosis. The action of either gene-product is required for an outwardly directed force that acts upon the spindle poles. We have selected mutations that suppress the temperature-sensitivity of a cin8-temperature-sensitive kip1-delta strain. The extragenic suppressors analyzed were all found to be alleles of the KAR3 gene. KAR3 encodes a distinct kinesin-related protein whose action antagonizes Cin8p/Kip1p function. All seven alleles analyzed were altered within the region of KAR3 that encodes the putative force-generating (or "motor") domain. These mutations also suppressed the inviability associated with the cin8-delta kip1-delta genotype, a property not shared by a deletion of KAR3. Other properties of the suppressing alleles revealed that they were not null for function. Six of the seven were unaffected for the essential karyogamy and meiosis properties of KAR3 and the seventh was dominant for the suppressing trait. Our findings suggest that despite an antagonistic relationship between Cin8p/Kip1p and Kar3p, aspects of their mitotic roles may be similar.
Sequence requirements for myosin gene expression and regulation in Caenorhabditis elegans.
Authors: Okkema P G , Harrison S W , Plunger V , Aryana A , Fire A
Published: January 2021

Four Caenorhabditis elegans genes encode muscle-type specific myosin heavy chain isoforms: myo-1 and myo-2 are expressed in the pharyngeal muscles; unc-54 and myo-3 are expressed in body wall muscles. We have used transformation-rescue and lacZ fusion assays to determine sequence requirements for regulated myosin gene expression during development. Multiple tissue-specific activation elements are present for all four genes. For each of the four genes, sequences upstream of the coding region are tissue-specific promoters, as shown by their ability to drive expression of a reporter gene (lacZ) in the appropriate muscle type. Each gene contains at least one additional tissue-specific regulatory element, as defined by the ability to enhance expression of a heterologous promoter in the appropriate muscle type. In rescue experiments with unc-54, two further requirements apparently independent of tissue specificity were found: sequences within the 3' non-coding region are essential for activity while an intron near the 5' end augments expression levels. The general intron stimulation is apparently independent of intron sequence, indicating a mechanistic effect of splicing. To further characterize the myosin gene promoters and to examine the types of enhancer sequences in the genome, we have initiated a screen of C. elegans genomic DNA for fragments capable of enhancing the myo-2 promoter. The properties of enhancers recovered from this screen suggest that the promoter is limited to muscle cells in its ability to respond to enhancers.
Population genetics of tandem repeats in centromeric heterochromatin: unequal crossing over and chromosomal divergence at the Responder locus of Drosophila melanogaster.
Authors: Cabot E L , Doshi P , Wu M L , Wu C I
Published: January 2021

The Responder (Rsp) locus in Drosophila melanogaster is the target locus of segregation distortion and is known to be comprised of a tandem array of 120-bp repetitive sequences. In this study, we first determined the large scale molecular structure of the Rsp locus, which extends over a region of 600 kb on the standard sensitive (cn bw) chromosome. Within the region, small Rsp repeat arrays are interspersed with non-Rsp sequences and account for 10-20% of the total sequences. We isolated and sequenced 32 Rsp clones from three different chromosomes. The main results are: (1) Rsp repeats isolated from the same chromosome are not more similar than those from different chromosomes. This implies either that there are more homologous exchanges at the Rsp locus than expected or, alternatively, that the second chromosomes of D. melanogaster have diverged from one another more recently at the centromeric heterochromatin than at the nearby euchromatin. (2) The repeats usually have a dimeric structure with an average difference of 16% between the left and right halves. The differences allow us to easily identify the products of unequal exchanges. Despite the large differences between the two halves, exchanges have occurred frequently and the majority of them fall within a 29-bp interval of identity between the two halves. Our data thus support the suggestion that recombination depends on short stretches of complete identity rather than long stretches of general homology. (3) Frequent unequal crossover events obscure the phylogenetic relationships between repeats; therefore, different parts of any single repeat could often have different phylogenetic histories. The high rate of unequal crossing over may also help explain the evolutionary dynamics of the Rsp locus.
Isolation and characterization of chromosome-gain and increase-in-ploidy mutants in yeast.
Authors: Chan C S , Botstein D
Published: January 2021

We have developed a colony papillation assay for monitoring the copy number of genetically marked chromosomes II and III in Saccharomyces cerevisiae. The unique feature of this assay is that it allows detection of a gain of the marked chromosomes even if there is a gain of the entire set of chromosomes (increase-in-ploidy). This assay was used to screen for chromosome-gain or increase-in-ploidy mutants. Five complementation groups have been defined for recessive mutations that confer an increase-in-ploidy (ipl) phenotype, which, in each case, cosegregates with a temperature-sensitive growth phenotype. Four new alleles of CDC31, which is required for spindle pole body duplication, were also recovered from this screen. Temperature-shift experiments with ipl1 cells show that they suffer severe nondisjunction at 37 degrees. Similar experiments with ipl2 cells show that they gain entire sets of chromosomes and become arrested as unbudded cells at 37 degrees. Molecular cloning and genetic mapping show that IPL1 is a newly identified gene, whereas IPL2 is allelic to BEM2, which is required for normal bud growth.
Genetic and phenotypic studies of hypomorphic lin-12 mutants in Caenorhabditis elegans.
Authors: Sundaram M , Greenwald I
Published: January 2021

The lin-12 gene of Caenorhabditis elegans is thought to encode a receptor for intercellular signals that specify certain cell fates during development. We describe several alleles of lin-12 that reduce but do not eliminate lin-12 activity (hypomorphic alleles). These alleles cause a novel egg-laying defective (Egl) phenotype in hermaphrodites as well as incompletely penetrant cell fate transformations seen with high penetrance in lin-12 null mutants. Characterization of the Egl phenotype revealed additional roles of lin-12 in the development of the egg-laying system that were not apparent from studying lin-12 null mutants: lin-12 activity is required for proper early vulval morphogenesis as well as for some unknown later aspect of egg-laying system development. Reversion of the Egl phenotype caused by one lin-12 hypomorphic allele was used to identify potential interacting genes as described in the accompanying paper.
Spo12 is a limiting factor that interacts with the cell cycle protein kinases Dbf2 and Dbf20, which are involved in mitotic chromatid disjunction.
Authors: Toyn J H , Johnston L H
Published: January 2021

The DBF2 and DBF20 genes of the budding yeast Saccharomyces cerevisiae encode a pair of structurally similar protein kinases. Although yeast with either gene deleted is viable, deletion of both genes is lethal. Thus, the Dbf2 and Dbf20 proteins are functional alternatives for an essential activity. In contrast to deletions, four different mutant alleles of DBF2 are lethal. Thus, the presence of a nonfunctional Dbf2 protein, rather than the lack of function per se, is inhibitory. Here we present genetic evidence that nonfunctional mutant Dbf2 protein blocks the function of Dbf20 protein by sequestering a common interacting protein encoded by SPO12. Even a single extra copy of SPO12 is sufficient to suppress the dbf2 defect. Since SPO12 appears to encode a limiting factor, it may be a rate limiting cofactor that is involved in the regulation of the Dbf2 and Dbf20 protein kinases. A corollary to the finding that one extra copy of SPO12 can suppress dbf2, is that the acquisition of an extra chromosome VIII, which carries the SPO12 locus, will also suppress dbf2. Indeed, physical analysis of chromosome copy number in dbf2 revertants able to grow at 37 degrees showed that the frequency of chromosome VIII acquisition increased when cells were incubated at the restrictive temperature, and reached a frequency of more than 100-fold the amount in wild-type yeast. This suggested that the dbf2 mutation was not only suppressed by an extra copy of chromosome VIII but also that the dbf2 mutation actually caused aberrant chromosomal segregation. Conventional assays for chromosome loss confirmed this proposal.
Mutations in the yeast PDR3, PDR4, PDR7 and PDR9 pleiotropic (multiple) drug resistance loci affect the transcript level of an ATP binding cassette transporter encoding gene, PDR5.
Authors: Dexter D , Moye-Rowley W S , Wu A L , Golin J
Published: January 2021

The yeast pleiotropic (multiple drug) resistance gene PDR5 encodes a product with homology to a large number of membrane transport proteins including the mammalian multiple drug resistance family. In this study, we identified four genes on chromosome II that affect the steady-state level of PDR5 transcript in addition to a previously identified positive regulator, PDR1. The genes in question are PDR3, PDR4, PDR7 and PDR9. We also analyzed the interaction between PDR5 and YAP1. YAP1 encodes a positive regulator with a leucine zipper motif that causes pleiotropic drug resistance when overproduced. YAP1-mediated pleiotropic drug resistance is not dependent on the presence of PDR5 and must act through other genes.
The genetic basis of sex ratio in Silene alba (= S. latifolia).
Authors: Taylor D R
Published: January 2021

A survey of maternal families collected from natural populations showed that the sex ratio in Silene alba was slightly female biased. Sex ratio varied among populations and among families within a female biased population. Crosses among plants from the most female biased population and the most male biased population showed that the sex ratio polymorphism was inherited through or expressed in the male parent. Males from one family in particular exhibited a severe female bias, characterized by less than 20% male progeny. The inheritance of sex ratio was investigated using a reciprocal crossing design. Sex ratios from reciprocal crosses were significantly different, indicating either sex-linkage or cytoplasmic inheritance of sex ratio. The sex ratios produced by males generally resembled the sex ratios produced by their male parents, indicating that the sex ratio modifier was Y linked. The maternal parent also significantly influenced sex ratio through an interaction with the genotype of the paternal parent. Sex ratio, therefore, is apparently controlled by several loci. Although sex ratio bias in this species may be due to deleterious alleles on the Y chromosome, it is more likely to involve an interaction between loci that cause the female bias and a Y-linked locus that enhances the proportion of males in the progeny.
Decline in heterozygosity under full-sib and double first-cousin inbreeding in Drosophila melanogaster.
Authors: Rumball W , Franklin I R , Frankham R , Sheldon B L
Published: January 2021

The effects of inbreeding on heterozygosities and reproductive fitness were determined by carrying out full-sib and double first-cousin inbreeding in Drosophila melanogaster populations for up to 18 generations. Parents were scored each generation for five or six polymorphic enzyme loci, and progeny numbers per pair were recorded. Inbreeding depression, in the form of significant reductions in progeny numbers and significant extinction of lines, was observed. Heterozygosity decreased at a significantly slower rate than predicted, being about 80% of expected. The full-sib and double first-cousin treatments showed similar disagreement with expectations over comparable ranges of inbreeding. Natural selection was shown to favor heterozygotes in the inbred lines. Associative overdominance was the most probable explanation for the slower than expected decline in heterozygosity.
Genetic characterization of pathogenic Saccharomyces cerevisiae isolates.
Authors: McCusker J H , Clemons K V , Stevens D A , Davis R W
Published: January 2021

Saccharomyces cerevisiae isolates from human patients have been genetically analyzed. Some of the characteristics of these isolates are very different from laboratory and industrial strains of S. cerevisiae and, for this reason, stringent genetic tests have been used to confirm their identity as S. cerevisiae. Most of these clinical isolates are able to grow at 42 degrees, a temperature that completely inhibits the growth of most other S. cerevisiae strains. This property can be considered a virulence trait and may help explain the presence of these isolates in human hosts. The ability to grow at 42 degrees is shown to be polygenic with primarily additive effects between loci. S. cerevisiae will be a useful model for the evolution and genetic analysis of fungal virulence and the study of polygenic traits.
Muller's ratchet under epistatic selection.
Authors: Kondrashov A S
Published: January 2021

In a finite asexual population mean fitness may decrease by a process known as Muller's ratchet, which proceeds if all individuals with the minimum number of deleterious alleles are randomly lost. If these alleles have independent effects on fitness, previous analysis suggested that the rate of this decrease either remains constant or, if accumulation of mutations leads to the decline of the population size, grows. Here I show that this conclusion is quite sensitive to the assumption of independence. If deleterious alleles have synergistic fitness effects, then, as the ratchet advances, the frequency of the best available genotype will necessarily increase, making its loss less and less probable. As a result, sufficiently strong synergistic epistasis can effectively halt the action of Muller's ratchet. Instead of being driven extinct, a finite asexual population could then survive practically indefinitely, although with lower mean fitness than without random drift.
Synergistic release from glucose repression by mig1 and ssn mutations in Saccharomyces cerevisiae.
Authors: Vallier L G , Carlson M
Published: January 2021

In the yeast Saccharomyces cerevisiae, glucose repression of SUC2 transcription requires the SSN6-TUP1 repressor complex. It has been proposed that the DNA-binding protein MIG1 secures SSN6-TUP1 to the SUC2 promoter. Here we show that a mig1 deletion does not cause nearly as dramatic a loss of repression as ssn6: glucose-grown mig1 mutants display 20-fold lower SUC2 expression than ssn6 mutants. Thus, repression by SSN6-TUP1 is not mediated solely by MIG1, but also involves MIG1-independent mechanisms. We report that mig1 partially restores SUC2 expression in mutants lacking the SNF1 protein kinase and show that mig1 is allelic to ssn1, a mutation selected as a suppressor of snf1. Other SSN genes identified in this selection were therefore candidates for a role in repression of SUC2. We show that mig1 acts synergistically with ssn2 through ssn5, ssn7, and ssn8 to relieve glucose repression of SUC2 and to suppress the requirement for SNF1. These findings indicate that the SSN proteins contribute to repression of SUC2, and the pleiotropic phenotypes of the ssn mutants suggest global roles in repression. Finally, the regulated SUC2 expression observed in snf1 mig1 mutants indicates that signals regarding glucose availability can be transmitted independently of the SNF1 protein kinase.
Superoxide dismutase (sod-1) null mutants of Neurospora crassa: oxidative stress sensitivity, spontaneous mutation rate and response to mutagens.
Authors: Chary P , Dillon D , Schroeder A L , Natvig D O
Published: January 2021

Enzymatic superoxide-dismutase activity is believed to be important in defense against the toxic effects of superoxide. Although superoxide dismutases are among the best studied proteins, numerous questions remain concerning the specific biological roles of the various superoxide-dismutase types. In part, this is because the proposed damaging effects of superoxide are manifold, ranging from inactivation of certain metabolic enzymes to DNA damage. Studies with superoxide-deficient mutants have proven valuable, but surprisingly few such studies have been reported. We have constructed and characterized Neurospora crassa mutants that are null for sod-1, the gene that encodes copper-zinc superoxide dismutase. Mutant strains are sensitive to paraquat and elevated oxygen concentrations, and they exhibit an increased spontaneous mutation rate. They appear to have near wild-type sensitive to near- and far-UV, heat shock and gamma-irradiation. Unlike the equivalent Saccharomyces cerevisiae mutant and the sodA sodB double mutant of Escherichia coli, they do not exhibit aerobic auxotrophy. These results are discussed in the context of an attempt to identify consensus phenotypes among superoxide dismutase-deficient mutants. N. crassa sod-1 null mutant strains were also employed in genetic and subcellular fractionation studies. Results support the hypothesis that a single gene (sod-1), located between Fsr-12 and leu-3 on linkage group I, is responsible for most or all CuZn superoxide dismutase activity in this organism.
Effective population sizes with multiple paternity.
Authors: Sugg D W , Chesser R K
Published: January 2021

While the concept of effective population size is of obvious applicability to many questions in population genetics and conservation biology, its utility has suffered due to a lack of agreement among its various formulations. Often, mathematical formulations for effective sizes apply restrictive assumptions that limit their applicability. Herein, expressions for effective sizes of populations that account for mating tactics, biases in sex ratios, and differential dispersal rates (among other parameters) are developed. Of primary interest is the influence of multiple paternity on the maintenance of genetic variation in a population. In addition to the standard inbreeding and variance effective sizes, intragroup (coancestral) and intergroup effective sizes also are developed. Expressions for effective sizes are developed for the beginning of nonrandom gene exchanges (initial effective sizes), the transition of gene correlations (instantaneous effective sizes), and the steady-state (asymptotic effective size). Results indicate that systems of mating that incorporate more than one male mate per female increase all effective sizes above those expected from polygyny and monogamy. Instantaneous and asymptotic sizes can be expressed relative to the fixation indices. The parameters presented herein can be utilized in models of effective sizes for the study of evolutionary biology and conservation genetics.
The population dynamics of maternal-effect selfish genes.
Authors: Wade M J , Beeman R W
Published: January 2021

We use population genetic methods to describe the expected population dynamics of the selfish-gene chromosomal factor, Medea (maternal-effect dominant embryonic arrest), recently discovered in flour beetles, genus Tribolium. In the absence of deleterious effects on gross fecundity, Medea factors spread to fixation for all degrees of maternal-effect lethality greater than zero and the rate of spread is proportional to the strength of the maternal-effect. The rate of spread when rare is very slow, on the order of the frequency squared p2, but this can be accelerated to order p when there is density regulation at the level of families as is known to occur for some genetic strains of flour beetles. When there are general deleterious effects of Medea on fecundity, affecting all offspring genotypes in addition to the genotype-specific maternal effect, then a stable interior polymorphism is possible. The location of the interior equilibrium and the probability of loss or fixation are sensitive to the degree of dominance of these fecundity effects.
Mutations in the unc-52 gene responsible for body wall muscle defects in adult Caenorhabditis elegans are located in alternatively spliced exons.
Authors: Rogalski T M , Gilchrist E J , Mullen G P , Moerman D G
Published: January 2021

The unc-52 gene in Caenorhabditis elegans produces several large proteins that function in the basement membrane underlying muscle cells. Mutations in this gene result in defects in myofilament assembly and in the attachment of the myofilament lattice to the muscle cell membrane. The st549 and ut111 alleles of unc-52 produce a lethal (Pat) terminal phenotype whereas the e444, e669, e998, e1012 and e1421 mutations result in viable, paralyzed animals. We have identified the sequence alterations responsible for these mutant phenotypes. The st549 allele has a premature stop codon in exon 7 that should result in the complete elimination of unc-52 gene function, and the ut111 allele has a Tc1 transposon inserted into the second exon of the gene. The five remaining mutations are clustered in a small interval containing three adjacent, alternatively spliced exons (16, 17 and 18). These mutations affect some, but not all of the unc-52-encoded proteins. Thirteen intragenic revertants of the e669, e998, e1012 and e1421 alleles have also been sequenced. The majority of these carry the original mutation plus a G to A transition in the conserved splice acceptor site of the affected exon. This result suggests that reversion of the mutant phenotype in these strains may be the result of exon-skipping.
Phenotypic and molecular characterization of SerD, a dominant allele of the Drosophila gene Serrate.
Authors: Thomas U , Jönsson F , Speicher S A , Knust E
Published: January 2021

The Drosophila gene Serrate (Ser) encodes a transmembrane protein with 14 epidermal growth factor--like repeats in its extracellular domain, which is required for the control of cell proliferation and pattern formation during wing development. Flies hetero- or homozygous for the dominant mutation SerD exhibit scalloping of the wing margin due to cell death during pupal stages. SerD is associated with an insertion of the transposable element Tirant in the 3' untranslated region of the gene, resulting in the truncation of the Ser RNA, thereby eliminating putative RNA degradation signals located further downstream. This leads to increased stability of Ser RNA and higher levels of Serrate protein. In wing discs of wild-type third instar larvae, the Serrate protein exhibits a complex expression pattern, including a strong stripe dorsal and a weaker stripe ventral to the prospective wing margin. Wing discs of SerD third instar larvae exhibit additional Serrate protein expression in the edge zone of the future wing margin, where it is normally not detectable. In these cells expression of wing margin specific genes, such as cut and wingless, is repressed. By using the yeast Gal4 system to induce locally restricted ectopic expression of Serrate in the edge zone of the prospective wing margin, we can reproduce all aspects of the SerD wing phenotype, that is, repression of wing margin-specific genes, scalloping of the wing margin and enhancement of the Notch haplo-insufficiency wing phenotype. This suggests that expression of the Serrate protein in the cells of the edge zone of the wing margin, where it is normally absent, interferes with the proper development of the margin.