bluuebunny/crossref_metadata_2025 huggingface dataset:
A genetic and molecular analysis of the 46C chromosomal region surrounding the FMRFamide neuropeptide gene in Drosophila melanogaster.
Authors: O'Brien M A , Roberts M S , Taghert P H
Published: January 2021

We have analyzed the FMRFamide neuropeptide gene region of Drosophila melanogaster. This gene maps to the 46C region of chromosome 2R; this interval previously was not well characterized. For this genetic and molecular analysis, we have used X-ray mutagenesis, EMS mutagenesis, and the recently reported local P element transposition method. We identified four overlapping deletions, two of which have proximal breakpoints that define a 50-60-kb region surrounding the FMRFamide gene in 46C. To this small region, we mapped three lethal complementation groups; 10 additional lethal complementation groups were mapped to more distal regions of 46CD. One of these groups corresponds to even-skipped, the other 12 are previously unidentified. Using various lines of evidence we excluded the possibility that FMRFamide corresponds to any of the three lethal complementation groups mapping to its immediate 50-60-kb vicinity. The positions of two of the three lethal complementation groups were identified with P elements using a local transposition scheme. The third lethal complementation group was excluded as being FMRFamide mutants by sequence analysis and by immunocytochemistry with proFMRFamide precursor-specific antibodies. This analysis has (1) provided a genetic map of the 46CD chromosomal region and a detailed molecular map of a portion of the 46C region and (2) provided additional evidence of the utility of local transposition for targeting nearby genes.
Retrotransposon-induced ectopic expression of cut causes the Om(1A) mutant in Drosophila ananassae.
Authors: Awasaki T , Juni N , Hamabata T , Yoshida K , Matsuda M , Tobari Y N , Hori S H
Published: January 2021

Optic morphology (Om) mutations in Drosophila ananassae map to at least 22 loci scattered throughout the genome. They are semidominant, neomorphic, nonpleiotropic, and are associated with the insertion of a retrotransposon, tom. The Om(1A) gene, which is cytogenetically linked to the cut locus, was cloned using a DNA fragment of the cut locus of Drosophila melanogaster as a probe. Three of the eight alleles of Om(1A) examined have insertion of the tom element within a putative cut region. The gamma-ray-induced revertants of Om(1A) are accompanied with cut lethal mutations and rearrangements within the cut coding region. In the eye imaginal discs of the Om(1A) mutants, differentiation of photoreceptor clusters is suppressed, abnormal cell death occurs in the center and the cut protein is expressed ectopically. D. melanogaster flies transformed with a chimeric cut gene under the control of a heat-inducible promoter show excessive cell death in the region anterior to the morphogenetic furrow, suppressed differentiation to photoreceptor clusters and defect in the imaginal eye morphology when subjected to temperature elevation. These findings suggest that the tom element inserted within the Om(1A) region induces ectopic cut expression in the eye imaginal discs, thus resulting in the Om(1A) mutant phenotype.
Sequences with the potential to form stem-and-loop structures are associated with coding-region duplications in animal mitochondrial DNA.
Authors: Stanton D J , Daehler L L , Moritz C C , Brown W M
Published: January 2021

Tandem duplications of gene-encoding regions occur in the mitochondrial DNA (mt DNA) of some individuals belonging to several species of whiptail lizards (genus Cnemidophorus). All or part of the duplicated regions of the mtDNAs from five different species were sequenced. In all, the duplication endpoints were within or immediately adjacent to sequences in tRNA, rRNA or protein genes that are capable of forming energetically stable stem-and-loop structures. In two of these mtDNAs, the duplication endpoints were also associated with a direct sequence repeat of 13 bp. The consistent association of stem-and-loop structures with duplication endpoints suggests that these structures may play a role in the duplication process. These data, combined with the absence of direct or palindromic repeats at three of the pairs of duplication endpoints, also suggest the existence of a mechanism for generating de novo duplications that is qualitatively different from those previously modeled.
The relationship of homologous synapsis and crossing over in a maize inversion.
Authors: Maguire M P , Riess R W
Published: January 2021

Frequency of homologous synapsis at pachytene for a relatively short heterozygous inversion was compared to the frequency of crossover occurrence within the inversion and to the frequency of the presence of a recombination nodule within the homologously synapsed inverted region. Crossover frequencies were estimated from bridge-fragment frequencies at anaphase I and anaphase II. Recombination nodules (RNs) were observed in electron micrographs. Results show very similar frequencies of homologous synapsis and the occurrence of reciprocal recombination within the inverted region, consistent with the interpretation that establishment of homologous synapsis in this case is related to at least commitment to the form of resolution of crossover intermediates which gives rise to reciprocal recombination, not conversion only, events. An RN was generally found at pachytene in homologously synapsed inverted regions.
Intragenic suppression of integration-defective IS10 transposase mutants.
Authors: Junop M S , Hockman D , Haniford D B
Published: January 2021

IS10 transposase mediates excision and integration reactions in Tn10/IS10 transposition. Mutations in IS10 transposase that specifically block integration have previously been identified; however, the mechanism by which these mutations block integration has not been established. One approach to defining the basis of this block is to identify ways in which the original defect can be corrected. The approach we have taken toward this end has been to isolate and characterize intragenic second site suppressors to two different integration-defective mutants. Of the second site suppressors identified, one, CY134, is of particular interest for two reasons. First, it suppresses at least seven different mutations that confer an integration-defective phenotype. Interestingly, these mutations map in two separate segments of transposase, designated patch I and patch II. Second, CY134 on its own has previously been shown to relax the target DNA sequence requirements for Tn10 integration. We provide evidence that suppression by CY134 is not simply a consequence of this mutation conferring a general "transposition up" phenotype, but rather is due to correcting the original defect. Possible mechanisms of suppression for both CY134 and other second site suppressors are considered.
Poisson-like fluctuation patterns of revertants of leucine auxotrophy (leu-500) in Salmonella typhimurium caused by delay in mutant cell division.
Authors: Dijkmans R , Kreps S , Mergeay M
Published: January 2021

Leu+ mutants from Salmonella typhimurium leu-500 strain MA412 arise at high frequencies and mutant colonies appear over a broad range of time on selective plates. This observation suggested that these Leu+ mutants might be induced or "directed."= If such a mechanism was responsible, mutants should originate on selective plates rather than in the preceding culture in nonselective conditions and should give rise to Poisson-like fluctuation curves upon plating of sister cultures on selective medium. Poisson-like distribution profiles were indeed observed for Leu+ mutants of S. typhimurium MA412. However, an explanation for the observed Poisson-like fluctuation patterns without a need for selection-induced mutations was found. Microscopical analysis and cell mass/viable count measurements showed that the size of Leu+ mutant cells was often much larger than those of nonmutants. This size difference was a stable characteristic of a large proportion of Leu+ mutants, was observed both in stationary and growing culture and did not measurably affect the division rates of the cells in nutrient broth. As the transition from normal-sized nonmutant to oversized mutant cells during the nonselective culture phase of the fluctuation experiment may have been accompanied by a period with no or few completed cell division cycles, the number of mutant offspring may have been smaller than that of sibling nonmutants. Such underrepresentation of mutants in the final culture is expected to give rise to Poisson-like fluctuation patterns without invoking "directed" mutations.
Somatic inactivation and reactivation of Ac associated with changes in cytosine methylation and transposase expression.
Authors: Brutnell T P , Dellaporta S L
Published: January 2021

Several metastable Ac alleles at the maize p locus were identified that produced novel pericarp variegation patterns. From the transmission analysis of pericarp sectors, we show that Ac inactivation is a somatic process. Ac excision from P and transactivation of an unlinked Ds was delayed or absent in plants with metastable Ac alleles. These decreases in Ac activity were correlated to increases in cytosine methylation at specific sites near the start of Ac transcription (open reading frame a; ORFa) and at sites in some flanking P sequence. Reactivation of inactive alleles was accompanied by decreased methylation of Ac and P sequences. Using a competitive polymerase chain reaction assay, steady state levels of ORFa transcript were quantitatively compared among the various metastable alleles. We propose that changes in the methylation profile of Ac correspond to changes in Ac activity through the differential accumulation of Ac transcript.
Distribution of exchanges upon homologous recombination of exogenous DNA in Xenopus laevis oocytes.
Authors: Carroll D , Lehman C W , Jeong-Yu S , Dohrmann P , Dawson R J , Trautman J K
Published: January 2021

Homologous recombination between DNA molecules injected into Xenopus oocyte nuclei was investigated by examining the recovery of information from differentially marked parental sequences. The injected recombination substrate was a linear DNA with terminal direct repeats of 1246 bp; one repeat differed from the other by eight single base-pair substitutions, distributed throughout the region of homology, each of which created or destroyed a restriction enzyme site. Recombination products were recovered and analyzed for their content of the diagnostic sites, either directly by Southern blot-hybridization or after cloning in bacteria. The majority (76%) of the cloned products appeared to be the result of simple exchanges-i.e., there was one sharp transition from sequences derived from one parent to sequences derived from the other. These simple exchanges were concentrated near the ends of the homologous interval and, thus, near the sites of the original molecular ends. Placing marked sites on only one side of the homologous overlap showed that marker recovery was governed largely by the positions of the molecular ends and not by the markers themselves. When a terminal nonhomology was present at one end of the substrate, the yield of recombinants was sharply decreased, but the pattern of exchanges was not affected, suggesting that products from end-blocked substrates arise by the same recombination pathway. Because of considerable evidence supporting a nonconservative, resection-annealing mechanism for recombination in oocytes, we interpret the distribution of exchanges as resulting from long-patch repair of extensive heteroduplex intermediates.
The murine dilute suppressor gene encodes a cell autonomous suppressor.
Authors: Moore K J , Swing D A , Copeland N G , Jenkins N A
Published: January 2021

The murine dilute suppressor gene (dsu) suppresses the coat-color phenotype of three pigment mutations, dilute (d), ashen (ash) and leaden (ln), that each produce adendritic melanocytes. Suppression is due to the ability of dsu to partially restore (ash and ln), or almost completely restore (d), normal melanocyte morphology. While the ash and ln gene products have yet to be identified, the d gene encodes a novel myosin heavy chain (myosin 12), which is speculated to be necessary for the elaboration, maintenance, and/or function of melanocyte cell processes. To begin to discriminate between different models of dsu action, we have produced aggregation chimeras between mice homozygous for dsu and mice homozygous for d to determine if dsu acts cell autonomously or cell nonautonomously. In addition, we have further refined the map location of dsu in order to examine a number of possible dsu candidate genes mapping in the region and to provide a genetic basis for the positional cloning of dsu.
Use of a chromosomal inverted repeat to demonstrate that the RAD51 and RAD52 genes of Saccharomyces cerevisiae have different roles in mitotic recombination.
Authors: Rattray A J , Symington L S
Published: January 2021

An intrachromosomal recombination assay that monitors events between alleles of the ade2 gene oriented as inverted repeats was developed. Recombination to adenine prototrophy occurred at a rate of 9.3 x 10(-5)/cell/generation. Of the total recombinants, 50% occurred by gene conversion without crossing over, 35% by crossover and 15% by crossover associated with conversion. The rate of recombination was reduced 3,000-fold in a rad52 mutant, but the distribution of residual recombination events remained similar to that seen in the wild type strain. In rad51 mutants the rate of recombination was reduced only 4-fold. In this case, gene conversion events unassociated with a crossover were reduced 18-fold, whereas crossover events were reduced only 2.5-fold. A rad51 rad52 double mutant strain showed the same reduction in the rate of recombination as the rad52 mutant, but the distribution of events resembled that seen in rad51. From these observations it is concluded that (i) RAD52 is required for high levels of both gene conversions and reciprocal crossovers, (ii) that RAD51 is not required for intrachromosomal crossovers, and (iii) that RAD51 and RAD52 have different functions, or that RAD52 has functions in addition to those of the Rad51/Rad52 protein complex.
The Neurospora transposon Tad is sensitive to repeat-induced point mutation (RIP).
Authors: Kinsey J A , Garrett-Engele P W , Cambareri E B , Selker E U
Published: January 2021

RIP (repeat-induced point mutation) efficiently mutates repeated sequences in the sexual phase of the Neurospora crassa life cycle. Nevertheless, an active LINE-like retrotransposon, Tad, was found in a N. crassa strain from Adiopodoumé. The possibility was tested that Tad might be resistant to RIP, or that the Adiopodoumé strain might be incompetent for RIP. Tad elements derived from the Adiopodoumé strain were found to be susceptible to RIP. In addition, strains lacking active Tad elements, including common laboratory strains and strains representing seven species of Neurospora, were found to have sequences closely related to Tad but with numerous mutations of the type resulting from RIP (G:C to A:T). Even the Adiopodoumé strain showed Tad-like elements with mutations characteristic of RIP. Results of crossing of an Adiopodoumé transformant with progeny of Adiopodoumé suggest that the Adiopodoumé strain is proficient at RIP. We conclude that Tad is an old transposable element that has been inactivated by RIP in most strains. Finding relics of RIP in both heterothallic and homothallic species of Neurospora implicates RIP across the genus.
The Drosophila homeotic mutation Nasobemia (AntpNs) and its revertants: an analysis of mutational reversion.
Authors: Talbert P B , Garber R L
Published: January 2021

The homeotic gene Antennapedia (Antp) controls determination of many different cell types in the thorax and abdomen of Drosophila melanogaster. The spontaneous mutant allele Nasobemia (AntpNs) and its revertants have been widely used to infer normal Antp gene function but have not themselves been thoroughly characterized. Our analysis reveals that AntpNs consists of an internal 25-kb partial duplication of the Antp gene as well as a complex insertion of > 40 kb of new DNA including two roo transposons. The duplication gives the mutant gene three Antp promoters, and transcripts from each of these are correctly processed to yield functional ANTP proteins. At least two of the promoters are ectopically active in the eye-antenna imaginal discs, leading to homeotic transformation of the adult head. A molecular and genetic description of several AntpNs revertants shows them to be diverse in structure and activity, including a restoration of the wild type, rearrangements separating two of the AntpNs promoters from the coding sequences, and protein nulls and hypomorphs affecting expression from all three of the promoters. Finally, one revertant has a suppressing lesion in the osa locus far away from Antp. These features explain the unusual homozygous viable nature of AntpNs, suggest a mechanism by which its homeotic transformation occurs, and exemplify the diversity of ways in which mutational reversion can take place.
The maize NCS2 abnormal growth mutant has a chimeric nad4-nad7 mitochondrial gene and is associated with reduced complex I function.
Authors: Marienfeld J R , Newton K J
Published: January 2021

The molecular basis of the maternally inherited, heteroplasmic NCS2 mutant of maize was investigated. Analysis of the NCS2 mtDNA showed that it closely resembles the progenitor cmsT mitochondrial genome, except that the mutant genome contains a fused nad4-nad7 gene and is deleted for the small fourth exon of nad4. The rearrangement has occurred at a 16-bp repeat present in the third intron of the nad4 gene and in the second intron of the nad7 gene. Transcripts containing exon 4 of the nad4 gene are greatly reduced in mtRNA preparations from heteroplasmic NCS2 plants; larger transcripts are associated with the first three nad4 exons. Identical 5' ends of the nad4 transcripts have been mapped 396 and 247 bp upstream of the start codon in mtRNAs from both NCS2 and related non-NCS plants. The putative transcription termination signal of nad4 is deleted in mutant DNA, resulting in the production of the unique longer transcripts. The complex transcript pattern associated with nad7 is also altered in the mutant. Both nad4 and nad7 encode subunits of complex I (NADH dehydrogenase) of the mitochondrial electron transfer chain. Oxygen uptake experiments show that the functioning of complex I is specifically reduced in mitochondria isolated from NCS2 mutant plants.
A genetic linkage map of the mouse using restriction landmark genomic scanning (RLGS).
Authors: Hayashizaki Y , Hirotsune S , Okazaki Y , Shibata H , Akasako A , Muramatsu M , Kawai J , Hirasawa T , Watanabe S , Shiroishi T
Published: January 2021

We have developed a multiplex method of genome analysis, restriction landmark genomic scanning (RLGS) that has been used to construct genetic maps in mice. Restriction landmarks are end-labeled restriction fragments of genomic DNA that are separated by using high resolution, two-dimensional gel electrophoresis identifying as many as two thousand landmark loci in a single gel. Variation for several hundred of these loci has been identified between laboratory strains and between these strains and Mus spretus. The segregation of more than 1100 RLGS loci has been analyzed in recombinant inbred (RI) strains and in two separate interspecific genetic crosses. Genetic maps have been derived that link 1045 RLGS loci to reference loci on all of the autosomes and the X chromosome of the mouse genome. The RLGS method can be applied to genome analysis in many different organisms to identify genomic loci because it uses end-labeling of restriction landmarks rather than probe hybridization. Different combinations of restriction enzymes yield different sets of RLGS loci providing expanded power for genetic mapping.
Role of reciprocal exchange, one-ended invasion crossover and single-strand annealing on inverted and direct repeat recombination in yeast: different requirements for the RAD1, RAD10, and RAD52 genes.
Authors: Prado F , Aguilera A
Published: January 2021

We have constructed novel DNA substrates (one inverted and three direct repeats) based on the same 0.6-kb repeat sequence to study deletions and inversions in Saccharomyces cerevisiae. Spontaneous deletions occur six to eight times more frequently than inversions, irrespective of the distance between the repeats. This difference can be explained by the observation that deletion events can be mediated by a recombination mechanism that can initiate within the intervening sequence of the repeats. Spontaneous and double-strand break (DSB)-induced deletions occur as RAD52-dependent and RAD52-independent events. Those deletion events initiated through a DSB in the unique intervening sequence require the Rad1/Rad10 endonuclease only if the break is distantly located from the flanking DNA repeats. We propose that deletions can occur as three types of recombination events: the conservative RAD52-dependent reciprocal exchange and the nonconservative events, one-ended invasion crossover, and single-strand annealing (SSA). We suggest that one-ended invasion is RAD52 dependent, whereas SSA is RAD52 independent. Whereas deletions, like inversions, occur through reciprocal exchange, deletions can also occur through SSA or one-ended invasion. We propose that the contribution of reciprocal exchange and one-ended invasion crossover vs. SSA events to overall spontaneous deletions is a feature specific for each repeat system, determined by the initiation event and the availability of the Rad52 protein. We discuss the role of the Rad1/Rad10 endonuclease on the initial steps of one-ended invasion crossover and SSA as a function of the location of the initiation event relative to the repeats. We also show that the frequency of recombination between repeats is the same independent of their location (whether on circular plasmids, linear minichromosomes, or natural chromosomes) and have similar RAD52 dependence.
Mutations affecting the chemosensory neurons of Caenorhabditis elegans.
Authors: Starich T A , Herman R K , Kari C K , Yeh W H , Schackwitz W S , Schuyler M W , Collet J , Thomas J H , Riddle D L
Published: January 2021

We have identified and characterized 95 mutations that reduce or abolish dye filling of amphid and phasmid neurons and that have little effect on viability, fertility or movement. Twenty-seven mutations occurred spontaneously in strains with a high frequency of transposon insertion. Sixty-eight were isolated after treatment with EMS. All of the mutations result in defects in one or more chemosensory responses, such as chemotaxis to ammonium chloride or formation of dauer larvae under conditions of starvation and overcrowding. Seventy-five of the mutations are alleles of 12 previously defined genes, mutations which were previously shown to lead to defects in amphid ultrastructure. We have assigned 20 mutations to 13 new genes, called dyf-1 through dyf-13. We expect that the genes represented by dye-filing defective mutants are important for the differentiation of amphid and phasmid chemosensilla.
Genetic adaptation to captivity and inbreeding depression in small laboratory populations of Drosophila melanogaster.
Authors: Latter B D , Mulley J C
Published: January 2021

The rate of adaptation to a competitive laboratory environment and the associated inbreeding depression in measures of reproductive fitness have been observed in populations of Drosophila melanogaster with mean effective breeding size of the order of 50 individuals. Two large wild-derived populations and a long-established laboratory cage population were used as base stocks, from which subpopulations were extracted and slowly inbred under crowded conditions over a period of 210 generations. Comparisons have been made of the competitive ability and reproductive fitness of these subpopulations, the panmictic populations produced from them by hybridization and random mating and the wild- or cage-base populations from which they were derived. After an average of approximately 180 generations in the laboratory, the wild-derived panmictic populations exceeded the resampled natural populations by 75% in fitness under competitive conditions. The cage-derived panmictic population, after a total of 17 years in the laboratory, showed a 90% superiority in competitive ability over the corresponding wild population. In the inbred lines derived from the wild-base stocks, the average rate of adaptation was estimated to be 0.33 +/- 0.06% per generation. However, the gain in competitive ability was more than offset by inbreeding depression at an initial rate of approximately 2% per generation. The effects of both adaptation and inbreeding on reproductive ability in a noncompetitive environment were found to be minor by comparison. The maintenance of captive populations under noncompetitive conditions can therefore be expected to minimize adaptive changes due to natural selection in the changed environment.
How often do duplicated genes evolve new functions?
Authors: Walsh J B
Published: January 2021

A recently duplicated gene can either fix a null allele (becoming a pseudogene) or fix an (advantageous) allele giving a slightly different function, starting it on the road to evolving a new function. Here we examine the relative probabilities of these two events under a simple model. Null alleles are assumed to be neutral; linkage effects are ignored, as are unequal crossing over and gene conversion. These assumptions likely make our results underestimates for the probability that an advantageous allele is fixed first. When new advantageous mutations are additive with selection coefficient s and the ratio of advantageous to null mutations is rho, the probability an advantageous allele is fixed first is ([1 - e-s]/[rho S] + 1)-1, where S = 4Nes with Ne the effective population size. The probability that a duplicate locus becomes a pseudogene, as opposed to evolving a new gene function, is high unless rhoS > 1. However, even if advantageous mutations are very rare relative to null mutations, for sufficiently large populations rhoS > 1 and new gene function, rather than pseudogene formation, is the expected fate of most duplicated genes.
The inbreeding effective population number in dioecious populations.
Authors: Nagylaki T
Published: January 2021

The inbreeding effective population number in a dioecious population with discrete, nonoverlapping generations is investigated for both autosomal and X-linked loci. The recursion relations for the probabilities of genic identity, and the effective population numbers are analyzed and compared in two cases: (i) the offspring identified by sex in the calculation of the probability of common parentage and (ii) the offspring not so identified. Case i gives the correct evolution of the probabilities of identity, but case ii has been more widely studied and applied. A general symmetric framework that reduces the number of parameters is developed and used to examine a wide variety of models of panmixia and monogamy. Cases i and ii agree in many, but not all, models.
Spontaneous mutation rate of modifiers of metabolism in Drosophila.
Authors: Clark A G , Wang L , Hulleberg T
Published: January 2021

A rigorous test of our understanding of evolutionary quantitative genetics would be to predict accurately the equilibrium distribution of a character from empirical estimates of the relevant parameters in a mutation-selection-drift balance model. An aspect of this problem that is amenable to experimental analysis is the distribution of the effects of new mutations. This study quantifies the divergence among 200 lines of Drosophila melanogaster as they accumulated mutations on the second chromosome and estimates the rate of increase of variation and covariation in metabolic characters. Amounts of stored triacylglycerol and glycogen and the activities of a series of 12 metabolic enzymes were assayed in a subset of lines at generations 0, 11, 22, 33 and 44. Analyses of the rate of increase in the among-line variance in each trait allowed estimation of Vm/Ve, the ratio of among-line variance added per generation to the environmental variance. Values of Vm/Ve for the second chromosome ranged from 0.0004 to 0.0289 per generation. Six of the 16 characters showed significant departure from a normal distribution, and several lines exhibited large changes in more than one character. The covariance of pairs of traits also was partitioned into a within-line component (environmental covariance, Cov(e)) and an among-line component (mutational covariance, Covm). Both variances and covariance among lines increased over time, as assessed by linear regression, whereas environmental covariance showed no such trend. Results indicate that the quantitative genetic parameters describing the variation in metabolic traits are similar to those of other continuous characters.
Estimating interference and linkage map distance from two-factor tetrad data.
Authors: Stahl F W , Lande R
Published: January 2021

We present methods for using the model of Foss, Lande, Stahl and Steinberg to estimate interference and map distances from two-factor tetrad data. We illustrate the application of the methods with data from Neurospora and from Saccharomyces.
The mechanism of recA polA lethality: suppression by RecA-independent recombination repair activated by the lexA(Def) mutation in Escherichia coli.
Authors: Cao Y , Kogoma T
Published: January 2021

The mechanism of recA polA lethality in Escherichia coli has been studied. Complementation tests have indicated that both the 5'-->3' exonuclease and the polymerization activities of DNA polymerase I are essential for viability in the absence of RecA protein, whereas the viability and DNA replication of DNA polymerase I-defective cells depend on the recombinase activity of RecA. An alkaline sucrose gradient sedimentation analysis has indicated that RecA has only a minor role in Okazaki fragment processing. Double-strand break repair is proposed for the major role of RecA in the absence of DNA polymerase I. The lexA(Def)::Tn5 mutation has previously been shown to suppress the temperature-sensitive growth of recA200(Ts) polA25::spc mutants. The lexA(Def) mutation can alleviate impaired DNA synthesis in the recA200(Ts) polA25::spc mutant cells at the restrictive temperature. recF+ is essential for this suppression pathway. recJ and recQ mutations have minor but significant adverse effects on the suppression. The recA200(Ts) allele in the recA200(Ts) polA25::spc lexA(Def) mutant can be replaced by delta recA, indicating that the lexA(Def)-induced suppression is RecA independent. lexA(Def) reduces the sensitivity of delta recA polA25::spc cells to UV damage by approximately 10(4)-fold. lexA(Def) also restores P1 transduction proficiency to the delta recA polA25::spc mutant to a level that is 7.3% of the recA+ wild type. These results suggest that lexA(Def) activates a RecA-independent, RecF-dependent recombination repair pathway that suppresses the defect in DNA replication in recA polA double mutants.
sli-1, a negative regulator of let-23-mediated signaling in C. elegans.
Authors: Jongeward G D , Clandinin T R , Sternberg P W
Published: January 2021

By screening for suppressors of hypomorphic mutations of let-23, a receptor tyrosine kinase necessary for vulval induction in Caenorhabditis elegans, we recovered > or = 12 mutations defining the sli-1 (suppressor of lineage defect) locus. sli-1 mutations suppress four of five phenotypes associated with hypomorphic alleles of let-23 but do not suppress let-23 null alleles. Thus, a sli-1 mutation does not bypass the requirement for functional let-23 but rather allows more potent LET-23-dependent signaling. Mutations at the sli-1 locus are otherwise silent with respect to vulval differentiation and cause only a low-penetrance abnormal head phenotype. Mutations at sli-1 also suppress the vulval defects but not other defects associated with mutations of sem-5, whose product likely interacts with LET-23 protein during vulval induction. Mutations at sli-1 suppress lin-2, lin-7 and lin-10 mutations but only partially suppress lin-3 and let-60 mutations and do not suppress a lin-45 mutation. The sli-1 locus displays dosage sensitivity: severe reduction of function alleles of sli-1 are semidominant suppressors; a duplication of the sli-1(+) region enhances the vulvaless phenotype of hypomorphic mutations of let-23. We propose that sli-1 is a negative regulator that acts at or near the LET-23-mediated step of the vulval induction pathway. Our analysis suggests that let-23 can activate distinct signaling pathways in different tissues: one pathway is required for vulval induction; another pathway is involved in hermaphrodite fertility and is not regulated by sli-1.
Restriction fragment length polymorphism mapping of quantitative trait loci for malaria parasite susceptibility in the mosquito Aedes aegypti.
Authors: Severson D W , Thathy V , Mori A , Zhang Y , Christensen B M
Published: January 2021

Susceptibility of the mosquito Aedes aegypti to the malarial parasite Plasmodium gallinaceum was investigated as a quantitative trait using restriction fragment length polymorphisms (RFLP). Two F2 populations of mosquitoes were independently prepared from pairwise matings between a highly susceptible and a refractory strain of A. aegypti. RFLP were tested for association with oocyst development on the mosquito midgut. Two putative quantitative trait loci (QTL) were identified that significantly affect susceptibility. One QTL, pgs[2,LF98], is located on chromosome 2 and accounted for 65 and 49% of the observed phenotypic variance in the two populations, respectively. A second QTL, pgs[3,MalI], is located on chromosome 3 and accounted for 14 and 10% of the observed phenotypic variance in the two populations, respectively. Both QTL exhibit a partial dominance effect on susceptibility, wherein the dominance effect is derived from the refractory parent. No indication of epistasis between these QTL was detected. Evidence suggests that either a tightly linked cluster of independent genes or a single locus affecting susceptibility to various mosquito-borne parasites and pathogens has evolved near the LF98 locus; in addition to P. gallinaceum susceptibility, this general genome region has previously been implicated in susceptibility to the filarial nematode Brugia malayi and the yellow fever virus.
Interval mapping of high growth (hg), a major locus that increases weight gain in mice.
Authors: Horvat S , Medrano J F
Published: January 2021

The high growth locus (hg) causes a major increase in weight gain and body size in mice. As a first step to map-based cloning of hg, we developed a genetic map of the hg-containing region using interval mapping of 403 F2 from a C57BL/6J-hghg x CAST/EiJ cross. The maximum likelihood position of hg was at the chromosome 10 marker D10Mit41 (LOD = 24.8) in the F2 females and 1.5 cM distal to D10Mit41 (LOD = 9.56) in the F2 males with corresponding LOD 2 support intervals of 3.7 and 5.4 cM, respectively. The peak LOD scores were significantly higher than the estimated empirical threshold LOD values. The localization of hg by interval mapping was supported by a test cross of F2 mice recombinant between the LOD 2 support interval and the flanking marker. The interval mapping and test-cross results indicate that hg is not allelic with candidate genes Igf1 or decorin (Dcn), a gene that was mapped close to hg in this study. The hg inheritance was recessive in females, although we could not reject recessive or additive inheritance in males. Possible causes for sex differences in peak LOD scores and for the distortion of transmission ratios observed in F2 males are discussed. The genetic map of the hg region will facilitate further fine mapping and cloning of hg, and allow searches for a homologous quantitative trait locus affecting growth in humans and domestic animals.
Reduced mtDNA diversity in the Ngöbé Amerinds of Panamá.
Authors: Kolman C J , Bermingham E , Cooke R , Ward R H , Arias T D , Guionneau-Sinclair F
Published: January 2021

Mitochondrial DNA (mtDNA) haplotype diversity was determined for 46 Ngöbé Amerinds sampled widely across their geographic range in western Panamá. The Ngöbé data were compared with mtDNA control region I sequences from two additional Amerind groups located at the northern and southern extremes of Amerind distribution, the Nuu-Chah-Nulth of the Pacific Northwest and the Chilean Mapuche and from one Na-Dene group, the Haida of the Pacific Northwest. The Ngöbé exhibit the lowest mtDNA control region sequence diversity yet reported for an Amerind group. Moreover, they carry only two of the four Amerind founding lineages first described by Wallace and coworkers. We posit that the Ngöbé passed through a population bottleneck caused by ethnogenesis from a small founding population and/or European conquest and colonization. Dating of the Ngöbé population expansion using the Harpending et al. approach to the analysis of pairwise genetic differences indicates a Ngöbé expansion at roughly 6800 years before present (range: 1850-14,000 years before present), a date more consistent with a bottleneck at Chibcha ethnogenesis than a conquest-based event.
Exact inbreeding coefficient and effective size of finite populations under partial sib mating.
Authors: Wang J
Published: January 2021

An exact recurrence equation for inbreeding coefficient is derived for a partially sib-mated population of N individuals mated in N/2 pairs. From the equation, a formula for effective size (Ne) taking second order terms of 1/N into consideration is derived. When the family sizes are Poisson or equally distributed, the formula reduces to Ne = [(4 - 3 beta) N/(4 - 2 beta)] + 1 or Ne = [(4 - 3 beta) N/(2 - 2 beta)] - 8/(4 - 3 beta), approximately. For the special case of sib-mating exclusion and Poisson distribution of family size, the formula simplifies to Ne = N + 1, which differs from the previous results derived by many authors by a value of one. Stochastic simulations are run to check our results where disagreements with others are involved.
The dominance theory of Haldane's rule.
Authors: Turelli M , Orr H A
Published: January 2021

"HALDANE's rule" states that, if species hybrids of one sex only are inviable or sterile, the afflicted sex is much more likely to be heterogametic (XY) than homogametic (XX). We show that most or all of the phenomena associated with HALDANE's rule can be explained by the simple hypothesis that alleles decreasing hybrid fitness are partially recessive. Under this hypothesis, the XY sex suffers more than the XX because X-linked alleles causing postzygotic isolation tend to have greater cumulative effects when hemizygous than when heterozygous, even though the XX sex carries twice as many such alleles. The dominance hypothesis can also account for the "large X effect," the disproportionate effect of the X chromosome on hybrid inviability/sterility. In addition, the dominance theory is consistent with: the long temporal lag between the evolution of heterogametic and homogametic postzygotic isolation, the frequency of exceptions to HALDANE's rule, puzzling Drosophila experiments in which "unbalanced" hybrid females, who carry two X chromosomes from the same species, remain fertile whereas F1 hybrid males are sterile, and the absence of cases of HALDANE's rule for hybrid inviability in mammals. We discuss several novel predictions that could lead to rejection of the dominance theory.
Specificities of the Saccharomyces cerevisiae rad6, rad18, and rad52 mutators exhibit different degrees of dependence on the REV3 gene product, a putative nonessential DNA polymerase.
Authors: Roche H , Gietz R D , Kunz B A
Published: January 2021

The Saccharomyces cerevisiae rad6, rad18, and rad52 mutants exhibit DNA repair deficiencies and distinct mutator phenotypes. DNA replication past unrepaired spontaneous damage might contribute to the specificities of these mutators. Because REV3 is thought to encode a DNA polymerase that specializes in translesion synthesis, we determined the REV3 dependence of the rad mutator specificities. Spontaneous mutagenesis at a plasmid-borne SUP4-o locus was examined in isogenic strains having combinations of normal or mutant REV3 and RAD6, RAD18, or RAD52 alleles. For the rad6 and rad18 mutators, the mutation rate increase relied largely, but not exclusively, on REV3 whereas the rad52 mutator was entirely REV3 dependent. The influence of REV3 on the specificity of the rad6 mutator differed markedly depending on the mutational class examined. However, the requirement of rev3 for the production of G.C-->T.A transversions by the rad18 mutator, which induces only these substitutions, was similar to that for rad6-mediated G.C-->T.A transversion. This supports a role for the Rad6-Rad18 protein complex in the control of spontaneous mutagenesis. The available data imply that the putative Rev3 polymerase can process a variety of spontaneous DNA lesions that normally are substrates for error-free repair.
sck1, a high copy number suppressor of defects in the cAMP-dependent protein kinase pathway in fission yeast, encodes a protein homologous to the Saccharomyces cerevisiae SCH9 kinase.
Authors: Jin M , Fujita M , Culley B M , Apolinario E , Yamamoto M , Maundrell K , Hoffman C S
Published: January 2021

Schizosaccharomyces pombe regulates intracellular cAMP levels, and thus cAMP-dependent protein kinase (PKA) activity, in response to changes in nutrient conditions. Mutations in any of eight git genes inhibit glucose repression of fbp1 transcription, alter the cell morphology, and cause a reduction in the growth rate. The eight git genes encode components of an adenylate cyclase activation pathway, adenylate cyclase itself, and the catalytic subunit of PKA. Three of these genes have been identified in other studies as regulators of meiosis. Here we show that the sck1 gene, cloned as a high copy number suppressor of a mutation in git3, is able to suppress the defects conferred by a mutation in any of these git genes. Sequence analysis suggests that sck1 encodes a protein most closely related to the Saccharomyces cerevisiae SCH9 protein kinase that had previously been identified as a high copy number suppressor of mutations in S. cerevisiae that reduce or eliminate PKA activity. Disruption of the sck1 gene causes a significant delay in exit from stationary phase when combined with a disruption of the pka1 (git6) gene encoding the catalytic subunit of PKA. However, the sck1 disruption by itself has little or no effect upon fbp1 transcription, meiosis, or exit from stationary phase, and does not enhance the constitutive fbp1 transcription observed in a pka1 mutant. Therefore, sck1 appears to function in a redundant fashion to pka1, but to varying degrees, in the pathways regulated by pka1.
Competition between mitochondrial haplotypes in distinct nuclear genetic environments: Drosophila pseudoobscura vs. D. persimilis.
Authors: Hutter C M , Rand D M
Published: January 2021

A test for coadaptation of nuclear and mitochondrial genomes was performed using the sibling species, Drosophila pseudoobscura and D. persimilis. Two lines of flies with "disrupted" cytonuclear genotypes were constructed by repeated backcrossing of males from one species to females carrying mitochondrial DNA (mtDNA) from the other species. Each "disrupted" strain was competed in population cages with the original stock of each species from which the recurrent males were obtained during the backcrossing. As such, the two species' mitochondrial types were competed reciprocally in the nuclear genetic environments of each species. The trajectories of mtDNA haplotypes were followed in discrete-generation population cages using a PCR-four-cutter approach. A significant increase in the frequency of D. pseudoobscura mtDNA was observed in each of four replicate cages with a D. pseudoobscura nuclear background. In the D. persimilis nuclear background, one cage actually showed an increase in frequency of D. pseudoobscura mtDNA, although together the four replicate cages show little change in frequency. These results were repeated after frequency perturbations and reinitiation of each cage. An analysis of fitness components revealed that fertility selection greatly outweighed viability selection in these cytonuclear competition experiments. The asymmetry of the fitnesses of the mtDNA haplotypes on the two genetic backgrounds is consistent in direction with the previously reported asymmetry of female fertility in backcrosses between these two species. While our experiments do not allow us to identify mtDNA as the sole source of fitness variation, at a minimum the data indicate a fitness association between nuclear fertility factors and the D. pseudoobscura mtDNA on its own genetic background.
Comparative analysis of QTLs affecting plant height and maturity across the Poaceae, in reference to an interspecific sorghum population.
Authors: Lin Y R , Schertz K F , Paterson A H
Published: January 2021

Correspondence among QTLs affecting height and/or flowering was investigated across the five races of sorghum, an interspecific sorghum F2 population, and 32 previously published sorghum, maize, rice, wheat, and barley populations revealing 185 QTLs or discrete mutants. Among nine QTLs mapped in the interspecific sorghum population (six affecting height and three affecting flowering), at least seven (78%) are associated with "conversion," backcross-introgression of alleles imparting reduced height or earlier flowering from cultivated sorghums into one or more exotic Sorghum bicolor races. One chromosomal region was "converted" in all S. bicolar races--in the interspecific F2, this region explained 54.8% of height variation (putatively the Dw2 gene) and 85.7% of flowering time variation (putatively Ma1). Comparative data suggest that Ma1 and Dw2 orthologs influence height and flowering of other Poaceae taxa and support classical dogma that the sorghum phenotypes attributed to Ma1 and Dw2 (respectively) are due to different genetic loci. Other sorghum QTLs also showed correspondence with those in other Poaceae, more frequently than would be expected by chance. Possible homoeologous QTLs were found within both the maize and sorghum genomes. Comparative QTL mapping provides a means to unify, and thereby simplify, molecular analysis of complex phenotypes.
Two-dimensional spreads of synaptonemal complexes from solanaceous plants. VI. High-resolution recombination nodule map for tomato (Lycopersicon esculentum).
Authors: Sherman J D , Stack S M
Published: January 2021

We have produced a high-resolution physical recombination map for tomato chromosomes by determining the frequency and distribution of recombination nodules (RNs) on tomato synaptonemal complexes (SCs). We present evidence that there is a 1:1 relationship between RNs and chiasmata. Every SC has at least one RN. There are no RNs at the ends of SCs, in kinetochores, or in the heterochromatic short arm of SC 2 that carries the nucleolus organizer. RNs are more common per unit length of SC in euchromatin compared with SC in heterochromatin . The average number of RNs per SC and the average number of RNs per SC arm are directly correlated with the length of SC in euchromatin. When SCs have only one RN, that RN occurs on the long arm more frequently than predicted based on SC arm length. Patterns of multiple Rns on SCs indicate RN (crossover) interference. Rns probably can occur anywhere on SCs in euchromatin, but RNs are not distributed randomly along SCs in euchromatin or in heterochromatin. The lengths of tomato's physical recombination (RN) map, classical genetic linkage map, and molecular linkage map all differ from each other for a variety of reasons.