bluuebunny/crossref_metadata_2025_split huggingface dataset:
The transposable element mariner mediates germline transformation in Drosophila melanogaster.
Authors: Lidholm D A , Lohe A R , Hartl D L 
Published: January 2021

Abstract
A vector for germline transformation in Drosophila melanogaster was constructed using the transposable element mariner. The vector, denoted pMlwB, contains a mariner element disrupted by an insertion containing the wild-type white gene from D. melanogaster, the beta-galactosidase gene from Escherichia coli and sequences that enable plasmid replication and selection in E. coli. The white gene is controlled by the promoter of the D. melanogaster gene for heat-shock protein 70, and the beta-galactosidase gene is flanked upstream by the promoter of the transposable element P as well as that of mariner. The MlwB element was introduced into the germline of D. melanogaster by co-injection into embryos with an active mariner element, Mos1, which codes for a functional transposase and serves as a helper. Two independent germline insertions were isolated and characterized. The results show that the MlwB element inserted into the genome in a mariner-dependent manner with the termini of the inverted repeats inserted at a TA dinucleotide. Both insertions exhibit an unexpected degree of germline and somatic stability, even in the presence of an active mariner element in the genetic background. These results demonstrate that the mariner transposable element, which is small (1286 bp) and relatively homogeneous in size among different copies, is nevertheless capable of promoting the insertion of the large (13.2 kb) MlwB element. Because of the widespread phylogenetic distribution of mariner among insects, these results suggest that mariner might provide a wide host-range transformation vector for insects.
Detecting marker-QTL linkage and estimating QTL gene effect and map location using a saturated genetic map.
Authors: Darvasi A , Weinreb A , Minke V , Weller J I , Soller M 
Published: January 2021

Abstract
A simulation study was carried out on a backcross population in order to determine the effect of marker spacing, gene effect and population size on the power of marker-quantitative trait loci (QTL) linkage experiments and on the standard error of maximum likelihood estimates (MLE) of QTL gene effect and map location. Power of detecting a QTL was virtually the same for a marker spacing of 10 cM as for an infinite number of markers and was only slightly decreased for marker spacing of 20 or even 50 cM. The advantage of using interval mapping as compared to single-marker analysis was slight. "Resolving power" of a marker-QTL linkage experiment was defined as the 95% confidence interval for the QTL map location that would be obtained when scoring an infinite number of markers. It was found that reducing marker spacing below the resolving power did not add appreciably to narrowing the confidence interval. Thus, the 95% confidence interval with infinite markers sets the useful marker spacing for estimating QTL map location for a given population size and estimated gene effect.
An attempt to hybridize Drosophila species using pole cell transplantation.
Authors: Lawrence P A , Ashburner M , Johnston P 
Published: January 2021

Abstract
We have made hybrid embryos in Drosophila by pole cell transplants, by transferring pole cells from two species, D. rajasekari and D. eugracilis, into sterile D. melanogaster hosts. These females were then mated to melanogaster males and the older these females were, the further their hybrid offspring developed. In the case of the rajasekari/melanogaster hybrids, the embryos form cuticle but had defective heads, while the eugracilis/melanogaster hatched as larvae that grew but did not moult to the second instar. Hybrid pole cells could be transferred to melanogaster hosts but they failed to make eggs.
Developmental analysis of two sex-determining genes, M and F, in the housefly, Musca domestica.
Authors: Hilfiker-Kleiner D , Dübendorfer A , Hilfiker A , Nöthiger R 
Published: January 2021

Abstract
In the housefly, Musca domestica, a single dominant factor, M, determines maleness. Animals hemi-or heterozygous for M are males, whereas those without M develop as females. In certain strains, however, both sexes are homozygous for M, and an epistatic dominant factor, FD, dictates female development. The requirement for these factors was analyzed by producing, with mitotic recombination, mosaic animals consisting of genetically male and female cells. Removal of FD from an M/M;FD/+ cell at any time of larval development, even in the last larval instar, resulted in sex-reversal, i.e., in the development of a male clone in an otherwise female fly. In contrast, when M was removed from M/+ cells, the resulting clones remained male despite their female genotype, even when the removal of M happened at embryonic stages. The occurrence of spontaneous gynandromorphs, however, shows that the loss of M in individual nuclei prior to blastoderm formation causes the affected cells to adopt the female pathway. These results are consistent with the hypothesis that M is the primary sex-determining signal which sets the state of activity of the key gene F at around the blastoderm stage. Parallels and differences to the sex-determining system of Drosophila are discussed.
Transposition pattern of the maize element Ds in Arabidopsis thaliana.
Authors: Bancroft I , Dean C 
Published: January 2021

Abstract
As part of establishing an efficient transposon tagging system in Arabidopsis using the maize elements Ac and Ds, we have analyzed the inheritance and pattern of Ds transposition in four independent Arabidopsis transformants. A low proportion (33%) of plants inheriting the marker used to monitor excision contained a transposed Ds. Selection for the transposed Ds increased this to at least 49%. Overall, 68% of Ds transpositions inherited with the excision marker were to genetically linked sites; however, the distribution of transposed elements varied around the different donor sites. Mapping of transposed Ds elements that were genetically unlinked to the donor site showed that a proportion (3 of 11 tested) integrated into sites which were still physically linked.
Maximum likelihood estimation of population parameters.
Authors: Fu Y X , Li W H 
Published: January 2021

Abstract
One of the most important parameters in population genetics is theta = 4Ne mu where Ne is the effective population size and mu is the rate of mutation per gene per generation. We study two related problems, using the maximum likelihood method and the theory of coalescence. One problem is the potential improvement of accuracy in estimating the parameter theta over existing methods and the other is the estimation of parameter lambda which is the ratio of two theta's. The minimum variances of estimates of the parameter theta are derived under two idealized situations. These minimum variances serve as the lower bounds of the variances of all possible estimates of theta in practice. We then show that Watterson's estimate of theta based on the number of segregating sites is asymptotically an optimal estimate of theta. However, for a finite sample of sequences, substantial improvement over Watterson's estimate is possible when theta is large. The maximum likelihood estimate of lambda = theta 1/theta 2 is obtained and the properties of the estimate are discussed.
The effect of deleterious mutations on neutral molecular variation.
Authors: Charlesworth B , Morgan M T , Charlesworth D 
Published: January 2021

Abstract
Selection against deleterious alleles maintained by mutation may cause a reduction in the amount of genetic variability at linked neutral sites. This is because a new neutral variant can only remain in a large population for a long period of time if it is maintained in gametes that are free of deleterious alleles, and hence are not destined for rapid elimination from the population by selection. Approximate formulas are derived for the reduction below classical neutral values resulting from such background selection against deleterious mutations, for the mean times to fixation and loss of new mutations, nucleotide site diversity, and number of segregating sites. These formulas apply to random-mating populations with no genetic recombination, and to populations reproducing exclusively asexually or by self-fertilization. For a given selection regime and mating system, the reduction is an exponential function of the total mutation rate to deleterious mutations for the section of the genome involved. Simulations show that the effect decreases rapidly with increasing recombination frequency or rate of outcrossing. The mean time to loss of new neutral mutations and the total number of segregating neutral sites are less sensitive to background selection than the other statistics, unless the population size is of the order of a hundred thousand or more. The stationary distribution of allele frequencies at the neutral sites is correspondingly skewed in favor of rare alleles, compared with the classical neutral result. Observed reductions in molecular variation in low recombination genomic regions of sufficiently large size, for instance in the centromere-proximal regions of Drosophila autosomes or in highly selfing plant populations, may be partly due to background selection against deleterious mutations.
Variance analysis of immunoglobulin alleles in natural populations of rabbit (Oryctolagus cuniculus): the extensive interallelic divergence at the b locus could be the outcome of overdominance-type selection.
Authors: van der Loo W 
Published: January 2021

Abstract
Population genetic data are presented which should contribute to evaluation of the hypothesis that the extraordinary evolutionary patterns observed at the b locus of the rabbit immunoglobulin light chain constant region can be the outcome of overdominance-type selection. The analysis of allele correlations in natural populations revealed an excess of heterozygotes of about 10% at the b locus while heterozygote excess was not observed at loci determining the immunoglobulin heavy chain. Data from the published literature, where homozygote advantage was suggested, were reevaluated and found in agreement with data here presented. Gene diversity was evenly distributed among populations and showed similarities with patterns reported for histocompatibility loci. Analysis of genotypic disequilibria revealed strong digenic associations between the leading alleles of heavy and light chain constant region loci in conjunction with trigenic disequilibria corresponding to a preferential association of b locus heterozygosity with the predominant allele of the heavy chain e locus. It is argued that this may indicate compensatory or nonadditive aspects of a putative heterozygosity enhancing mechanism, implying that effects at the light chain might be more pronounced in populations fixed for the heavy chain polymorphism.
Somatic variegation and germinal mutability reflect the position of transposable element Dissociation within the maize R gene.
Authors: Alleman M , Kermicle J L 
Published: January 2021

Abstract
The R gene regulates the timing and tissue-specificity of anthocyanin deposition during maize development. The Ac/Ds system of transposable elements was used to induce insertional mutants of the R-sc:124 allele during two cycles of mutagenesis. Of 43 unstable, spotted-aleurone mutants generated, 42 contain inserts of the Ds6 transposable element differing only in the position and orientation of the element. The remaining mutant, r-sc:m1, contained an insert of a Ds element of the approximate size of the Ds1 transposable element. The patterns of somatic variegation of these mutants, resulting from excision of Ds, define a spectrum of phenotypes ranging from sparse to dense variegation. The sparsely variegated mutants produce few germinal revertants but relatively many stable null derivative alleles; densely variegated mutants produce many germinal revertants and few stable null derivatives. Molecular analysis shows that the sparsely variegated alleles are caused by Ds6 insertions in protein coding regions of R-sc:124 whereas the densely variegated mutants result from insertions in introns or in flanking regions of the gene. The excision rate of Ds6 from R, estimated as the proportion of R genomic DNA restriction fragments lacking the element, was uniform regardless of position, orientation or whether the element was inserted in R-sc:124 or another R allele. The excision rate was greater, however, for the mutable alleles involving the Ds element from r-sc:m1. These data indicate that, although the excision rates are uniform for a given Ds element, the somatic and germinal mutability patterns of alleles associated with that element vary widely and depend primarily on the position of the transposable element within coding or noncoding regions of the gene.
Genetic characterization of tube and pelle, genes required for signaling between Toll and dorsal in the specification of the dorsal-ventral pattern of the Drosophila embryo.
Authors: Hecht P M , Anderson K V 
Published: January 2021

Abstract
tube and pelle are two of the maternally transcribed genes required for dorsal-ventral patterning of the Drosophila embryo. Females homozygous for strong alleles of tube or pelle produce embryos that lack all ventral and lateral embryonic pattern elements. By analyzing the phenotypes caused by 24 pelle and 9 tube alleles, we have defined characteristic features of the two genes, including the extremely variable phenotypes of a number of tube alleles and the antimorphic character of a number of pelle alleles. Double mutant females carrying dominant ventralizing alleles of Toll and dorsalizing alleles of tube or pelle produce dorsalized embryos, suggesting that tube and pelle act downstream of the membrane protein Toll in the signaling pathway that defines the embryonic dorsal-ventral pattern. Both tube and pelle are also important zygotically for survival: at least 30% of the zygotes lacking either tube or pelle die before adult stages, while 90-95% of tube- pelle- double mutant zygotes die. We discuss the phenotypes of tube-pelle double mutants in the context of whether the two proteins interact directly.
Genetic and molecular analysis of the X chromosomal region 14B17-14C4 in Drosophila melanogaster: loss of function in NONA, a nuclear protein common to many cell types, results in specific physiological and behavioral defects.
Authors: Stanewsky R , Rendahl K G , Dill M , Saumweber H 
Published: January 2021

Abstract
We have performed a genetic analysis of the 14C region of the X chromosome of Drosophila melanogaster to isolate loss of function alleles of no-on-transient A (nonA; 14C1-2; 1-52.3). NONA is a nuclear protein common to many cell types, which is present in many puffs on polytene chromosomes. Sequence data suggest that the protein contains a pair of RNA binding motifs (RRM) found in many single-strand nucleic acid binding proteins. Hypomorphic alleles of this gene, which lead to aberrant visual and courtship song behavior, still contain normally distributed nonA RNA and NONA protein in embryos, and in all available alleles NONA protein is present in puffs of third instar larval polytene chromosomes. We find that complete loss of this general nuclear protein is semilethal in hemizygous males and homozygous cell lethal in the female germline. Surviving males show more extreme defects in nervous system function than have been described for the hypomorphic alleles. Five other essential genes that reside within this region have been partially characterized.
Suppressors of glp-1, a gene required for cell communication during development in Caenorhabditis elegans, define a set of interacting genes.
Authors: Maine E M , Kimble J 
Published: January 2021

Abstract
The glp-1 gene is essential for two cell interactions that control cell fate in Caenorhabditis elegans: induction of anterior pharynx in the embryo and induction of mitotic proliferation in the germ line. To identify other genes involved in these cell interactions, we have isolated suppressors of two temperature sensitive alleles of glp-1. Each of 14 recessive suppressors rescues both embryonic and germline glp-1(ts) defects. These suppressors are extragenic and define a set of six genes designated sog, for suppressor of glp-1. Suppression of glp-1 is the only obvious phenotype associated with sog mutations. Mutations in different sog genes show allele-specific intergenic noncomplementation, suggesting that the sog gene products may interact. In addition, we have analyzed a semidominant mutation that suppresses only the glp-1 germline phenotype and has a conditional feminized phenotype of its own. None of the suppressors rescues a glp-1 null mutation and therefore they do not bypass a requirement for glp-1. Distal tip cell function remains necessary for germline proliferation in suppressed animals. These suppressor mutations identify genes that may encode other components of the glp-1 mediated cell-signaling pathway or regulate glp-1 expression.
Chloroplast DNA diversity among trees, populations and species in the California closed-cone pines (Pinus radiata, Pinus muricata and Pinus attenuata).
Authors: Hong Y P , Hipkins V D , Strauss S H 
Published: January 2021

Abstract
The amount, distribution and mutational nature of chloroplast DNA polymorphisms were studied via analysis of restriction fragment length polymorphisms in three closely related species of conifers, the California closed-cone pines-knobcone pine: Pinus attenuata Lemm.; bishop pine: Pinus muricata D. Don; and Monterey pine: Pinus radiata D. Don. Genomic DNA from 384 trees representing 19 populations were digested with 9-20 restriction enzymes and probed with cloned cpDNA fragments from Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco] that comprise 82% chloroplast genome. Up to 313 restriction sites were surveyed, and 25 of these were observed to be polymorphic among or within species. Differences among species accounted for the majority of genetic (haplotypic) diversity observed [Gst = 84(+/- 13)%]; nucleotide diversity among species was estimated to be 0.3(+/- 0.1)%. Knobcone pine and Monterey pine displayed almost no genetic variation within or among populations. Bishop pine also showed little variability within populations, but did display strong population differences [Gst = 87(+/- 8)%] that were a result of three distinct geographic groups. Mean nucleotide diversity within populations was 0.003(+/- 0.002)%; intrapopulation polymorphisms were found in only five populations. This pattern of genetic variation contrasts strongly with findings from study of nuclear genes (allozymes) in the group, where most genetic diversity resides within populations rather than among populations or species. Regions of the genome subject to frequent length mutations were identified; estimates of subdivision based on length variant frequencies in one region differed strikingly from those based on site mutations or allozymes. Two trees were identified with a major chloroplast DNA inversion that closely resembled one documented between Pinus and Pseudotsuga.
Effective sizes for subdivided populations.
Authors: Chesser R K , Rhodes O E , Sugg D W , Schnabel A 
Published: January 2021

Abstract
Many derivations of effective population sizes have been suggested in the literature; however, few account for the breeding structure and none can readily be expanded to subdivided populations. Breeding structures influence gene correlations through their effects on the number of breeding individuals of each sex, the mean number of progeny per female, and the variance in the number of progeny produced by males and females. Additionally, hierarchical structuring in a population is determined by the number of breeding groups and the migration rates of males and females among such groups. This study derives analytical solutions for effective sizes that can be applied to subdivided populations. Parameters that encapsulate breeding structure and subdivision are utilized to derive the traditional inbreeding and variance effective sizes. Also, it is shown that effective sizes can be determined for any hierarchical level of population structure for which gene correlations can accrue. Derivations of effective sizes for the accumulation of gene correlations within breeding groups (coancestral effective size) and among breeding groups (intergroup effective size) are given. The results converge to traditional, single population measures when similar assumptions are applied. In particular, inbreeding and intergroup effective sizes are shown to be special cases of the coancestral effective size, and intergroup and variance effective sizes will be equal if the population census remains constant. Instantaneous solutions for effective sizes, at any time after gene correlation begins to accrue, are given in terms of traditional F statistics or transition equations. All effective sizes are shown to converge upon a common asymptotic value when breeding tactics and migration rates are constant. The asymptotic effective size can be expressed in terms of the fixation indices and the number of breeding groups; however, the rate of approach to the asymptote is dependent upon dispersal rates. For accurate assessment of effective sizes, initial, instantaneous or asymptotic, the expressions must be applied at the lowest levels at which migration among breeding groups is nonrandom. Thus, the expressions may be applicable to lineages within socially structured populations, fragmented populations (if random exchange of genes prevails within each population), or combinations of intra- and interpopulation discontinuities of gene flow. Failure to recognize internal structures of populations may lead to considerable overestimates of inbreeding effective size, while usually underestimating variance effective size.
The pheromone receptors inhibit the pheromone response pathway in Saccharomyces cerevisiae by a process that is independent of their associated G alpha protein.
Authors: Hirsch J P , Cross F R 
Published: January 2021

Abstract
Dominant mutations at the DAF2 locus confer resistance to the cell-cycle arrest that normally occurs in MATa cells exposed to alpha-factor. One of these alleles, DAF2-2, has also been shown to suppress the constitutive signaling phenotype of null alleles of the gene encoding the alpha subunit of the G protein involved in pheromone signaling. These observations indicate that DAF2-2 inhibits transmission of the pheromone response signal. The DAF2-2 mutation has two effects on the expression of a pheromone inducible gene, FUS1. In DAF2-2 cells, FUS1 RNA is present at an increased basal level but is no longer fully inducible by pheromone. Cloning of DAF2-2 revealed that it is an allele of STE3, the gene encoding the a-factor receptor. STE3 is normally an alpha-specific gene, but is inappropriately expressed in a cells carrying a STE3DAF2-2 allele. The two effects of STE3DAF2-2 alleles on the pheromone response pathway are the result of different functions of the receptor. The increased basal level of FUS1 RNA is probably due to stimulation of the pathway by an autocrine mechanism, because it required at least one of the genes encoding a-factor. Suppression of a null allele of the G alpha subunit gene, the phenotype associated with the inhibitory function of STE3, was independent of a-factor. This suppression was also observed when the wild-type STE3 gene was expressed in a cells under the control of an inducible promoter. Inappropriate expression of STE2 in alpha cells was able to suppress a point mutation, but not a null allele, of the G alpha subunit gene. The ability of the pheromone receptors to block the pheromone response signal in the absence of the G alpha subunit indicates that these receptors interact with another component of the signal transduction pathway.