bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transposable element numbers in cosmopolitan inversions from a natural population of Drosophila melanogaster.
Authors: Sniegowski P D , Charlesworth B 
Published: January 2021

Abstract
Population studies of the distribution of transposable elements (TEs) on the chromosomes of Drosophila melanogaster have suggested that their copy number increase due to transposition is balanced by some form of natural selection. Theory suggests that, as a consequence of deleterious ectopic meiotic exchange between TEs, selection can favor genomes with lower TE copy numbers. This predicts that TEs should be less deleterious, and hence more abundant, in chromosomal regions in which recombination is reduced. To test this, we surveyed the abundance and locations of 10 families of TEs in recombination-suppressing chromosomal inversions from a natural population. The sample of 49 chromosomes included multiple independent isolates of seven different inversions and a corresponding set of standard chromosomes. For all 10 TE families pooled, copy numbers were significantly higher overall within low frequency inversions than within corresponding regions of standard chromosomes. TEs occupied chromosomal sites at significantly higher frequencies within the In(3R)Mo and In(3R)K inversions than within the corresponding regions of standard 3R chromosomes. These results are consistent with the predictions of the ectopic exchange model.
Molecular genetics of the brown (b)-locus region of mouse chromosome 4. I. Origin and molecular mapping of radiation- and chemical-induced lethal brown deletions.
Authors: Rinchik E M , Bell J A , Hunsicker P R , Friedman J M , Jackson I J , Russell L B 
Published: January 2021

Abstract
Over a period of many years, germ-cell mutagenesis experiments using the mouse specific-locus test have generated numerous radiation- and chemical-induced alleles of the brown (b; Tyrp 1) locus in mouse chromosome 4. We describe here the origin, maintenance and initial molecular characterization of 28 b mutations that are prenatally lethal when homozygous. Each of these mutations is deleted for Tyrp 1 sequences, and each of 25 mutations tested further is deleted for at least one other locus defined by molecular clones previously found to be closely linked to b by interspecific backcross analysis. A panel of DNAs from mice carrying a lethal b mutation and a Mus spretus chromosome 4 was used in the fine structure mapping of these molecularly defined loci. The deletional nature of each of these prenatally lethal mutations is consistent with the hypothesis that the null phenotype at b has an effect only on the quality (color) of eumelanin produced in melanocytes. The resulting deletion map provides a framework on which to build future molecular-genetic and biological analyses of this region of mouse chromosome 4.
Molecular genetics of the brown (b)-locus region of mouse chromosome 4. II. Complementation analyses of lethal brown deletions.
Authors: Rinchik E M 
Published: January 2021

Abstract
Numerous new mutations at the brown (b) locus in mouse chromosome 4 have been recovered over the years in germ-cell mutagenesis experiments performed at the Oak Ridge National Laboratory. A large series of radiation- and chemical-induced b mutations known to be chromosomal deletions, and also known to be prenatally lethal when homozygous, were analyzed by pairwise complementation crosses as well as by pseudodominance tests involving flanking loci defined by externally visible phenotypes. These crosses were designed to determine the extent of each deletion on the genetic and phenotype map of the chromosomal region surrounding the b locus; the crosses also provided basic data that assigned deletions to complementation groups and defined four new loci associated with aberrancies in normal development. Specifically, the pseudodominance tests identified deletions that include the proximally mapping whirler (wi) and the distally mapping depilated (dep) genes, thereby bracketing these loci defined by visible developmental abnormalities with landmarks (deletion breakpoints) that are easily identified on the physical map. Furthermore, the complementation crosses, which were supplemented with additional crosses that allowed determination of the gross time of lethality of selected deletions, defined four new loci required for normal development. Homozygous deletion of one of these loci (b-associated fitness, baf) results in a runting syndrome evident during postnatal development; deletion of one locus [l(4)2Rn] causes death in the late gestation/neonatal period; and deletion of either of two loci [l(4)1Rn or l(4)3Rn] results in embryonic death, most likely in pre-, peri- or postimplantation stages. The placement of these new functionally defined loci on the evolving molecular map of the b region should be useful for continuing the analysis of the roles played in development by genes in this segment of chromosome 4.
Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers.
Authors: Grattapaglia D , Sederoff R 
Published: January 2021

Abstract
We have used a "two-way pseudo-testcross" mapping strategy in combination with the random amplified polymorphic DNA (RAPD) assay to construct two moderate density genetic linkage maps for species of Eucalyptus. In the cross between two heterozygous individuals many single-dose RAPD markers will be heterozygous in one parent, null in the other and therefore segregate 1:1 in their F1 progeny following a testcross configuration. Meiosis and gametic segregation in each individual can be directly and efficiently analyzed using RAPD markers. We screened 305 primers of arbitrary sequence, and selected 151 to amplify a total of 558 markers. These markers were grouped at LOD 5.0, theta = 0.25, resulting in the maternal Eucalyptus grandis map having a total of 240 markers into 14 linkage groups (1552 cM) and the paternal Eucalyptus urophylla map with 251 markers in 11 linkage groups (1101 cM) (n = 11 in Eucalyptus). Framework maps ordered with a likelihood support &gt; or = 1000:1 were assembled covering 95% of the estimated genome size in both individuals. Characterization of genome complexity of a sample of 48 mapped random amplified polymorphic DNA (RAPD) markers indicate that 53% amplify from low copy regions. These are the first reported high coverage linkage maps for any species of Eucalyptus and among the first for any hardwood tree species. We propose the combined use of RAPD markers and the pseudo-testcross configuration as a general strategy for the construction of single individual genetic linkage maps in outbred forest trees as well as in any highly heterozygous sexually reproducing living organisms. A survey of the occurrence of RAPD markers in different individuals suggests that the pseudo-testcross/RAPD mapping strategy should also be efficient at the intraspecific level and increasingly so with crosses of genetically divergent individuals. The ability to quickly construct single-tree genetic linkage maps in any forest species opens the way for a shift from the paradigm of a species index map to the heterodox proposal of constructing several maps for individual trees of a population, therefore mitigating the problem of linkage equilibrium between marker and trait loci for the application of marker assisted strategies in tree breeding.
Molecular evolution of the metallothionein gene Mtn in the melanogaster species group: results from Drosophila ananassae.
Authors: Stephan W , Rodriguez V S , Zhou B , Parsch J 
Published: January 2021

Abstract
Three distinctly different alleles of the metallothionein gene Mtn have been identified in natural Drosophila melanogaster populations: Mtn.3, Mtn1, and Dp(Mtn1), where the latter designates a tandem duplication of Mtn1. In Drosophila simulans, only Mtn.3-type alleles have been found. It has been suggested that Mtn.3 is the ancestral allele and demonstrated that a presumed two-step transition from Mtn.3 to Mtn1 to Dp(Mtn1) is accompanied by an approximate 5-fold increase in RNA levels. We analyzed the evolutionary genetics of the Mtn locus of Drosophila ananassae, a distant relative of D. melanogaster and D. simulans within the melanogaster species group. The Mtn gene of D. ananassae is most similar to Mtn.3: (i) it is identical with Mtn.3 at the amino acid level, but differs from Mtn1 in its terminal codon; (ii) its 3' UTR contains a characteristic extra DNA segment of about 50 bp which is present in Mtn.3, but lacking in Mtn1; (iii) duplications of Mtn were not found in a worldwide sample of 110 wild D. ananassae chromosomes. However, the intron of the Mtn gene in D. ananassae is only 69 bp long, whereas the length of the Mtn.3 and Mtn1 introns is 265 bp; and it lacks a polypyrimidine stretch upstream of the 3' splice site in contrast to the much greater pyrimidine-richness found in the Mtn.3 and Mtn1 introns. A short intron (67 bp) was also identified in a D. pseudoobscura Mtn allele, suggesting that the short intron is the ancestral form and that the transition from the short to the long intron occurred within the melanogaster species group.(ABSTRACT TRUNCATED AT 250 WORDS)
Length variation in mitochondrial DNA of the minnow Cyprinella spiloptera.
Authors: Broughton R E , Dowling T E 
Published: January 2021

Abstract
Length differences in animal mitochondrial DNA (mtDNA) are common, frequently due to variation in copy number of direct tandem duplications. While such duplications appear to form without great difficulty in some taxonomic groups, they appear to be relatively short-lived, as typical duplication products are geographically restricted within species and infrequently shared among species. To better understand such length variation, we have studied a tandem and direct duplication of approximately 260 bp in the control region of the cyprinid fish, Cyprinella spiloptera. Restriction site analysis of 38 individuals was used to characterize population structure and the distribution of variation in repeat copy number. This revealed two length variants, including individuals with two or three copies of the repeat, and little geographic structure among populations. No standard length (single copy) genomes were found and heteroplasmy, a common feature of length variation in other taxa, was absent. Nucleotide sequence of tandem duplications and flanking regions localized duplication junctions in the phenylalanine tRNA and near the origin of replication. The locations of these junctions and the stability of folded repeat copies support the hypothesized importance of secondary structures in models of duplication formation.
Selection on silent sites in the rodent H3 histone gene family.
Authors: DeBry R W , Marzluff W F 
Published: January 2021

Abstract
Selection promoting differential use of synonymous codons has been shown for several unicellular organisms and for Drosophila, but not for mammals. Selection coefficients operating on synonymous codons are likely to be extremely small, so that a very large effective population size is required for selection to overcome the effects of drift. In mammals, codon-usage bias is believed to be determined exclusively by mutation pressure, with differences between genes due to large-scale variation in base composition around the genome. The replication-dependent histone genes are expressed at extremely high levels during periods of DNA synthesis, and thus are among the most likely mammalian genes to be affected by selection on synonymous codon usage. We suggest that the extremely biased pattern of codon usage in the H3 genes is determined in part by selection. Silent site G + C content is much higher than expected based on flanking sequence G + C content, compared to other rodent genes with similar silent site base composition but lower levels of expression. Dinucleotide-mediated mutation bias does affect codon usage, but the affect is limited to the choice between G and C in some fourfold degenerate codons. Gene conversion between the two clusters of histone genes has not been an important force in the evolution of the H3 genes, but gene conversion appears to have had some effect within the cluster on chromosome 13.
Three additional linkage groups that repress transcription and meiotic recombination in the mating-type region of Schizosaccharomyces pombe.
Authors: Thon G , Cohen A , Klar A J 
Published: January 2021

Abstract
The mating-type genes of Schizosaccharomyces pombe are found at three locations in the same chromosomal region. These genes are in an active configuration at the mat1 locus and in an inactive configuration at the mat2 and mat3 loci. The mechanism that represses transcription of mat2 and mat3 also inactivates other promoters introduced nearby and is accompanied by a block to meiotic recombination in the mat2-mat3 interval, suggesting that this mechanism involves a particular chromatin structure. We present evidence that the transcription and recombination blocks require three newly defined trans-acting loci, clr2, clr3 and clr4, in addition to the previously identified clr1, rik1 and swi6 loci. We also investigated the role of mat2 cis-acting sequences in silencing. Four cis-acting elements that repress mat2 in a plasmid context were previously identified. Deletion of two of these elements proved to have little effect in a chromosomal context. However, when combined with mutations in trans-acting genes, deletion of the same two elements greatly enhanced mat2 expression. The observed cumulative effects suggest a redundancy in the silencing mechanism.
The mec-8 gene of Caenorhabditis elegans affects muscle and sensory neuron function and interacts with three other genes: unc-52, smu-1 and smu-2.
Authors: Lundquist E A , Herman R K 
Published: January 2021

Abstract
Mutations in the Caenorhabditis elegans gene mec-8 were previously shown to cause defects in mechanosensation and in the structure and dye filling of certain chemosensory neurons. Using noncomplementation screens, we have identified eight new mec-8 alleles and a deficiency that uncovers the locus. Strong mec-8 mutants exhibit an incompletely penetrant cold-sensitive embryonic and larval arrest, which we have correlated with defects in the attachment of body muscle to the hypodermis and cuticle. Mutations in mec-8 strongly enhance the mutant phenotype of unc-52(viable) mutations; double mutants exhibit an unconditional arrest and paralysis at the twofold stage of embryonic elongation, a phenotype characteristic of lethal alleles of unc-52, a gene previously shown to encode a homolog of the core protein of heparan sulfate proteoglycan, found in basement membrane, and to be involved in the anchorage of myofilament lattice to the muscle cell membrane. We have identified and characterized four extragenic recessive suppressors of a mec-8; unc-52(viable) synthetic lethality. The suppressors, which define the genes smu-1 and smu-2, can weakly suppress all mec-8 mutant phenes. They also suppress the muscular dystrophy conferred by an unc-52(viable) mutation.
Structure, expression and duplication of genes which encode phosphoglyceromutase of Drosophila melanogaster.
Authors: Currie P D , Sullivan D T 
Published: January 2021

Abstract
We report here the isolation and characterization of genes from Drosophila that encode the glycolytic enzyme phosphoglyceromutase (PGLYM). Two genomic regions have been isolated that have potential to encode PGLYM. Their cytogenetic localizations have been determined by in situ hybridization to salivary gland chromosomes. One gene, Pglym78, is found at 78A/B and the other, Pglym87, at 87B4,5 of the Drosophila polytene map. Pglym78 transcription follows a developmental pattern similar to other glycolytic genes in Drosophila, i.e., substantial maternal transcript deposited during oogenesis; a decline in abundance in the first half of embryogenesis; a subsequent increase in the second half of embryogenesis which continues throughout larval life; a decline in pupae and a second increase to a plateau in adults. This transcript has been mapped by cDNA and genomic sequence comparison, RNase protection, and primer extension. Using similar analyses transcripts of Pglym87 could not be detected. Pglym78 has two introns which interrupt the coding region, while the Pglym87 gene lacks introns. This and other features support a model of retrotransposition mediated gene duplication for the origin of Pglym87. The apparent absence of a complete, intact coding frame and transcript suggest that Pglym87 is a pseudogene. However, retention of reading frame and codon bias suggests that Pglym87 may retain coding function, or may have been inactivated recently, substantially after the time of duplication, or that the molecular evolution of Pglym87 is unusual. Similarities of the unusual molecular evolution of Pglym87 and other proposed pseudogenes are discussed.
Mutations in calphotin, the gene encoding a Drosophila photoreceptor cell-specific calcium-binding protein, reveal roles in cellular morphogenesis and survival.
Authors: Yang Y , Ballinger D 
Published: January 2021

Abstract
Calphotin is a Drosophila photoreceptor cell-specific protein expressed very early in eye development, at the time when cell-type decisions are being made. Calphotin is a very hydrophobic and proline-rich protein which lacks obvious transmembrane domains. The cDNA encoding Calphotin was mapped to a region removed by a set of existing chromosomal deletions. Mutations that alter photoreceptor cell structure and development were isolated that fail to complement these deletions. These mutations fall into two classes. Class I mutations alter the structure of the rhabdomere, a photoreceptor cell organelle specialized for phototransduction. Class II mutations have rough eyes, due to misorientation of the rhabdomeres and photoreceptor cell death. Transformation rescue of these phenotypes in transgenic flies bearing calphotin genomic DNA indicates that both classes of mutations are in the calphotin gene. Analysis of these mutations suggest that Calphotin plays important roles in both rhabdomere development and in photoreceptor cell survival.
Possible loss of length conservation and reciprocity during recombination or conversion in tandem arrays.
Authors: Fletcher H L 
Published: January 2021

Abstract
Recombination or conversion between arrays of repeated sequences need not be conservative for length because two single strands of DNA from one chromatid may form heteroduplexes in different registers on the other participating duplex. This can cause an overall change in repeat number. Loss of length conservation is equally possible whether models of recombination initiated by single-strand transfer or double-strand break are applicable. Length changing conversion will frequently produce a characteristic insertion within a deletion, often appearing as a double deletion such as are frequently found in new variants of human minisatellite MS32. There is no apparent means of preserving parity during length-changing conversion or recombination, and if the changes are biased then the overall copy number will increase or decrease according to that bias. The observation that arrays persist suggests that any bias in these arrays will be toward gains. An equilibrium may be reached where gains, which may be largely independent of array length, equal losses from the array-length-dependent processes of intrachromatid recombination and repeated unequal sister chromatid exchanges.
Dosage compensation of the period gene in Drosophila melanogaster.
Authors: Cooper M K , Hamblen-Coyle M J , Liu X , Rutila J E , Hall J C 
Published: January 2021

Abstract
The period (per) gene is located on the X chromosome of Drosophila melanogaster. Its expression influences biological clocks in this fruit fly, including the one that subserves circadian rhythms of locomotor activity. Like most X-linked genes in Drosophila, per is under the regulatory control of gene dosage compensation. In this study, we assessed the activity of altered or augmented per+ DNA fragments in transformants. Relative expression levels in male and female adults were inferred from periodicities associated with locomotor behavioral rhythms, and by histochemically assessing beta-galactosidase levels in transgenics carrying different kinds of per-lacZ fusion genes. The results suggest that per contains multipartite regulatory information for dosage compensation within the large first intron and also within the 3' half of this genetic locus.
Reversible changes in the composition of the population of mtDNAs during dedifferentiation and regeneration in tobacco.
Authors: Kanazawa A , Tsutsumi N , Hirai A 
Published: January 2021

Abstract
Differences in the composition of the population of mtDNAs between green plants and calli of tobacco were detected by DNA filter hybridization analysis. The altered composition of the population of mtDNAs observed in calli returned to the composition typical of green plants during the process of regeneration. Quantitative assays revealed that the changes were associated with the differentiation and dedifferentiation of cells since the extent of the change in composition depended on the degree of differentiation of a population of cells. The sequence that accumulated in dedifferentiated cells was shown to be a product of recombination mediated by a 9-nucleotide repeated element, one of which is located at the 5' region of atp6. Although the recombinant sequence was not detected by a hybridization procedure in green plants, its presence was identified by a more sensitive polymerase chain reaction method. The recombination event was shown to result in a deletion that prevents reverse recombination. Therefore, the reversion from the altered composition to the normal state of the population of mtDNAs during regeneration is explained not by recombination but by the preferential amplification of subgenomic mtDNA molecules.
Three independent forms of regulation affect expression of HO, CLN1 and CLN2 during the cell cycle of Saccharomyces cerevisiae.
Authors: Breeden L , Mikesell G 
Published: January 2021

Abstract
The G1 cyclins (CLNs) bind to and activate the CDC28 kinase during the G1 to S transition in Saccharomyces cerevisiae. Two G1 cyclins are regulated at the RNA level so that their RNAs peak at the G1/S boundary. In this report we show that the cell cycle regulation of CLN1 and CLN2 is partially determined by the restricted expression of SW14, a known trans-activator of SCB elements. When SWI4 is constitutively expressed or deleted, cell cycle regulation of CLN1/2 is reduced but not eliminated. In the absence of SwI6, another known regulator of both SCB and MCB elements, cell cycle regulation of the CLNs is also reduced, and the Start-dependence of HO transcription is eliminated. This indicates that SwI6 also plays an important role in the normal cell cycle regulation of all three promoters. When both SwI6 activity and the transcriptional regulation of SW14 are eliminated, cell cycle regulation is further reduced, indicating that these are two independent pathways of regulation. However, a twofold fluctuation in transcript levels still persists under these conditions. This reveals a third source of cell cycle control, which could affect SwI4 activity post-transcriptionally, or reflect the existence of another unidentified regulator of these promoters.