bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytotype control of Drosophila melanogaster P element transposition: genomic position determines maternal repression.
Authors: Misra S , Buratowski R M , Ohkawa T , Rio D C 
Published: January 2021

Abstract
P element transposition in Drosophila is controlled by the cytotype regulatory state: in P cytotype, transposition is repressed, whereas in M cytotype, transposition can occur. P cytotype is determined by a combination of maternally inherited factors and chromosomal P elements in the zygote. Transformant strains containing single elements that encoded the 66-kD P element protein zygotically repressed transposition, but did not display the maternal repression characteristic of P cytotype. Upon mobilization to new genomic positions, some of these repressor elements showed significant maternal repression of transposition in genetic assays, involving a true maternal effect. Thus, the genomic position of repressor elements can determine the maternal vs. zygotic inheritance of P cytotype. Immunoblotting experiments indicate that this genomic position effect does not operate solely by controlling the expression level of the 66-kD repressor protein during oogenesis. Likewise, P element derivatives containing the hsp26 maternal regulator sequence expressed high levels of the 66-kD protein during oogenesis, but showed no detectable maternal repression. These data suggest that the location of a repressor element in the genome may determine maternal inheritance of P cytotype by a mechanism involving more than the overall level of expression of the 66-kD protein in the ovary.
Unusual mitochondrial genome organization in cytoplasmic male sterile common bean and the nature of cytoplasmic reversion to fertility.
Authors: Janska H , Mackenzie S A 
Published: January 2021

Abstract
Spontaneous reversion to pollen fertility and fertility restoration by the nuclear gene Fr in cytoplasmic male sterile common bean (Phaseolus vulgaris L.) are associated with the loss of a large portion of the mitochondrial genome. To understand better the molecular events responsible for this DNA loss, we have constructed a physical map of the mitochondrial genome of a stable fertile revertant line, WPR-3, and the cytoplasmic male sterile line (CMS-Sprite) from which it was derived. This involved a cosmid clone walking strategy with comparative DNA gel blot hybridizations. Mapping data suggested that the simplest model for the structure of the CMS-Sprite genome consists of three autonomous chromosomes differing only in short, unique regions. The unique region contained on one of these chromosomes is the male sterility-associated 3-kb sequence designated pvs. Based on genomic environments surrounding repeated sequences, we predict that chromosomes can undergo intra- and intermolecular recombination. The mitochondrial genome of the revertant line appeared to contain only two of the three chromosomes; the region containing the pvs sequence was absent. Therefore, the process of spontaneous cytoplasmic reversion to fertility likely involves the disappearance of an entire mitochondrial chromosome. This model is supported by the fact that we detected no evidence of recombination, excision or deletion events within the revertant genome that could account for the loss of a large segment of mitochondrial DNA.
Paramutation, an allelic interaction, is associated with a stable and heritable reduction of transcription of the maize b regulatory gene.
Authors: Patterson G I , Thorpe C J , Chandler V L 
Published: January 2021

Abstract
The b gene of maize encodes a transcriptional activator of anthocyanin pigment biosynthetic genes. Certain b alleles undergo paramutation: a unidirectional, heritable alteration of one allele caused by the presence of another allele. B-I (intensely pigmented plant) is always changed to B' (weakly pigmented plant) in the B'/B-I heterozygote, such that all progeny receive the B' allele. The "new" B', which was B-I in the previous generation, is weakly pigmented and fully capable of changing another B-I allele into B'. It was not previously known whether paramutation is associated with altered b expression, altered B protein function or both. Our results show that B' acts in trans to suppress the transcription of B-I, with transcription remaining low in subsequent generations, even when the original B' allele segregates away. The products of B-I and B' are equally capable of activating the transcription of their target genes, indicating they are functionally equivalent. Genomic restriction maps, DNA sequence and methylation of B' and B-I were compared. Despite dramatic differences in phenotype and transcription of B' and B-I, no evidence for rearrangements, changes in sequence or changes in methylation was found. These results provide no support for models involving "dominant negative" proteins, gene conversion or transposable element interactions. We suggest that b paramutation involves a physical interaction between the alleles that suppresses transcription and promotes a change in chromatin structure that is heritable.
Molecular characterization of duplicate cytosolic phosphoglucose isomerase genes in Clarkia and comparison to the single gene in Arabidopsis.
Authors: Thomas B R , Ford V S , Pichersky E , Gottlieb L D 
Published: January 2021

Abstract
The nucleotide sequence of PgiC1-a which encodes a cytosolic isozymes of phosphoglucose isomerase (PGIC; EC 5.3.1.9) in Clarkia lewisii, a wildflower native to California, is described and compared to the previously published sequence of the duplicate PgiC2-a from the same genome. Both genes have the same structure of 23 exons and 22 introns located in identical positions, and they encode proteins of 569 amino acids. Exon and inferred protein sequences of the two genes are 96.4% and 97.2% identical, respectively. Intron sequences are 88.2% identical. The high nucleotide similarity of the two genes is consistent with previous genetic and biosystematic findings that suggest the duplication arose within Clarkia. A partial sequence of PgiC2-b was also obtained. It is 99.5% identical to PgiC2-a in exons and 99.7% in introns. The nucleotide sequence of the single PgiC from Arabidopsis thaliana was also determined for comparison to the Clarkia genes. The A. thaliana PgiC has 21 introns located at positions identical to those in Clarkia PgiC1 and PgiC2, but lacks the intron that divides Clarkia exons 21 and 22. The A. thaliana PGIC protein is shorter, with 560 amino acids, and differs by about 17% from the Clarkia PGICs. The PgiC in A. thaliana was mapped to a site 20 cM from restriction fragment length polymorphism marker 331 on chromosome 5.
Longevity-determining genes in Caenorhabditis elegans: chromosomal mapping of multiple noninteractive loci.
Authors: Ebert R H , Cherkasova V A , Dennis R A , Wu J H , Ruggles S , Perrin T E , Shmookler Reis R J 
Published: January 2021

Abstract
We have used chromosome mapping with polymorphic markers to define genetic components governing life span in the nematode Caenorhabditis elegans. A complex recombinant-inbred population was derived from an interstrain cross, yielding &gt; 1000 genotypes, each a composite of homozygous segments from the two parental strains. Genotypes were analyzed for the last-surviving 1-5% of worms in aging cohorts, and for young controls, by multiplex polymerase chain reaction using polymorphic markers to distinguish the parental alleles. We identified five regions of the genome at which one parental allele was significantly enriched in long-lived subpopulations. At four of five loci, the same alleles were selected in aging cohorts maintained under two different conditions, implying that these genes determine life span in differing environments.
Analysis of mutations in the sqt-1 and rol-6 collagen genes of Caenorhabditis elegans.
Authors: Kramer J M , Johnson J J 
Published: January 2021

Abstract
Different mutations in the sqt-1 and rol-6 collagen genes of Caenorhabditis elegans can cause diverse changes in body morphology and display different genetic attributes. We have determined the nucleotide alterations in 15 mutant alleles of these genes. Three mutations in sqt-1 and one in rol-6 that cause dominant right-handed helical twisting (RRol) of animals are arginine to cysteine replacements. These mutations are all within a short conserved sequence, on the amino terminal side of the Gly-X-Y repeats, that is found in all C. elegans cuticle collagens. A recessive RRol mutation of rol-6 is a replacement of one of the same conserved arginines by histidine. In contrast, three sqt-1 mutations that cause recessive left-handed helical twisting (LRol) are replacements of a conserved carboxy-terminal cysteine residue with either tyrosine or serine. These results suggest that disulfide bonding is important in collagen organization and that a deficit or surplus of disulfides may cause cuticle alterations of opposite handedness. In contrast to other collagens, glycine replacement mutations in the Gly-X-Y repeats of sqt-1 cause very mild phenotypes. Nonsense mutations of both sqt-1 and rol-6 cause nearly, but not totally, wild-type phenotypes. A nonsense mutation in sqt-1 suppresses the phenotype of rol-6 RRol mutations, suggesting that rol-6 collagen function is dependent on the presence of sqt-1 collagen. Mutations of sqt-1 are not suppressed by a rol-6 nonsense mutation, however, indicating that sqt-1 collagen can function independently of rol-6.
Two maize genes are each targeted predominantly by distinct classes of Mu elements.
Authors: Hardeman K J , Chandler V L 
Published: January 2021

Abstract
The Mutator transposable element system of maize has been used to isolate mutations at many different genes. Six different classes of Mu transposable elements have been identified. An important question is whether particular classes of Mu elements insert into different genes at equivalent frequencies. To begin to address this question, we used a small number of closely related Mutator plants to generate multiple independent mutations at two different genes. The overall mutation frequency was similar for the two genes. We then determined what types of Mu elements inserted into the genes. We found that each of the genes was preferentially targeted by a different class of Mu element, even when the two genes were mutated in the same plant. Possible explanations for these findings are discussed. These results have important implications for cloning Mu-tagged genes as other genes may also be resistant or susceptible to the insertion of particular classes of Mu elements.
Application of a random walk model to geographic distributions of animal mitochondrial DNA variation.
Authors: Neigel J E , Avise J C 
Published: January 2021

Abstract
In rapidly evolving molecules, such as animal mitochondrial DNA, mutations that delineate specific lineages may not be dispersed at sufficient rates to attain an equilibrium between genetic drift and gene flow. Here we predict conditions that lead to nonequilibrium geographic distributions of mtDNA lineages, test the robustness of these predictions and examine mtDNA data sets for consistency with our model. Under a simple isolation by distance model, the variance of an mtDNA lineage's geographic distribution is expected be proportional to its age. Simulation results indicated that this relationship is fairly robust. Analysis of mtDNA data from natural populations revealed three qualitative distributional patterns: (1) significant departure of lineage structure from equilibrium geographic distributions, a pattern exhibited in three rodent species with limited dispersal; (2) nonsignificant departure from equilibrium expectations, exhibited by two avian and two marine fish species with potentials for relatively long-distance dispersal; and (3) a progression from nonequilibrium distributions for younger lineages to equilibrium distributions for older lineages, a condition displayed by one surveyed avian species. These results demonstrate the advantages of considering mutation and genealogy in the interpretation of mtDNA geographic variation.
Plasmid suppressors active in the sexual cycle of Neurospora intermedia.
Authors: Yang X , Griffiths A J 
Published: January 2021

Abstract
We have discovered that, in certain crosses of natural isolates of Neurospora intermedia, linear and circular mitochondrial plasmids of the maternal parent are not transmitted to the progeny. This contrasts with the maternal transmission of organellar genetic elements generally observed in crosses between laboratory strains and between other natural isolates. Formally, failure of plasmid transmission is a type of plasmid suppression. The present cases represent the first report of plasmid suppressors in natural populations of fungi. Strains used as female parents can transmit or not transmit plasmids depending on the strain used as male parent. Males that act to suppress in one cross fail to suppress in others. Therefore, the suppression of plasmids depends on a strain-specific interaction and is not determined exclusively by the males. Since suppression is a specific interaction we inferred that it must be genetically based and tested this hypothesis by seeking segregation of suppressed and nonsuppressed phenotypes in octads. Segregation of the original full suppression of all plasmids was indeed observed in each of the three sets of testcrosses examined. The interaction type of suppression must be initiated in ascogenous tissue during the sexual cycle. It is a nonautonomous type of suppression, affecting all descendent cells. In any one case of suppression, either one, several, or all plasmids can be lost. Both linear and circular plasmids can be eliminated by the same suppressor genotype. In addition, several strains were found to contain suppressors that act after ascospore delineation. This autonomous type of suppression has been observed previously in laboratory strains, but not in natural isolates. All the cases of plasmid suppression identified in this study involved a range of apparently neutral circular and linear plasmids. Using one senescent Kalilo strain of N. intermedia, we did not detect any case of suppression of the senescence-determining linear plasmid kalDNA.
Frequent loss of the En transposable element after excision and its relation to chromosome replication in maize (Zea mays L.).
Authors: Dash S , Peterson P A 
Published: January 2021

Abstract
A model of En transposition during chromosome replication is presented following a study of somatic events associated with the transposition of En in the endosperm tissue of the maize kernel. Two supporting assays, the excision and the postexcision events, were used in following these events. The excision of the En transposon has been monitored in the starch-producing endosperm tissue by using the wx-844 autonomously mutable allele, and events after excision have been monitored by using various reporter alleles of the En-1 (Spm-dSpm) system. The initial observations revealed an unusually large amount of loss of the En transposon following its excision from the wx-844 allele. Subsequent analysis of the somatic events using the a2-m1 reporter allele to monitor the dosage of En suggested that the large amount of loss would result from the transposition of En during chromosome replication. Transposition of En from a replicated segment of the chromosome to another site that has also undergone replication explains most of the somatic events observed.
Molecular and cytogenetical characterization of the 10A1-2 band and adjoining region in the Drosophila melanogaster polytene X chromosome.
Authors: Kozlova T u , Semeshin V F , Tretyakova I V , Kokoza E B , Pirrotta V , Grafodatskaya V E , Belyaeva E S , Zhimulev I F 
Published: January 2021

Abstract
Some 300 kb of DNA from the 9F12-10A7 X chromosome region (seven bands) uncovered by Df(1)vL3 were cloned and 31 break points of chromosome rearrangements within the region were mapped. Positions of 12 genes found earlier in genetic saturation experiments, transcripts and P element-induced mutations were located on the physical map using either chromosome rearrangements or Southern blot hybridizations. Data on the position of the break points, genes and polytene chromosome bands allow the following conclusions to be made. (1) The size of the bands in the region varies between 4 kb (10A6 and 7) and 183-195 kb (10A1-2). The compaction ratio of DNA in bands varies from 8-36 (10A6 + 7) to 151-161 (10A1-2). Therefore, fine and thick bands appear to have different kinds of DNP packaging. (2) The bands differ in genetic content. Fine bands contain from one to three genes. In contrast, the 10A1-2 band contains three genes and at least six transcribed DNA fragments. (3) Comparison of genetic and physical maps shows that in this region 0.01 centiMorgan corresponds to 3.3 kb of DNA.
Gene marker loss induced by the transposable element, En, in maize.
Authors: Cormack J , Peterson P A 
Published: January 2021

Abstract
The En/Spm transposable element system in maize includes the functional element, En/Spm and the receptor element I/dSpm. An En receptor has been found that shows En-induced breakage. This En-responsive receptor (designated I836518) is located on the short arm of chromosome 9, proximal to Wx. In the presence of En, markers distal to the receptor show a loss of gene expression. Kernels heterozygous for aleurone and endosperm marker genes have a variegated appearance. The hypothesis is advanced that this variegation represents a physical loss of the chromosome segments carrying the genes distal to the receptor position. It is the first case of an En-controlled breakage event.
Epistasis analysis of suppressor mutations that allow HO expression in the absence of the yeast SW15 transcriptional activator.
Authors: Stillman D J , Dorland S , Yu Y 
Published: January 2021

Abstract
We have examined mutations which overcome the requirement for SW15-dependent transcriptional activation of the Saccharomyces cerevisiae HO gene. We show that the RPD3 gene is the same as SDI2, and that SIN4 is the same as the TSF3 and SDI3 genes. We have also identified a new swi5 suppressor, RGR1. The RGR1 gene was identified originally as a negative regulator of SUC2. Epistasis analysis indicates that six swi5 suppressor genes function in four distinct pathways, with RPD3 and SIN3 in one pathway, RGR1 and SIN4 in a second pathway, and SDI4 and SIN5 each in distinct pathways. Finally, we show that complete suppression of the swi5 defect in HO expression by sin5 requires the wild-type ACE2 gene. This suggests that one function of SIN5 is to prevent ACE2, a SWI5 homolog, from activating HO expression.
The small ribosomal subunit RNA isoforms in Plasmodium cynomolgi.
Authors: Corredor V , Enea V 
Published: January 2021

Abstract
We report the isolation, characterization and analysis of the small subunit rRNA genes in Plasmodium cynomolgi (Ceylon). As in other Plasmodium species, these genes are present in low copy number, are unlinked and form two types that are distinct in sequence and are expressed stage specifically. The asexually expressed (type A) genes are present in four copies in the Ceylon- and in five copies in the Berok-strain. Surprisingly, the sexually expressed (type B) gene is present in a single copy. The vast majority of the differences between gene types is confined to the variable regions. The pattern of divergence is different from that observed in Plasmodium berghei or in Plasmodium falciparum. Analysis of the small subunit rRNA sequences of P. cynomolgi, P. berghei and P. falciparum, indicates that the two gene types do not evolve independently but rather interact (through gene conversion or some form of recombination) to such an extent as to erase whatever stage-specific sequence signatures they may have had in the last common ancestor.
Evolutionary conservation of the structure and expression of alternatively spliced Ultrabithorax isoforms from Drosophila.
Authors: Bomze H M , López A J 
Published: January 2021

Abstract
In Drosophila melanogaster, alternatively spliced mRNAs from the homeotic gene Ultrabithorax (Ubx) encode a family of structurally distinct homeoprotein isoforms. The developmentally regulated expression patterns of these isoforms suggest that they have specialized stage- and tissue-specific functions. To evaluate the functional importance of UBX isoform diversity and gain clues to the mechanism that regulates processing of Ubx RNAs, we have investigated whether the Ubx RNAs of other insects undergo similar alternative splicing. We have isolated and characterized Ubx cDNA fragments from D. melanogaster, Drosophila pseudoobscura, Drosophila hydei and Drosophila virilis, species separated by as much as 60 million years of evolution, and have found that three aspects of Ubx RNA processing have been conserved. (1) These four species exhibit identical patterns of optional exon use in a region adjacent to the homeodomain. (2) These four species produce the same family of UBX protein isoforms with identical amino acid sequences in the optional exons, even though the common amino-proximal region has undergone substantial divergence. The nucleotide sequences of the optional exons, including third positions of rare codons, have also been conserved strongly, suggesting functional constraints that are not limited to coding potential. (3) The tissue- and stage-specific patterns of expression of different UBX isoforms are identical among these Drosophila species, indicating that the developmental regulation of the alternative splicing events has also been conserved. These findings argue for an important role of alternative splicing in Ubx function. We discuss the implications of these results for models of UBX protein function and the mechanism of alternative splicing.
The role of macronuclear DNA sequences in the permanent rescue of a non-mendelian mutation in Paramecium tetraurelia.
Authors: You Y , Scott J , Forney J 
Published: January 2021

Abstract
The paramecium tetraurelia mutant called d48 has a complete copy of the A surface protein gene in its micronuclei, but lacks the A gene in the macronucleus. Previous experiments have shown that microinjection of a plasmid containing the entire A gene or a large portion of the gene into the macronucleus of d48 rescued the cell line after formation of a new macronucleus (autogamy). Here we show that several different regions of the A gene can rescue d48, but 100% of the activity cannot be localized to a single, defined region. Inversion of a sequence contained within an A gene plasmid had no measurable effect on rescue efficiency and co-injection of two different plasmids results in enhancement of rescue activity despite the non-contiguous form of the DNA sequences. Both these results suggest that no specific product (RNA or protein) with defined end points is made from the rescuing fragment. A unique restriction site was created in the A gene and used to demonstrate that the injected DNA does not serve as a direct template for the synthesis of the new macronuclear DNA. Models to explain the action of the injected DNA are discussed.