scholarly journals Dynamics of R1 and R2 Elements in the rDNA Locus of Drosophila simulans

Genetics ◽  
2001 ◽  
Vol 158 (4) ◽  
pp. 1557-1567 ◽  
Author(s):  
César E Pérez-González ◽  
Thomas H Eickbush
Keyword(s):  
Copy Number ◽  
Rdna Locus ◽  
Drosophila Simulans ◽  
Rrna Gene ◽  
Ltr Retrotransposons ◽  
Pcr Assay ◽  
X Chromosomes ◽  
Low Copy Number ◽  
The Many ◽  
The Individual

Abstract The mobile elements R1 and R2 insert specifically into the rRNA gene locus (rDNA locus) of arthropods, a locus known to undergo concerted evolution, the recombinational processes that preserve the sequence homogeneity of all repeats. To monitor how rapidly individual R1 and R2 insertions are turned over in the rDNA locus by these processes, we have taken advantage of the many 5′ truncation variants that are generated during the target-primed reverse transcription mechanism used by these non-LTR retrotransposons for their integration. A simple PCR assay was designed to reveal the pattern of the 5′ variants present in the rDNA loci of individual X chromosomes in a population of Drosophila simulans. Each rDNA locus in this population was found to have a large, unique collection of 5′ variants. Each variant was present at low copy number, usually one copy per chromosome, and was seldom distributed to other chromosomes in the population. The failure of these variants to spread to other units in the same rDNA locus suggests a strong recombinational bias against R1 and R2 that results in the individual copies of these elements being rapidly lost from the rDNA locus. This bias suggests a significantly higher frequency of R1 and R2 retrotransposition than we have previously suggested.

scholarly journals Spontaneous mutations in maize pollen are frequent in some lines and arise mainly from retrotranspositions and deletions

2019 ◽  
Vol 116 (22) ◽  
pp. 10734-10743 ◽  
Author(s):  
Hugo K. Dooner ◽  
Qinghua Wang ◽  
Jun T. Huang ◽  
Yubin Li ◽  
Limei He ◽  
...  
Keyword(s):  
Copy Number ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Ltr Retrotransposons ◽  
Spontaneous Mutations ◽  
Maize Pollen ◽  
Genome Wide ◽  
Autonomous Element ◽  
Low Copy Number ◽  
Female Germline

While studying spontaneous mutations at the maizebronze(bz) locus, we made the unexpected discovery that specific low-copy number retrotransposons are mobile in the pollen of some maize lines, but not of others. We conducted large-scale genetic experiments to isolate newbzmutations from severalBzstocks and recovered spontaneous stable mutations only in the pollen parent in reciprocal crosses. Most of the new stablebzmutations resulted from either insertions of low-copy number long terminal repeat (LTR) retrotransposons or deletions, the same two classes of mutations that predominated in a collection of spontaneouswxmutations [Wessler S (1997)The Mutants of Maize, pp 385–386]. Similar mutations were recovered at the closely linkedshlocus. These events occurred with a frequency of 2–4 × 10−5in two lines derived from W22 and in 4Co63, but not at all in B73 or Mo17, two inbreds widely represented in Corn Belt hybrids. Surprisingly, the mutagenic LTR retrotransposons differed in the active lines, suggesting differences in the autonomous element make-up of the lines studied. Some active retrotransposons, likeHopscotch,Magellan, andBs2, aBs1variant, were described previously; others, likeFotoandFocouin 4Co63, were not. By high-throughput sequencing of retrotransposon junctions, we established that retrotranposition ofHopscotch,Magellan, andBs2occurs genome-wide in the pollen of active lines, but not in the female germline or in somatic tissues. We discuss here the implications of these results, which shed light on the source, frequency, and nature of spontaneous mutations in maize.

scholarly journals Detection of plant species-specific dna (barley and soybean) in blood, muscle tissue, organs and gastrointestinal contents of rabbit.

2010 ◽  
Vol 18 (2) ◽  
pp. 83 ◽  
Author(s):  
 R. Tudisco ◽  
S. Calabrò ◽  
F. Bovera ◽  
M.I. Cutrignelli ◽  
A. Nizza ◽  
...  
Keyword(s):  
Muscle Tissue ◽  
Dna Sequences ◽  
Soybean Meal ◽  
Copy Number ◽  
Barley Grain ◽  
Melting Curve Analysis ◽  
Rrna Gene ◽  
Plant Dna ◽  
Low Copy Number ◽  
Soybean Lectin

The aim of this study was to detect plant DNA sequences from low copy number genes of barley grain and soybean meal, the latter being subjected to solvent extraction process, in blood, liver, kidney, spleen, muscle tissue and digesta (duodenum, caecum and faeces from rectal ampulla) of rabbits. For fattening, Hyla rabbits (20 males and 20 females) were fed a diet including barley grain (15%) and soybean meal (12%). Animals were slaughtered at 74 d of age (2 ± 0.2 kg live weight) and samples collected from each animal. The quality of each DNA sample was verified using the UNIV P/Q primers used to amplify a mammalian specifi c portion of mtDNA 16S rRNA gene. The presence of plant DNA was subsequently ascertained on the same DNA samples, as well as on barley and soybean (control). Two classes of plant DNA sequences were monitored via real-time PCR, using SYBR® Green I Dye: a high copy number chloroplast gene (trnl) and a low copy number specific for barley (metal-dependent hydrolase-like protein) and soybean (lectin) genes. Melting curve analysis was used to identify the PCR products. The chloroplast fragment detection frequency was higher (P<0.01) in muscle (90%), liver (80%), kidney (80%) and spleen (80%) than in blood (40%) and digesta samples. In the latter, chloroplast DNA was found in 40 and 30% of duodenum and caecum contents respectively, and in 30% of faeces. The specificity of the amplicons obtained was checked by sequencing and annotation. In the samples positive for chloroplast fragments, the frequency of detection of barley specific sequence was higher (P<0.01) in liver (62.5%), kidney (62.5%), spleen (62.5%) and digesta (100%) than in blood (25%) and muscle (22.2%) samples. The soybean lectin gene was not detected in animal samples, although it was seen in plant samples. Results confirm that, except for gastrointestinal tract (GIT), plant single copy genes are more difficult to identify in animal samples.

scholarly journals Abnormality in Initiation Program of DNA Replication Is Monitored by the Highly Repetitive rRNA Gene Array on Chromosome XII in Budding Yeast

2006 ◽  
Vol 27 (2) ◽  
pp. 568-578 ◽  
Author(s):  
Satoru Ide ◽  
Keiichi Watanabe ◽  
Hiromitsu Watanabe ◽  
Katsuhiko Shirahige ◽  
Takehiko Kobayashi ◽  
...  
Keyword(s):  
Dna Damage ◽  
Copy Number ◽  
Temperature Shift ◽  
Rdna Locus ◽  
Dna Lesions ◽  
Dna Damage Checkpoint ◽  
Rrna Gene ◽  
Origin Firing ◽  
Rdna Copy ◽  
Rdna Copy Number

ABSTRACT We have shown previously that perturbation of origin firing in chromosome replication causes DNA lesions and triggers DNA damage checkpoint control, which ensures genomic integrity by stopping cell cycle progression until the lesions are repaired or by inducing cell death if they are not properly repaired. This was based on the observation that the temperature-sensitive phenotype of orc1-4 and orc2-1 mutants required a programmed action of the RAD9-dependent DNA damage checkpoint. Here, we report that DNA lesions in the orc mutants are induced much more quickly and frequently within the rRNA gene (rDNA) locus than at other chromosomal loci upon temperature shift. orc mutant cells with greatly reduced rDNA copy numbers regained the ability to grow at restrictive temperatures, and the checkpoint response after the temperature shift became weak in these cells. In orc2-1 cells, completion of chromosomal duplication was delayed specifically on chromosome XII, where the rDNA array is located, and the delay was partially suppressed when the rDNA copy number was reduced. These results suggest that the rDNA locus primarily signals abnormalities in the initiation program to the DNA damage checkpoint and that the rDNA copy number modulates the sensitivity of this monitoring function.

scholarly journals The distribution of transposable elements on X chromosomes from a natural population of Drosophila simulans

1995 ◽  
Vol 66 (2) ◽  
pp. 159-166 ◽  
Author(s):  
Sergey V. Nuzhdin
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Transposable Element ◽  
Natural Population ◽  
Copy Number ◽  
Polytene Chromosomes ◽  
Distal Region ◽  
Drosophila Simulans ◽  
Chromosome Band ◽  
X Chromosomes

SummaryThe distribution of 13 transposable element families along 15 X chromosomes from an African natural population of Drosophila simulans was determined by in situ hybridization to polytene chromosomes. The transposable elements cloned from Drosophila melanogaster all hybridized with Drosophila simulans chromosomes. The number of copies per family was 3·5 times lower in the latter species and correlated with the copy number per family in Drosophila melanogaster. With the exception of 297, the copy number per chromosome followed a Poisson distribution. Element frequencies per chromosome band were generally low. However, several sites of the distal region and the base of the X chromosome had high frequencies of occupation. Elements had higher abundance at the base of the chromosome compared to distal regions. Overall, the distribution of transposable elements in Drosophila simulans is similar to that found in Drosophila melanogaster. These data provide evidence for the operation of a force (or forces) opposing transpositional increase in copy number, and that this force is weaker at the bases of chromosomes, consistent with the idea that recombination between elements at non-homologous sites contains TE copy number. The reduction in copy number of all TE families in Drosophila simulans compared to Drosophila melanogaster can be explained by stronger selection against transposable element multiplication and/or lower rates of transposition in Drosophila simulans.

A Handbook to Eddic Poetry: Myths and Legends of Early Scandinavia, ed. Carolyne Larrington, Judy Quinn, and Brittany Schorn. Cambridge: Cambridge University Press, 2016, xii, 413 pp., 12 b/w ill.

Mediaevistik ◽  
2018 ◽  
Vol 31 (1) ◽  
pp. 366-366
Author(s):  
Albrecht Classen
Keyword(s):  
Old Norse ◽  
Entire Volume ◽  
Cambridge University ◽  
Critical Studies ◽  
Individual Contributions ◽  
The Many ◽  
The Individual ◽  
Made In ◽  
Scandinavian Literature

Eddic poetry constitutes one of the most important genres in Old Norse or Scandinavian literature and has been studied since the earliest time of modern-day philology. The progress we have made in that field is impressive, considering the many excellent editions and translations, not to mention the countless critical studies in monographs and articles. Nevertheless, there is always a great need to revisit, to summarize, to review, and to digest the knowledge gained so far. The present handbook intends to address all those goals and does so, to spell it out right away, exceedingly well. But in contrast to traditional concepts, the individual contributions constitute fully developed critical article, each with a specialized topic elucidating it as comprehensively as possible, and concluding with a section of notes. Those are kept very brief, but the volume rounds it all off with an inclusive, comprehensive bibliography. And there is also a very useful index at the end. At the beginning, we find, following the table of contents, a list of the contributors, unfortunately without emails, a list of translations and abbreviations of the titles of Eddic poems in the Codex Regius and then elsewhere, and a very insightful and pleasant introduction by Carolyne Larrington. She briefly introduces the genre and then summarizes the essential points made by the individual authors. The entire volume is based on the Eddic Network established by the three editors in 2012, and on two workshops held at St. John’s College, Oxford in 2013 and 2014.

Individuality and Beyond

2019 ◽  
Author(s):  
Benedetta Zavatta
Keyword(s):  
Moral Autonomy ◽  
First Line ◽  
Philosophical Interpretation ◽  
Individual Personality ◽  
The World ◽  
Regulative Ideal ◽  
Personal Library ◽  
The Many ◽  
The Individual ◽  
The Impact

Based on an analysis of the marginal markings and annotations Nietzsche made to the works of Emerson in his personal library, the book offers a philosophical interpretation of the impact on Nietzsche’s thought of his reading of these works, a reading that began when he was a schoolboy and extended to the final years of his conscious life. The many ideas and sources of inspiration that Nietzsche drew from Emerson can be organized in terms of two main lines of thought. The first line leads in the direction of the development of the individual personality, that is, the achievement of critical thinking, moral autonomy, and original self-expression. The second line of thought is the overcoming of individuality: that is to say, the need to transcend one’s own individual—and thus by definition limited—view of the world by continually confronting and engaging with visions different from one’s own and by putting into question and debating one’s own values and certainties. The image of the strong personality that Nietzsche forms thanks to his reading of Emerson ultimately takes on the appearance of a nomadic subject who is continually passing out of themselves—that is to say, abandoning their own positions and convictions—so as to undergo a constant process of evolution. In other words, the formation of the individual personality takes on the form of a regulative ideal: a goal that can never be said to have been definitively and once and for all attained.

scholarly journals Haptoglobin Duplicon, Hemoglobin, and Vitamin C: Analyses in the British Women’s Heart and Health Study and Caerphilly Prospective Study

2014 ◽  
Vol 2014 ◽  
pp. 1-5 ◽  
Author(s):  
Philip A. I. Guthrie ◽  
Mohammad R. Abdollahi ◽  
Tom Gaunt ◽  
Debbie A. Lawlor ◽  
Yoav Ben-Shlomo ◽  
...  
Keyword(s):  
Vitamin C ◽  
Copy Number ◽  
Health Study ◽  
Free Hemoglobin ◽  
Pcr Assay ◽  
Partial Duplication ◽  
Haptoglobin Genotype ◽  
Haptoglobin Gene ◽  
Apparent Association ◽  
Quantitative Pcr Assay

Background. Haptoglobin acts as an antioxidant by limiting peroxidative tissue damage by free hemoglobin. The haptoglobin gene allele Hp2 comprises a 1.7 kb partial duplication. Relative to allele Hp1, Hp2 carriers form protein multimers, suboptimal for hemoglobin scavenging.Objective. To examine the association of haptoglobin genotype with a range of phenotypes, with emphasis on vitamin C and hemoglobin levels.Methods. We applied a quantitative PCR assay for the duplication junction to two population cohorts including 2747 British women and 1198 British men. We examined the association of haptoglobin duplicon copy number with hemoglobin and vitamin C and used the copy number to complete a phenome scan.Results.Hemoglobin concentrations were greater in those with Hp2,2 genotype, in women only (Hp1,1 13.45 g/dL, Hp1,2 13.49 g/dL, Hp2,2 13.61 g/dL;P=0.002), though statistically there was no evidence of a difference between the sexes (zvalue = 1.2,P=0.24). Haptoglobin genotype was not associated with vitamin C or any other phenotype in either cohort.Conclusions. Our results do not support association of haptoglobin genotype with vitamin C or with other phenotypes measured in two population cohorts. The apparent association between haptoglobin genotype and hemoglobin in the women’s cohort merits further investigation.

scholarly journals Entangling Lattice-Trapped Bosons with a Free Impurity: Impact on Stationary and Dynamical Properties

Entropy ◽  
2021 ◽  
Vol 23 (3) ◽  
pp. 290
Author(s):  
Maxim Pyzh ◽  
Kevin Keiler ◽  
Simeon I. Mistakidis ◽  
Peter Schmelcher
Keyword(s):  
Structural Changes ◽  
Many Body ◽  
Wide Range ◽  
Entropy Measures ◽  
Particle Level ◽  
The Many ◽  
The One ◽  
Tunneling Dynamics ◽  
The Individual ◽  
Trapped Bosons

We address the interplay of few lattice trapped bosons interacting with an impurity atom in a box potential. For the ground state, a classification is performed based on the fidelity allowing to quantify the susceptibility of the composite system to structural changes due to the intercomponent coupling. We analyze the overall response at the many-body level and contrast it to the single-particle level. By inspecting different entropy measures we capture the degree of entanglement and intraspecies correlations for a wide range of intra- and intercomponent interactions and lattice depths. We also spatially resolve the imprint of the entanglement on the one- and two-body density distributions showcasing that it accelerates the phase separation process or acts against spatial localization for repulsive and attractive intercomponent interactions, respectively. The many-body effects on the tunneling dynamics of the individual components, resulting from their counterflow, are also discussed. The tunneling period of the impurity is very sensitive to the value of the impurity-medium coupling due to its effective dressing by the few-body medium. Our work provides implications for engineering localized structures in correlated impurity settings using species selective optical potentials.

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