scholarly journals Fixation of transposable elements in the Drosophila melanogaster genome

2005 ◽  
Vol 85 (3) ◽  
pp. 195-203 ◽  
Author(s):  
XULIO MASIDE ◽  
STAVROULA ASSIMACOPOULOS ◽  
BRIAN CHARLESWORTH
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Genomic Dna ◽  
Molecular Level ◽  
Hybridization Technique ◽  
Small Interfering Rnas ◽  
Heterochromatin Formation ◽  
Large Clusters

We have investigated at the molecular level four cases in which D. melanogaster middle repetitive DNA probes consistently hybridized to a particular band on chromosomes sampled from a D. melanogaster natural population. Two corresponded to true fixations of a roo and a Stalker element, and the others were artefacts of the in situ hybridization technique caused by the presence of genomic DNA flanking the transposable elements (TEs) in the probes. The two fixed elements are located in the β-heterochromatin (20A and 80B, respectively) and are embedded in large clusters of other elements, many of which may also be fixed. We also found evidence that this accumulation is an ongoing process. These results support the hypothesis that TEs accumulate in the non-recombining part of the genome. Their implications for the effects of TEs on determining the chromatin structure of the host genomes are discussed in the light of recent evidence for the role of TE-derived small interfering-RNAs as cis-acting determinants of heterochromatin formation.

Effects of transposable elements on the expression of the forked gene of Drosophila melanogaster.

Genetics ◽  
1993 ◽  
Vol 135 (2) ◽  
pp. 507-526 ◽  
Author(s):  
K K Hoover ◽  
A J Chien ◽  
V G Corces
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Molecular Level ◽  
Northern Analysis ◽  
Fibrillar Structure ◽  
Transcript Analysis ◽  
Coding Region ◽  
Pupal Development ◽  
Gypsy Retrotransposon

Abstract The products of the forked gene are involved in the formation and/or maintenance of a temporary fibrillar structure within the developing bristle rudiment of Drosophila melanogaster. Mutations in the forked locus alter this structure and result in aberrant development of macrochaetae, microchaetae and trichomes. The locus has been characterized at the molecular level by walking, mutant characterization and transcript analysis. Expression of the six forked transcripts is temporally restricted to mid-late pupal development. At this time, RNAs of 6.4, 5.6, 5.4, 2.5, 1.9 and 1.1 kilobases (kb) are detected by Northern analysis. The coding region of these RNAs has been found to be within a 21-kb stretch of genomic DNA. The amino terminus of the proteins encoded by the 5.4- and 5.6-kb forked transcripts contain tandem copies of ankyrin-like repeats that may play an important role in the function of forked-encoded products. The profile of forked RNA expression is altered in seven spontaneous mutations characterized during this study. Three forked mutations induced by the insertion of the gypsy retrotransposon contain a copy of this element inserted into an intron of the gene. In these mutants, the 5.6-, 5.4- and 2.5-kb forked mRNAs are truncated via recognition of the polyadenylation site in the 5' long terminal repeat of the gypsy retrotransposon. These results help explain the role of the forked gene in fly development and further our understanding of the role of transposable elements in mutagenesis.

Using genomic slot blot hybridization to assess intergeneric Saccharum x Erianthus hybrids (Andropogoneae – Saccharinae)

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 428-432 ◽  
Author(s):  
P. Besse ◽  
C. L. McIntyre ◽  
D. M. Burner ◽  
C. G. de Almeida
Keyword(s):  
Genomic Dna ◽  
Blot Hybridization ◽  
Female Parent ◽  
Saccharum Officinarum ◽  
Rapid Screening ◽  
Hybridization Technique ◽  
Slot Blot ◽  
Saccharum Species ◽  
Slot Blot Hybridization

The use of genomic slot blot hybridization enabled the differentiation of hybrids from selfs in Saccharum × Erianthus intergeneric crosses in which Saccharum was used as the female parent. Based on the genomic in situ hybridization technique, slot blots of DNA from the parents and the progeny were blocked with the Saccharum parent DNA and hybridized with the labelled male Erianthus genomic DNA. This technique allowed a rapid screening for hybrids and was sensitive enough to detect a 1/20 dilution of Erianthus in Saccharum DNA, which should enable the detection of most partial hybrids. The genomic slot blot hybridization technique was shown to be potentially useful for assessing crosses involving Saccharum species with either Old World Erianthus section Ripidium or North American Erianthus (= Saccharum) species. The effectiveness of the technique was assessed on 144 progeny of a Saccharum officinarum × Erianthus arundinaceus cross, revealing that 43% of the progeny were selfs. The importance of this test as a tool to support intergeneric breeding programs is discussed.Key words: slot blot, Erianthus, genomic DNA, Saccharum, sugarcane.

scholarly journals Efficacy of Clarithromycin Depends on the Bacterial Density in Clarithromycin-Heteroresistant Helicobacter pylori Infections: An In Situ Detected Susceptibility and Quantitative Morphometry-Based Retrospective Study

2021 ◽  
Vol 27 ◽  
Author(s):  
Jewel Ju Ea Kim ◽  
Ildikó Kocsmár ◽  
György Miklós Buzás ◽  
Ildikó Szirtes ◽  
Orsolya Rusz ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Retrospective Study ◽  
Bacterial Population ◽  
Tissue Sample ◽  
Bacterial Density ◽  
Resistant Bacteria ◽  
Hybridization Technique ◽  
Predictive Role

The global rise in clarithromycin (Cla) resistance is considered to be the main contributor of Helicobacter pylori (Hp) eradication failures. In nearly half of the Cla-resistant Hp infections, Cla-susceptible bacteria are simultaneously present with the Cla-resistant ones (Cla-heteroresistance). The proportion of resistant bacteria in the bacterial population (R-fraction) and its predictive role for the use of Cla-based therapies in Cla-heteroresistant infections has not yet been investigated. Our retrospective study analyzed gastric biopsy samples of 62 Hp-positive patients with Cla-heteroresistant infection. Fluorescence In Situ Hybridization technique was used to visualize the coexistence of resistant and susceptible bacteria within one tissue sample. R-fraction was quantified on multichannel microimages by digital morphometry. Resistant bacteria had a patchy distribution within the whole bacterial population causing high diversity among the investigated areas. Patients were subdivided into two major groups according to whether a Cla-based eradication attempt was conducted before or after the biopsy sampling. R-fraction was significantly lower among cases having only one previous Cla-based eradication attempt vs. those that had multiple previous eradications, including at least one Cla-containing therapy (0.41 vs. 0.89, p = 0.0308). Majority of the patients without previous eradication attempt had successful eradication with Cla-containing regimen (59.26%), verified by a negative 13C-urea breath test or control biopsy. Multivariable model indicated that the therapeutic outcome using Cla-based regimens depended on the bacterial density rather than the R-fraction. Our study raises the potential use of Cla-containing eradication therapies in certain Cla-heteroresistant Hp infections, taking into account the possible predictive role of bacterial density.

scholarly journals Induction of Copper-Zinc Superoxide Dismutase in Gerbil Hippocampus after Ischemia

1993 ◽  
Vol 13 (1) ◽  
pp. 135-144 ◽  
Author(s):  
Tomohiro Matsuyama ◽  
Hisamasa Michishita ◽  
Hitoshi Nakamura ◽  
Masato Tsuchiyama ◽  
Souichiro Shimizu ◽  
...  
Keyword(s):  
Superoxide Dismutase ◽  
In Situ Hybridization ◽  
Control Level ◽  
Antioxidant Defenses ◽  
Hybridization Technique ◽  
Copper Zinc Superoxide Dismutase ◽  
Pyramidal Layer ◽  
Endogenous Antioxidant

To assess the role of Cu-Zn superoxide dismutase (CuZnSOD) in regulating cellular antioxidant defenses, we studied the induction of CuZnSOD mRNA by an in situ hybridization technique and of CuZnSOD protein by an immunocytochemical method in the gerbil hippocampus following 5 min of transient global ischemia. For hybridization, we synthesized 48-mer oligonucleotide (base 465–512) complementary to rat CuZnSOD mRNA. Northern blot analysis showed hybridization to a single band of molecular weight 0.65 kb. After 5 min of ischemia, the signal became stronger at 3 and 24 h and returned to the control level 3 days later. In situ hybridization histochemistry revealed an increase in labeling throughout the hippocampus, especially in the granular layer 3 h following ischemia. The increase was prolonged only in the CA1 pyramidal layer after 24 h and was eliminated within 3 days or later. Conversely, analysis by Western blotting revealed that the insult produced few effects on the induction of CuZnSOD protein. Immunocytochemistry for CuZnSOD revealed a reduced immunostaining in the CA1 pyramidal layer at 24 h of recirculation when the persistent expression of CuZnSOD mRNA was shown in the same area. Our findings suggest that the expression of endogenous CuZnSOD is temporarily stimulated by an ischemic insult without increasing the protein level. The prolonged increase in mRNA and the decrease in the protein of CuZnSOD in the CA, neurons seem to imply an important role of the endogenous antioxidant enzyme that protects against the detrimental effects of superoxide radicals on delayed neuronal death.

scholarly journals The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. I. Element frequencies and distribution

1992 ◽  
Vol 60 (2) ◽  
pp. 103-114 ◽  
Author(s):  
Brian Charlesworth ◽  
Angela Lapid ◽  
Darlene Canada
Keyword(s):  
Population Dynamics ◽  
Drosophila Melanogaster ◽  
Linkage Disequilibrium ◽  
Transposable Elements ◽  
Copy Number ◽  
Polytene Chromosomes ◽  
Chromosome Band ◽  
High Frequencies ◽  
Copy Numbers

SummaryData were collected on the distribution of nine families of transposable elements among second and third chromosomes isolated from a natural population of Drosophila melanogaster, by means of in situ hybridization of element probes to polytene chromosomes. It was found that the copy numbers per chromosome in the distal sections of the chromosome arms followed a Poisson distribution. Elements appeared to be distributed randomly along the distal sections of the chromosome arms. There was no evidence for linkage disequilibrium in the distal sections of the chromosomes, but some significant disequilibrium was detected in proximal regions. There were many significant correlations between different element families with respect to the identity of the sites that were occupied in the sample. There were also significant correlations between families with respect to sites at which elements achieved relatively high frequencies. Element frequencies per chromosome band were generally low in the distal sections, but were higher proximally. These results are discussed in the light of models of the population dynamics of transposable elements. It is concluded that they provide strong evidence for the operation of a force or forces opposing transpositional increase in copy number. The data suggest that the rate of transposition perelement per generation is of the order of 10−4, for the elements included in this study.

scholarly journals Rates of movement of transposable elements on the second chromosome of Drosophila melanogaster

2000 ◽  
Vol 75 (3) ◽  
pp. 275-284 ◽  
Author(s):  
XULIO MASIDE ◽  
STAVROULA ASSIMACOPOULOS ◽  
BRIAN CHARLESWORTH
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Polytene Chromosomes ◽  
Mutation Accumulation ◽  
Long Terminal Repeats ◽  
Significant Difference ◽  
Transposable Element Copy ◽  
Excision Rate

The rates of movement of 11 families of transposable elements of Drosophila melanogaster were studied by means of in situ hybridization of probes to polytene chromosomes of larvae from a long-term mutation accumulation experiment. Replicate mutation-accumulation lines carrying second chromosomes derived from a single common ancestral chromosome were maintained by backcrosses of single males heterozygous for a balancer chromosome and a wild-type chromosome, and were scored after 116 generations. Twenty-seven transpositions and 1 excision were detected using homozygous viable and fertile second chromosomes, for a total of 235056 potential sources of transposition events and a potential 252880 excision events. The overall transposition rate per element per generation was 1·15×10−4 and the excision rate was 3·95×10−6. The single excision (of a roo element) was due to recombination between the element's long terminal repeats. A survey of the five most active elements among nine homozygous lethal lines revealed no significant difference in the estimates of transposition and excision rates from those from viable lines. The excess of transposition over excision events is in agreement with the results of other in situ hybridization experiments, and supports the conclusion that replicative increase in transposable element copy number is opposed by selection. These conclusions are compared with those from other studies, and with the conclusions from population surveys of element frequencies.

scholarly journals Mapping candidate genes for Drosophila melanogaster resistance to the parasitoid wasp Leptopilina boulardi

2006 ◽  
Vol 88 (2) ◽  
pp. 81-91 ◽  
Author(s):  
M. HITA ◽  
E. ESPAGNE ◽  
F. LEMEUNIER ◽  
L. PASCUAL ◽  
Y. CARTON ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Candidate Genes ◽  
Resistance Gene ◽  
Molecular Level ◽  
Single Gene ◽  
Parasitoid Wasp ◽  
Male Recombination ◽  
Leptopilina Boulardi

Drosophila melanogaster resistance against the parasitoid wasp Leptopilina boulardi is under the control of a single gene (Rlb), with two alleles, the resistant one being dominant. Using strains bearing deletions, we previously demonstrated that the 55E2–E6; 55F3 region on chromosome 2R is involved in the resistance phenomenon. In this paper, we first restricted the Rlb containing region by mapping at the molecular level the breakpoints of the Df(2R)Pc66, Df(2R)P34 and Df(2R)Pc4 deficiencies, using both chromosomal in situ hybridization and Southern analyses. The resistance gene was localized in a 100 kb fragment, predicted to contain about 10 different genes. Male recombination genetic experiments were then performed, leading to identification of two possible candidates for the Rlb gene. Potential involvement of one of this genes, edl/mae, is discussed.

MOLECULAR CLONING OF α-AMYLASE GENES FROM DROSOPHILA MELANOGASTER. I. CLONE ISOLATION BY USE OF A MOUSE PROBE

Genetics ◽  
1985 ◽  
Vol 110 (2) ◽  
pp. 299-312
Author(s):  
Robert M Gemmill ◽  
Jack N Levy ◽  
Winifred W Doane
Keyword(s):  
Drosophila Melanogaster ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Cdna Sequence ◽  
Lambda Phage ◽  
Hybridization Probe ◽  
Class A ◽  
Class B ◽  
Small Set

ABSTRACT A cloned ä-amylase cDNA sequence from the mouse is homologous to a small set of DNA sequences from Drosophila melanogaster under appropriate conditions of hybridization. A number of recombinant lambda phage that carry homologous Drosophila genomic DNA sequences were isolated using the mouse clone as a hybridization probe. Putative amylase clones hybridized in situ to one or the other of two distinct sites in polytene chromosome 2R and were assigned to one of two classes, A and B. Clone λDm32, representing class A, hybridizes within chromosome section 53CD. Clone λDm65 of class B hybridizes within section 54A1-B1. Clone λDm65 is homologous to a 1450- to 1500-nucleotide RNA species, which is sufficiently long to code for α-amylase. No RNA homologous to λDm32 was detected. We suggest that the class B clone, λDm65, contains the functional Amy structural gene(s) and that class A clones contain an amylase pseudogene.

Accumulation of Transposable Elements in Autosomes and Giant Sex Chromosomes of Omophoita (Chrysomelidae: Alticinae)

2018 ◽  
Vol 156 (4) ◽  
pp. 215-222 ◽  
Author(s):  
Lucas A.M. Rosolen ◽  
Marcelo R. Vicari ◽  
Mara C. Almeida
Keyword(s):  
Transposable Elements ◽  
Sex Chromosomes ◽  
Chromosomal Rearrangements ◽  
Dna Double Strand Breaks ◽  
Sequencing Data ◽  
High Accumulation ◽  
Strand Breaks ◽  
Cytogenetic Studies

Coleoptera is the most diverse order among insects, and comparative molecular cytogenetic studies in this group are lacking. The species of Omophoita (Oedionychina) possess a karyotype of 2n = 22 = 10II+X+Y. They are interesting models for evolutionary cytogenetic studies due to giant sex chromosomes which are asynaptic during meiosis. Transposable elements (TEs) confer plasticity and mobility to genomes and are considered hotspots for DNA double-strand breaks and chromosomal rearrangements. The objective of the present study was to verify the role of TEs in the karyotype and in the size expansion of the giant sex chromosomes in Omophoita. Thus, different TEs were characterized in the Omophoita genome and localized in the chromosomes by fluorescence in situ hybridization (FISH). The DNA sequencing data revealed identity with TE families Tc1/Mariner and RTE/L1-56_XT. FISH showed signals of all TEs in the karyotypes and a high accumulation in the sex chromosomes of the 3 Omophoita species analyzed. These data suggest that the genome size expansion and the origin of the giant sex chromosomes of Omophoita are due to an intensive genomic invasion of TEs, as those characterized here as Tc1/Mariner-Ooc and RTE-Ooc. Differences in the chromosomal location of the TEs among the 3 species indicate that they have participated in the karyotype differentiation in Omophoita.

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