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Results for “insertion, inversion”

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At least 541 records · Page 30Linked to original sources

PubMed1995

A rapid PCR-based test for the endogenous viral element ev3 of chickens.

A short fragment of chicken genomic DNA encompassing the insertion site of the endogenous avian leucosis viral element ev3 was isolated using the inverse polymerase chain reaction (inverse PCR) technique. The nucleotide sequence of the unoccupied site was used to design PCR primers that can be used to unambiguously determine the genetic status of any chicken, with respect to ev3. Screening of a small number of individuals from exotic breeds of chickens suggested that the frequency of ev3 is highly variable. The ev3 integration site shows a high degree of sequence homology with the macrophage-specific tyrosine kinase gene, bmk, in mice.

Animals↗

PubMed1991

Development of an efficient transposon tagging system in Arabidopsis thaliana.

We are currently developing a transposon tagging system in Arabidopsis thaliana using the maize transposable elements Ac and Ds. In order to make the system as efficient as possible, four different antibiotic resistance markers have been tested for their usefulness in monitoring excision and reinsertion of transposons in the Arabidopsis genome. Owing to the low transposition frequency of wild-type Ac in Arabidopsis we have also tested a number of modifications to the Ac element. Deletion of the CpG-rich region in the transposase 5' untranslated leader was found to significantly increase the activity of Ac in Arabidopsis. In our first non-targeted tagging experiment, 200 individuals with an inherited transposed Ac element have been collected and their progeny are being screened in families of twelve for segregation of mutant phenotypes. A two-element system, using Ac and Ds, is also being developed and a way of stabilising the Ds-induced mutations by counter selecting plants carrying the transposase source is being investigated. The Agrobacterium T-DNA insertions carrying the different transposons are currently being mapped onto the Arabidopsis RFLP map. Inverse polymerase chain reaction (IPCR) is being used to generate flanking DNA probes, that will be used on the RFLP blots to map the T-DNA relative to the other known markers. Once the first few have been mapped the first targeted tagging experiment will be initiated.

Arabidopsis↗

PubMed2000

Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms.

Recent work suggests that restriction-modification gene complexes are mobile genetic elements that insert themselves into the genome and cause various genome rearrangements. In the present work, the complete genome sequences of Pyrococcus horikoshii and Pyrococcus abyssi, two species in a genus of hyperthermophilic archaeon (archaebacterium), were compared to detect large genome polymorphisms linked with restriction-modification gene homologs. Sequence alignments, GC content analysis, and codon usage analysis demonstrated the diversity of these homologs and revealed a possible case of relatively recent acquisition (horizontal transfer). In two cases out of the six large polymorphisms identified, there was insertion of a DNA segment with a modification gene homolog, accompanied by target deletion (simple substitution). In two other cases, homologous DNA segments carrying a modification gene homolog were present at different locations in the two genomes (transposition). In both cases, substitution (insertion/deletion) in one of the two loci was accompanied by inversion of adjacent chromosomal segment. In the fifth case, substitution by a DNA segment carrying type I restriction, modification, and specificity gene homologs was likewise accompanied by adjacent inversion. In the last case, two homologous DNA segments, were found at different loci in the two genomes (transposition), but only one of them had insertion of a modification homolog and an unknown ORF. The possible relationship of these polymorphisms to attack by restriction enzymes on the chromosome will be discussed.

Chromosome Inversion↗

PubMed2001

Sequence analysis of HIV-1 insertion sites in peripheral blood lymphocytes.

An essential component of the HIV-1 life cycle involves insertion in the genome of an infected cell. The site of HIV-1 integration has the potential to disrupt a gene and perturb a normal cellular function. To begin to address whether disease pathogenesis may correlate with the site of insertion, flanking cellular sequences at these HIV integrated regions were directly amplified from peripheral blood mononuclear cells DNA from a broad range of infected individuals using an inverse polymerase chain reaction strategy. Amplified flanking regions were sequenced and examined for similarity to the nucleic acid database. In this group of analyzed samples, the HIV-1 provirus was inserted within non-coding regions throughout the genome of the infected host, in which 7/14 sites were positioned in close proximity to different Alu repetitive elements while 2/14 sites were located within intron sequences. Insertions were also detected at sites without a specific gene designation but not within short tandem repetitive sequences, telomeres or centromeric repeat regions. Altogether, it is expected that this approach will yield new information on sites of integration by HIV-1 that may be associated with the pathogenic manifestations of disease progression.

Base Sequence↗

PubMed1999

Electrical impedance properties of normal and chronically infarcted left ventricular myocardium.

BACKGROUND: Previous reports have disclosed that a significant difference exists between the electrical impedance properties of healthy and chronically infarcted ventricular myocardium. PURPOSE: To assess the potential utility of electrical impedance as the basis for mapping in chronically infarcted left ventricular myocardium. Specifically: (1) to delineate electrical impedance properties of healthy and chronically infarcted ventricular myocardium, with special emphasis on the infarction border zone; (2) to correlate impedance properties with tissue histology; (3) to correlate impedance properties with electrogram amplitude and duration; (4) To demonstrate that endocardial impedance can be measured effectively in vivo using an electrode mounted on a catheter inserted percutaneously. METHODS: An ovine model of chronic left ventricular infarction was utilized. Sites of healthy myocardium, densely infarcted myocardium and the infarction border zone were investigated. Bulk impedance was measured in vitro using capacitor cell, four-electrode and unipolar techniques. Epicardial and endocardial impedances were measured in vivo using four-electrode and unipolar techniques. Impedance was measured at multiple frequencies. Electrographic amplitude, duration and amplitude/duration ratio were measured using bipolar electrograms during sinus rhythm. Quantitation of tissue content of myocytes, collagen, elastin and neurovascular elements was performed. RESULTS: Densely infarcted myocardial impedance was significantly lower than healthy myocardium. Impedance gradually decreased in the border zone transitioning between healthy myocardium and dense infarction. Decreasing impedance correlated with a decrease in tissue myocyte content. The magnitude of the difference in impedance between densely infarcted and healthy myocardium increased as the measurement frequency decreased. Healthy myocardium exhibited a marked frequency dependence in its impedance properties; this phenomenon was not observed in densely infarcted myocardium. There was a direct association between impedance and both electrogram amplitude and amplitude/duration ratio. There was an inverse association between impedance and electrogram duration. Endocardial impedance, measured in vivo using a electrode catheter inserted percutaneously, was demonstrated to distinguish between healthy and infarcted myocardium. CONCLUSIONS: The electrical impedance properties of healthy and infarcted left ventricular myocardium differ markedly. The properties of the infarction border zone are intermediate between healthy and infarcted myocardium. Impedance may be a useful assay of cardiac tissue content and adaptable for cardiac mapping in vivo. Condensed Abstract. To delineate the electrical impedance properties of healthy and chronically infarcted left ventricular myocardium emphasizing the infarction border zone, impedance was measured in chronically infarcted ovine hearts. Densely infarcted myocardial impedance was significantly lower than healthy myocardium. Impedance gradually decreased in the infarction border zone in transition between healthy myocardium and dense infarction. This correlated with a decreasing myocyte content. The magnitude of the difference in impedance between densely infarcted and healthy myocardium increased as measurement frequency decreased. There was a direct association between impedance and electrogram characteristics. Endocardial impedance, measured in vivo using an electrode catheter inserted percutaneously, distinguished between healthy and infarcted myocardium

Action Potentials↗

PubMed1997

Large chromosomal inversions occur in Pseudomonas aeruginosa clone C strains isolated from cystic fibrosis patients.

An analysis of the chromosomal structure of 21 Pseudomonas aeruginosa clone C genotypes of various origins was carried out. The circular chromosomes showed various insertions and deletions which did not alter the gene order in 6 environmental and one ear isolate in comparison with strain PAO and strain C. However, the chromosome structure differed by at least one large inversion in 50% of the genotypes (7/14) isolated from cystic fibrosis patients. Recombination endpoints were scattered throughout the chromosome. All but one inversion included the terminus of replication which was displaced by the recombination events. The rearrangements shifted the positions of the rrn operons with respect to the origin of replication, but the transcription of the rrn operons remained in the same direction as replication. The exclusive detection of inversions in isolates from cystic fibrosis lungs, which represent an atypical habitat for P. aeruginosa, supports the theory that peculiar features of this new ecological niche may select, cause or tolerate genomic changes.

Chromosome Inversion↗

PubMed1999

Velocity selective radiofrequency pulse trains.

The incorporation of velocity-encoding gradient pulses in RF-pulse trains is proposed and examined. Velocity selective perturbation is shown to be analogous in many respects to the well established use of trains of short RF-pulses for chemical shift selective perturbation. Velocity selective perturbation is viable in a biomedical setting only if additional RF refocusing pulses are inserted between the individual RF-pulse elements. Aspects of velocity selective excitation saturation and inversion are examined, and new inversion pulse trains proposed. The selective perturbation of both flowing and stationary spins is demonstrated in phantoms and possible biomedical applications of these pulse trains are discussed.

Magnetic Resonance Spectroscopy↗

PubMed1999

Analysis of bleomycin-induced chromosomal aberrations in Chinese hamster primary embryonic cells by FISH using arm-specific painting probes.

Chinese hamster primary embryonic cells (at G1 phase) were treated with 1.0 or 3.0 microg/ml bleomycin and chromosomal aberrations in first division metaphases were analysed by fluorescence in situ hybridization (FISH) using arm-specific painting probes for chromosomes 3, 4, 8 and 9. We observed that bleomycin induced all classes of chromosome-type aberrations very efficiently. The interesting findings were: (i) the frequency of induced interstitial translocations (i.e. insertions) was approximately equal to that of reciprocal translocations; (ii) the frequency of induced pericentric inversions was higher than that of centric rings. In our earlier studies, we found that X-rays induced a low frequency of interstitial translocations in comparison with reciprocal translocations and equal frequencies of centric rings and pericentric inversions. These data suggest that bleomycin differs from X-rays with respect to the induction of some specific types of aberrations. The results of a chi2 test examining the hypothesis that formed aberrations among the chromosomes or chromosome arms are randomly distributed on the basis of their relative lengths revealed a differential involvement of these chromosomes in the aberrations following exposure to bleomycin. In general, chromosome 8 was found to be more involved in induced aberrations than expected, chromosome 4 was randomly involved, whereas chromosomes 3 and 9 were less involved. This study demonstrates the utility of arm-specific painting probes for efficient detection of a large variety of chromosomal aberrations induced by bleomycin.

Animals↗

PubMed2003

The incidence of inhibitor development according to specific mutations--and treatment?

The spectrum of mutations in the factor VIII (FVIII) gene was investigated in a cohort of patients with severe haemophilia A, together with the relationship between mutation type and inhibitor development DNA analysis was undertaken on 55 previously untreated patients in the Recombinate PUP mutation study who had all received the same clotting factor treatment and underwent regular monitoring for inhibitor development. Overall, 35% of patients with 'severe molecular defects'--intron 22 inversions, large deletions or stop mutations--developed an inhibitor. None of the patients with small insertions or deletions developed inhibitors. The patient numbers in this study were too small for analysis of mutation location effect and therefore an analysis of a large electronic patient database, HAMSTeRS, was undertaken. This revealed that 40% of patients with large deletions and 35% of patients with nonsense mutations developed inhibitors. This large database of information allowed further stratification by examination of the location of mutations within the FVIII gene and the type of sequence affected by the mutation. Nonsense and missense mutations in the light chain were associated with a higher risk of inhibitor formation than those occurring in the heavy chain. Small deletions or insertions affecting an A residue in a run of A residues were associated with a lower risk of inhibitor formation than deletions or insertions affecting other sequences. Splicing errors demonstrated the lowest inhibitor risk of any mutation type. These results may enable patients at higher risk of inhibitor formation to be identified. This may have consequences for the design of clinical trials and treatment options available to high-risk patients.

Antibody Specificity↗

PubMed2006

Reconstructing contiguous regions of an ancestral genome.

This article analyzes mammalian genome rearrangements at higher resolution than has been published to date. We identify 3171 intervals, covering approximately 92% of the human genome, within which we find no rearrangements larger than 50 kilobases (kb) in the lineages leading to human, mouse, rat, and dog from their most recent common ancestor. Combining intervals that are adjacent in all contemporary species produces 1338 segments that may contain large insertions or deletions but that are free of chromosome fissions or fusions as well as inversions or translocations >50 kb in length. We describe a new method for predicting the ancestral order and orientation of those intervals from their observed adjacencies in modern species. We combine the results from this method with data from chromosome painting experiments to produce a map of an early mammalian genome that accounts for 96.8% of the available human genome sequence data. The precision is further increased by mapping inversions as small as 31 bp. Analysis of the predicted evolutionary breakpoints in the human lineage confirms certain published observations but disagrees with others. Although only a few mammalian genomes are currently sequenced to high precision, our theoretical analyses and computer simulations indicate that our results are reasonably accurate and that they will become highly accurate in the foreseeable future. Our methods were developed as part of a project to reconstruct the genome sequence of the last ancestor of human, dogs, and most other placental mammals.

Algorithms↗

PubMed2003

Identification of Actinobacillus pleuropneumoniae genes important for survival during infection in its natural host.

Actinobacillus pleuropneumoniae is a strict respiratory tract pathogen of swine and is the causative agent of porcine pleuropneumonia. We have used signature-tagged mutagenesis (STM) to identify genes required for survival of the organism within the pig. A total of 2,064 signature-tagged Tn10 transposon mutants were assembled into pools of 48 each, and used to inoculate pigs by the endotracheal route. Out of 105 mutants that were consistently attenuated in vivo, only 11 mutants showed a >2-fold reduction in growth in vitro compared to the wild type, whereas 8 of 14 mutants tested showed significant levels of attenuation in pig as evidenced from competitive index experiments. Inverse PCR was used to generate DNA sequence of the chromosomal domains flanking each transposon insertion. Only one sibling pair of mutants was identified, but three apparent transposon insertion hot spots were found--an anticipated consequence of the use of a Tn10-based system. Transposon insertions were found within 55 different loci, and similarity (BLAST) searching identified possible analogues or homologues for all but four of these. Matches included proteins putatively involved in metabolism and transport of various nutrients or unknown substances, in stress responses, in gene regulation, and in the production of cell surface components. Ten of the sequences have homology with genes involved in lipopolysaccharide and capsule production. The results highlight the importance of genes involved in energy metabolism, nutrient uptake and stress responses for the survival of A. pleuropneumoniae in its natural host: the pig.

ATP-Binding Cassette Transporters↗

PubMed2003

Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18.

We present the 4.8-Mb complete genome sequence of Salmonella enterica serovar Typhi strain Ty2, a human-specific pathogen causing typhoid fever. A comparison with the genome sequence of recently isolated S. enterica serovar Typhi strain CT18 showed that 29 of the 4,646 predicted genes in Ty2 are unique to this strain, while 84 genes are unique to CT18. Both genomes contain more than 200 pseudogenes; 9 of these genes in CT18 are intact in Ty2, while 11 intact CT18 genes are pseudogenes in Ty2. A half-genome interreplichore inversion in Ty2 relative to CT18 was confirmed. The two strains exhibit differences in prophages, insertion sequences, and island structures. While CT18 carries two plasmids, one conferring multiple drug resistance, Ty2 has no plasmids and is sensitive to antibiotics.

Adenosine Triphosphatases↗

PubMed1977

Acute inversion of the uterus.

Eight successive cases of acute puerperal inversion of the uterus are presented. The incidence was one in 26,364 deliveries. Fundal insertion of the placenta, adherent placenta and low parity were significant factors in our cases. Two patients were given halothane anesthesia to relax uterine retraction and cervical ring. Vaginal repositioning was successful in seven cases. One patient required abdominal repositioning. Apart from iron deficiency anemia, the postoperative period was uneventful.

Female↗

PubMed1992

Fis plays a role in Tn5 and IS50 transposition.

The Fis (factor for inversion stimulation) protein of Escherichia coli was found to influence the frequency of transposon Tn5 and insertion sequence IS50 transposition. Fis stimulated both Tn5 and IS50 transposition events and also inhibited IS50 transposition in Dam-bacteria. This influence was not due to regulation by Fis of the expression of the Tn5 transposition proteins. We localized, by DNase I footprinting, one Fis site overlapping the inside end of IS50 and give evidence to strongly suggest that when Fis binds to this site, IS50 transposition is inhibited. The Fis site at the inside end overlaps three Dam GATC sites, and Fis bound efficiently only to the unmethylated substrate. Using a mobility shift assay, we also identified another potential Fis site within IS50. Given the growth phase-dependent expression of Fis and its differential effect on Tn5 versus IS50 transposition in Dam-bacteria, we propose that the high levels of Fis present during exponential growth stimulate transposition events and might bias those events toward Tn5 and away from IS50 transposition.

Adenine↗

PubMed2003

Resources for targeted insertional and deletional mutagenesis in Arabidopsis.

The maize transposons Activator (Ac) and Dissociation (Ds) are active in many monocots and dicots, including Arabidopsis. We describe a new Ac-derived transposon construct, designated the Ds-loxP T-DNA, which can be used for both insertional and deletional mutagenesis. There are loxP sites in both orientations on both the transposon and the donor site T-DNA and an arrangement of marker genes that permits selection of transposition events, as well as deletions and inversions extending from the donor site to a transposon reinserted on either side of it. We show that Cre-mediated deletions and inversions occur at a high frequency. The tendency of Ac-Ds transposons to reinsert near the donor site can be used to target both insertional and deletional mutagenesis, but efficient exploitation of this property requires a library of mapped marked donor sites distributed in the genome. We have created a population of independent Ds T-DNA transformants and we have mapped an initial set of 75 Ds T-DNA integration sites. We assessed the potential efficiency of targeted mutagenesis by detecting Ds reinsertion events at several loci over a 400 kb interval from each of two donor sites with different Ds T-DNA constructs. The distribution of reinsertion sites is similar around the two tested loci, with roughly 10, 4, and ca. 1% of reinsertions detected within 1-2 kb of sites 10, 100, and 200-400 kb from the donor site, respectively. To facilitate the use of this targeted mutagenesis system. we have constructed a searchable database of the mapped Ds T-DNA integration sites.

Arabidopsis↗

PubMed1991

Construction of an IS946-based composite transposon in Lactococcus lactis subsp. lactis.

An artificial composite transposon was constructed based on the lactococcal insertion sequence IS946. A 3.0-kb element composed of the pC194 cat gene (Cmr) flanked by inversely repeated copies of IS946 was assembled on pBluescript KS+. When subcloned into the shuttle vector pSA3 (Emr), two putative transposons were created on the recombinant plasmid pTRK128: the 3.0-kb Cmr element (Tn-CmA) and an inverse 11.5-kb Emr element (Tn-EmA). pTRK128 was electroporated into the recombination-deficient strain Lactococcus lactis MMS362, which contains the self-transmissible plasmid pRS01. An MMS362 Cmr Emr transformant was used to assay for transposition events via conjugal mobilization of pTRK128-encoded Cmr or Emr to L. lactis LM2345. Transfer of either marker alone occurred at frequencies of ca. 2 x 10(-4) per input donor. Approximately 19% of the Emr transconjugants were Cms, indicating loss of the cat gene marker. No Cmr Ems transconjugants were recovered (n = 550). Plasmid analysis showed that the Cms Emr isolates contained a single large plasmid that was determined to be a cointegrate between pRS01 and the Tn-EmA element. A 32P-labeled pSA3 probe hybridized specifically to pTRK128 sequences and revealed different junction fragments within each of the cointegrate plasmids. DNA sequence analysis of the Tn-EmA::pRS01 junctions from a representative cointegrate verified transposition by Tn-EmA. This represents the first example of a functional composite transposon in the genus Lactococcus and serves as an experimental tool and model for the genetic analyses of transposons in these organisms.

Base Sequence↗

PubMed2000

Relationship between factor VIII mutation type and inhibitor development in a cohort of previously untreated patients treated with recombinant factor VIII (Recombinate). Recombinate PUP Study Group.

A cohort of 79 previously untreated patients (PUPs) with moderate-severe haemophilia A (baseline Factor VIII < or =2%) were enrolled in a study to evaluate the safety, efficacy and immunogenicity of recombinant factor VIII (r-FVIII, Recombinate). Blood samples were obtained retrospectively from a total 55 PUPs who were investigated for the spectrum of FVIII gene mutations responsible for their haemophilia. FVIII gene inversion mutations were found in 27 (49%) patients. Two patients had partial gene deletions. The remaining 26 patients were then screened for mutations in the FVIII gene coding region using conformation sensitive gel electrophoresis. Point mutations were identified in 22 (85%) of the patients and 14 of these mutations were novel. Study subjects were monitored for the development of FVIII inhibitors throughout the study. A total of 23 of the 73 evaluable subjects (including one subject with a low inhibitor titer at baseline) demonstrated an inhibitor on one or more occasions; 11 (15%) were persistent. Inhibitors were detected in patients with partial gene deletions and inversions and in three of eight patients with missense mutations. No inhibitors were found in 11 patients with small insertions or deletions resulting in an alteration of the protein translation reading frame (frameshift mutations). The results corroborate the observation that mutation type is an important determinant of the propensity to develop inhibitory anti-FVIII antibody.

Antibody Formation↗

PubMed1980

Site-specific X-chromosome rearrangements from hybrid dysgenesis in Drosophila melanogaster.

When the germ line of Drosophila males is destabilized by a syndrome known as hybrid dysgenesis, X-chromosome rearrangements are found in up to 10 percent of the gametes produced. Some of these aberrations are simple inversions, but many are complex multibreak rearrangements. Furthermore, most of the breakpoints fall into a few highly localized positions on the chromosome. These positions are mostly at points of intercalary heterochromatin and may vary from one strain to the next. the results suggest that they may represent points of insertion of mobile DNA sequences.

Animals↗