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Results for “insertion, inversion”

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PubMed1999

Genomic loci of the Porphyromonas gingivalis insertion element IS1126.

The Porphyromonas gingivalis genome contains multiple copies of insertion element IS1126. When chromosomal DNA digests of different strains were probed with IS1126, between 25 and 35 hybridizing fragments per genome were detected, depending on the strain. Unrelated strains had very different restriction fragment length polymorphism (RFLP) patterns. When different laboratory copies of a specific strain were examined, the IS1126 RFLP patterns were very similar but small differences were observed, indicating that element-associated changes had occurred during laboratory passage. Within the next year, genome sequencing, assembly, and annotation for P. gingivalis W83 will be completed. Because repetitive elements complicate the assembly of randomly sequenced DNA fragments, we isolated and sequenced the flanking regions of IS1126 copies in strain W83. We also isolated and sequenced the flanking regions of IS1126 copies in strain ATCC 33277 in order to compare insertion sites in phylogenetically divergent strains. We identified 37 new sequences flanking IS1126 from strain ATCC 33277 and 30 from strain W83. The insertion element was found between genes except where it transposed into another insertion element. Examination of identifiable flanking genes or open reading frames indicated that the insertion sites were different in the two strains, except that both strains possess an insertion adjacent to the Lys-gingipain gene (J. P. Lewis and F. L. Macrina, Infect. Immun. 66:3035-3042, 1998). Most of the genes or sequences flanking IS1126 in ATCC 33277 were present in W83 but were contiguous and not insertion element associated. Thus, where genes were identified in both strains, their order was maintained, indicating that the two genomes are organized similarly, but the loci of IS1126 are different. In both strains, insertion element-associated duplicated target sites were lost from several copies of IS1126, providing evidence of homologous recombination between elements. Larger organizational differences between the genomes, such as deletions and inversions, may result from insertion element-mediated recombination events.

DNA Transposable Elements↗

PubMed1990

The origin of a double insertion of homogeneously staining regions in the house mouse (Mus musculus musculus).

A high resolution analysis of the G-band patterns of normal and aberrant chromosomes 1, bearing two linked insertions of homogeneously staining regions (HSRs) in the house mouse (Mus musculus musculus) reveals the inverted pattern of the euchromatic region between the HSRs. On the basis of this analysis a hypothesis on the origin of the aberrant chromosome is put forward: the double insertion is a result of an inversion of the chromosome 1 of Mus musculus domesticus bearing a single insertion of HSR. The proximal breakpoint is localized inside the HSR, and the distal one between subbands E3 and E4.

Animals↗

PubMed1992

A local algorithm for DNA sequence alignment with inversions.

A dynamic programming algorithm to find all optimal alignments of DNA subsequences is described. The alignments use not only substitutions, insertions and deletions of nucleotides but also inversions (reversed complements) of substrings of the sequences. The inversion alignments themselves contain substitutions, insertions and deletions of nucleotides. We study the problem of alignment with non-intersecting inversions. To provide a computationally efficient algorithm we restrict candidate inversions to the K highest scoring inversions. An algorithm to find the J best non-intersecting alignments with inversions is also described. The new algorithm is applied to the regions of mitochondrial DNA of Drosophila yakuba and mouse coding for URF6 and cytochrome b and the inversion of the URF6 gene is found. The open problem of intersecting inversions is discussed.

Algorithms↗

PubMed1999

Generation of a widespread Drosophila inversion by a transposable element.

Although polymorphic inversions in Drosophila are very common, the origin of these chromosomal rearrangements is unclear. The breakpoints of the cosmopolitan inversion 2j of D. buzzatii were cloned and sequenced. Both breakpoints contain large insertions corresponding to a transposable element. It appears that the two pairs of target site duplications generated upon insertion were exchanged during the inversion event, and that the inversion arose by ectopic recombination between two copies of the transposon that were in opposite orientations. This is apparently the mechanism by which transposable elements generate natural inversions in Drosophila.

Animals↗

PubMed1990

[The causes of appearance of a double insertion of homogeneously staining regions in the chromosome 1 of house mouse (Mus musculus musculus)].

A high resolution analysis of G-band pattern of normal and aberrant chromosome 1 bearing two linked insertions of homogeneously staining regions (HSRs) in the house mouse (Mus musculus musculus) reveals an inverted pattern of the euchromatic region between the HSRs. On the basis of this analysis, a hypothesis on the causes for appearance of the aberrant chromosome was put forward: the double insertion is a result of inversion of the chromosome 1 of Mus musculus domesticus bearing a single long insertion. The proximal breakpoint is localized inside the HSR and the distal one--between subbands E3 and E4. From the point of view of these data, new symbols for the aberrations are proposed: Ls (HSR, 1C5) 1Icg--for the proximal insertion, Is(HSR, 1D)21cg--for the distal one, In (1) 1Icg--for the inverted region, including the bands D, E1-E3 and the insertion Is(HSR 1D)21cg.

Animals↗

PubMed1996

[Ascending intramedullary nailing of the femur. Technique. Initial results. Indications].

Some fractures of the distal third of the femur are not good indications for the centromedular locked nailing technique where the nail in inserted through the greater trochanter. Indeed, unsatisfactory reduction and stabilization are often obtained. Inversely, when the nail is inserted upwardly from the knee joint after drilling an orifice in the trochlea and the condyles, the mechanical locking is very close to the knee joint and, when the subtrochanter region is reached, the nail automatically aligns the fracture. The implant temporarily used was a centromedular tibial nail rotated by 180 degrees and mechanically locked near the knee under fluoroscopic control near the lesser trochanter. Five trauma cases were treated with this technique. Early results have been encouraging, similar to those obtained for nailing with closed surgery. These results would suggest that upward nailing should be conceived for particular indications: fractures of the supracondyle area, spiral and comminutive fractures of the distal third of the femur, certain fractures of the supra and inter condyle area.

Adult↗

PubMed1991

Site-specific retrotransposons of the trypanosomatid protozoa.

Retrotransposons are mobile genetic elements that have invaded a wide variety of organisms. While these mobile elements share gene homologies and structural features with retroviruses, they have lost the ability to produce infectious particles. Typically these elements are 5-10 kilobases (kb) in length, are conserved in their structural organization and are present in many copies in the genomes into which they have integrated(1). Retrotransposons generally interrupt their host genome promiscuously and thus cause a variety of random effects. In general, their insertion results in mutations, inversions, deletions or rearrangements among host sequences. All of these changes are thought to add to the plasticity of the host genome and thus contribute to a faster pace of evolutionary development. However, because of the random nature of insertions, it has been difficult to attribute any one specific function to these diverse elements. Here, Serap Aksoy describes a newly recognized family of mobile elements that are different from most retrotransposons in that they have the ability to integrate into specific host sequences.

Journal Article↗

PubMed1980

Structure of a cloned circular Moloney murine leukemia virus DNA molecule containing an inverted segment: implications for retrovirus integration.

Closed circular Moloney murine leukemia virus (M-MuLV) DNA was prepared from recently infected cells and cloned in a lambda vector. Four classes of cloned M-MuLV inserts were found: Class I, full length 8.8-kilobase (kb) inserts with two tandem long terminal repeats (LTRs) of 600 base pairs; class 2, 8.2-kb inserts with a single copy of a LTR; class 3, M-MuLV DNA inserts with various portions deleted; and class 4, an 8.8-kb insert with an internal sequence inversion. Determination of nucleotide sequence at the junction between the two LTRs from a class 1 insert suggested that circularization occurred by blunt-end ligation of an 8.8-kb linear DNA. The class 4 molecule had an inversion that was flanked by inverted LTRs, each of which had lost two terminal base pairs at the inversion end points. Also, four base pairs that were present only once in standard M-MuLV DNA were duplicated at either end of the inversion. This molecule was interpreted as resulting from an integrative inversion in which M-MuLV DNA has integrated into itself. Its analysis thus provided explicit information concerning the mechanism by which retrovirus DNA integrates into host cell DNA. Models of retrovirus integration based on bacterial DNA transposition mechanisms are proposed.

Bacteriophage lambda↗

PubMed2006

The impact of sequence divergence and DNA mismatch repair on homeologous recombination in Arabidopsis.

We examined the effects of substrate divergence and DNA mismatch repair (MMR) on recombination in Arabidopsis thaliana. Relative to the frequency observed in plants with a homologous construct (0% divergence), recombination was decreased 4.1-, 9.6-, 11.7- or 20.3-fold, respectively, in lines with constructs containing 0.5%, 2%, 4% or 9% divergence between the recombination substrates. To evaluate the contribution of the MMR system in this decrease, 12 independent reporter lines (two or three lines per reporter construct) were crossed to an AtMSH2 T-DNA insertional mutant. We examined the recombination frequency in progeny homozygous for a reporter T-DNA and homozygous either for the wild type or the mutant allele of AtMSH2. The loss of MMR activity led to a two- to ninefold increase in homeologous recombination and the size of the increase did not seem to correlate with the amount of divergence. Inversely, complementation of the insertional mutant with a wild-type cDNA of AtMSH2 reduced recombination. Our results demonstrate clearly that sequence divergence can dramatically reduce the recombination frequency in plants and that the MMR system plays a part in this decrease.

Alleles↗

PubMed1984

Proteus mirabilis chromosome mobilization by plasmid D: a physical characterization.

Plasmid D, a hybrid of plasmids P-lac and R1 drd19, mediates polarized chromosome mobilization from one origin in Proteus mirabilis strain PM5006, while the parental plasmids neither individually nor combined mobilize this chromosome. To elucidate its acquired mobilizing ability plasmid D was characterized physically in relation to P-lac and R1 drd19. Restriction patterns of these plasmids were compared and it was shown that D consists of P-lac and only the r-determinant (r-det) of R1 drd19. A mechanism for the formation of plasmid D, via transduction of the r-det and subsequent transposon-like integration into P-lac, involving insertion sequence IS1, was suggested. Evidence for aberration in plasmid D DNA as a result of r-det integration into P-lac was attributed to IS1 elements which flank the r-det. Recombination regions of parental plasmid DNA were located on HindIII fragments alpha and beta of plasmid D and were subsequently inserted in vitro into IncP-1 plasmid RP4 that fails to mobilize the P. mirabilis chromosome. RP4::HindIII alpha plasmids did not mobilize the latter chromosome, but rendered the Proteus host lac+. RP4::HindIII beta plasmids pMC1 and pMC17, containing the fragment in opposite orientations, mobilized the P. mirabilis chromsome. For pMC17, mobilization was indistinguishable from that of plasmid D, i.e. having the same orientation and the same single origin. However, mobilization promoted by pMC1 was from two distinctly different origins, different from that of pMC17. This apparently deviates from known examples where inversion of homologous DNA inserted into plasmids leads to mobilization from the same origin but in reverse direction.

Chromosome Mapping↗

PubMed1994

A three-season comparative analysis of the chromosomal distribution of P and hobo mobile elements in a natural population of Drosophila melanogaster.

An analysis on the chromosomal distribution of P and hobo elements in a Greek natural population extending over three seasons showed that the P elements were more abundant in the population than hobos. The copy number distribution per chromosome arm was in general random. The X chromosome had more P copies and the 3R arm more hobos in all three collections. Significant seasonal differences were not observed for these two elements in relation to the total number of insertions per haploid genome. There were, however, certain seasonal differences. They involved the copy number variability, the intra-arm distribution, the distribution along the chromosomes, and the spread and occupancy frequencies. There were no significant differences between the copy numbers of the two elements carried by the standard and the corresponding inverted regions for a number of inversions found in the population. Finally, three out of the five cosmopolitan inversions were found to have hobo insertions at or very near the one of the two breakpoints. Three out of the total had P insertions at or very near the one of the two breakpoints in some squashes and two of the three endemic inversions had a hobo insertion at or very near the one breakpoint, while the third had a P insertion.

Animals↗

PubMed1997

Heterogeneity in the breakpoints in balanced rearrangements involving band 12p13 in hematologic malignancies identified by fluorescence in situ hybridization: TEL (ETV6 ) is involved in only one half.

Using fluorescence in situ hybridization (FISH) and probes located on 12p12.1 to 13.3, we studied the breakpoints of 23 patients who had various hematologic malignant diseases and who had 12p13-balanced translocations (21 patients), inversion (1 patient), or insertion (1 patient). Among them, 14 patients had breakpoints within YAC964c10, which contains the TEL (ETV6 ) gene and in 12 of these with balanced translocations or insertion, the FISH results suggested that TEL was involved. Two of the 14 patients, patients no. 13 and 14, had breakpoints in YAC 964C10 that were centromeric to TEL but telomeric to KIP1. In the other 9 patients whose breakpoints did not fall within the YAC, the breakpoints were found telomeric to the YAC in at least three different locations on distal 12p. These results indicated that TEL was involved in only half (12 of 23) of the patients with balanced 12p13 rearrangements and that there probably were several other breakpoint cluster regions on 12p13, suggesting that genes other than TEL were involved in these rearrangements.

Adult↗

PubMed1994

Nucleotide sequence analysis of genes essential for capsular polysaccharide biosynthesis in Streptococcus pneumoniae type 19F.

Previous studies have shown that the capsular polysaccharide synthesis (cps) locus of the type 19F Streptococcus pneumoniae strain SSZ was closely linked to a copy of the insertion sequence IS1202 (J.K. Morona, A. Guidolin, R. Morona, D. Hansman, and J.C. Paton, J. Bacteriol. 176:4437-4443, 1994). In the present study, we used plasmid insertion and rescue and inverse PCR to clone 6,322 bp of flanking DNA upstream of IS1202. Sequence analysis indicated that this region contains six complete open reading frames (ORFs) and one partial ORF that are arranged as a single transcriptional unit. Chromosomal disruption of any of these ORFs in a smooth-type 19F strain leads to a rough (unencapsulated) phenotype, indicating that this operon is essential for capsule production. The ORFs have therefore been designated cps19fA to cps19fG, where cps19fA is the first gene of the type 19F cps locus. Furthermore, many of the gene products from this incomplete operon exhibit strong similarities to proteins known to be involved in the production of capsular polysaccharide, exopolysaccharide, teichoic acid, enterobacterial common antigen, and lipopolysaccharide from numerous other bacterial species. This has allowed us to propose functions for many of the type 19F cps gene products. Southern hybridization studies reveal that cps19fA and cps19fB are conserved among all 12 pneumococcal serotypes tested, whereas genes downstream of cps19fB are conserved among some, but not all, of the serotypes tested.

Amino Acid Sequence↗

PubMed2005

High incidence of proviral integrations in the Hoxa locus in a new model of E2a-PBX1-induced B-cell leukemia.

Relevant mouse models of E2a-PBX1-induced pre-B cell leukemia are still elusive. We now report the generation of a pre-B leukemia model using E2a-PBX1 transgenic mice, which lack mature and precursor T-cells as a result of engineered loss of CD3epsilon expression (CD3epsilon(-/-)). Using insertional mutagenesis and inverse-PCR, we show that B-cell leukemia development in the E2a-PBX1 x CD3epsilon(-/-) compound transgenic animals is significantly accelerated when compared to control littermates, and document several known and novel integrations in these tumors. Of all common integration sites, a small region of 19 kb in the Hoxa gene locus, mostly between Hoxa6 and Hoxa10, represented 18% of all integrations in the E2a-PBX1 B-cell leukemia and was targeted in 86% of these leukemias compared to 17% in control tumors. Q-PCR assessment of expression levels for most Hoxa cluster genes in these tumors revealed an unprecedented impact of the proviral integrations on Hoxa gene expression, with tumors having one to seven different Hoxa genes overexpressed at levels up to 6600-fold above control values. Together our studies set the stage for modeling E2a-PBX1-induced B-cell leukemia and shed new light on the complexity pertaining to Hox gene regulation. In addition, our results show that the Hoxa gene cluster is preferentially targeted in E2a-PBX1-induced tumors, thus suggesting functional collaboration between these oncogenes in pre-B-cell tumors.

Animals↗

PubMed1994

The search for homology does not limit the rate of extrachromosomal homologous recombination in mammalian cells.

Mouse LTK- cells were transfected with a pair of defective Herpes simplex virus thymidine kinase (tk) genes. One tk gene had an 8-bp insertion mutation while the second gene had a 100-bp inversion. Extrachromosomal homologous recombination leading to the reconstruction of a functional tk gene was monitored by selecting for tk positive cells using medium supplemented with hypoxanthine/aminopterin/thymidine. To assess whether the search for homology may be a rate-limiting step of recombination, we asked whether the presence of an excess number of copies of a tk gene possessing both the insertion and inversion mutations could inhibit recombination between the singly mutated tk genes. Effective competitive inhibition would require that homology searching (homologous pairing) occur rapidly and efficiently. We cotransfected plasmid constructs containing the singly mutated genes in the presence or absence of competitor sequences in various combinations of linear or circular forms. We observed effective inhibition by the competitor DNA in six of the seven combinations studied. A lack of inhibition was observed only when the insertion mutant gene was cleaved within the insertion mutation and cotransfected with the two other molecules in circular form. Additional experiments suggested that homologous interactions between two DNA sequences may compete in trans with recombination between two other sequences. We conclude that homology searching is not a rate-limiting step of extrachromosomal recombination in mammalian cells. Additionally, we speculate that a limiting factor is involved in a recombination step following homologous pairing and has a high affinity for DNA termini.

Animals↗

PubMed1996

A complex five breakpoint intrachromosomal rearrangement ascertained through two recombinant offspring.

Intrachromosomal rearrangements usually result from three of fewer breaks. We report a complex intrachromosomal rearrangement resulting from five breaks in one chromosome 10 of a phenotypically normal father of two developmentally delayed children. GTG-banding analysis of the father's rearranged chromosome 10 suggested in initial pericentric inversion followed by an insertion from the short arm into the terminal band of the long arm [der(10) (pter-->p13::q21.2-->p12.2::q22.1::-->q26.3::q22.1-->q 21.2::p12.2-->p13::q26.3-->qter)]. To our knowledge, this rearrangement is the most complex ever reported in a single chromosome. Both children inherited a recombinant chromosome 10 with loss of the insertion and the segment distal to it [rec(10)der(pter-->p13: :q21.2-->p12.2::q22.1-->q26.3:)]. Mechanisms for both rearrangements are proposed.

Child↗

PubMed2001

[Principles of shoulder prosthesis implantation].

Patients with an intact rotator cuff and a humeral head that is centered in the glenoid fossa will benefit from both: a hemiarthroplasty and a total shoulder arthroplasty. However, the functional outcome following total shoulder arthroplasty is superior to that of hemiarthroplasty. Superior migration or mal-positioning of the humeral head in the anterior or posterior direction are generally associated with a maximum active flexion of 90 degrees and a high rate of loosening of the glenoid component. Total shoulder arthroplasty leads to superior results in patients with osteoarthritis and mal-positioning of the humeral head in the posterior direction. However, if the head can not be centralized in the glenoid fossa a significant risk of glenoid loosening remains. A superior functional outcome of total shoulder arthroplasty in patients with rheumatoid arthritis can be observed. On the other hand inferior bone quality and a rotator cuff might lead to loosening of the glenoid component. Radiographic signs of glenoid loosening are frequently observed. However, these hardly require operative revisions. If a glenoid component can not be inserted, a bipolar or inverse prosthesis might be considered an alternative.

Arthritis, Rheumatoid↗

PubMedDate not supplied

Single and tandem stents in sheep iliac arteries: is there a difference in patency?

PURPOSE: To compare patency and neointima formation of single and tandem arterial stents. METHODS: In each of six sheep, two Memotherm nitinol stents (tandem stents) were inserted into the external iliac artery on one side and a single stent into the artery on the opposite side. The size of the iliac lumen was assessed in the proximal, middle, and distal segments of the stents by intravascular ultrasound (IVUS) before, immediately after, and 1 month after implantation when the sheep were killed. Neointimal thickness was determined in the proximal, middle, and distal segments of each stent by light microscopy. RESULTS: All stents remained patent. There was no significant difference in lumen and neointimal thickness between single and tandem stents. Cranial tandem stents showed a significantly wider lumen and smaller neointimal thickness than caudal tandem stents. In the proximal and distal segments, the lumen of the stents was significantly smaller and the neointimal thickness greater than in the middle segment; differences in neointimal thickness were significant only between the proximal and the middle segment. CONCLUSION: In an experimental setting, tandem stents did not interfere with one another with regard to patency and neointima formation when compared with a single contralateral stent. Neointimal thickening after stent insertion seems to be inversely related to the original arterial diameter.

Angiography↗