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Results for “insertion, inversion”

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PubMed1998

[Nephritic colic due to indinavir].

OBJECTIVE: Evaluate the frequency and assess curative and preventive measures against urinary lithiasis in patients treated with indinavir. PATIENTS AND METHODS: Fourteen HIV seropositive patients who developed severe and acute flank pain were included. Four of the patients receiving 800 mg indinavir t.i.d. had fever (38.5 degrees C) or delayed secretion (> 2 h). Delay from indinavir treatment onset was 1 to 321 days. During the same period, 155 patients had been treated with indinavir. Clinical features, radiology and laboratory results were recorded in addition to an analysis of the lithiasis if possible. RESULTS: Transient moderate renal failure occurred in 8 patients. Mean urine pH was 6. Serum phosphorus, calcium, and uric acid, liver tests and urinalysis were normal. A JJ ureteral stent was inserted in 4 cases due to complications. In all cases, fluids, analgesics and antispasmodics provided favorable outcome. Inversely, nonsteroid antiinflammatory drugs given in 2 patients had a deleterious effect on renal function. The lithiasis was eliminated in 3 cases and infrared spectrophotometry demonstrated a structure compatible with indinavir monohydrate. CONCLUSION: The formation of urinary lithiasis is a frequent complication of indinavir therapy (9%). Hyperhydration and urine acidification are usually successful but emergency drainage is required in approximately 3% of cases. Nonsteroidal antiinflammatory drugs should be avoided due to the risk of renal toxicity. A precise evaluation of fluid intake and diet, drug associations and personal history is needed to recognize patients at risk of recurrent lithiasis formation.

Acute Kidney Injury↗

PubMed2002

Microphthalmia with linear skin defects syndrome (MLS): a male with a mosaic paracentric inversion of Xp.

The microphthalmia with linear skin defects syndrome (MLS) is an X-linked dominant disorder with male lethality. In the majority of the patients reported, the MLS syndrome is caused by segmental monosomy of the Xp22.3 region. To date, five male patients with MLS and 46,XX karyotype ("XX males") have been described. Here we report on the first male case with MLS and an XY complement. The patient showed agenesis of the corpus callosum, histiocytoid cardiomyopathy, and lactic acidosis but no microphthalmia, and carried a mosaic subtle inversion of the short arm of the X chromosome in 15% of his peripheral blood lymphocytes, 46,Y,inv(X)(p22.13 approximately 22.2p22.32 approximately 22.33)[49]/46,XY[271]. By fluorescence IN SITU hybridization (FISH), we showed that YAC 225H10 spans the breakpoint in Xp22.3. End-sequencing and database analysis revealed a YAC insert of at least 416 kb containing the genes HCCS and AMELX, and exons 2-16 of ARHGAP6. Molecular cytogenetic data suggest that the Xp22.3 inversion breakpoint is located in intron 1 of ARHGAP6, the gene encoding the Rho GTPase activating protein 6. Future molecular studies in karyotypically normal female MLS patients to detect submicroscopic rearrangements including the ARHGAP6 gene as well as mutation screening of ARHGAP6 in patients with no obvious chromosomal rearrangements will clarify the role of this gene in MLS syndrome.

Chromosome Inversion↗

PubMed1994

Aligning genomes with inversions and swaps.

The decision about what operators to allow and how to charge for these operations when aligning strings that arise in a biological context is the decision about what model of evolution to assume. Frequently the operators used to construct an alignment between biological sequences are limited to deletion, insertion, or replacement of a character or block of characters, but there is biological evidence for the evolutionary operations of exchanging the positions of two segments in a sequence and the replacement of a segment by its reversed complement. In this paper we describe a family of heuristics designed to compute alignments of biological sequences assuming a model of evolution with swaps and inversions. The heuristics will necessarily be approximate since the appropriate way to charge for the evolutionary events (delete, insert, substitute, swap, and invert) is not known. The paper concludes with a pairwise comparison of 20 Picornavirus genomes, and a detailed comparison of the hepatitis delta virus with the citrus exocortis viroid.

Amino Acid Sequence↗

PubMed1985

[Chromosomal inversion accompanied by an enhancement of uridine phosphorylase gene expression in Escherichia coli K-12].

In thymine requiring auxotrophs of Escherichia coli the uridine phosphorylase enzyme (udp gene) can catalyze nonspecifically conversion of thymine to thymidine. By selection for effective utilization of exogenous thymine, it is possible to isolate forms with increased expression of the udp gene. Mutants with increased gene expression were isolated from the strain with transposon Tn10 within the metE gene closely linked to udp. Some mutants (designated udpPf) losing Tn10 but retaining the Met- phenotype are characterized by disturbance of recombination in the metE-udp region: they do not form Met+ transductants in P1 transduction with the wild-type donor strain. However, recovery of homology in the chromosomal metE-udp region takes place with low frequency in P1 transduction using the strain with Tn10 insertion in metE as a donor. Data obtained in transductional and conjugational experiments demonstrate that the udpPf1 mutant studied is an inversion extending about 3 min of the E. coli chromosome and including the region of chromosomal replication origin (oriC).

Chromosome Inversion↗

PubMed2006

First myringotomy with insertion of a modified Goode T-Tube: changing the perforation paradigm.

BACKGROUND: Goode T-Tubes (Medtronic Xomed, Inc) have a bad reputation because of their residual tympanic perforation rate. However, these long-term tubes are mostly used in patients with chronic middle ear problems. On the other hand, "safer," short-term tubes may need to be reinserted in up to 20% of children. OBJECTIVE: To demonstrate that modified Goode T-Tubes inserted at the first myringotomy in normal children leave a perforation rate comparable to the rate reported in the literature for short-term tubes and may be extracted safely in the outpatient clinic when eustachian tube function is thought to be adequate. METHOD: This prospective study followed 58 children (100 ears) who had their modified Goode T-Tubes electively removed in the clinic, from October 2003 to November 2004. RESULTS: We found only one persistent perforation at the third follow-up (mean time 5.2 months). The tubes had been in place for an average of 2.9 years. The perforation healing rate was inversely related to intubation duration. Adenotonsillectomy seemed to favourably influence the speed of healing. The perforations healed faster when tubes were inserted for chronic middle ear effusion compared with recurrent acute otitis media. Age, gender, and the site of intubation were not related to persistent perforation. All of the tubes spontaneously extruded (13) healed without perforation. CONCLUSION: Modified Goode T-Tubes inserted at the first myringotomy and electively extracted allow for a longer middle ear ventilation period and have a perforation rate comparable to that of short-term tubes.

Child, Preschool↗

PubMed1985

Genes aroA and serC of Salmonella typhimurium constitute an operon.

Genetic analysis of aroA554::Tn10 derivatives of two mouse-virulent Salmonella typhimurium strains, "FIRN" and "WRAY," and of a nonreverting derivative of each constructed for use as a live vaccine, showed the site of the insertion among mapped aroA point mutants. The WRAY live-vaccine strain gave no aro+ recombinants in crosses with aroA point mutations to one side of the insertion, indicating a deletion from Tn10 through the sites of these point mutations. The FIRN live-vaccine strain gave wild-type recombinants with all tested point mutants; it probably has a deletion or inversion extending from Tn10 into aroA but not as far as the nearest point mutation. Some tetracycline-sensitive mutants of aroA554::Tn10 strains required serine and pyridoxine, indicating loss of serC function, and some that were found to be SerC- did not produce gas from glucose, indicating a loss of pfl function. These results show the gene order pfl-serC-aroA, as in Escherichia coli. Ampicillin enrichment applied to pools of tetracycline-sensitive mutants of strains with Tn10 insertions near aroA (i.e., zbj::Tn10 strains) yielded Aro- SerC- Pfl-, Aro- SerC+ Pfl+, and Aro- SerC- Pfl+ mutants but none which were Aro+ SerC-. All of the mutants are explicable by deletions or inversions extending clockwise from zbj::Tn10 into or through an operon comprising serC (promoter-proximal) and aroA. Such an operon was also shown by the identification of two Tn10 insertions causing phenotype Aro- SerC-, each able to revert to Aro+ SerC+ by precise excision. serC corresponds to the open reading frame promoter-proximal to aroA that was identified elsewhere by base sequencing of a cloned aroA segment of S. typhimurium (Comai et al., Science 221:370-371, 1983). Both serine and chorismate are precursors of enterochelin; this may be why serC and aroA are in a single operon.

Bacterial Vaccines↗

PubMedDate not supplied

Genomic distribution of P elements in Drosophila willistoni and a search for their relationship with chromosomal inversions.

According to the recent-invasion hypothesis, Drosophila melanogaster may have acquired its P elements in a fairly recent process of horizontal transmission between species. Drosophila willistoni has been identified as the potential donor species in that transfer process. A most remarkable feature of D. willistoni is its extensive chromosomal polymorphism due to inversions-the adaptiveness of which has been the subject of many classical studies on evolutionary genetics. In this article, we further extend the study of P elements in D. willistoni, focusing on the possible role they may play in the generation of chromosomal inversions. Our results may be summarized as follows. P-homologous sequences were detected in South American populations of D. willistoni. In two of them, a recently collected wild population and an old laboratory stock, the P insertion sites were located in the polytene chromosomes. Several hybridization sites were mapped in all major chromosome arms of the natural population, which was also chromosomally polymorphic; in the laboratory population, nearly devoid of inversions, hybridization sites were found to be confined to the chromocenter. In the wild population, 10 of the 24 P hybridized sites coincided with several inversions break points and another five sites located themselves very close to those points. The results are discussed within the context of evolutionary hypotheses.

Animals↗

PubMed2004

An intragenic deletion/inversion event in the DMD gene determines a novel exon creation and results in a BMD phenotype.

Duchenne and Becker Muscular Dystrophy (DMD and BMD) are caused, in the majority of cases, by deletions in the dystrophin gene ( DMD). Here we describe the unprecedented case of a BMD patient carrying a large out-of-frame intragenic deletion, together with an inversion in the DMD gene, resulting in the inclusion of a novel exon in the transcript. Multiplex PCR amplification revealed the presence of a 48-52 exon deletion, but transcript analysis identified two unexpected products, neither of them including exon 53. The shorter mRNA derived from the juxtaposition of exons 47-54 (in-frame), while the longer one resulted from the inclusion of a novel 73-bp exon between exons 47 and 54. Sequence analysis revealed that the inserted sequence derived from an inverted portion of intron 53; its inclusion is predicted to determine protein truncation. The presence of a genomic inversion involving exon 53 and flanking regions was confirmed, and inversion/deletion breakpoints were sequenced. The inverted 73-bp sequence displays splicing signals at both ends and thus it is probably recognized as a novel exon when the partially inverted hnRNA is processed. These findings highlight the importance of mRNA analysis on patients that, based on routine DNA screenings, do not follow the reading-frame rule. This is the first reported patient carrying both an intragenic deletion and inversion in the DMD locus. This case might provide further insight into both the mechanisms that determine genomic rearrangements in the DMD locus and the molecular signals that drive exon inclusion.

Adult↗

PubMed1979

Phase variation in Salmonella: genetic analysis of a recombinational switch.

The alternative expression of Salmonella genes H1 and H2, which specify different flagellar antigens, results in the oscillation of phenotype known as phase variation. This alternation is controlled by the inversion of an 800-base-pair sequence of DNA adjacent to, or including part of, the H2 gene. The invertable region was presumed to regulate the function of a promoter and to include specific sites at which a recombinational event, resulting in the inversion, could occur. Here we report genetic manipulations of hybrid lambda phage carrying the H2 gene that were used to define the H2 promoter region and the recombinational sites. The H2 gene fragment was inserted on a hybrid lambda phage next to the cheW gene, which lacked a promoter element. In the resulting fusion, cheW gene activity was restored, the expression of the H2 and cheW genes was controlled coordinately by the inversion, and the polarity of transcription and location of the H2 gene could be determined. Evidence from this type of gene fusion suggested that the H2 gene promoter is included in the inversion region. Hybrid H2 phage were constructed that contained substitutions for regions of the H2 gene. In contrast to hybrid lambda containing the H2 gene, which alternate between "on" and "off" states, several substituted lambdaH2 were fixed in the "on" state. A site necessary for the recombinational event must have been removed in these fixed lambdaH2.

Bacterial Proteins↗

PubMed1998

[Mutation bursts of the yellow gene in a natural Drosophila melanogaster population is connected with insertion of the hobo transposon].

In 1981, a recurrent local burst of high mutability and high allele frequency of the yellow gene was recorded in the natural population of Drosophila melanogaster from Uman', Ukraine. A detailed genetic analysis showed that hypomorphic alleles y2 prevailed during the mutation burst. Mutations were strictly allele-specific and occurred only in two directions: from y2 to y+ and from y+ to y2. Alleles y2 isolated from the natural population differed in the degree of instability of mutant and wild-type derivatives, expression of the mutant phenotype, and complementation properties. In this work, the insertion nature of all unstable alleles derived from the natural population is confirmed by direct molecular methods. The mutation burst at the yellow locus is shown to result from insertion of a defective hobo copy. Six mutations y2 independently isolated from the natural population were caused by an insertion of hobo in the same site of the yellow regulatory region. The hobo copies were identical according to the restriction map. In three y2 alleles, the mutant phenotype was associated with inversion between hobo copies, one of which was located in the yellow locus and the other, in another unidentified region of the X chromosome. The remaining y2 alleles were associated with deletions that were located in the vicinity of the hobo insertion site and in the region of yellow enhancers.

Alleles↗

PubMed1993

Differential electron capture mass spectral response of pentafluorobenzoyl derivatives of platelet activating factor alkyl chain homologs.

The electron capture mass spectrometric response of pentafluorobenzoyl ester derivatives of platelet-activating factor alkyl chain homologs has been found to be inversely proportional to their alkyl chain length. This phenomenon was observed when either the gas chromatograph or direct insertion probe was utilized for sample introduction. A similar differential response was also obtained for a series of fatty alcohols, analyzed as pentafluorobenzoyl esters. These studies demonstrate that multiple standard curves must be prepared for analysis of platelet-activating factor and related lipids in order to obtain accurate quantification.

Benzoates↗

PubMed1994

Invasion of the hobo transposable element studied by in situ hybridization on polytene chromosomes of Drosophila melanogaster.

The invasion kinetics of hobo transposable element in the Drosophila melanogaster genome was studied by in situ hybridization on the polytene chromosomes. Six independent lines of Drosophila melanogaster flies that had been previously transformed by microinjection of the pHFL1 plasmid containing a complete hobo element were followed over 50 generations. We observed that hobo elements were scattered on each of the chromosome arms, with more insertion sites on the 3R arm. The total number of insertion sites remains quite small, between four and six, at generation 52. On the 2R arm, a short inversion appeared once at generation 52. Most of the integration sites reported here were already described for several transposons but some of them appear to be hotspots for hobo elements.

Animals↗

PubMed1982

Molecular cloning of AKR xenotropic murine leukemia virus unintegrated proviral DNA.

Suprahelical proviral DNA of AKR xenotropic murine leukemia virus was purified from agarose gels and cloned in lambda Charon 28 DNA (BamHI sites). Nine viral DNA recombinants were identified and mapped with 12 restriction endonucleases. Three calsses of cloned viral DNA inserts were found: (1) Six inserts were apparently full-length 9.0-kb DNA with tandem long terminal repeat (LTR) elements; (2) two inserts contained DNAs with deletions in or adjacent to the LTR regions; (3) a single isolate contained an inversion of 2.3 kb around the LTR in the envelope gene.

AKR murine leukemia virus↗

PubMed1998

Multiple genome rearrangement and breakpoint phylogeny.

Multiple alignment of macromolecular sequences generalizes from N = 2 to N > or = 3 the comparison of N sequences which have diverged through the local processes of insertion, deletion and substitution. Gene-order sequences diverge through non-local genome rearrangement processes such as inversion (or reversal) and transposition. In this paper we show which formulations of multiple alignment have counterparts in multiple rearrangement. Based on difficulties inherent in rearrangement edit-distance calculation and interpretation, we argue for the simpler "breakpoint analysis." Consensus-based multiple rearrangement of N > or = 3 orders can be solved exactly through reduction to instances of the Travelling Salesman Problem (TSP). We propose a branch-and-bound solution to TSP particularly suited to these instances. Simulations show how non-uniqueness of the solution is attenuated with increasing numbers of data genomes. Tree-based multiple alignment can be achieved to a great degree of accuracy by decomposing the tree into a number of overlapping 3-stars centered on the non-terminal nodes, and solving the consensus-based problem iteratively for these nodes until convergence. Accuracy improves with very careful initializations at the non-terminal nodes. The degree of non-uniqueness of solutions depends on the position of the node in the tree in terms of path length to the terminal vertices.

Algorithms↗

PubMedDate not supplied

Molecular mechanisms for transposition of drug-resistance genes and other movable genetic elements.

Transposition is proposed to be responsible for the rapid evolution of multiply drug-resistant bacterial strains. Transposons, which carry the genes encoding drug resistance, are linear pieces of DNA that range in size from 2.5 to 23 kilobase pairs and always contain at their ends nucleotide sequences repeated in inverse order. In some transposons the terminal inverted repeat sequences are capable of independent movement and are called insertion sequences. Transposons carry a gene that encodes transposase(s), the enzyme(s) responsible for recombination of the transposon into another DNA molecule. Studies on transposable genetic elements in bacteria have not only given insight into the spread of antibiotic resistance but also into the process of DNA movement.

Anti-Bacterial Agents↗

PubMed1992

Genomic diversity and organization of virulence genes in the pathogenic anaerobe Clostridium perfringens.

Pulsed-field gel electrophoresis has been used to assess genomic diversity and to identify virulence regions in 10 strains, representing all five serotypes, of the anaerobic pathogen Clostridium perfringens. Detailed physical and gene maps of the approximately 3.6 Mb circular chromosomes have been established in eight cases and used to deduce a consensus map. With one exception the chromosomal arrangement was relatively constant and map comparison allowed three hypervariable regions to be identified. One of these was associated with the enterotoxin gene, cpe, which is an important cause of human diarrhoea following the ingestion of food contaminated with C. perfringens. Another variable region spanning the major virulence gene plc, which encodes the cytolytic toxin, alpha, was located near oriC in all cases whereas the gene for another lethal typing toxin, epsilon, was borne by an episome. It now seems likely that the serological variations, and the changes in the pathogenic spectrum which constitute the C. perfringens typing system, may be due entirely to the loss, or acquisition, of extrachromosomal genetic elements.

Chromosome Deletion↗

PubMedDate not supplied

Analyses of the ribosomal DNA region in Nosema bombycis NIS 001.

Ribosomal DNA (rDNA) containing small subunit (SSU) rDNA and both flanking regions in the entomopathogenic microsporidian Nosema bombycis NIS 001 was amplified from genomic DNA with a primer set based on the sequence of an inverse polymerase chain reaction (PCR)-derived fragment. In this fragment, SSU rDNA was divided by a 618-bp insert at nt 599, and 5S rDNA was located downstream of the SSU rDNA, fragmented by 284-bp intergenic spacer. In addition, the 48-bp 3'-end of large subunit (LSU) rDNA was located 118 bp upstream of the fragmented SSU rDNA. In the amplicon, the region upstream of the LSU rDNA was a homologue of the C-terminal CHARLIE8 transposon-like element of human GTF2IRD2. In this organism, another fragmented SSU rDNA, which was divided by a 231-bp insert at nt 50, was also detected. Both the intact (insertless) and fragmented SSU rDNAs clustered with LSU rDNA and 5S rDNA and the intergenic sequences between SSU rDNA and 5S rDNA were divergent in an organism. Reverse transcription (RT)-PCR assay indicated that not only the intact SSU rDNA but also the fragmened SSU rDNA were transcribed in N. bombycis.

Animals↗

PubMed2003

Molecular analysis of incHI1 antimicrobial resistance plasmids from Salmonella serovar Typhi strains associated with typhoid fever.

The first outbreak of multidrug-resistant (MDR) typhoid fever in Vietnam was in 1993, and by 1995 nearly 90% of cases were MDR. Plasmid HCM1, sequenced in full, is an incHI1 plasmid from Salmonella enterica serovar Typhi strain CT18, isolated in Vietnam in 1993. Restriction analysis shows that pHCM1 shares a restriction fragment length polymorphism (RFLP) pattern with plasmids isolated from the first outbreak and 10 of 17 MDR plasmids isolated from sporadic cases occurring at the same time in Vietnam. A core region of pHCM1 has significant DNA sequence similarity to plasmid R27, isolated in 1961 from S. enterica in the United Kingdom. There are five regions of DNA in pHCM1 which are not present in R27. Two of these are putative acquisition regions; the largest is 34.955 kbp in length and includes sequences of several antibiotic resistance genes and several insertion sequences. The borders of this region are defined by two identical IS10 left elements, associated with an inversion of DNA or with a truncated Tn10 element. The second, smaller region is 14.751 kbp and carries a trimethoprim resistance gene dfr14A cassette associated with a class 1 integrase. In 1993 to 1994, restriction analysis revealed some variations in the structures of Salmonella serovar Typhi MDR plasmids which were mapped to the two putative acquisition regions and three smaller variable regions. In 1996 a single RFLP type, RFLP7, was found to carry the dfrA7 and sul-1 genes, which were not present on R27 or pHCM1. This plasmid type appears to have a selective advantage over other plasmids with the same resistance phenotype.

Conjugation, Genetic↗