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Results for “insertion, inversion”

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PubMed2000

CBFB/MYH11 fusion in a patient with AML-M4Eo and cytogenetically normal chromosomes 16.

We present a unique case of acute myeloid leukemia M4Eo (AML-M4Eo) with a CBFB/MYH11 fusion transcript and a trisomy 22, but in whom cytogenetic analyses did not disclose an inv(16). Fluorescence in situ hybridization (FISH) analysis with chromosome arm-specific painting probes as well as with the c40 and c36 cosmids also revealed no evidence for an inv(16), whereas the application of locus-specific probes confirmed the presence of a masked inv(16). The results of our comprehensive FISH investigations indicate that the events leading to this masked inv(16) were complex and concurred with deletions on both the long and short arms. The most likely explanation for the formation of the relevant CBFB/MYH11 fusion is an insertion of parts of the MYH11 into the CBFB gene, although it is also possible that it was formed by a double inversion.

Adolescent↗

PubMed2003

Self-incompatibility (S) locus region of the mutated S6-haplotype of sour cherry (Prunus cerasus) contains a functional pollen S allele and a non-functional pistil S allele.

This study characterizes the S6m-haplotype, a mutated S6-haplotype with an altered HindIII cut site, of sour cherry (Prunus cerasus). Inheritance and pollination studies of S-haplotypes from reciprocal crosses between 'Erdi Botermo' (EB; S4S6mSa) and 'Rheinische Schattenmorelle' (RS; S6SaSbSc) revealed that the S6m-haplotype conferred unilateral incompatibility with a non-functional pistil component and a functional pollen component. Expression analyses of S6-RNase and SFB6, a candidate gene for pollen-S, in the S6m-haplotype showed that SFB6 was transcribed in EB pollen, but S6-RNase was not transcribed in EB styles. These results were consistent with data from the inheritance and pollination studies. Inverse PCR for the flanking regions of S6-RNase in the S6- and S6m-haplotypes revealed an approximately 2600 bp insertion present at approximately 800 bp upstream of the S6-RNase in the S6m-haplotype, which is responsible for the alternation of the HindIII cut site and a possible cause of inhibition of the transcription of S6-RNase. SFB6 was present downstream of S6-RNase in both the S6- and S6m-haplotypes and expressed in the same way, supporting the idea that SFB is a good candidate for pollen-S in Prunus.

Alleles↗

PubMed2004

The repair of double-strand breaks in plants: mechanisms and consequences for genome evolution.

The efficient repair of double-strand breaks (DSBs) in genomic DNA is important for the survival of all organisms. In recent years, basic mechanisms of DSB repair in somatic plant cells have been elucidated. DSBs are mainly repaired by non-homologous end-joining (NHEJ). The repair can be associated with deletions, but also insertions due to copying genomic sequences from elsewhere into the break. Species-specific differences of NHEJ have been reported and an inverse correlation of deletion size to genome size has been postulated, indicating that NHEJ might contribute significantly to evolution of genome size. DSB repair by homologous recombination (HR) might also influence genome organization. Whereas homology present in an allelic or an ectopic position is hardly used for repair, the use of homologous sequences in close proximity to the break is frequent. A 'single-strand annealing' mechanism that leads to sequence deletions between direct repeats is particularly efficient. This might explain the accumulation of single long terminal repeats of retroelements in cereal genomes. The conservative 'synthesis-dependent strand annealing' mechanism, resulting in conversions without crossovers is also prominent and seems to be significant for the evolution of tandemly arranged gene families such as resistance genes. Induction of DSBs could be used as a means for the controlled manipulation of plant genomes in an analogous way for the use of marker gene excision and site-specific integration.

Biotechnology↗

PubMed2005

A genetic selection for supercoiling mutants of Escherichia coli reveals proteins implicated in chromosome structure.

Chromosomes are divided into topologically independent regions, called domains, by the action of uncharacterized barriers. With the goal of identifying domain barrier components, we designed a genetic selection for mutants with reduced negative supercoiling of the Escherichia coli chromosome. We employed a strain that contained two chromosomally located reporter genes under the control of a supercoiling-sensitive promoter and used transposon mutagenesis to generate a wide range of mutants. We subjected the selected mutants to a series of secondary screens and identified five proteins as modulators of chromosomal supercoiling in vivo. Three of these proteins: H-NS, Fis and DksA, have clear ties to chromosome biology. The other two proteins, phosphoglucomutase (Pgm) and transketolase (TktA), are enzymes involved in carbohydrate metabolism and have not previously been shown to affect DNA. Deletion of any of the identified genes specifically affected chromosome topology, without affecting plasmid supercoiling. We suggest that at least H-NS, Fis and perhaps TktA assist directly in the supercoiling of domains by forming topological barriers on the E. coli chromosome.

Bacterial Proteins↗

PubMed1999

MR imaging-guided radio-frequency thermal ablation in the pancreas in a porcine model with a modified clinical C-arm system.

PURPOSE: To test the hypotheses that (a) magnetic resonance (MR) imaging-guided radio-frequency (RF) thermal ablation in the pancreas is safe and feasible in a porcine model and (b) induced thermal lesion size can be predicted with MR imaging monitoring. MATERIALS AND METHODS: MR imaging-guided RF ablation was performed in the pancreas of six pigs. A 17-gauge monopolar RF probe was inserted into the pancreas with MR imaging guidance, and RF was applied for 10 minutes. After postprocedural imaging (T2-weighted, short inversion time inversion-recovery [STIR], and T1-weighted imaging before and after intravenous administration of gadodiamide), the pigs were observed for 7 days and follow-up MR images were acquired. The pigs were sacrificed, and pathologic examination was performed. RESULTS: Successful RF probe placement was accomplished in all pigs; the interventional procedure took 46-80 minutes. Thermal lesions were 12-15 mm perpendicular to the probe track and were best seen on STIR and contrast material-enhanced T1-weighted images with a radiologic and/or pathologic mean difference in RF lesion diameter of 1.7 mm +/- 1.0 (SD) and 0.8 mm +/- 1.2, respectively. Diarrhea was the only side effect during the 1-week follow-up; no clinical signs of pancreatitis occurred. CONCLUSION: MR imaging-guided RF thermal ablation in the pancreas is feasible and safe. Induced thermal lesion size can best be monitored with STIR and contrast-enhanced T1-weighted images. In the future, RF ablation may offer an alternative treatment option for pancreatic cancer.

Animals↗

PubMed1998

Neurophysiological modeling of voiding in rats: urethral nerve response to urethral pressure and flow.

In male urethan-anesthetized rats, activity was measured in nerves that run over the proximal urethra. The urethral nerve response to stepwise urethral perfusion could be described by a four-parameter model (fit error < 6%). At the onset of perfusion, the urethra was closed and the pressure increased with the infused volume. The nerve activity (NA) increased linearly with this inserted volume to a maximum (NAmax), which was proportional to the instantaneous pressure. The duration of this first episode (delta t) was inversely proportional to the perfusion rate. After infusion of a fixed volume, the urethra opened and the NA decreased with a time constant phi -1 (approximately 1.8 s) to an elevated level (NAlevel). NAlevel was linearly related to the steady-state pressure. Accordingly, sensors in the urethra are sensitive to pressure rather than to the perfusion rate. The parameters NAmax, NAlevel, and delta t showed very good reproducibility (SD approximately 19% of mean). The measured activity was most likely afferent and conducted to the major pelvic ganglion.

Animals↗

PubMed2004

Modification of an existing chromosomal inversion to engineer a balancer for mouse chromosome 15.

Chromosomal inversions are valuable genetic tools for mutagenesis screens, where appropriately marked inversions can be used as balancer chromosomes to recover and maintain mutations in the corresponding chromosomal region. For any inversion to be effective as a balancer, it should exhibit both dominant and recessive visible traits; ideally the recessive trait should be a fully penetrant lethality in which inversion homozygotes die before birth. Unfortunately, most inversions recovered by classical radiation or chemical mutagenesis techniques do not have an overt phenotype in either the heterozygous or the homozygous state. However, they can be modified by relatively simple procedures to make them suitable as an appropriately marked balancer. We have used homologous recombination to modify, in embryonic stem cells, the recessive-lethal In(15)21Rk inversion to endow it with a dominant-visible phenotype. Several ES cell lines were derived from inversion heterozygotes, and a keratin-14 (K14) promoter-driven agouti minigene was introduced onto the inverted chromosome 15 in the ES cells by gene targeting. Mice derived from the targeted ES cells carry the inverted chromosome 15 and, at the same time, exhibit lighter coat color on their ears and tails, making this modified In(15)21Rk useful as a balancer for proximal mouse chromosome 15.

Animals↗

PubMed2001

[Cloning of AHA gene from Amaranthus hypochondriacus and it's aphid inhibitory effect in transgenic tabacco plants].

Using total DNA isolated from Amaranthus hypochondriacus as template, Amaranthus hypochondriacus agglutinin AHA gene was amplified by PCR and cloned. Sequence analysis results showed that this gene is consisted of 2453 base pairs including one 1538 bp intron and two exons of 212 bp and 703 bp respectively. After inverse PCR amplification, coding region of AHA gene was obtained. AHA gene with it's intron (AHAg) and withou intron (AHAc) were inserted downstream of 35S promotor in the binary vector pBin438 resulting in the construction of two plant expression vectors pBAHAg and pBAHAc repectively. Leave explants of Nicotinana tabacum var. SR1 were transformed with A. tumefaciens LBA4404 harbouring the above expression vectors. Results from PCR and Southern blot analysis showed that AHA genes were inserted into the genome of transformed tobacco plants. Immunodot blot analysis indicated that AHA was expressed in transgenic plants. The results from insect bioassay with peach aphid (Mizus persicae) showed that the transgenic plants of pBAHAg and pBAHAc were aphid resistant, evidenced by a 57%-48% reduction in insect population density, some plants were more than 85%. The aphid resistance of transgenic plants transformed with AHAg gene as judged by aphid inhibition rate was higher than that of plants transormed with AHAc gene indicating that the intron in AHAg may be favorable for expression of AHA in transgenic plants.

Animals↗

PubMed1995

Actinomycin D stimulates the transcription of rRNA minigenes transfected into mouse cells. Implications for the in vivo hypersensitivity of rRNA gene transcription.

The in vivo hypersensitivity of eukaryotic rRNA gene transcription to actinomycin D has long been known, but this effect could not be reproduced in model systems and its molecular mechanisms remain uncertain. We studied the action of actinomycin D using mouse rRNA minigenes (with RNA polymerase I promoter and terminator signals), carrying truncated mouse or human rDNA inserts, which are faithfully transcribed upon transient transfection into mouse cells. Low concentrations (0.01-0.08 micrograms/ml) of actinomycin D caused within 1-2 h a 2-7-fold stimulation of the transcription of rRNA minigenes which is inversely related to the size of the rDNA transcript. With transcripts longer than 3 kb the effect was reversed and at 4 kb a practically complete inhibition of the formation of full-length transcripts was observed, accompanied, however, by an enhanced accumulation of unfinished rDNA transcripts. The dependence of actinomycin D action on transcript length was also observed with lacZ gene segments of different size inserted into the mouse rRNA minigenes. The transcription initiation of endogenous rRNA genes was also stimulated by the low doses of actinomycin D as indicated by the enhanced synthesis of unfinished rDNA transcripts (spanning mainly the 5' external transcribed spacer), whereas the synthesis of full-length transcripts was abolished. Removal of actinomycin D from the medium caused within 8-24 h a dramatic increase of the transcription from all rRNA minigenes tested. This stimulation was also inversely related to the size of the transcripts and varied from twofold to fivefold for the 3-4-kb transcripts to about 50-80-fold for the basic minigene transcript (395 nucleotides). The amount of endogenous aborted rDNA transcripts was also markedly increased, but the synthesis of full-length transcripts was not restored even 24 h after removal of the drug. The present results reproduce in a model cellular system the in vivo hypersensitivity of rRNA gene transcription to actinomycin D and reveal that the major factor involved is the size of the rRNA gene transcript. This effect requires only the basic rRNA gene promoter and terminator signals and does not depend on the G + C content of the RNA polymerase I transcripts. We suggest that at low concentrations, the intercalation of actinomycin D changes the conformation of DNA in the promoter region in a manner that stimulates the transcription of both endogenous and transfected rRNA genes.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed2005

The effect of slow interfacial kinetics on the chronoamperometric response of composite lithiated graphite electrodes and on the calculation of the chemical diffusion coefficient of Li ions in graphite.

This paper deals with a study of the shape of the chronoamperometric response (current, I, vs time, t) and, eventually, the mechanism of Li-ions insertion and deinsertion to/from composite graphite electrodes obtained by a small-amplitude (incremental) technique, such as potentiostatic intermittent titration (PITT). The dependences of log I, the Cottrell parameter It(1/2), and the differential parameter d log I/d log t on the process duration (vs log t) were carefully examined both for single- and two-phase coexistence domains. log I vs log t curves for single-phase domains were characterized by a single monotonic curve with a gradually increasing slope. In contrast, the same curves for two-phase domains consist of two sequential downward concave lines. Both types of response were explained by using the cell-impedance-control model. To separate the contributions of solid-state diffusion, Ohmic drops, and slow interfacial charge-transfer kinetics to the chronoamperometric response, the data were presented in the form of the inverse Cottrell parameter, (It(1/2))(-1) vs t(-1/2), from which the chemical diffusion coefficient (D) could be obtained. Refined values of D for Li insertion into graphite obtained herein agree very well with values of the component diffusion coefficient obtained from quasielastic neutron scattering for Li insertion into HOPG, reported in the literature.

Journal Article↗

PubMed1999

Generation of adenovirus vectors devoid of all viral genes by recombination between inverted repeats.

Direct or inverse repeated sequences are important functional features of prokaryotic and eukaryotic genomes. Considering the unique mechanism, involving single-stranded genomic intermediates, by which adenovirus (Ad) replicates its genome, we investigated whether repetitive homologous sequences inserted into E1-deleted adenoviral vectors would affect replication of viral DNA. In these studies we found that inverted repeats (IRs) inserted into the E1 region could mediate predictable genomic rearrangements, resulting in vector genomes devoid of all viral genes. These genomes (termed DeltaAd.IR) contained only the transgene cassette flanked on both sides by precisely duplicated IRs, Ad packaging signals, and Ad inverted terminal repeat sequences. Generation of DeltaAd.IR genomes could also be achieved by coinfecting two viruses, each providing one inverse homology element. The formation of DeltaAd.IR genomes required Ad DNA replication and appeared to involve recombination between the homologous inverted sequences. The formation of DeltaAd. IR genomes did not depend on the sequence within or adjacent to the inverted repeat elements. The small DeltaAd.IR vector genomes were efficiently packaged into functional Ad particles. All functions for DeltaAd.IR replication and packaging were provided by the full-length genome amplified in the same cell. DeltaAd.IR vectors were produced at a yield of approximately 10(4) particles per cell, which could be separated from virions with full-length genomes based on their lighter buoyant density. DeltaAd.IR vectors infected cultured cells with the same efficiency as first-generation vectors; however, transgene expression was only transient due to the instability of deleted genomes within transduced cells. The finding that IRs present within Ad vector genomes can mediate precise genetic rearrangements has important implications for the development of new vectors for gene therapy approaches.

Adenoviridae↗

PubMed2000

Insertion with long target duplication: a mechanism for gene mobility suggested from comparison of two related bacterial genomes.

The complete genome sequences of two closely related organisms--two Helicobacter pylori strains--have recently become available. Comparison of these genomes at single base pair level has suggested the presence of a mechanism for bacterial gene mobility--insertion with long target duplications. This mechanism is formally similar to classical transposon insertion, but the duplication is much longer, often in the range of 100bp. Restriction and/or modification enzyme genes are often within or adjacent to the insertion. A similar process may have mediated insertion of the cag(+) pathogenicity island in H. pylori. A similar structure was identified in comparisons between Neisseria meningitidis and Neisseria gonorrhoeae genomes. We hypothesize that this mechanism, as well as two other types of polymorphism linked with restriction-modification genes (insertion accompanied by target deletion and a tripartite structure composed of substitution/inversion/deletion), have resulted from attack by restriction enzymes on the chromosome.

Base Sequence↗

PubMed2001

Early and multiple Ac transpositions in rice suitable for efficient insertional mutagenesis.

A GFP excision assay was developed to monitor the excision of Ac introduced into rice by Agrobacterium-mediated transformation. The presence of a strong double enhancer element of the CaMV 35S promoter adjacent to the Ac promoter induced very early excision, directly after transformation into the plant cell, exemplified by the absence of Ac in the T-DNA loci. Excision fingerprint analysis and characterization of transposition events from related regenerants revealed an inverse correlation between the number of excision events and transposed Ac copies, with single early excisions after transformation generating Ac amplification. New transpositions were generated at a frequency of 15-50% in different lines, yielding genotypes bearing multiple insertions, many of which were inherited in the progeny. The sequence of DNA flanking Ac in three representative lines provided a database of insertion tagged sites suitable for the identification of mutants of sequenced genes that can be examined for phenotypes in a reverse genetics strategy to elucidate gene function. Remarkably, two-thirds of Ac tagged sites showing homology to sequences in public databases were in predicted genes. A clear preference of transposon insertions in genes that are either predicted by protein coding capacity or by similarity to ESTs suggests that the efficiency of recovering knockout mutants of genes could be about three times higher than random. Linked Ac transposition, suitable for targeted tagging, was documented by segregation analysis of a crippled Ac element and by recovery of a set of six insertions in a contiguous sequence of 70 kb from chromosome 6 of rice.

Base Sequence↗

PubMed2006

Hb Jambol: a new hyperunstable hemoglobin causing severe hemolytic anemia.

We describe a new hyperunstable beta-chain variant due to a complex genomic rearrangement. The abnormal hemoglobin (Hb) was found as a de novo mutation in a 2-year-old Bulgarian girl with severe hemolytic anemia. The mutation was detected through RNA/DNA analysis. It represents a complex genomic rearrangement involving an insertion of 23 nts after IVS-II-535 (derived by triplication of the 12-nts adjacent sequence and subsequent deletion of 1 nt), a deletion of 310 nts extending from IVS-II-550 to the first nt of Cd 108 and an insertion of 28 nts at the deletion junctions (derived from the inverted sequence between nts +3,707 and +3,734 3' to the beta-globin gene termination codon). At the protein level this mutation leads to a deletion of 4 amino acid residues (Leu-Leu-Glu-Asn) at positions 105-108 and an insertion of 9 residues (Val-Pro-Ser-Val-Thr-Leu-Phe-Phe-Asp) at the same location, creating an abnormal elongated beta-chain of 151 amino acid residues. This highly unstable variant was named 'Hb Jambol' after the geographic location in which the patient resides.

Amino Acid Sequence↗

PubMed1999

Type 1 fimbriation and phase switching in a natural Escherichia coli fimB null strain, Nissle 1917.

Escherichia coli Nissle 1917 has been used as a probiotic against intestinal disorders for many decades. It is a good colonizer of the human gut and has been reported to be able to express type 1 fimbriae. Type 1 fimbriae are surface organelles which mediate alpha-D-mannose-sensitive binding to various host cell surfaces. The expression is phase variable, and two tyrosine recombinases, FimB and FimE, mediate the inversion of the fimbrial phase switch. Current evidence suggests that FimB can carry out recombination in both directions, whereas FimE-catalyzed switching is on to off only. We show here that under liquid shaking growth conditions, Nissle 1917 did not express type 1 fimbriae, due to a truncation of the fimB gene by an 1,885-bp insertion element. Despite its fimB null status, Nissle 1917 was still capable of off-to-on switching of the phase switch and expressing type 1 fimbriae when grown under static conditions. This phase switching was not catalyzed by FimE, by truncated FimB, or by information residing within the insertion element. No further copies of fimB seemed to be present on the chromosome of Nissle 1917, suggesting that another tyrosine recombinase in Nissle 1917 is responsible for the low-frequency off-to-on inversion of the phase switch that is strongly favored under static growth conditions. This is the first report documenting the non-FimB- or non-FimE-catalyzed inversion of the fim switch.

Amino Acid Sequence↗

PubMed1984

Trisomy 1q24----1q41 in two sibs with an insertion in an inverted chromosome 4.

We report two patients whose karyotype revealed an additional segment 1q inserted into an inverted chromosome 4. The patients were partially trisomic for the region 1q24----1q41, karyotype 46,XY or XX, inv ins(4;1)inv(4)(q28;q24q41)(p15 . 3q28), while in the mother the chromosomal aberration was balanced. The inserted segment was inverted. In six patients from three other families with insertions, the segment 1q25----1q32 was inserted into the short arm of chromosome 1. In another patient, the segment 1q25----1q42 of the mother was inverted and inserted into the long arm of chromosome 6. These findings suggest an increased susceptibility for a segment of the long arm of chromosome 1 to be inserted and inverted in rearrangements.

Abnormalities, Multiple↗

PubMed1993

The XbaI-BlnI-CeuI genomic cleavage map of Salmonella enteritidis shows an inversion relative to Salmonella typhimurium LT2.

We have established the genomic cleavage map of Salmonella enteritidis strain SSU7998 using pulsed-field gel electrophoresis. The chromosome of 4600 kb was analysed by XbaI (16 fragments), I-CeuI (7 fragments) and BlnI (12 fragments); the genome also contains a plasmid of 60 kb. Cleavage sites of I-Ceul, in the large subunit ribosomal RNA gene, are conserved from Salmonella typhimurium and Escherichia coli K-12, and the XbaI and BlnI sites in glt-tRNA are also conserved, but other sites are less conserved. Transposon Tn10, located at 60 different positions in the chromosome of S. typhimurium, was transduced by bacteriophage P22 into S. enteritidis and the insertion mapped using the XbaI and BlnI sites on Tn10. Gene order in S. enteritidis is identical to S. typhimurium LT2 and similar to E. coli K-12 except for an inversion of 815 kb, which covers the terminus region including T1 and T2. Endpoints are in the NDZs, or non-divisible zones, in which inversion endpoints were not detected in experiments in E. coli K-12 and S. typhimurium LT2. This inversion resembles the inversion between S. typhimurium and E. coli, but is longer at both ends.

Chromosome Inversion↗

PubMed2003

HIV insertions within and proximal to host cell genes are a common finding in tissues containing high levels of HIV DNA and macrophage-associated p24 antigen expression.

HIV integration within host cell genomic DNA is a requisite step of the viral infection cycle. Yet, characteristics of the sites of provirus integration within the host genome remain obscure. The authors present evidence that in diseased tissues showing a high level of HIV DNA and macrophage-associated HIV p24 antigen expression from end stage forms of HIV disease, HIV-1 integration sites were favored within genes and transcriptionally active host cell genomic loci. Using an inverse PCR (IPCR) technique that identified dominant integrated forms of HIV, clonal IPCR products were isolated from AIDS dementia, AIDS lymphoma, and angioimmunoblastic lymphadenopathy tissues. Thirty of 34 disease-associated HIV-1 insertions were identified within annotated and hypothetical genes, an unexpected but highly nonrandom genetic coding region association (p <.026). The 1% sensitivity thresholds used for HIV IPCR suggested some form of selective expansion of cells containing these HIV proviruses. Consistent with this interpretation were the HIV-1 insertion sites identified within introns of genes that encoded for factors associated with signal transduction, apoptosis, and transcription regulation. In addition, HIV-1 proviruses were frequently found proximal to genes that encoded for receptor-associated, signal transduction-associated, transcription-associated, and translation-associated proteins. HIV-1 integration within host cell genomic DNA potentially represents a significant insertional mutagenic event. In certain cases, provirus insertions may mediate the dysregulation of specific gene expression events, providing mechanisms contributing to the pathogenesis associated with certain AIDS-related diseases.

Chromosomes, Human↗